Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 109 of 121
Found at i:18524848 original size:23 final size:25
Alignment explanation
Indices: 18524808--18524855 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
18524798 CCTAATCAAA
* *
18524808 ATTTTAAATTTAATATATTTTTATT
1 ATTTTAAATTTAAAATATTATTATT
18524833 ATTTT-AA-TTAAAATATTATTATT
1 ATTTTAAATTTAAAATATTATTATT
18524856 TTATTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 2 0.10
25 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTAAATTTAAAATATTATTATT
Found at i:18524871 original size:23 final size:22
Alignment explanation
Indices: 18524815--18524871 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
18524805 AAAATTTTAA
*
18524815 ATTTAATATATTTTTATTATTTT
1 ATTTAATATA-TATTATTATTTT
*
18524838 AATTAA-A-ATATTATTATTTT
1 ATTTAATATATATTATTATTTT
18524858 ATTTATATATATAT
1 ATTTA-ATATATAT
18524872 ATCAATTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 15 0.54
21 2 0.07
22 2 0.07
23 9 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTAATATATATTATTATTTT
Found at i:18525292 original size:22 final size:23
Alignment explanation
Indices: 18525267--18525312 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
18525257 TTAATCTTTG
*
18525267 TATATTTC-ATTT-TTTTATTATT
1 TATAATTCAATTTATTTT-TTATT
18525289 TATAATTCAATTTATTTTTTATT
1 TATAATTCAATTTATTTTTTATT
18525312 T
1 T
18525313 TAAGCACAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 10 0.48
24 4 0.19
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (23 bp):
TATAATTCAATTTATTTTTTATT
Found at i:18528116 original size:25 final size:27
Alignment explanation
Indices: 18528087--18528153 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 27
18528077 TTTGATTTAT
18528087 ATTTATTAAAA-AAATTATTT-TATTC
1 ATTTATTAAAATAAATTATTTATATTC
18528112 ATTTA--AATAATAAATTATTTATATTC
1 ATTTATTAA-AATAAATTATTTATATTC
*
18528138 ATTTAATTAAATTAAA
1 ATTT-ATTAAAATAAA
18528154 CAAACTCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
23 2 0.06
24 2 0.06
25 14 0.40
26 9 0.26
27 1 0.03
28 5 0.14
29 2 0.06
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTATTAAAATAAATTATTTATATTC
Found at i:18528225 original size:19 final size:19
Alignment explanation
Indices: 18528198--18528245 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
18528188 ACGAACGTAT
*
18528198 ATAAATAAATACATTCATAA
1 ATAAATAAATA-AATCATAA
18528218 AT-AATAAATAAATCATAA
1 ATAAATAAATAAATCATAA
*
18528236 TTAAATAAAT
1 ATAAATAAAT
18528246 TTAAACAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.32
19 15 0.60
20 2 0.08
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAATAAATAAATCATAA
Found at i:18528300 original size:14 final size:14
Alignment explanation
Indices: 18528220--18528300 Score: 56
Period size: 14 Copynumber: 5.5 Consensus size: 14
18528210 ATTCATAAAT
18528220 AATAAATAAATCATA
1 AATAAATAAAT-ATA
* *
18528235 ATTAAATAAATTTA
1 AATAAATAAATATA
* *
18528249 AACAAATAGATCATA
1 AATAAATAAAT-ATA
*
18528264 AACGAACATAAATA-A
1 AA-TAA-ATAAATATA
*
18528279 ACTCAAATAAATATA
1 AAT-AAATAAATATA
18528294 AATAAAT
1 AATAAAT
18528301 CTTAAAATAA
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
14 21 0.42
15 21 0.42
16 3 0.06
17 5 0.10
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (14 bp):
AATAAATAAATATA
Found at i:18528317 original size:23 final size:20
Alignment explanation
Indices: 18528271--18528318 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 20
18528261 ATAAACGAAC
*
18528271 ATAAATAAACTCAAATAAAT
1 ATAAATAAACTAAAATAAAT
18528291 ATAAATAAATCTTAAAATAAAAT
1 ATAAATAAA-C-TAAAAT-AAAT
18528314 ATAAA
1 ATAAA
18528319 AATATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 1 0.04
22 5 0.21
23 9 0.38
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (20 bp):
ATAAATAAACTAAAATAAAT
Found at i:18528362 original size:11 final size:11
Alignment explanation
Indices: 18528342--18528386 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
18528332 TAATATTATT
18528342 ATAAATAAATA
1 ATAAATAAATA
*
18528353 ATAAAAAAATA
1 ATAAATAAATA
* *
18528364 ATAATTGAATA
1 ATAAATAAATA
*
18528375 ATAAACAAATA
1 ATAAATAAATA
18528386 A
1 A
18528387 ATTTTAAATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (11 bp):
ATAAATAAATA
Found at i:18535684 original size:20 final size:20
Alignment explanation
Indices: 18535659--18535718 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
18535649 AAGATTCATA
18535659 TATATTGATTTAAATTTATT
1 TATATTGATTTAAATTTATT
* *
18535679 TATATTCATTTAAGATTTGTT
1 TATATTGATTTAA-ATTTATT
*
18535700 AAT-TTG-TTTAAATTTATT
1 TATATTGATTTAAATTTATT
18535718 T
1 T
18535719 TGTTATAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 6 0.18
19 5 0.15
20 14 0.42
21 8 0.24
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.60
Consensus pattern (20 bp):
TATATTGATTTAAATTTATT
Found at i:18537047 original size:31 final size:31
Alignment explanation
Indices: 18536995--18537053 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
18536985 ATTTCGAATA
** *
18536995 AAATCAATTATAATTTTATATATATATATAT
1 AAATCAATTATAATTAAATATAAATATATAT
18537026 AAATCAAATTA-AATTAAATATAAATATA
1 AAATC-AATTATAATTAAATATAAATATA
18537054 ATATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 19 0.79
32 5 0.21
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (31 bp):
AAATCAATTATAATTAAATATAAATATATAT
Found at i:18540071 original size:20 final size:20
Alignment explanation
Indices: 18540046--18540085 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18540036 TCCTCAAACA
18540046 AAGGAAGCCAATCAAAGTTT
1 AAGGAAGCCAATCAAAGTTT
18540066 AAGGAAGCCAATCAAAGTTT
1 AAGGAAGCCAATCAAAGTTT
18540086 TTACTGGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGGAAGCCAATCAAAGTTT
Found at i:18543980 original size:125 final size:127
Alignment explanation
Indices: 18543747--18544002 Score: 383
Period size: 125 Copynumber: 2.0 Consensus size: 127
18543737 AGGAAAGGGT
*
18543747 TATAAGTACTATGATTTGATTTGAATTCCAGACCTGCTCGATGTCAGTTCTCAGTGGCCACACAA
1 TATAAGTACTATGATTTGATTTGAATTCCAGACCTGCTCGACGTCAG-TCT-AGTGGCCACACAA
18543812 ACCAACTGATTTAAGCTCCCTTACACACAACATTTTCATTAAAACGTTTAAAACCCAATAATCC
64 ACCAACTGATTTAAGCTCCCTTACACACAACATTTTCATTAAAACGTTTAAAACCCAATAATCC
* **
18543876 TATAAGTGCTATGATTTGATTTGAATTCCAGACCTGCTCGACGTCAG-CT-GTGG-CAGCATGAA
1 TATAAGTACTATGATTTGATTTGAATTCCAGACCTGCTCGACGTCAGTCTAGTGGCCA-CACAAA
* * * * *
18543938 TCAACTGATTTAAGCTGCCTTACACACCACATTTTCATTAAAACTTTTAAACCCCAATAATCC
65 CCAACTGATTTAAGCTCCCTTACACACAACATTTTCATTAAAACGTTTAAAACCCAATAATCC
18544001 TA
1 TA
18544003 ATTATCACAT
Statistics
Matches: 117, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
124 2 0.02
125 68 0.58
127 2 0.02
129 45 0.38
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (127 bp):
TATAAGTACTATGATTTGATTTGAATTCCAGACCTGCTCGACGTCAGTCTAGTGGCCACACAAAC
CAACTGATTTAAGCTCCCTTACACACAACATTTTCATTAAAACGTTTAAAACCCAATAATCC
Found at i:18546776 original size:62 final size:65
Alignment explanation
Indices: 18546673--18546795 Score: 198
Period size: 62 Copynumber: 1.9 Consensus size: 65
18546663 CCGGTCCTTC
*
18546673 GTTTATCTATGACCATGAATGATTATTGCCTTGGACCGGCAATTGTTGAAGACTTCAGCTTGTGT
1 GTTTATCTATGACCAT-AATGATTATTGCCATGGACCGGCAATTGTTGAAGACTTCAGCTTGTGT
18546738 T
65 T
*
18546739 GTTTATCTATGA-C-T-ATGATTATTGCCATGGACTGGCAATTGTTGAAGACTTCAGCTT
1 GTTTATCTATGACCATAATGATTATTGCCATGGACCGGCAATTGTTGAAGACTTCAGCTT
18546796 CTATGTCGTC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
62 41 0.75
64 1 0.02
65 1 0.02
66 12 0.22
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (65 bp):
GTTTATCTATGACCATAATGATTATTGCCATGGACCGGCAATTGTTGAAGACTTCAGCTTGTGTT
Found at i:18546981 original size:27 final size:27
Alignment explanation
Indices: 18546927--18546996 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
18546917 CTCACGTCAG
* *
18546927 CTGTATAAGAAAGTTC--GATCATCAA
1 CTGTATAACAGAGTTCAAGATCATCAA
18546952 CTGTATAACAGAGTTCAAGATCATCAA
1 CTGTATAACAGAGTTCAAGATCATCAA
18546979 CTGTATAACAGAGTTCAA
1 CTGTATAACAGAGTTCAA
18546997 TCAGGTACGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 14 0.34
27 27 0.66
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (27 bp):
CTGTATAACAGAGTTCAAGATCATCAA
Found at i:18548381 original size:21 final size:22
Alignment explanation
Indices: 18548357--18548404 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
