Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 183 of 195
Found at i:31378825 original size:21 final size:21
Alignment explanation
Indices: 31378799--31378838 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
31378789 AAAAAATATT
31378799 TTATTATTAAT-ATTAATTTAA
1 TTATTA-TAATAATTAATTTAA
31378820 TTATTATAATAATTAATTT
1 TTATTATAATAATTAATTT
31378839 CACTTCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTATAATAATTAATTTAA
Found at i:31394163 original size:27 final size:27
Alignment explanation
Indices: 31394125--31394179 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
31394115 ACAAAATTAA
*
31394125 ACTAAAATCTTACAACATTATAGTGGT
1 ACTAAAATCTTACAACAGTATAGTGGT
*
31394152 ACTAAAATCTTACAATAGTATAGTGGT
1 ACTAAAATCTTACAACAGTATAGTGGT
31394179 A
1 A
31394180 ATTTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (27 bp):
ACTAAAATCTTACAACAGTATAGTGGT
Found at i:31399080 original size:18 final size:18
Alignment explanation
Indices: 31399057--31399096 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
31399047 TTGAACTCGG
31399057 TATGAACTAAAAAATGTT
1 TATGAACTAAAAAATGTT
* *
31399075 TATGAACTCAGAAATGTT
1 TATGAACTAAAAAATGTT
31399093 TATG
1 TATG
31399097 TCCTTCTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (18 bp):
TATGAACTAAAAAATGTT
Found at i:31403165 original size:2 final size:2
Alignment explanation
Indices: 31403154--31403187 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
31403144 AGCGCTTTGC
31403154 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31403188 TGTAGTCCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31412311 original size:23 final size:24
Alignment explanation
Indices: 31412280--31412339 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 24
31412270 TAAAAAAACT
* *
31412280 AATACATTTTA-TTATTTTATTTA
1 AATAAATTTTATTTATTATATTTA
31412303 AATAAATTTATATTTTTATTATATTTA
1 AATAAATTT-TA--TTTATTATATTTA
31412330 AATAAATTTT
1 AATAAATTTT
31412340 TAAACTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 8 0.26
24 2 0.06
26 1 0.03
27 20 0.65
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
AATAAATTTTATTTATTATATTTA
Found at i:31412423 original size:59 final size:57
Alignment explanation
Indices: 31412291--31412459 Score: 162
Period size: 59 Copynumber: 2.8 Consensus size: 57
31412281 ATACATTTTA
* * * *
31412291 TTATTTTATTTAAATAAATTTAT-ATT-TTTATTATATTTAAATAAATTTTTAAACT
1 TTATTTTATTTAAATAAATTTTTAATTATTAATTTTATTTAAATAAATTTGTAAACT
* * *
31412346 TTAATTTATATCATAATAAATTTTTAATTATTAATTTTATTTAAATAAATTTGTAATATT
1 TTATTTTAT-TTA-AATAAATTTTTAATTATTAATTTTATTTAAATAAATTTGTAA-ACT
*
31412406 TTATTTGTATTTAAATAAAATTTTAATATAAATTAATTTTTTATTTGAAATAAA
1 TTATTT-TATTTAAATAAATTTTTAAT-T--ATTAA--TTTTATTT-AAATAAA
31412460 ATTTTATTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
55 8 0.09
56 2 0.02
57 10 0.11
58 3 0.03
59 36 0.39
60 10 0.11
61 3 0.03
62 5 0.05
64 8 0.09
65 7 0.08
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (57 bp):
TTATTTTATTTAAATAAATTTTTAATTATTAATTTTATTTAAATAAATTTGTAAACT
Found at i:31412433 original size:30 final size:29
Alignment explanation
Indices: 31412291--31412434 Score: 129
Period size: 30 Copynumber: 5.0 Consensus size: 29
31412281 ATACATTTTA
31412291 TTATTTTATTTAAAT-AAA-TTT-ATATTT
1 TTATTTTATTTAAATAAAATTTTAATA-TT
* * *
31412318 TTATTATATTTAAATAAATTTTTAA-ACT
1 TTATTTTATTTAAATAAAATTTTAATATT
* * *
31412346 TTAATTTATATCATAATAAATTTTTAAT-TAT
1 TTATTTTAT-TTA-AATAAAATTTTAATAT-T
*
31412377 TAATTTTATTTAAAT-AAATTTGTAATATT
1 TTATTTTATTTAAATAAAATTT-TAATATT
31412406 TTATTTGTATTTAAATAAAATTTTAATAT
1 TTATTT-TATTTAAATAAAATTTTAATAT
31412435 AAATTAATTT
Statistics
Matches: 94, Mismatches: 12, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