18548347 CTCAAATTTA
18548357 ATAAAATATTA-TTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
18548378 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
18548400 ATAAA
1 ATAAA
18548405 TATAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:18548405 original size:21 final size:20
Alignment explanation
Indices: 18548356--18548407 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
18548346 ACTCAAATTT
18548356 AATA-AAATATTATTTTTAA
1 AATATAAATATTATTTTTAA
18548375 AATATAAAATATTATTTTTTAA
1 AATAT-AAATATTA-TTTTTAA
18548397 AATATAAATAT
1 AATATAAATAT
18548408 AAAATTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.13
21 14 0.47
22 12 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATAAATATTATTTTTAA
Found at i:18548419 original size:10 final size:9
Alignment explanation
Indices: 18548398--18548437 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
18548388 ATTTTTTAAA
18548398 ATATAAA-T
1 ATATAAATT
18548406 ATA-AAATT
1 ATATAAATT
18548414 ATAT-AATT
1 ATATAAATT
18548422 ATATAAATAT
1 ATATAAAT-T
18548432 ATATAA
1 ATATAA
18548438 TTGAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 3 0.11
8 15 0.54
9 3 0.11
10 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATATAAATT
Found at i:18548419 original size:16 final size:18
Alignment explanation
Indices: 18548398--18548437 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
18548388 ATTTTTTAAA
18548398 ATATAAATATA-AAAT-T
1 ATATAAATATATAAATAT
*
18548414 ATATAATTATATAAATAT
1 ATATAAATATATAAATAT
18548432 ATATAA
1 ATATAA
18548438 TTGAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 4 0.19
18 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAAATATATAAATAT
Found at i:18548427 original size:18 final size:18
Alignment explanation
Indices: 18548398--18548448 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
18548388 ATTTTTTAAA
*
18548398 ATATAAATATA-AAAT-T
1 ATATAATTATATAAATAT
18548414 ATATAATTATATAAATAT
1 ATATAATTATATAAATAT
18548432 ATATAATTGA-ATAAATA
1 ATATAATT-ATATAAATA
18548449 AGTAAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 10 0.32
17 4 0.13
18 16 0.52
19 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
ATATAATTATATAAATAT
Found at i:18556428 original size:13 final size:13
Alignment explanation
Indices: 18556410--18556434 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18556400 CCATTGAAAC
18556410 TGTAAAAAAAAAT
1 TGTAAAAAAAAAT
18556423 TGTAAAAAAAAA
1 TGTAAAAAAAAA
18556435 AATGCATGAA
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:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
TGTAAAAAAAAAT
Found at i:18557712 original size:2 final size:2
Alignment explanation
Indices: 18557705--18557735 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18557695 TCAATTGGTA
*
18557705 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18557736 GAAATGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:18558945 original size:17 final size:15
Alignment explanation
Indices: 18558923--18558965 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
18558913 TTAGAATTTG
18558923 GTTTTAGGGTTTACAGA
1 GTTTTAGGGTTTA-A-A
*
18558940 GTTTTAGGGCTTAAA
1 GTTTTAGGGTTTAAA
18558955 -TTTTAGGGTTT
1 GTTTTAGGGTTT
18558966 TGGATTTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 10 0.42
15 1 0.04
16 1 0.04
17 12 0.50
ACGTcount: A:0.21, C:0.05, G:0.28, T:0.47
Consensus pattern (15 bp):
GTTTTAGGGTTTAAA
Found at i:18559006 original size:30 final size:29
Alignment explanation
Indices: 18558953--18559032 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 29
18558943 TTAGGGCTTA
18558953 AATTTTAGGGTTTT-GGATTTGAGAGTTTG
1 AATTTTAGGGTTTTAGG-TTTGAGAGTTTG
18558982 AATTTTAGGGTTTTAAGGTTTGAGAGTTTG
1 AATTTTAGGGTTTT-AGGTTTGAGAGTTTG
* *
18559012 GATTTTAAGGTTTTGAGGTTT
1 AATTTTAGGGTTTT-AGGTTT
18559033 AAGGCTTTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 14 0.30
30 30 0.65
31 2 0.04
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (29 bp):
AATTTTAGGGTTTTAGGTTTGAGAGTTTG
Found at i:18559189 original size:14 final size:14
Alignment explanation
Indices: 18559154--18559234 Score: 51
Period size: 14 Copynumber: 5.7 Consensus size: 14
18559144 GGCTTAAGGA
*
18559154 TTTAGGGTTTGA-T
1 TTTAGGGTTTTAGT
*
18559167 GTTTGGGGTTTTAGT
1 -TTTAGGGTTTTAGT
* *
18559182 TTTAGGGTTTGGAGGG
1 TTTAGGGTTT-TA-GT
**
18559198 TTTAGGG-CCTAGT
1 TTTAGGGTTTTAGT
18559211 TTTAGGGTTTT-GTT
1 TTTAGGGTTTTAG-T
18559225 TTTAGGGTTT
1 TTTAGGGTTT
18559235 AAGGTTTGAG
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
13 9 0.18
14 32 0.63
15 2 0.04
16 8 0.16
ACGTcount: A:0.11, C:0.02, G:0.36, T:0.51
Consensus pattern (14 bp):
TTTAGGGTTTTAGT
Found at i:18559294 original size:30 final size:28
Alignment explanation
Indices: 18559216--18559294 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 28
18559206 CTAGTTTTAG
*
18559216 GGTTTTGTTTTTAGGGTTT-AAGGTTTGA
1 GGTTTTGATTTTA-GGTTTGAAGGTTTGA
*
18559244 GATTTTGATTTTAGGATTTGAAGGGTTTGA
1 GGTTTTGATTTTAGG-TTTGAA-GGTTTGA
*
18559274 GGTTTTGATCTTAGAGTTTGA
1 GGTTTTGATTTTAG-GTTTGA
18559295 GATTTTAGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.05
28 14 0.33
29 2 0.05
30 24 0.56
31 1 0.02
ACGTcount: A:0.19, C:0.01, G:0.30, T:0.49
Consensus pattern (28 bp):
GGTTTTGATTTTAGGTTTGAAGGTTTGA
Found at i:18559342 original size:21 final size:21
Alignment explanation
Indices: 18559295--18559351 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
18559285 TAGAGTTTGA
*
18559295 GATTTTAGGGTTTAGGGCTTT
1 GATTTTAGGGTTTAAGGCTTT
18559316 GATTTTAGGGTTTAAGG-TTT
1 GATTTTAGGGTTTAAGGCTTT
* *
18559336 CGGTTTTAAGGTTTAA
1 -GATTTTAGGGTTTAA
18559352 TTTTTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 3 0.09
21 29 0.91
ACGTcount: A:0.19, C:0.04, G:0.30, T:0.47
Consensus pattern (21 bp):
GATTTTAGGGTTTAAGGCTTT
Found at i:18559493 original size:3 final size:3
Alignment explanation
Indices: 18559485--18559514 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
18559475 TTATGAAAAT
18559485 TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
18559515 TTTTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18559535 original size:18 final size:18
Alignment explanation
Indices: 18559512--18559546 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18559502 ATTATTATAT
18559512 ATTTTTTAATTT-TAATTA
1 ATTTTTT-ATTTGTAATTA
18559530 ATTTTTTATTTGTAATT
1 ATTTTTTATTTGTAATT
18559547 CTTCAACATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTTTTTATTTGTAATTA
Found at i:18561578 original size:110 final size:110
Alignment explanation
Indices: 18561427--18561654 Score: 312
Period size: 110 Copynumber: 2.1 Consensus size: 110
18561417 TCATGTCTGA
* * * *
18561427 AGGTTTTATAGAATCGACTAGGATAATACCGTAAGTTAAAAAATAAAGAATCGATCGAAACAGCA
1 AGGTCTTATAGAATCGACTAGGATAATACCGTAAATAAAAAAATAAAGAATCGATCGAAACAACA
** * *
18561492 TCGTAAATTGAAATTATGCCCGAAAGTCTTAAAGATTATGTTCGG
66 TCGTAAATCAAAATTATACCCGAAAGTCTTAAAGATTATGTTCAG
* * * * *
18561537 AGGTCTTATAGAATCGACTGGGATAATATCGTAAATAAAAAAATAAAGAATTGATCGAGACAATA
1 AGGTCTTATAGAATCGACTAGGATAATACCGTAAATAAAAAAATAAAGAATCGATCGAAACAACA
* *
18561602 TCGTGAATCAAAATTATACCTGAAAGTCTTAAAGATTATGTTCAG
66 TCGTAAATCAAAATTATACCCGAAAGTCTTAAAGATTATGTTCAG
*
18561647 AAGTCTTA
1 AGGTCTTA
18561655 AAAATCATGC
Statistics
Matches: 102, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
110 102 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (110 bp):
AGGTCTTATAGAATCGACTAGGATAATACCGTAAATAAAAAAATAAAGAATCGATCGAAACAACA
TCGTAAATCAAAATTATACCCGAAAGTCTTAAAGATTATGTTCAG
Found at i:18561784 original size:22 final size:22
Alignment explanation
Indices: 18561743--18561785 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18561733 ACCGCGAATT
* *
18561743 AAAATTATACCCGGAGGTCTTA
1 AAAATTATACCCGAAAGTCTTA
*
18561765 AAAATTATACTCGAAAGTCTT
1 AAAATTATACCCGAAAGTCTT
18561786 TGAAATCATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (22 bp):
AAAATTATACCCGAAAGTCTTA
Found at i:18563974 original size:8 final size:8
Alignment explanation
Indices: 18563963--18564017 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 8
18563953 TAATTGAATA
18563963 TATTTTTT
1 TATTTTTT
18563971 TATTTTTT
1 TATTTTTT
18563979 TATTTTTT
1 TATTTTTT
18563987 TATCTTTTT
1 TAT-TTTTT
**
18563996 GCTTTTTT
1 TATTTTTT
*
18564004 TGTTTATTT
1 TATTT-TTT
18564013 T-TTTT
1 TATTTT