27 14 0.15
28 15 0.16
29 19 0.20
30 32 0.34
31 14 0.15
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (29 bp):
TTATTTTATTTAAATAAAATTTTAATATT
Found at i:31412464 original size:18 final size:17
Alignment explanation
Indices: 31412408--31412468 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
31412398 GTAATATTTT
*
31412408 ATTTGTATTTAAATAAA
1 ATTTTTATTTAAATAAA
* * *
31412425 ATTTTAATATAAATTAA
1 ATTTTTATTTAAATAAA
*
31412442 TTTTTTATTTGAAATAAA
1 ATTTTTATTT-AAATAAA
31412460 A-TTTTATTT
1 ATTTTTATTT
31412469 TGATATAAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
17 28 0.82
18 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTTATTTAAATAAA
Found at i:31412470 original size:18 final size:18
Alignment explanation
Indices: 31412418--31412477 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
31412408 ATTTGTATTT
* *
31412418 AAATAAAATTTTAATAT-
1 AAATAAAATTTTATTTTG
* *
31412435 AAAT-TAATTTTTTATTTG
1 AAATAAAATTTTAT-TTTG
31412453 AAATAAAATTTTATTTTG
1 AAATAAAATTTTATTTTG
*
31412471 ATATAAA
1 AAATAAA
31412478 TAAAAAAAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
16 6 0.18
17 6 0.18
18 14 0.42
19 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (18 bp):
AAATAAAATTTTATTTTG
Found at i:31413418 original size:15 final size:17
Alignment explanation
Indices: 31413398--31413430 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
31413388 CTTTAAGATT
31413398 ATCTAAA-AAAAT-TAA
1 ATCTAAATAAAATATAA
31413413 ATCTAAATAAAATATAA
1 ATCTAAATAAAATATAA
31413430 A
1 A
31413431 AACACTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
ATCTAAATAAAATATAA
Found at i:31414981 original size:16 final size:16
Alignment explanation
Indices: 31414962--31414995 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
31414952 TATATATATA
31414962 TGAATAAATTTAAATT
1 TGAATAAATTTAAATT
*
31414978 TGAATAATTTTAAATT
1 TGAATAAATTTAAATT
31414994 TG
1 TG
31414996 GATTGAACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (16 bp):
TGAATAAATTTAAATT
Found at i:31416356 original size:9 final size:9
Alignment explanation
Indices: 31416331--31416364 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
31416321 TTTATTCATT
31416331 ATTTTTTTA
1 ATTTTTTTA
31416340 ATTATTTTTA
1 ATT-TTTTTA
*
31416350 ATTTTTTTC
1 ATTTTTTTA
31416359 ATTTTT
1 ATTTTT
31416365 GTATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:31417309 original size:20 final size:20
Alignment explanation
Indices: 31417284--31417322 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
31417274 GATAAAAGTG
31417284 TTAAATTTTTAA-TTTAATAA
1 TTAAA-TTTTAATTTTAATAA
31417304 TTAAATTTTAATTTTAATA
1 TTAAATTTTAATTTTAATA
31417323 TTTTTTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAATTTTAATTTTAATAA
Found at i:31421090 original size:114 final size:117
Alignment explanation
Indices: 31420945--31421178 Score: 413
Period size: 116 Copynumber: 2.0 Consensus size: 117
31420935 CCTATACTAT
*
31420945 TTTTATTTTTTTATCATTCAAGTCTAATGCAATG-AAAAAAA-ATAATTTTCATTCCTCTAATTT
1 TTTTATTTTTTTATCATTCAAGTCCAATGCAATGAAAAAAAAGATAATTTTCATTCCTCTAATTT
31421008 CTTTTTTCTTTTTCTGCCAAATATAATATTAATGAAATTTTTTAGTTGTTAA
66 CTTTTTTCTTTTTCTGCCAAATATAATATTAATGAAATTTTTTAGTTGTTAA
*
31421060 TTTTA-TTTTTTATCATTCAAG-CCAATTGCAATGAAAAAAAAGATAATTTTCATTCCTCTGATT
1 TTTTATTTTTTTATCATTCAAGTCCAA-TGCAATGAAAAAAAAGATAATTTTCATTCCTCTAATT
31421123 TCTTTTTTCTTTTTCTGCCAAATATAATATTAATGAAATTTTTTAGTTGTTAA
65 TCTTTTTTCTTTTTCTGCCAAATATAATATTAATGAAATTTTTTAGTTGTTAA
31421176 TTT
1 TTT
31421179 GGTTTTTATT
Statistics
Matches: 114, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
113 3 0.03
114 23 0.20
115 12 0.11
116 76 0.67