18564018 AAAATGCGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
7 1 0.02
8 30 0.73
9 10 0.24
ACGTcount: A:0.09, C:0.04, G:0.04, T:0.84
Consensus pattern (8 bp):
TATTTTTT
Found at i:18570648 original size:15 final size:15
Alignment explanation
Indices: 18570611--18570649 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
18570601 TTAAAGGTTA
*
18570611 GGGTTTTAGATTTTG
1 GGGTTTTGGATTTTG
*
18570626 GAGTTTTGGATTTTG
1 GGGTTTTGGATTTTG
18570641 GGGTTTTGG
1 GGGTTTTGG
18570650 TTTGAGTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.38, T:0.51
Consensus pattern (15 bp):
GGGTTTTGGATTTTG
Found at i:18570685 original size:21 final size:19
Alignment explanation
Indices: 18570630--18570688 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 19
18570620 ATTTTGGAGT
*
18570630 TTTGGATTTTGGGGTTTTGG
1 TTTGG-TTTTAGGGTTTTGG
*
18570650 TTTGAGTTTCAAGGGTTTTAGG
1 TTTG-GTTT-TAGGGTTTT-GG
18570672 ATTTGGTTTTAGGGTTT
1 -TTTGGTTTTAGGGTTT
18570689 AAAGAGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 7 0.22
21 15 0.47
22 6 0.19
23 4 0.12
ACGTcount: A:0.12, C:0.02, G:0.34, T:0.53
Consensus pattern (19 bp):
TTTGGTTTTAGGGTTTTGG
Found at i:18570699 original size:17 final size:15
Alignment explanation
Indices: 18570664--18570719 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 15
18570654 AGTTTCAAGG
*
18570664 GTTTTAGGATTT-G-
1 GTTTTAGGGTTTAGA
18570677 GTTTTAGGGTTTAAAGA
1 GTTTTAGGGTTT--AGA
18570694 GTTTTAGGGTTTAGA
1 GTTTTAGGGTTTAGA
18570709 -TTTTAGGGTTT
1 GTTTTAGGGTTT
18570720 TGGGGTTTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
13 11 0.29
14 11 0.29
15 3 0.08
16 1 0.03
17 12 0.32
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (15 bp):
GTTTTAGGGTTTAGA
Found at i:18570700 original size:30 final size:31
Alignment explanation
Indices: 18570655--18570719 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
18570645 TTTGGTTTGA
* * *
18570655 GTTTCAAGGGTTTTAGGATTT-GGTTTTAGG
1 GTTTAAAGAGTTTTAGGATTTAGATTTTAGG
*
18570685 GTTTAAAGAGTTTTAGGGTTTAGATTTTAGG
1 GTTTAAAGAGTTTTAGGATTTAGATTTTAGG
18570716 GTTT
1 GTTT
18570720 TGGGGTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.20, C:0.02, G:0.31, T:0.48
Consensus pattern (31 bp):
GTTTAAAGAGTTTTAGGATTTAGATTTTAGG
Found at i:18570705 original size:8 final size:8
Alignment explanation
Indices: 18570676--18570757 Score: 55
Period size: 8 Copynumber: 10.6 Consensus size: 8
18570666 TTTAGGATTT
18570676 GGTTTTAG
1 GGTTTTAG
*
18570684 GGTTTAAAG
1 GGTTT-TAG
*
18570693 AGTTTTAG
1 GGTTTTAG
18570701 GG-TTTA-
1 GGTTTTAG
*
18570707 GATTTTAG
1 GGTTTTAG
*
18570715 GGTTTTGG
1 GGTTTTAG
*
18570723 GGTTTGAG
1 GGTTTTAG
*
18570731 AG-TTT-G
1 GGTTTTAG
*
18570737 GATTTTAG
1 GGTTTTAG
*
18570745 GGTTTTGG
1 GGTTTTAG
18570753 GGTTT
1 GGTTT
18570758 GAAAGTTTTC
Statistics
Matches: 54, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
6 2 0.04
7 13 0.24
8 33 0.61
9 6 0.11
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.48
Consensus pattern (8 bp):
GGTTTTAG
Found at i:18570725 original size:22 final size:22
Alignment explanation
Indices: 18570694--18570749 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
18570684 GGTTTAAAGA
*
18570694 GTTTTAGGGTTT-AGATTTTAGG
1 GTTTTAGGGTTTGAGAGTTT-GG
*
18570716 GTTTTGGGGTTTGAGAGTTTGG
1 GTTTTAGGGTTTGAGAGTTTGG
*
18570738 ATTTTAGGGTTT
1 GTTTTAGGGTTT
18570750 TGGGGTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (22 bp):
GTTTTAGGGTTTGAGAGTTTGG
Found at i:18570743 original size:30 final size:29
Alignment explanation
Indices: 18570702--18570820 Score: 107
Period size: 30 Copynumber: 4.0 Consensus size: 29
18570692 GAGTTTTAGG
*
18570702 GTTTAGATTTTAGGGTTTTGGGGTTTGAGA
1 GTTTGGATTTT-GGGTTTTGGGGTTTGAGA
*
18570732 GTTTGGATTTTAGGGTTTTGGGGTTTGAAA
1 GTTTGGATTTT-GGGTTTTGGGGTTTGAGA
** *
18570762 GTTTTCATTTTGGG-TTTGAAGGGTTTAAG-
1 GTTTGGATTTTGGGTTTTG--GGGTTTGAGA
* * *
18570791 GTTTAGGATTTTTGATTTTAGGGTTTGAGA
1 GTTT-GGATTTTGGGTTTTGGGGTTTGAGA
18570821 TTTTAGAGTT
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
28 4 0.06
29 15 0.21
30 50 0.69
31 3 0.04
ACGTcount: A:0.18, C:0.01, G:0.34, T:0.48
Consensus pattern (29 bp):
GTTTGGATTTTGGGTTTTGGGGTTTGAGA
Found at i:18570969 original size:30 final size:30
Alignment explanation
Indices: 18570933--18570990 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
18570923 TAGGGTTCGA
*
18570933 GGTTTGG-GATTTTGATTTTAGGATTTGAAG
1 GGTTTGGTG-TTTCGATTTTAGGATTTGAAG
*
18570963 GGTTTGGTGTTTCGATTTTAGGGTTTGA
1 GGTTTGGTGTTTCGATTTTAGGATTTGA
18570991 GATTTTGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (30 bp):
GGTTTGGTGTTTCGATTTTAGGATTTGAAG
Found at i:18571374 original size:3 final size:3
Alignment explanation
Indices: 18571343--18571409 Score: 52
Period size: 3 Copynumber: 23.7 Consensus size: 3
18571333 TAAAAAAATA
* * * * *
18571343 TAT TTT TAT TCT TAT TAT CAT CAT T-T TAT TAT TAT GAT T-T T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
18571388 TAT TTT TAT T-T TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
18571410 AAACATCAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 8 0.16
3 43 0.84
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:18574984 original size:25 final size:23
Alignment explanation
Indices: 18574956--18575024 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
18574946 ATTTTTTTAA
18574956 AATATCTCAAAATTATATATTTTTT
1 AATATCT-AAAATTAT-TATTTTTT
* *
18574981 AATATCTAAAACTCTTATTTTTT
1 AATATCTAAAATTATTATTTTTT
* *
18575004 TATATTTTAAAATTATT-TTTT
1 AATA-TCTAAAATTATTATTTT
18575025 ACTTTTTAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 15 0.41
24 15 0.41
25 7 0.19
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (23 bp):
AATATCTAAAATTATTATTTTTT
Found at i:18575024 original size:20 final size:20
Alignment explanation
Indices: 18574999--18575038 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18574989 AAACTCTTAT
18574999 TTTTTTA-TATTTTAAAATTA
1 TTTTTTACT-TTTTAAAATTA
*
18575019 TTTTTTACTTTTTAACATTA
1 TTTTTTACTTTTTAAAATTA
18575039 AAAATCATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTTACTTTTTAAAATTA
Found at i:18576423 original size:35 final size:36
Alignment explanation
Indices: 18576343--18576424 Score: 91
Period size: 35 Copynumber: 2.3 Consensus size: 36
18576333 CATATTATAT
18576343 TTAAATATTTAATTTAAAATTAATTAATAATAAATAAA
1 TTAAA-ATTTAATTTAAAATTAA-TAATAATAAATAAA
* *
18576381 --AATATTTAATTTAAAATTAA-AATCATTAAA-AAA
1 TTAAAATTTAATTTAAAATTAATAAT-AATAAATAAA
18576414 TTAAAATTTAA
1 TTAAAATTTAA
18576425 CAAATTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
33 6 0.16
34 5 0.13
35 25 0.66
36 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (36 bp):
TTAAAATTTAATTTAAAATTAATAATAATAAATAAA
Found at i:18576424 original size:15 final size:16
Alignment explanation
Indices: 18576393--18576432 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
18576383 TATTTAATTT
18576393 AAAATTAAAATCATTAA
1 AAAATTAAAAT-ATTAA
18576410 AAAATTAAAAT-TTAA
1 AAAATTAAAATATTAA
*
18576425 CAAATTAA
1 AAAATTAA
18576433 TACAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
17 11 0.50
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTAAAATATTAA
Found at i:18579010 original size:32 final size:33
Alignment explanation
Indices: 18578952--18579014 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
18578942 CTGAAACAGA
18578952 ACGGGTTGATCAAACATATATAAAATATGAAATC
1 ACGGGTTGATCAAACA-ATATAAAATATGAAATC
18578986 ACGGGTTGATCAAAC-ATATAAAATATGAA
1 ACGGGTTGATCAAACAATATAAAATATGAA
18579015 TTCATGCTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 14 0.48
34 15 0.52
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (33 bp):
ACGGGTTGATCAAACAATATAAAATATGAAATC
Found at i:18579673 original size:13 final size:14
Alignment explanation
Indices: 18579651--18579681 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
18579641 TTCAAATATA
*
18579651 TAATTTTTAATTAT
1 TAATTTTAAATTAT
18579665 TAATTTTAAATTAT
1 TAATTTTAAATTAT
18579679 TAA
1 TAA
18579682 ATATGATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TAATTTTAAATTAT
Found at i:18580654 original size:27 final size:26
Alignment explanation
Indices: 18580624--18580682 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
18580614 TTTTCTTTAT
18580624 TTATTTATTTTTTTAAATATTCTAA-AA
1 TTATTTATTTTTTT-AATA-TCTAACAA
* * *
18580651 TTATATCTTTTTTTAATATCTAACAC
1 TTATTTATTTTTTTAATATCTAACAA
18580677 TTATTT
1 TTATTT
18580683 TTTATGATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 5 0.19
26 10 0.37
27 12 0.44
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (26 bp):
TTATTTATTTTTTTAATATCTAACAA
Found at i:18581725 original size:68 final size:69
Alignment explanation
Indices: 18581596--18581732 Score: 267
Period size: 68 Copynumber: 2.0 Consensus size: 69
18581586 GTCTTTAACT
18581596 AAACTTTAGTTTAATTAATTAATTAATTACTTCACTTGATTGTATATAATTTAATTATTAATTAT
1 AAACTTTAGTTTAATTAATTAATTAATTACTTCACTTGATTGTATATAATTTAATTATTAATTAT
18581661 CACA
66 CACA
18581665 AAACTTTAGTTTAATTAATTAATTAATTAC-TCACTTGATTGTATATAATTTAATTATTAATTAT
1 AAACTTTAGTTTAATTAATTAATTAATTACTTCACTTGATTGTATATAATTTAATTATTAATTAT
18581729 CACA
66 CACA
18581733 CTTCATGAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 38 0.56
69 30 0.44
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.47
Consensus pattern (69 bp):
AAACTTTAGTTTAATTAATTAATTAATTACTTCACTTGATTGTATATAATTTAATTATTAATTAT
CACA
Found at i:18582469 original size:18 final size:18
Alignment explanation
Indices: 18582446--18582484 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
18582436 TGATAAAAAA
18582446 AAACATTGAAGTTATTTT
1 AAACATTGAAGTTATTTT
18582464 AAACATTGAAGTTATTTT
1 AAACATTGAAGTTATTTT
18582482 AAA
1 AAA
18582485 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (18 bp):
AAACATTGAAGTTATTTT
Found at i:18584810 original size:32 final size:33
Alignment explanation
Indices: 18584752--18584814 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
18584742 CTGAAACAGA
18584752 ACGGGTTGATCAAACATATATAAAATATGAAATC
1 ACGGGTTGATCAAACA-ATATAAAATATGAAATC
18584786 ACGGGTTGATCAAAC-ATATAAAATATGAA
1 ACGGGTTGATCAAACAATATAAAATATGAA
18584815 TTCATGCTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 14 0.48
34 15 0.52
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (33 bp):
ACGGGTTGATCAAACAATATAAAATATGAAATC
Found at i:18586468 original size:23 final size:24
Alignment explanation
Indices: 18586396--18586469 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
18586386 TATTTACTTT
*
18586396 TTAAATGTTTCAAAATTATATTTTT-
1 TTAAATATTT-AAAATTAT-TTTTTA
* * *
18586421 TTAAATATTTAAAACTCTTACTTTA
1 TTAAATATTTAAAATTATT-TTTTA
*
18586446 TTATAT-TTTAAAATTATTTTTTA
1 TTAAATATTTAAAATTATTTTTTA
18586469 T
1 T
18586470 GATTTTTTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
23 6 0.15
24 19 0.49
25 14 0.36
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.57
Consensus pattern (24 bp):
TTAAATATTTAAAATTATTTTTTA
Found at i:18586686 original size:14 final size:13
Alignment explanation
Indices: 18586631--18586714 Score: 51
Period size: 14 Copynumber: 6.1 Consensus size: 13
18586621 AAAAACAAAA
**
18586631 TATTATTACATAT
1 TATTATTATTTAT
* *
18586644 AATTATTAATTTAA
1 TATTATT-ATTTAT
* * *
18586658 TATTTTTAATAAT
1 TATTATTATTTAT
18586671 TATTTATTATTTAT
1 TA-TTATTATTTAT
*
18586685 TATAATTTATTTTAT
1 TATTA-TTA-TTTAT
18586700 TATTATTATTATAT
1 TATTATTATT-TAT
18586714 T
1 T
18586715 TACATTTAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
13 15 0.29
14 28 0.54
15 9 0.17
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:18586702 original size:18 final size:17
Alignment explanation
Indices: 18586658--18586715 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
18586648 ATTAATTTAA
* * *
18586658 TATTTTTAATAATTATT
1 TATTTTTTATTATAATT
*
18586675 TATTATTTATTATAATT
1 TATTTTTTATTATAATT
*
18586692 TATTTTATTATTATTATT
1 TATTTT-TTATTATAATT
18586710 ATATTT
1 -TATTT
18586716 ACATTTAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 18 0.55
18 10 0.30
19 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTTTTATTATAATT
Found at i:18586716 original size:18 final size:18
Alignment explanation
Indices: 18586669--18586716 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
18586659 ATTTTTAATA
18586669 ATTATTTA-TTATTTATT
1 ATTATTTATTTATTTATT
*
18586686 ATAATTTATTT-TATTATT
1 ATTATTTATTTAT-TTATT
18586704 ATTATTATATTTA
1 ATTATT-TATTTA
18586717 CATTTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 8 0.32
18 12 0.48
19 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTATTTATTTATTTATT
Found at i:18586784 original size:27 final size:26
Alignment explanation
Indices: 18586673--18586788 Score: 80
Period size: 27 Copynumber: 4.4 Consensus size: 26
18586663 TTAATAATTA
* *
18586673 TTTATTATTTATTATAATTTATTTTA-
1 TTTATTATTT-TAATAATTAATTTTAT
* * *
18586699 -TTATTATTATT-ATATTTACATTTAAA
1 TTTATTATT-TTAATAATTA-ATTTTAT
* *
18586725 TATA-TATTTTTATAATTAATTTTAAT
1 TTTATTATTTTAATAATTAATTTT-AT
18586751 TTTATTATTTTAATAATTAATTTT-T
1 TTTATTATTTTAATAATTAATTTTAT
18586776 TTATCATTATTTT
1 TT-T-ATTATTTT
18586789 TAATTTCATC
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
24 5 0.07
25 23 0.32
26 16 0.22
27 28 0.39
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTATTATTTTAATAATTAATTTTAT
Found at i:18586791 original size:21 final size:20
Alignment explanation
Indices: 18586731--18586794 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
18586721 TAAATATATA
*
18586731 TTTTTATAATTAATTTTAATT
1 TTTTTAT-ATTATTTTTAATT
* * **
18586752 TTATTATTTTAATAATTAATT
1 TTTTTATATT-ATTTTTAATT
18586773 TTTTTATCATTATTTTTAATT
1 TTTTTAT-ATTATTTTTAATT
18586794 T
1 T
18586795 CATCAAAATC
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTATATTATTTTTAATT
Found at i:18587062 original size:16 final size:16
Alignment explanation
Indices: 18587025--18587062 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
18587015 AAGGATAATG
18587025 ATTTT-ATGGATTAAA
1 ATTTTAATGGATTAAA
**
18587040 AAGTTAATGGATTAAA
1 ATTTTAATGGATTAAA
18587056 ATTTTAA
1 ATTTTAA
18587063 AAAGTTTATG
Statistics
Matches: 18, Mismatches: 4, Indels: 1
0.78 0.17 0.04
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (16 bp):
ATTTTAATGGATTAAA
Found at i:18587062 original size:24 final size:24
Alignment explanation
Indices: 18587035--18587081 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
18587025 ATTTTATGGA
*
18587035 TTAAAAAGTTAATGGATTAAAATT
1 TTAAAAAGTTAATGAATTAAAATT
*
18587059 TTAAAAAGTTTATGAATTAAAAT
1 TTAAAAAGTTAATGAATTAAAAT
18587082 AATAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (24 bp):
TTAAAAAGTTAATGAATTAAAATT
Found at i:18587322 original size:35 final size:35
Alignment explanation
Indices: 18587276--18587393 Score: 127
Period size: 35 Copynumber: 3.4 Consensus size: 35
18587266 TTTAGCTTAA
18587276 TTAATTAATTAATTACTTCACTTGATTGTATATAAT
1 TTAA-TAATTAATTACTTCACTTGATTGTATATAAT
* *** *
18587312 TTAATCATTAATTA--TCACAAAATT-TATTTTAA-
1 TTAATAATTAATTACTTCACTTGATTGTA-TATAAT
18587344 TTAATTAATTAATTACTTCACTTGATTGTATATAAT
1 TTAA-TAATTAATTACTTCACTTGATTGTATATAAT
*
18587380 TTAATTATTAATTA
1 TTAATAATTAATTA
18587394 TCACACTTCA
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
32 6 0.09
33 20 0.31
35 29 0.45
36 10 0.15
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (35 bp):
TTAATAATTAATTACTTCACTTGATTGTATATAAT
Found at i:18587347 original size:68 final size:68
Alignment explanation
Indices: 18587272--18587398 Score: 245
Period size: 68 Copynumber: 1.9 Consensus size: 68
18587262 AAACTTTAGC
18587272 TTAATTAATTAATTAATTACTTCACTTGATTGTATATAATTTAATCATTAATTATCACAAAATTT
1 TTAATTAATTAATTAATTACTTCACTTGATTGTATATAATTTAATCATTAATTATCACAAAATTT
18587337 ATT
66 ATT
*
18587340 TTAATTAATTAATTAATTACTTCACTTGATTGTATATAATTTAATTATTAATTATCACA
1 TTAATTAATTAATTAATTACTTCACTTGATTGTATATAATTTAATCATTAATTATCACA
18587399 CTTCATGAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (68 bp):
TTAATTAATTAATTAATTACTTCACTTGATTGTATATAATTTAATCATTAATTATCACAAAATTT
ATT
Found at i:18593363 original size:172 final size:175
Alignment explanation
Indices: 18593076--18593390 Score: 451
Period size: 172 Copynumber: 1.8 Consensus size: 175
18593066 TTTGTATGAC
* * * ****
18593076 GGTATATTGAAGGTATTTTACAGTAGAAAACGCCTTTAATAATTTTTAAAATTTTTCAAAGGAAA
1 GGTATATTGAAGGCATTTTACAATAGAAAACGCATTTAATAATGCCCAAAATTTTTCAAAGGAAA
18593141 ATATTGAAGGCGTCTGTTATTAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAGGCATATT
66 ATATTGAAGGCGTCTGTTATTAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAGGCATATT
18593206 G-AAG-GCATTTTATAATAAAAGACACCTTTAATAATCCTATCGT
131 GAAAGCGCATTTTATAATAAAAGACACCTTTAATAATCCTATCGT
* * *
18593249 GGTATATTGAAGGCATTTTATAATAGAAGATGCATTTAATAATGCCCAAAA-TTTT-AAAGGAAA