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.50
Consensus pattern (117 bp):
TTTTATTTTTTTATCATTCAAGTCCAATGCAATGAAAAAAAAGATAATTTTCATTCCTCTAATTT
CTTTTTTCTTTTTCTGCCAAATATAATATTAATGAAATTTTTTAGTTGTTAA
Found at i:31421989 original size:24 final size:24
Alignment explanation
Indices: 31421962--31422010 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
31421952 TTTTTAAAAA
31421962 TTTTAAATTAT-ATTATTTTTATCT
1 TTTTAAATTATCA-TATTTTTATCT
* *
31421986 TTTTTATTTATCATATTTTTATCT
1 TTTTAAATTATCATATTTTTATCT
31422010 T
1 T
31422011 ATATTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTAAATTATCATATTTTTATCT
Found at i:31422020 original size:24 final size:24
Alignment explanation
Indices: 31421975--31422028 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
31421965 TAAATTATAT
*
31421975 TATTTTTATCTTTTTTATTTATCA
1 TATTTTTATCTTTATTATTTATCA
31421999 TATTTTTATCTTATATTATTATATCA
1 TATTTTTATCTT-TATTATT-TATCA
31422025 TATT
1 TATT
31422029 CTAAATTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 12 0.44
25 6 0.22
26 9 0.33
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTTTATCTTTATTATTTATCA
Found at i:31424150 original size:25 final size:25
Alignment explanation
Indices: 31424114--31424163 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
31424104 TTAGGGCACA
31424114 TGGGGAGAGATTGGGTGGGGTGGGG
1 TGGGGAGAGATTGGGTGGGGTGGGG
* *
31424139 TGGGGAGGGATTGGGTGTGGTGGGG
1 TGGGGAGAGATTGGGTGGGGTGGGG
31424164 CGTTGGGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.10, C:0.00, G:0.68, T:0.22
Consensus pattern (25 bp):
TGGGGAGAGATTGGGTGGGGTGGGG
Found at i:31424438 original size:19 final size:20
Alignment explanation
Indices: 31424416--31424455 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
31424406 TGTATCGAAA
*
31424416 TTTTAATATTT-TTTTGTTG
1 TTTTAATATTTATATTGTTG
*
31424435 TTTTGATATTTATATTGTTG
1 TTTTAATATTTATATTGTTG
31424455 T
1 T
31424456 CAATTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.70
Consensus pattern (20 bp):
TTTTAATATTTATATTGTTG
Found at i:31430266 original size:18 final size:18
Alignment explanation
Indices: 31430174--31430279 Score: 76
Period size: 18 Copynumber: 6.1 Consensus size: 18
31430164 CTTTTATTTT
*
31430174 TGATACATTTGAGGTGAA
1 TGATACATTTGAGGTGGA
* * *
31430192 AGATATATTT-A--AGGA
1 TGATACATTTGAGGTGGA
*
31430207 TGATACATTT-ATGGTGGG
1 TGATACATTTGA-GGTGGA
* * **
31430225 GGATACATTTGTGGTAAA
1 TGATACATTTGAGGTGGA
*
31430243 TAATACATTTGAGGTGGA
1 TGATACATTTGAGGTGGA
*
31430261 TGATACATTTAAGGTGGA
1 TGATACATTTGAGGTGGA
31430279 T
1 T
31430280 AATAACCATA
Statistics
Matches: 64, Mismatches: 20, Indels: 8
0.70 0.22 0.09
Matches are distributed among these distances:
15 11 0.17
17 1 0.02
18 52 0.81
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (18 bp):
TGATACATTTGAGGTGGA
Found at i:31430282 original size:36 final size:36
Alignment explanation
Indices: 31430176--31430283 Score: 89
Period size: 36 Copynumber: 3.1 Consensus size: 36
31430166 TTTATTTTTG
* * *
31430176 ATACATTTGAGGTGAAAGATATATTTAA---GGATG
1 ATACATTTGAGGTGGAAGATACATTTAAGGTGGATA
** ** **
31430209 ATACATTT-ATGGTGGGGGATACATTTGTGGTAAATA
1 ATACATTTGA-GGTGGAAGATACATTTAAGGTGGATA
*
31430245 ATACATTTGAGGTGGATGATACATTTAAGGTGGATA
1 ATACATTTGAGGTGGAAGATACATTTAAGGTGGATA
31430281 ATA
1 ATA
31430284 ACCATACGGA
Statistics
Matches: 55, Mismatches: 15, Indels: 7
0.71 0.19 0.09
Matches are distributed among these distances:
32 1 0.02
33 20 0.36
36 33 0.60
37 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (36 bp):
ATACATTTGAGGTGGAAGATACATTTAAGGTGGATA
Found at i:31434325 original size:19 final size:20
Alignment explanation
Indices: 31434291--31434330 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