1 GGTATATTGAAGGCATTTTACAATAGAAAACGCATTTAATAATGCCCAAAATTTTTCAAAGG-AA
* * * *
18593312 AATATTGAAGGCGTCTGTTATTAACAAACACTTTTC-GTAATGGATTACTAAGTTTGAGGGTATA
65 AATATTGAAGGCGTCTGTTATTAACAAACAC-CTTCAGTAATGGATTACTAAGTTTAAAGGCATA
18593376 TTGAAAGCGCATTTT
129 TTGAAAGCGCATTTT
18593391 CGAATAAATG
Statistics
Matches: 124, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
171 5 0.04
172 65 0.52
173 47 0.38
174 7 0.06
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (175 bp):
GGTATATTGAAGGCATTTTACAATAGAAAACGCATTTAATAATGCCCAAAATTTTTCAAAGGAAA
ATATTGAAGGCGTCTGTTATTAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAGGCATATT
GAAAGCGCATTTTATAATAAAAGACACCTTTAATAATCCTATCGT
Found at i:18611981 original size:20 final size:22
Alignment explanation
Indices: 18611939--18611983 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
18611929 ATTTGCATTA
*
18611939 TATTTTTTTCAATATATTATTG
1 TATTATTTTCAATATATTATTG
*
18611961 TATTATTTT-AAT-TATTTTTG
1 TATTATTTTCAATATATTATTG
18611981 TAT
1 TAT
18611984 AAAAGTGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 3 0.14
22 8 0.38
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TATTATTTTCAATATATTATTG
Found at i:18623649 original size:27 final size:27
Alignment explanation
Indices: 18623609--18623671 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
18623599 CTAAATCATC
* * *
18623609 CAACACCTGTGTTTCACTACCAAAGTT
1 CAACACTTGAGTTTCACCACCAAAGTT
*
18623636 CAACACTTGAGTTTCACCACCAAGGTT
1 CAACACTTGAGTTTCACCACCAAAGTT
*
18623663 CAAAACTTG
1 CAACACTTG
18623672 GGTCTCCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CAACACTTGAGTTTCACCACCAAAGTT
Found at i:18624862 original size:16 final size:16
Alignment explanation
Indices: 18624837--18624869 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
18624827 AATTGAATAA
18624837 TAAATACA-TTTAAAT
1 TAAATACATTTTAAAT
18624852 TAAATTACATTTTAAAT
1 TAAA-TACATTTTAAAT
18624869 T
1 T
18624870 CTTAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 4 0.25
17 8 0.50
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATACATTTTAAAT
Found at i:18625266 original size:25 final size:25
Alignment explanation
Indices: 18625204--18625255 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
18625194 TAGTTGCTAA
*
18625204 TTGCTACATTCATTTTAAGAAATTC
1 TTGCTACCTTCATTTTAAGAAATTC
18625229 TTGCTACCTTCATTTTAAGAAATTC
1 TTGCTACCTTCATTTTAAGAAATTC
18625254 TT
1 TT
18625256 TGCACTGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (25 bp):
TTGCTACCTTCATTTTAAGAAATTC
Found at i:18629471 original size:3 final size:3
Alignment explanation
Indices: 18629463--18629490 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
18629453 AGACAGTTGG
18629463 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
18629491 CTAGCTTTTG
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:18629746 original size:3 final size:3
Alignment explanation
Indices: 18629732--18629767 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
18629722 GCTATTTTTC
*
18629732 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18629768 AAAATAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:18629781 original size:12 final size:12
Alignment explanation
Indices: 18629766--18629790 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18629756 TATTATTATT
18629766 ATAAAATAAATA
1 ATAAAATAAATA
18629778 ATAAAATAAATA
1 ATAAAATAAATA
18629790 A
1 A
18629791 AATAGTAAAA
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:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAATAAATA
Found at i:18629793 original size:17 final size:17
Alignment explanation
Indices: 18629769--18629806 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
18629759 TATTATTATA
18629769 AAAT-AAATAATAAAAT
1 AAATAAAATAATAAAAT
*
18629785 AAATAAAATAGTAAAAT
1 AAATAAAATAATAAAAT
*
18629802 TAATA
1 AAATA
18629807 TATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATAAAATAATAAAAT
Found at i:18630281 original size:16 final size:16
Alignment explanation
Indices: 18630262--18630312 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
18630252 AATATTTTAA
18630262 TAATTTAATATGTAAT
1 TAATTTAATATGTAAT
18630278 TAATTTTATATTATGTTAA-
1 TAA-TTTA-A-TATG-TAAT
18630297 -AATTTAATATGTAAT
1 TAATTTAATATGTAAT
18630312 T
1 T
18630313 TAATAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
14 3 0.10
15 4 0.14
16 4 0.14
17 8 0.28
18 3 0.10
19 4 0.14
20 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TAATTTAATATGTAAT
Found at i:18633946 original size:41 final size:41
Alignment explanation
Indices: 18633877--18633974 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 41
18633867 GTCTTCATGC
* * * * *
18633877 ATAAAGAGCATGAAACAGGTGCATATGGCCTTCATGCGTAA
1 ATAAATAGTATGAAATAGGTACACATGGCCTTCATGCGTAA
* *
18633918 ATAGATAGTATGAAATAGGTACACATGGCCTTCATGTGTAA
1 ATAAATAGTATGAAATAGGTACACATGGCCTTCATGCGTAA
*
18633959 ATAAATAGTATAAAAT
1 ATAAATAGTATGAAAT
18633975 TCATTGACAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (41 bp):
ATAAATAGTATGAAATAGGTACACATGGCCTTCATGCGTAA
Found at i:18637251 original size:61 final size:61
Alignment explanation
Indices: 18637175--18637311 Score: 154
Period size: 61 Copynumber: 2.2 Consensus size: 61
18637165 AGAAAAAGGT
* *
18637175 ATTATAATAAGTTTGACCAAATAT-AGTAA-AAGGGCATTTCTATAATTAT-AGTTTGAGGAGC
1 ATTATAATAATTTTGACCAAATATGA-TAATAAGGGCATTTCTATAATTATGA-TATGAGGA-C
* * * * * *
18637236 ATTACAATAATTTTGATCAATTATGATAATAAGGGCATTTTTGTAATTATGATATGAGGAT
1 ATTATAATAATTTTGACCAAATATGATAATAAGGGCATTTCTATAATTATGATATGAGGAC
18637297 ATTATAATAATTTTG
1 ATTATAATAATTTTG
18637312 GTTGATTATA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
61 37 0.58
62 26 0.41
63 1 0.02
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (61 bp):
ATTATAATAATTTTGACCAAATATGATAATAAGGGCATTTCTATAATTATGATATGAGGAC
Found at i:18645793 original size:15 final size:15
Alignment explanation
Indices: 18645775--18645804 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18645765 TAAAATGCAT
18645775 TTAGATTGAAAGAAG
1 TTAGATTGAAAGAAG
*
18645790 TTAGATTTAAAGAAG
1 TTAGATTGAAAGAAG
18645805 AACTCAAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (15 bp):
TTAGATTGAAAGAAG
Found at i:18646921 original size:17 final size:18
Alignment explanation
Indices: 18646887--18646923 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
18646877 AATTGTTAAC
18646887 AGTTTATATTAATGTTTAT
1 AGTTTATATT-ATGTTTAT
18646906 AGTTTATATT-TGTTTAT
1 AGTTTATATTATGTTTAT
18646923 A
1 A
18646924 TTATCCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (18 bp):
AGTTTATATTATGTTTAT
Found at i:18646955 original size:19 final size:19
Alignment explanation
Indices: 18646931--18646971 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
18646921 ATATTATCCA
*
18646931 ATGGACAAGTATGCTTTAT
1 ATGGACAAGCATGCTTTAT
18646950 ATGGACAAGCATGCTTTAT
1 ATGGACAAGCATGCTTTAT
18646969 ATG
1 ATG
18646972 TACAGGGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (19 bp):
ATGGACAAGCATGCTTTAT
Found at i:18649872 original size:11 final size:11
Alignment explanation
Indices: 18649858--18649882 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18649848 ATTCACATGC
18649858 ATTTCAACCAA
1 ATTTCAACCAA
18649869 ATTTCAACCAA
1 ATTTCAACCAA
18649880 ATT
1 ATT
18649883 AATAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (11 bp):
ATTTCAACCAA
Found at i:18650919 original size:40 final size:40
Alignment explanation
Indices: 18650867--18650944 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
18650857 CTTCACACAT
*
18650867 TTTTTTTAATTTTAAATGAAATTACTTAATTACTTTTTTA
1 TTTTTTAAATTTTAAATGAAATTACTTAATTACTTTTTTA
*
18650907 TTTTTTAAATTTTAAGTGAAATTACTTAATTACTTTTT
1 TTTTTTAAATTTTAAATGAAATTACTTAATTACTTTTT
18650945 CTCAAACTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (40 bp):
TTTTTTAAATTTTAAATGAAATTACTTAATTACTTTTTTA
Found at i:18651065 original size:34 final size:34
Alignment explanation
Indices: 18651027--18651095 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
18651017 ACAAGTCTCT
* *
18651027 AGATTTACAGATTTGAAAA-CTTTTAAAAATTTTC
1 AGATTCACA-ATTTCAAAAGCTTTTAAAAATTTTC
* *
18651061 AGATTCACATTTTCAAAAGCTTTTAAAAGTTTTC
1 AGATTCACAATTTCAAAAGCTTTTAAAAATTTTC
18651095 A
1 A
18651096 TCCCACATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 7 0.23
34 23 0.77
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.41
Consensus pattern (34 bp):
AGATTCACAATTTCAAAAGCTTTTAAAAATTTTC
Found at i:18660251 original size:102 final size:104
Alignment explanation
Indices: 18659998--18660284 Score: 330
Period size: 105 Copynumber: 2.8 Consensus size: 104
18659988 ATCCACACCT
* * * * * *
18659998 GGTGAAGGGACTTTTGTTTCTGTGGAGTCTATTTCCATATTGGAGAAATCAGTACTTTCAGCCTT
1 GGTGAAGGAACTTTTGTTTCTATGGGGTCTATTTCCATTTTGGAGACATCAGTACTTTCAACCTT
* *
18660063 AGGCTGCTGAGAAGCTTCAACATCATCATCTTCCAGTGGC
66 AGGCTGCTGAGAAGCTTCAACACCATCA-CTTCAAGTGGC
* * * * *
18660103 GGTGAAGGAGCTTTTGTTTCCATGGGCTCTATTTCCATATTT-GAGACATCTGTGCTTTCAACCT
1 GGTGAAGGAACTTTTGTTTCTATGGGGTCTATTTCCAT-TTTGGAGACATCAGTACTTTCAACCT
* * * *
18660167 TTGGCTGATGAGAAGCTTCAGCACCGA-CA-TTCAATTGG-
65 TAGGCTGCTGAGAAGCTTCAACACC-ATCACTTCAAGTGGC
** * *
18660205 GGTGAAGGAACTTTTGTTTCTATGGGGTCTATTTTTATTTTGGAGACATCAGCATTTTCAACCTT
1 GGTGAAGGAACTTTTGTTTCTATGGGGTCTATTTCCATTTTGGAGACATCAGTACTTTCAACCTT
18660270 AGGCTGCTGAGAAGC
66 AGGCTGCTGAGAAGC
18660285 CTCCGCATGA
Statistics
Matches: 151, Mismatches: 28, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
101 3 0.02
102 65 0.43
103 7 0.05
105 73 0.48
106 3 0.02
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (104 bp):
GGTGAAGGAACTTTTGTTTCTATGGGGTCTATTTCCATTTTGGAGACATCAGTACTTTCAACCTT
AGGCTGCTGAGAAGCTTCAACACCATCACTTCAAGTGGC
Found at i:18660306 original size:102 final size:102
Alignment explanation
Indices: 18659998--18660299 Score: 313
Period size: 102 Copynumber: 2.9 Consensus size: 102
18659988 ATCCACACCT
* * * * * *
18659998 GGTGAAGGGACTTTTGTTTCTGTGGAGTCTATTTCCATATTGGAGAAATCAGTACTTTCAGCCTT
1 GGTGAAGGAACTTTTGTTTCTATGGGGTCTATTTCCATTTTGGAGACATCAGTACTTTCAACCTT
* * * *
18660063 AGGCTGCTGAGAAGCTTCAACATCATCATCTTCCAGTGGC
66 AGGCTGCTGAGAAGCTTC--C-GCATGATCTTCAATTGGC
* * * * *
18660103 GGTGAAGGAGCTTTTGTTTCCATGGGCTCTATTTCCATATTT-GAGACATCTGTGCTTTCAACCT
1 GGTGAAGGAACTTTTGTTTCTATGGGGTCTATTTCCAT-TTTGGAGACATCAGTACTTTCAACCT
* * * *
18660167 TTGGCTGATGAGAAGCTTCAGCACCGA-CATTCAATTGG-
65 TAGGCTGCTGAGAAGCTTCCGCA-TGATC-TTCAATTGGC
** * *
18660205 GGTGAAGGAACTTTTGTTTCTATGGGGTCTATTTTTATTTTGGAGACATCAGCATTTTCAACCTT
1 GGTGAAGGAACTTTTGTTTCTATGGGGTCTATTTCCATTTTGGAGACATCAGTACTTTCAACCTT
*
18660270 AGGCTGCTGAGAAGCCTCCGCATGATCTTC
66 AGGCTGCTGAGAAGCTTCCGCATGATCTTC
18660300 TGATTGGAGC
Statistics
Matches: 159, Mismatches: 33, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
101 8 0.05
102 74 0.47
103 8 0.05
105 67 0.42
106 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (102 bp):
GGTGAAGGAACTTTTGTTTCTATGGGGTCTATTTCCATTTTGGAGACATCAGTACTTTCAACCTT
AGGCTGCTGAGAAGCTTCCGCATGATCTTCAATTGGC
Found at i:18661737 original size:69 final size:70
Alignment explanation
Indices: 18661562--18661737 Score: 228
Period size: 72 Copynumber: 2.5 Consensus size: 70
18661552 TTCAGAGAAT
* * * * *
18661562 GCTCTGCTTCAAATTTAGAATTATTCTCAACCATGGCAGGTACCTCCACTGTGCCTGACTTATCT
1 GCTCTGATTCAAATTCAGAATTGTTCTCAACCATAGCAGGTACATCCACTGTGCCTGACTTATCT
18661627 GGATAAG
66 GG--AAG
* * * *
18661634 GCTCTGATTCACATTCAGAATTGTTCTTAACCATAGCAGGTGCATCCACTGTGCCTGATTTATCT
1 GCTCTGATTCAAATTCAGAATTGTTCTCAACCATAGCAGGTACATCCACTGTGCCTGACTTATCT
*
18661699 GG-GG
66 GGAAG
*
18661703 GCTCTGATTCATATTCAGAATTGTTCTCAACCATA
1 GCTCTGATTCAAATTCAGAATTGTTCTCAACCATA
18661738 CCTGGTGTGT
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
69 34 0.37
72 58 0.63
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (70 bp):
GCTCTGATTCAAATTCAGAATTGTTCTCAACCATAGCAGGTACATCCACTGTGCCTGACTTATCT
GGAAG
Found at i:18661760 original size:69 final size:69
Alignment explanation
Indices: 18661562--18661769 Score: 193
Period size: 72 Copynumber: 3.0 Consensus size: 69
18661552 TTCAGAGAAT
* * * * ** * * * *
18661562 GCTCTGCTTCAAATTTAGAATTATTCTCAACCATGGCAGGTACCTCCACTGTGCCTGACTTATCT
1 GCTCTGATTCACATTCAGAATTGTTCTCAACCATACCAGGTGCATCCACTGTACCTGACATATCT
*
18661627 GGATAAG
66 GG---GG
* * * **
18661634 GCTCTGATTCACATTCAGAATTGTTCTTAACCATAGCAGGTGCATCCACTGTGCCTGATTTATCT
1 GCTCTGATTCACATTCAGAATTGTTCTCAACCATACCAGGTGCATCCACTGTACCTGACATATCT
18661699 GGGG
66 GGGG
* * **
18661703 GCTCTGATTCATATTCAGAATTGTTCTCAACCATACCTGGTGTGTCCAAC-GTACCTGACATATC
1 GCTCTGATTCACATTCAGAATTGTTCTCAACCATACCAGGTGCATCC-ACTGTACCTGACATATC
18661767 TGG
65 TGG
18661770 ACAGGTAACA
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
69 56 0.48
70 2 0.02
72 58 0.50
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (69 bp):
GCTCTGATTCACATTCAGAATTGTTCTCAACCATACCAGGTGCATCCACTGTACCTGACATATCT
GGGG
Found at i:18665761 original size:6 final size:6
Alignment explanation
Indices: 18665751--18665815 Score: 67
Period size: 6 Copynumber: 10.8 Consensus size: 6
18665741 TGGTAGTTGG
* * * * *
18665751 GGAGGT TGAGGT GGAGGT GGAGGT AGAGGT GAAGGT GAAGGT GAAGGT
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT
* *
18665799 GAAGGT GAAGGT GGAGG
1 GGAGGT GGAGGT GGAGG
18665816 ATTAGGTTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.26, C:0.00, G:0.57, T:0.17
Consensus pattern (6 bp):
GGAGGT
Found at i:18665768 original size:12 final size:12
Alignment explanation
Indices: 18665759--18665815 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
18665749 GGGGAGGTTG
*
18665759 AGGTGGAGGTGG
1 AGGTGGAGGTGA
*
18665771 AGGTAGAGGTGA
1 AGGTGGAGGTGA
*
18665783 AGGTGAAGGTGA
1 AGGTGGAGGTGA
*
18665795 AGGTGAAGGTGA
1 AGGTGGAGGTGA
18665807 AGGTGGAGG
1 AGGTGGAGG
18665816 ATTAGGTTCG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.28, C:0.00, G:0.56, T:0.16
Consensus pattern (12 bp):
AGGTGGAGGTGA
Found at i:18665772 original size:18 final size:18
Alignment explanation
Indices: 18665753--18665815 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 18
18665743 GTAGTTGGGG
* *
18665753 AGGTTGAGGTGGAGGTGG
1 AGGTTGAGGTGAAGGTGA
*
18665771 AGGTAGAGGTGAAGGTGA
1 AGGTTGAGGTGAAGGTGA
18665789 AGG-TGAAGGTGAAGGTGA
1 AGGTTG-AGGTGAAGGTGA
*
18665807 AGGTGGAGG
1 AGGTTGAGG
18665816 ATTAGGTTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
17 1 0.03
18 36 0.95
19 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.56, T:0.17
Consensus pattern (18 bp):
AGGTTGAGGTGAAGGTGA
Found at i:18666885 original size:16 final size:16
Alignment explanation
Indices: 18666843--18666911 Score: 68
Period size: 16 Copynumber: 4.3 Consensus size: 16
18666833 CGACCCGATA
*
18666843 TATATAATTATT-TGTT
1 TATATAATT-TTATATT
* *
18666859 TATTTAGTTTTATATT
1 TATATAATTTTATATT
* *
18666875 TATATATTTTTATACT
1 TATATAATTTTATATT
*
18666891 TATTTAATTTTATATT
1 TATATAATTTTATATT
18666907 TATAT
1 TATAT
18666912 TAAAAATAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
15 2 0.05
16 40 0.95
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.65
Consensus pattern (16 bp):
TATATAATTTTATATT
Found at i:18667656 original size:22 final size:22
Alignment explanation
Indices: 18667631--18667674 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
18667621 TATATATTTA
* * *
18667631 TATTTGTATCTCTAGAATTAAG
1 TATTTGCATCCCTAAAATTAAG
18667653 TATTTGCATCCCTAAAATTAAG
1 TATTTGCATCCCTAAAATTAAG
18667675 GACAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (22 bp):
TATTTGCATCCCTAAAATTAAG
Found at i:18679924 original size:13 final size:14
Alignment explanation
Indices: 18679892--18679926 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
18679882 GTTCCGTTTG
18679892 TTTTGTAAAAAATAA
1 TTTT-TAAAAAATAA
18679907 TTTTTAAAAAATAA
1 TTTTTAAAAAATAA
18679921 TTTTTA
1 TTTTTA
18679927 TATTTTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TTTTTAAAAAATAA
Found at i:18680126 original size:18 final size:18
Alignment explanation
Indices: 18680105--18680260 Score: 95
Period size: 18 Copynumber: 8.4 Consensus size: 18
18680095 AATTTTACTT
18680105 ATAAATAATATTATATTA
1 ATAAATAATATTATATTA
*
18680123 ATAAATAATTAATATATACTA
1 ATAAATAA-T-AT-TATATTA
18680144 ATAAAT-A-A-TA-ATTA
1 ATAAATAATATTATATTA
18680158 ATAAATAATATTATATTA
1 ATAAATAATATTATATTA
* * * * * *
18680176 TTATATATTAATAAATAA
1 ATAAATAATATTATATTA
* * *
18680194 ATAATATTCTAATCTTTTAATAA
1 ATAA-A---TAATATTAT-ATTA
18680217 ATAAATAATATTATATTA
1 ATAAATAATATTATATTA
* *
18680235 ATAAATATTATGATATTA
1 ATAAATAATATTATATTA
*
18680253 ATTAATAA
1 ATAAATAA
18680261 ATAATATAGT
Statistics
Matches: 104, Mismatches: 22, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
14 9 0.09
15 3 0.03
16 1 0.01
17 3 0.03
18 51 0.49
19 9 0.09
20 3 0.03