31434281 AAAAGAATTG
*
31434291 ACAACAATATAAATATCAAA
1 ACAACAATAAAAATATCAAA
*
31434311 ACAACAA-AAAAATATTAAA
1 ACAACAATAAAAATATCAAA
31434330 A
1 A
31434331 TTCAAATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.17
Consensus pattern (20 bp):
ACAACAATAAAAATATCAAA
Found at i:31434552 original size:13 final size:12
Alignment explanation
Indices: 31434536--31434566 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31434526 AAAAAATTTT
*
31434536 AAAAATTAATTA
1 AAAAATTAAATA
31434548 AAAAATTAAATA
1 AAAAATTAAATA
31434560 AAAAATT
1 AAAAATT
31434567 CAACCCCCAC
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAATTAAATA
Found at i:31442641 original size:49 final size:49
Alignment explanation
Indices: 31442576--31442673 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
31442566 AAATGTGCAA
* * *
31442576 ACTTTTGGCATGAGAGATAACAGTGACCTCTATTTCATGAAAAAATGAC
1 ACTTTTGGCATAAGAGATAACAATGACCTCTATTTCATAAAAAAATGAC
*
31442625 ACTTTTGGCATAAGAGATAACAATGACCTCTGTTTCATAAAAAAATGAC
1 ACTTTTGGCATAAGAGATAACAATGACCTCTATTTCATAAAAAAATGAC
31442674 TTCCAGCATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (49 bp):
ACTTTTGGCATAAGAGATAACAATGACCTCTATTTCATAAAAAAATGAC
Found at i:31449722 original size:22 final size:21
Alignment explanation
Indices: 31449697--31449737 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
31449687 CTGTATATTT
31449697 ATATTTGCATCTCTAGAAATAA
1 ATATTTGCATCTCTA-AAATAA
*
31449719 ATATTTGTATCTCTAAAAT
1 ATATTTGCATCTCTAAAAT
31449738 TAATGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (21 bp):
ATATTTGCATCTCTAAAATAA
Found at i:31455813 original size:24 final size:24
Alignment explanation
Indices: 31455786--31455834 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
31455776 CATTAGAAAT
31455786 TGTG-AAAAAACTAAAAAATAAAAC
1 TGTGTAAAAAA-TAAAAAATAAAAC
* *
31455810 TGTGTAAAAAATTAAAAGTAAAAC
1 TGTGTAAAAAATAAAAAATAAAAC
31455834 T
1 T
31455835 AAATGTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.61, C:0.06, G:0.10, T:0.22
Consensus pattern (24 bp):
TGTGTAAAAAATAAAAAATAAAAC
Found at i:31465844 original size:18 final size:18
Alignment explanation
Indices: 31465809--31465857 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
31465799 TGAAAATTAT
31465809 ATAAAAATATATACAATGATA
1 ATAAAAAT-TA-A-AATGATA
* *
31465830 ATACAAATTAAAATGTTA
1 ATAAAAATTAAAATGATA
31465848 ATAAAAATTA
1 ATAAAAATTA
31465858 TATATAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 15 0.60
19 1 0.04
20 2 0.08
21 7 0.28
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (18 bp):
ATAAAAATTAAAATGATA
Found at i:31474174 original size:29 final size:29
Alignment explanation
Indices: 31474142--31474215 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 29
31474132 TTTTATTCAG
31474142 ATAAATCTTTATATTTTT-A-TTGTATCCAA
1 ATAAAT-TTT-TATTTTTAATTTGTATCCAA
31474171 ATAAATTTTTATTCTTTAATTTGTATCCAA
1 ATAAATTTTTATT-TTTAATTTGTATCCAA
31474201 ATAAATTTTTATTTT
1 ATAAATTTTTATTTT
31474216 AAACAAAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
27 4 0.10
28 6 0.14
29 9 0.21
30 23 0.55
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (29 bp):
ATAAATTTTTATTTTTAATTTGTATCCAA
Found at i:31474343 original size:28 final size:29
Alignment explanation
Indices: 31474311--31474386 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 29
31474301 TTTGAATGCA
* * *
31474311 AATTAAAAATTGAGAGTTTGTTTGGTTG-
1 AATTAAAAATTAAGAATTTGTTTGGATGT
*
31474339 AATTAAAAGTTAAGAATTTGTTTGGATGT
1 AATTAAAAATTAAGAATTTGTTTGGATGT
*
31474368 AA-TAAAAATATAATAATTT
1 AATTAAAAAT-TAAGAATTT
31474387 ATTTAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 30 0.75
29 10 0.25