21 12 0.12
22 5 0.05
23 8 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (18 bp):
ATAAATAATATTATATTA
Found at i:18680213 original size:27 final size:27
Alignment explanation
Indices: 18680148--18680231 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
18680138 ATACTAATAA
*
18680148 ATAATA-ATTAATAAATAATATTATATT
1 ATAATATATTAATAAATAA-ATAATATT
*
18680175 ATTATATATTAATAAATAAATAATATT
1 ATAATATATTAATAAATAAATAATATT
* * *
18680202 CTAATCTTTTAATAAATAAATAATATT
1 ATAATATATTAATAAATAAATAATATT
18680229 ATA
1 ATA
18680232 TTAATAAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
27 37 0.76
28 12 0.24
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
ATAATATATTAATAAATAAATAATATT
Found at i:18680229 original size:59 final size:62
Alignment explanation
Indices: 18680110--18680244 Score: 168
Period size: 59 Copynumber: 2.2 Consensus size: 62
18680100 TACTTATAAA
* *
18680110 TAATATTATATTAATAAATAATTAATATATACTAATAAATAATAATTAATAAATAATATTATAT
1 TAATA-TATATTAATAAATAAATAATATATACTAAT-AATAATAATAAATAAATAATATTATAT
* * **
18680174 TATTATATATTAATAAATAAATAATAT-T-CTAAT-CTTTTAATAAATAAATAATATTATAT
1 TAATATATATTAATAAATAAATAATATATACTAATAATAATAATAAATAAATAATATTATAT
*
18680233 TAATAAATATTA
1 TAATATATATTA
18680245 TGATATTAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
59 32 0.51
61 5 0.08
62 1 0.02
63 21 0.33
64 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (62 bp):
TAATATATATTAATAAATAAATAATATATACTAATAATAATAATAAATAAATAATATTATAT
Found at i:18680275 original size:22 final size:23
Alignment explanation
Indices: 18680210--18680338 Score: 102
Period size: 23 Copynumber: 5.7 Consensus size: 23
18680200 TTCTAATCTT
*
18680210 TTAATAAATAA-ATAATATTATA
1 TTAATAAATAATATAATATTACA
* *
18680232 TTAATAAATATTATGATATTA-A
1 TTAATAAATAATATAATATTACA
*
18680254 TTAATAAATAATATAGTATTA-A
1 TTAATAAATAATATAATATTACA
* * * *
18680276 TATAATGAATTACAAAATATTACA
1 T-TAATAAATAATATAATATTACA
* * * *
18680300 TTAATTAATAATATTATAATATA
1 TTAATAAATAATATAATATTACA
* *
18680323 CTAATAACTAATATAA
1 TTAATAAATAATATAA
18680339 AAAATAATAA
Statistics
Matches: 83, Mismatches: 21, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
22 31 0.37
23 50 0.60
24 2 0.02
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAATAAATAATATAATATTACA
Found at i:18680314 original size:18 final size:17
Alignment explanation
Indices: 18680108--18680315 Score: 61
Period size: 18 Copynumber: 12.6 Consensus size: 17
18680098 TTTACTTATA
*
18680108 AATAATATTATATTAATA
1 AATAATATTA-ATTAATT
*
18680126 AAT-A-ATTAATATATACT
1 AATAATATTAAT-TA-ATT
* *
18680143 AATAAATAATAATTAATA
1 AAT-AATATTAATTAATT
18680161 AATAATATTATATT-ATT
1 AATAATATTA-ATTAATT
* *
18680178 -AT-ATATTAATAAATA
1 AATAATATTAATTAATT
*
18680193 AATAATATT--CTAA-T
1 AATAATATTAATTAATT
* * *
18680207 -CT--T-TTAATAAATA
1 AATAATATTAATTAATT
*
18680220 AATAATATTATATTAATA
1 AATAATATTA-ATTAATT
* *
18680238 AATATTATGATATTAATT
1 AATAATATTA-ATTAATT
*
18680256 AATAA-A-TAA-TATAGT
1 AATAATATTAATTA-ATT
* *
18680271 ATTAATA-TAATGAATT
1 AATAATATTAATTAATT
*
18680287 ACAAAATATTACATTAATT
1 A-ATAATATTA-ATTAATT
18680306 AATAATATTA
1 AATAATATTA
18680316 TAATATACTA
Statistics
Matches: 136, Mismatches: 31, Indels: 46
0.64 0.15 0.22
Matches are distributed among these distances:
10 2 0.01
11 1 0.01
12 2 0.01
13 1 0.01
14 5 0.04
15 19 0.14
16 19 0.14
17 27 0.20
18 45 0.33
19 10 0.07
20 5 0.04
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (17 bp):
AATAATATTAATTAATT
Found at i:18680440 original size:16 final size:17
Alignment explanation
Indices: 18680387--18680455 Score: 54
Period size: 18 Copynumber: 4.1 Consensus size: 17
18680377 AACATAATAG
* *
18680387 TTTAATATTAAATATTT
1 TTTAATAATAAATAATT
*
18680404 TATTAA-AATACAATTATTT
1 T-TTAATAATA-AA-TAATT
*
18680423 TTTAAT-ATTAATAA-T
1 TTTAATAATAAATAATT
18680438 TTTAATAATAAATAATT
1 TTTAATAATAAATAATT
18680455 T
1 T
18680456 CAATATACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
15 7 0.17
16 9 0.21
17 8 0.19
18 12 0.29
19 6 0.14
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAATAATAAATAATT
Found at i:18680442 original size:15 final size:15
Alignment explanation
Indices: 18680422--18680462 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
18680412 TACAATTATT
*
18680422 TTTTAATATTAATAA
1 TTTTAATATAAATAA
18680437 TTTTAATAATAAATAA
1 TTTTAAT-ATAAATAA
*
18680453 TTTCAATATA
1 TTTTAATATA
18680463 CTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAATATAAATAA
Found at i:18681320 original size:18 final size:19
Alignment explanation
Indices: 18681278--18681320 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
18681268 CCGAATTGAG
18681278 TTATATATTTTTCATAATT
1 TTATATATTTTTCATAATT
18681297 TATATATATATTTT-A-AATT
1 T-TATATAT-TTTTCATAATT
18681316 TTATA
1 TTATA
18681321 AAATAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 8 0.36
21 4 0.18
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATATATTTTTCATAATT
Found at i:18686715 original size:25 final size:25
Alignment explanation
Indices: 18686651--18686725 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 25
18686641 AATACAATGT
* *
18686651 TAATAGAAAGTTGTG-AATATTTAA
1 TAATAGAAAGTTCTGAAATATATAA
* * * * *
18686675 TCAGAGAAACTACTGAAATATATGA
1 TAATAGAAAGTTCTGAAATATATAA
* *
18686700 TAATAGAAAGTTCTGAAGTATTTAA
1 TAATAGAAAGTTCTGAAATATATAA
18686725 T
1 T
18686726 CAGATGCTTT
Statistics
Matches: 36, Mismatches: 14, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
24 10 0.28
25 26 0.72
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.33
Consensus pattern (25 bp):
TAATAGAAAGTTCTGAAATATATAA
Found at i:18694048 original size:30 final size:30
Alignment explanation
Indices: 18694012--18694097 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
18694002 CTTATTTTCG
*
18694012 TTCAATTAAATAAAAATAAATATTTAA-AGC
1 TTCAATTAAATAAAAATAAATATTTAATA-A
** *
18694042 TTCAATTATGTGAAAATAAATATTTAATAA
1 TTCAATTAAATAAAAATAAATATTTAATAA
* *
18694072 TTTAATCAAATAAAAAATAAATATTT
1 TTCAATTAAAT-AAAAATAAATATTT
18694098 GACGACTCAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
30 31 0.69
31 14 0.31
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (30 bp):
TTCAATTAAATAAAAATAAATATTTAATAA
Found at i:18699579 original size:26 final size:28
Alignment explanation
Indices: 18699550--18699603 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
18699540 AAAACTTTCC
18699550 AAACATTA-ATATA-TTTTTATTTTTTA
1 AAACATTATATATATTTTTTATTTTTTA
* *
18699576 AAACATTATTTCTATTTTTTATTTTTTA
1 AAACATTATATATATTTTTTATTTTTTA
18699604 TTTTTTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.33
27 3 0.12
28 13 0.54
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (28 bp):
AAACATTATATATATTTTTTATTTTTTA
Found at i:18699600 original size:7 final size:7
Alignment explanation
Indices: 18699588--18699612 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18699578 ACATTATTTC
18699588 TATTTTT
1 TATTTTT
18699595 TATTTTT
1 TATTTTT
18699602 TATTTTT
1 TATTTTT
18699609 TATT
1 TATT
18699613 CACATAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TATTTTT
Found at i:18699917 original size:15 final size:15
Alignment explanation
Indices: 18699894--18699932 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
18699884 AATGAATCAA
*
18699894 AATTCAAAAAAATTT
1 AATTCAAAAAAATTC
* *
18699909 AATTTAAAATAATTC
1 AATTCAAAAAAATTC
18699924 AATTCAAAA
1 AATTCAAAA
18699933 CGCACCGCCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTCAAAAAAATTC
Found at i:18705560 original size:29 final size:30
Alignment explanation
Indices: 18705526--18705602 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
18705516 TATTTAATTT
18705526 TATATTTTTATATATATT-ATATTAATAAAA
1 TATATTTTTATATATATTAAT-TTAATAAAA
18705556 T-TATTATTTGATAT-T-TTAATTTAATAAAA
1 TATATT-TTT-ATATATATTAATTTAATAAAA
*
18705585 TACTATATTTATATATAT
1 TA-TATTTTTATATATAT
18705603 CAAGTTAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
29 20 0.51
30 11 0.28
31 8 0.21
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (30 bp):
TATATTTTTATATATATTAATTTAATAAAA
Found at i:18706299 original size:20 final size:18
Alignment explanation
Indices: 18706276--18706340 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 18
18706266 TAAATATTTA
18706276 AAAAATATAAAAATTTTCT
1 AAAAATATAAAAATTTT-T
**
18706295 AAAAATCATAACAAAAATTT
1 AAAAAT-ATAA-AAATTTTT