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.41
Consensus pattern (29 bp):
AATTAAAAATTAAGAATTTGTTTGGATGT
Found at i:31475897 original size:13 final size:13
Alignment explanation
Indices: 31475879--31475904 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31475869 ATTCGATCTG
31475879 AATTATTTTTATT
1 AATTATTTTTATT
31475892 AATTATTTTTATT
1 AATTATTTTTATT
31475905 TACATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTATTTTTATT
Found at i:31479397 original size:2 final size:2
Alignment explanation
Indices: 31479390--31479426 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
31479380 CCATGCATAT
31479390 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
31479427 TTGAGCTGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:31483243 original size:17 final size:18
Alignment explanation
Indices: 31483208--31483249 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
31483198 TTAAACTCCC
*
31483208 TTTTATTTTCTTGTAGTT
1 TTTTATTTTCCTGTAGTT
*
31483226 TTTTCTTTTCCTGT-GTT
1 TTTTATTTTCCTGTAGTT
*
31483243 TATTATT
1 TTTTATT
31483250 ATTATTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (18 bp):
TTTTATTTTCCTGTAGTT
Found at i:31483250 original size:3 final size:3
Alignment explanation
Indices: 31483242--31483298 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
31483232 TTTCCTGTGT
31483242 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31483290 TTA TTA TTA
1 TTA TTA TTA
31483299 AGCGACAGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31495930 original size:15 final size:15
Alignment explanation
Indices: 31495910--31495947 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
31495900 CTCCAGCACT
31495910 TCATCATCAAACTCA
1 TCATCATCAAACTCA
*
31495925 TCATCATCAATCTCA
1 TCATCATCAAACTCA
*
31495940 TGATCATC
1 TCATCATC
31495948 TTGATCTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.32
Consensus pattern (15 bp):
TCATCATCAAACTCA
Found at i:31496063 original size:3 final size:3
Alignment explanation
Indices: 31496053--31496103 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
31496043 CATCTCCAGA
* *
31496053 CAT C-T CAT CAT CAT CAT CAT CAT CAT CGT CAT CAT CAC CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
31496100 CAT C
1 CAT C
31496104 GAGGTTTTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.29, C:0.37, G:0.02, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:31506483 original size:24 final size:23
Alignment explanation
Indices: 31506456--31506518 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 23
31506446 TAATGGCAAT
31506456 AAATTTTGAATTTTACAATTTATA
1 AAATTTT-AATTTTACAATTTATA
*
31506480 AAATCTTT-ATAATTACAATTTATA
1 AAAT-TTTAAT-TTTACAATTTATA
31506504 AAATTTTTAATTTTA
1 AAA-TTTTAATTTTA
31506519 TAAGTTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
23 2 0.06
24 25 0.76
25 6 0.18
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (23 bp):
AAATTTTAATTTTACAATTTATA
Found at i:31507767 original size:18 final size:18
Alignment explanation
Indices: 31507731--31507774 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31507721 TATTATATTA
* * *
31507731 ATTAATTTTACTTTTATC
1 ATTATTTTTAATTTCATC
31507749 ATTATTTTTAATTTCATC
1 ATTATTTTTAATTTCATC
31507767 ATCTATTT
1 AT-TATTT
31507775 AAATAAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTATTTTTAATTTCATC
Found at i:31509152 original size:17 final size:18
Alignment explanation
Indices: 31509120--31509157 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
31509110 TTTATTTAAA
*
31509120 AAAAATTAAAATATATAT
1 AAAAACTAAAATATATAT
*
31509138 AAAAACTAAAA-ATATGT
1 AAAAACTAAAATATATAT
31509155 AAA
1 AAA
31509158 TTCAATATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAACTAAAATATATAT
Found at i:31509233 original size:13 final size:13
Alignment explanation
Indices: 31509214--31509250 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
31509204 ATTTGATTCG
31509214 AATTTAATATATA
1 AATTTAATATATA
*
31509227 TATTTAATATATA
1 AATTTAATATATA
31509240 AATTTAATATA
1 AATTTAATATA
31509251 AATCAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATTTAATATATA
Found at i:31528320 original size:14 final size:14
Alignment explanation
Indices: 31528301--31528328 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31528291 CCTAATAAAT
31528301 ATATAGCAATCAAG
1 ATATAGCAATCAAG
31528315 ATATAGCAATCAAG
1 ATATAGCAATCAAG
31528329 GATAACTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
ATATAGCAATCAAG
Found at i:31538087 original size:2 final size:2
Alignment explanation
Indices: 31538082--31538112 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
31538072 AGAAAAAAAA
*
31538082 AC AC AC AC AC AC AC AC AC AC AC AT AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
31538113 ACCCTAGTAA
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:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:31543445 original size:24 final size:23
Alignment explanation
Indices: 31543412--31543456 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
31543402 AGCTTTGCAC
* *
31543412 AATTTTATGCTAAGAGAGTTTGA
1 AATTTTATGCCAAGAAAGTTTGA
31543435 AATTTCTATGCCAAGAAAGTTT
1 AATTT-TATGCCAAGAAAGTTT
31543457 AACGTTTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (23 bp):
AATTTTATGCCAAGAAAGTTTGA
Found at i:31547748 original size:13 final size:13
Alignment explanation
Indices: 31547732--31547829 Score: 67
Period size: 13 Copynumber: 7.7 Consensus size: 13
31547722 TAAAGCCTTG
31547732 AAATAAAATCCC-A
1 AAATAAAA-CCCTA
31547745 AAATAAAACCCTA
1 AAATAAAACCCTA
*
31547758 AAATAAAACCATA
1 AAATAAAACCCTA
*
31547771 AACT-AAACCCTA
1 AAATAAAACCCTA
* * * *
31547783 GAGTAAAA-TCTT
1 AAATAAAACCCTA
* *
31547795 AAATGAAATCCTA
1 AAATAAAACCCTA
* *
31547808 AAATCAAACCTTA
1 AAATAAAACCCTA
*
31547821 AAATGAAAC
1 AAATAAAAC
31547830 TTTAAAACCC
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
12 19 0.29
13 47 0.71
ACGTcount: A:0.57, C:0.19, G:0.04, T:0.19
Consensus pattern (13 bp):
AAATAAAACCCTA
Found at i:31547797 original size:25 final size:25
Alignment explanation
Indices: 31547750--31547822 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 25
31547740 TCCCAAAATA
31547750 AAACCCTAAAATAAAACCATAAACT
1 AAACCCTAAAATAAAACCATAAACT
* * * *
31547775 AAACCCTAGAGTAAAATCTTAAA-T
1 AAACCCTAAAATAAAACCATAAACT
* * *
31547799 GAAATCCTAAAATCAAACCTTAAA
1 -AAACCCTAAAATAAAACCATAAA
31547823 ATGAAACTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 1 0.03
25 37 0.97
ACGTcount: A:0.55, C:0.21, G:0.04, T:0.21
Consensus pattern (25 bp):
AAACCCTAAAATAAAACCATAAACT
Found at i:31547850 original size:33 final size:33
Alignment explanation
Indices: 31547813--31547921 Score: 148
Period size: 33 Copynumber: 3.3 Consensus size: 33
31547803 TCCTAAAATC
* * *
31547813 AAACCTTAAAATGAAACTTTAAAACCCTATATG
1 AAACCCTAAAATAAAACTTTAAAACCCTAGATG
*
31547846 AAACCCTAAAATAAAACCTT-AAACCCTTAGATG
1 AAACCCTAAAATAAAACTTTAAAACCC-TAGATG
* *
31547879 AAACCCTAAAATAAAACTTTAAATCCTTAGATG
1 AAACCCTAAAATAAAACTTTAAAACCCTAGATG
31547912 AAACCCTAAA
1 AAACCCTAAA
31547922 TCTTAGGTGA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 6 0.09
33 57 0.85
34 4 0.06
ACGTcount: A:0.50, C:0.21, G:0.06, T:0.24
Consensus pattern (33 bp):
AAACCCTAAAATAAAACTTTAAAACCCTAGATG
Found at i:31547868 original size:13 final size:13
Alignment explanation
Indices: 31547722--31547836 Score: 58
Period size: 13 Copynumber: 9.0 Consensus size: 13
31547712 CGTAAATTTT
* *
31547722 TAAAGCCTTGAAA
1 TAAAACCTTAAAA
*
31547735 TAAAATCC-CAAAA
1 TAAAA-CCTTAAAA
*
31547748 TAAAACCCTAAAA
1 TAAAACCTTAAAA
* *
31547761 TAAAACCATAAAC
1 TAAAACCTTAAAA
* * *
31547774 T-AAACCCTAGAG
1 TAAAACCTTAAAA
*
31547786 TAAAATCTT-AAA
1 TAAAACCTTAAAA
*
31547798 TGAAATCC-TAAAA
1 T-AAAACCTTAAAA
*
31547811 TCAAACCTTAAAA
1 TAAAACCTTAAAA
* *
31547824 TGAAACTTTAAAA
1 TAAAACCTTAAAA
31547837 CCCTATATGA
Statistics
Matches: 77, Mismatches: 19, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
12 18 0.23
13 57 0.74
14 2 0.03
ACGTcount: A:0.55, C:0.18, G:0.05, T:0.22
Consensus pattern (13 bp):
TAAAACCTTAAAA
Found at i:31547932 original size:19 final size:20
Alignment explanation
Indices: 31547898--31547940 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
31547888 AATAAAACTT
31547898 TAAATCCTTAGATGAAACCC
1 TAAATCCTTAGATGAAACCC
*
31547918 TAAAT-CTTAGGTGAAACCC
1 TAAATCCTTAGATGAAACCC
31547937 TAAA
1 TAAA
31547941 CTTTCAGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.26
Consensus pattern (20 bp):
TAAATCCTTAGATGAAACCC
Found at i:31555310 original size:13 final size:13
Alignment explanation
Indices: 31555294--31555318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31555284 AATCCTGCGC
31555294 AGAAATCAGTTTA
1 AGAAATCAGTTTA
31555307 AGAAATCAGTTT
1 AGAAATCAGTTT
31555319 TTGATTTGAA
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AGAAATCAGTTTA
Found at i:31556706 original size:13 final size:12
Alignment explanation
Indices: 31556665--31556702 Score: 55
Period size: 11 Copynumber: 3.4 Consensus size: 12
31556655 ATATAATACG
31556665 ATAATA-AAATA
1 ATAATATAAATA
31556676 A-AATATAAA-A
1 ATAATATAAATA
31556686 ATAATATAAATA
1 ATAATATAAATA
31556698 ATAAT
1 ATAAT
31556703 TATATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.25
11 12 0.50
12 6 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:31562386 original size:8 final size:8
Alignment explanation
Indices: 31562378--31562416 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
31562368 TCATATGTAT
*
31562378 ATATATAT
1 ATATATAC
31562386 ATATATAC
1 ATATATAC
*
31562394 ATACATAC
1 ATATATAC
*
31562402 ATACATAC
1 ATATATAC
31562410 ATATATA
1 ATATATA
31562417 TAAGGGACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAC
Found at i:31562390 original size:12 final size:12
Alignment explanation
Indices: 31562375--31562416 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
31562365 AATTCATATG
* *
31562375 TATATATATATA
1 TATATACATACA
31562387 TATATACATACA
1 TATATACATACA
*
31562399 TACATACATACA
1 TATATACATACA
31562411 TATATA
1 TATATA
31562417 TAAGGGACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (12 bp):
TATATACATACA
Found at i:31578913 original size:21 final size:20
Alignment explanation
Indices: 31578889--31578935 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
31578879 ACTAGGGCTC
*
31578889 TATTTTTATTTTCATACATAA
1 TATTTTTATGTTC-TACATAA
* *
31578910 TATTTGTATGTTCTTCATAA
1 TATTTTTATGTTCTACATAA
31578930 -ATTTTT
1 TATTTTT
31578936 TTATATATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 5 0.23
20 6 0.27
21 11 0.50
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (20 bp):
TATTTTTATGTTCTACATAA
Found at i:31581469 original size:2 final size:2
Alignment explanation
Indices: 31581462--31581491 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31581452 AAAGAACTTG
31581462 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31581492 GAACCTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31582941 original size:2 final size:2
Alignment explanation
Indices: 31582934--31582966 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31582924 CCTTTCTTGG