18706315 AAAAATATATAAAATTTTAT
1 AAAAATATA-AAAATTTT-T
18706335 AAAAAT
1 AAAAAT
18706341 TACAAAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 14 0.37
20 19 0.50
21 5 0.13
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATATAAAAATTTTT
Found at i:18706315 original size:40 final size:39
Alignment explanation
Indices: 18706271--18706371 Score: 116
Period size: 40 Copynumber: 2.6 Consensus size: 39
18706261 TTATTTAAAT
*
18706271 ATTTAAAAAATATAAAAATTTTCTAAAAATCATAACAAAA
1 ATTTAAAAAATATAAAAATTTTCTAAAAATCACAA-AAAA
* *
18706311 ATTT-AAAAATATATAAAATTTTATAAAAATTACAAAAAA
1 ATTTAAAAAATATA-AAAATTTTCTAAAAATCACAAAAAA
* * *
18706350 GTTAAAAAAAT-TAAATATTTTC
1 ATTTAAAAAATATAAAAATTTTC
18706372 ATTAAATAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
38 7 0.13
39 17 0.33
40 28 0.54
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (39 bp):
ATTTAAAAAATATAAAAATTTTCTAAAAATCACAAAAAA
Found at i:18706348 original size:20 final size:20
Alignment explanation
Indices: 18706274--18706362 Score: 51
Period size: 20 Copynumber: 4.5 Consensus size: 20
18706264 TTTAAATATT
* * *
18706274 TAAAAAATATAAAAATTTTC
1 TAAAAATTACAAAAATTTTA
18706294 TAAAAATCATAACAAAAA--TT-
1 TAAAAAT--T-ACAAAAATTTTA
*
18706314 TAAAAATATA-TAAAATTTTA
1 TAAAAAT-TACAAAAATTTTA
**
18706334 TAAAAATTACAAAAAAGTTA
1 TAAAAATTACAAAAATTTTA
*
18706354 AAAAAATTA
1 TAAAAATTA
18706363 AATATTTTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
17 4 0.07
18 1 0.02
19 6 0.11
20 35 0.64
21 2 0.04
22 1 0.02
23 6 0.11
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (20 bp):
TAAAAATTACAAAAATTTTA
Found at i:18706599 original size:17 final size:19
Alignment explanation
Indices: 18706562--18706604 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
18706552 AAGAAATTTT
*
18706562 AATATTTTTAAAAACTAAA
1 AATATTTCTAAAAACTAAA
*
18706581 AA-ATTTCTAAAAA-TCAA
1 AATATTTCTAAAAACTAAA
18706598 AATATTT
1 AATATTT
18706605 TTTATATTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 14 0.67
19 2 0.10
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AATATTTCTAAAAACTAAA
Found at i:18707154 original size:18 final size:18
Alignment explanation
Indices: 18707114--18707155 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
18707104 AGCTTGATCA
18707114 TATTT-TTTAATCAAGCT
1 TATTTATTTAATCAAGCT
*
18707131 TCATTTATTTATTCAAGCT
1 T-ATTTATTTAATCAAGCT
18707150 TATTTA
1 TATTTA
18707156 ACATGCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 9 0.41
19 12 0.55
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.55
Consensus pattern (18 bp):
TATTTATTTAATCAAGCT
Found at i:18708823 original size:12 final size:12
Alignment explanation
Indices: 18708806--18708836 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
18708796 CTTATATCAA
18708806 TTTTTTATAAAT
1 TTTTTTATAAAT
*
18708818 TTTTTTATATAT
1 TTTTTTATAAAT
18708830 TTTTTTA
1 TTTTTTA
18708837 ACTTTTCCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTATAAAT
Found at i:18716260 original size:16 final size:16
Alignment explanation
Indices: 18716223--18716261 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
18716213 AGCAAGTACT
* *
18716223 CCATGTCCATTTTATG
1 CCATGACCATTTAATG
18716239 CTCATGACCATTTAATG
1 C-CATGACCATTTAATG
18716256 CCATGA
1 CCATGA
18716262 TTAAGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (16 bp):
CCATGACCATTTAATG
Found at i:18716876 original size:20 final size:18
Alignment explanation
Indices: 18716833--18716881 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
18716823 AACAATTATG
18716833 AATATAATCTATTTATATA
1 AATATAAT-TATTTATATA
*
18716852 AATATAATTATTTCTATTCA
1 AATATAATTATTTATA-T-A
18716872 AATATAATTA
1 AATATAATTA
18716882 CTTAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.26
19 9 0.33
20 11 0.41
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
AATATAATTATTTATATA
Found at i:18717811 original size:26 final size:26
Alignment explanation
Indices: 18717782--18717836 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
18717772 TATTTTTTAA
* *
18717782 TTATTTATTTAATTTTATAATTATTT
1 TTATATATTTAATTTTATAATTATAT
*
18717808 TTATATATTTAATTTTATATTTATAT
1 TTATATATTTAATTTTATAATTATAT
18717834 TTA
1 TTA
18717837 AAATAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TTATATATTTAATTTTATAATTATAT
Found at i:18717818 original size:20 final size:22
Alignment explanation
Indices: 18717768--18717817 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
18717758 ATTTGATATA
*
18717768 TATATATTTTTTAATTATTTAT
1 TATATATTTTATAATTATTTAT
18717790 T-TA-ATTTTATAATTATTT-T
1 TATATATTTTATAATTATTTAT
18717809 TATATATTT
1 TATATATTT
18717818 AATTTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 16 0.64
21 6 0.24
22 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATATATTTTATAATTATTTAT
Found at i:18719094 original size:17 final size:18
Alignment explanation
Indices: 18719063--18719096 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18719053 TTTAATATCT
18719063 AATTTGTTATATTTTAAA
1 AATTTGTTATATTTTAAA
*
18719081 AATTT-TTATTTTTTAA
1 AATTTGTTATATTTTAA
18719097 TATTAAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
AATTTGTTATATTTTAAA
Found at i:18719967 original size:16 final size:16
Alignment explanation
Indices: 18719948--18719978 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18719938 TTTAATATTG
*
18719948 AATATTTGTATGGTCA
1 AATATTTCTATGGTCA
18719964 AATATTTCTATGGTC
1 AATATTTCTATGGTC
18719979 GAAGAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (16 bp):
AATATTTCTATGGTCA
Found at i:18726212 original size:6 final size:6
Alignment explanation
Indices: 18726201--18726234 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
18726191 AGGAGAGAAG
*
18726201 AAAGGA AAAGGA ATAGGA AAAGGA AAAGGA AAAG
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAG
18726235 AAGGTCCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (6 bp):
AAAGGA
Found at i:18726778 original size:22 final size:22
Alignment explanation
Indices: 18726753--18726795 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18726743 AAATTTTAAT
* *
18726753 AATAAATATATAAATTTAATAA
1 AATAAAAAAATAAATTTAATAA
*
18726775 AATAAAAAAATATATTTAATA
1 AATAAAAAAATAAATTTAATA
18726796 TTTTATATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAAAAAAATAAATTTAATAA
Found at i:18726820 original size:25 final size:25
Alignment explanation
Indices: 18726791--18726846 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
18726781 AAAATATATT
* * *
18726791 TAATATTTTATATTAATATGAATTA
1 TAATATTTAATATTAATATAAAATA
* *
18726816 TAATATTTAATTTTTATATAAAATA
1 TAATATTTAATATTAATATAAAATA
18726841 TAATAT
1 TAATAT
18726847 AAATACATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTTAATATTAATATAAAATA
Found at i:18726841 original size:32 final size:30
Alignment explanation
Indices: 18726786--18726848 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 30
18726776 ATAAAAAAAT
*
18726786 ATATTTAATATTTTATATTAATATGAATTATA
1 ATATTTAATATTTTATATAAATAT-AA-TATA
18726818 ATATTTAAT-TTTTATATAAAATATAATATA
1 ATATTTAATATTTTATAT-AAATATAATATA
18726848 A
1 A
18726849 ATACATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 5 0.17
31 10 0.34
32 14 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
ATATTTAATATTTTATATAAATATAATATA
Found at i:18726890 original size:32 final size:33
Alignment explanation
Indices: 18726839--18726914 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 33
18726829 TTATATAAAA
18726839 TATAATATAAATACATAAATT-TTAATATTT-TT
1 TATAATATAAATACATAAATTATTAA-ATTTATT
*
18726871 TATAATATAAATTA-TTAAATTATTAAATTTATT
1 TATAATATAAA-TACATAAATTATTAAATTTATT
* *
18726904 TAAAATTTAAA
1 TATAATATAAA
18726915 AAATACACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
32 21 0.55
33 17 0.45
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (33 bp):
TATAATATAAATACATAAATTATTAAATTTATT
Found at i:18727274 original size:20 final size:21
Alignment explanation
Indices: 18727228--18727277 Score: 84
Period size: 22 Copynumber: 2.4 Consensus size: 21
18727218 CGAAATTAAT
18727228 TAAATATTATTTTTTAAAATA
1 TAAATATTATTTTTTAAAATA
18727249 TAAAATATTATTTTTT-AAATA
1 T-AAATATTATTTTTTAAAATA
18727270 TAAATATT
1 TAAATATT
18727278 TAAAAATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.25
21 7 0.25
22 14 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAATATTATTTTTTAAAATA
Done.