31582934 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31582967 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31582971 original size:2 final size:2
Alignment explanation
Indices: 31582966--31582991 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31582956 TCTCTCTCTC
31582966 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
31582992 AAATATCATC
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):
TA
Found at i:31584330 original size:28 final size:26
Alignment explanation
Indices: 31584299--31584358 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 26
31584289 AAGATTAATT
31584299 TAAATTAATATATTTATATTTA-AAAACA
1 TAAATTAATATA--TATATTTATAAAA-A
31584327 TAAATTAATATATATATTTATAAAAA
1 TAAATTAATATATATATTTATAAAAA
31584353 -AAATTA
1 TAAATTA
31584359 CGTAAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 6 0.19
26 9 0.29
27 4 0.13
28 12 0.39
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAATTAATATATATATTTATAAAAA
Found at i:31584367 original size:26 final size:26
Alignment explanation
Indices: 31584299--31584368 Score: 63
Period size: 26 Copynumber: 2.6 Consensus size: 26
31584289 AAGATTAATT
*
31584299 TAAATTAATATATTTATATTTAAAAACA
1 TAAATTAATA-A-ATATATTTAAAAACA
*
31584327 TAAATTAATATATATATTTATAAAA-A
1 TAAATTAATAAATATATTTA-AAAACA
*
31584353 -AAATTACGTAAATATA
1 TAAATTA-ATAAATATA
31584369 CATAATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 6 0.17
26 16 0.44
27 4 0.11
28 10 0.28
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (26 bp):
TAAATTAATAAATATATTTAAAAACA
Found at i:31599864 original size:22 final size:22
Alignment explanation
Indices: 31599838--31599879 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31599828 TATATTTATA
* *
31599838 TTTGTATCTCTAGAATTAAATG
1 TTTGTATCCCTAAAATTAAATG
31599860 TTTGTATCCCTAAAATTAAA
1 TTTGTATCCCTAAAATTAAA
31599880 AACAGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (22 bp):
TTTGTATCCCTAAAATTAAATG
Found at i:31600046 original size:24 final size:24
Alignment explanation
Indices: 31600018--31600070 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
31600008 AATATACATT
31600018 CAATTTTA-CTCTTAGTTTTCTACA
1 CAATTTTATCTCTTAGTTTT-TACA
* *
31600042 CAATTTTATTTCTTAGTTTTTCCA
1 CAATTTTATCTCTTAGTTTTTACA
31600066 CAATT
1 CAATT
31600071 ACTTGTGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.53
Consensus pattern (24 bp):
CAATTTTATCTCTTAGTTTTTACA
Found at i:31610368 original size:24 final size:26
Alignment explanation
Indices: 31610331--31610404 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 26
31610321 AAGATATTAC
*
31610331 ATATTTATTTTATATAATATTAAT-A
1 ATATTTATTATATATAATATTAATGA
* *
31610356 ATA-TTATTATATACAA-ATTCATGA
1 ATATTTATTATATATAATATTAATGA
*
31610380 ATATTTATAAATATATTAATATTAA
1 ATATTTAT-TATATA-TAATATTAA
31610405 ATTAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
23 5 0.13
24 15 0.39
25 7 0.18
26 5 0.13
27 2 0.05
28 4 0.11
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (26 bp):
ATATTTATTATATATAATATTAATGA
Found at i:31612288 original size:21 final size:21
Alignment explanation
Indices: 31612264--31612307 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
31612254 AAACCATATA
31612264 CAAAGGACCCTATTCTGGTCT
1 CAAAGGACCCTATTCTGGTCT
*
31612285 CAAAGGACCCTGTTCTGGTCT
1 CAAAGGACCCTATTCTGGTCT
31612306 CA
1 CA
31612308 TATATACTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (21 bp):
CAAAGGACCCTATTCTGGTCT
Found at i:31625199 original size:15 final size:15
Alignment explanation
Indices: 31625179--31625208 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31625169 CTAACTGTGG
31625179 TAGTATTGCTAATTA
1 TAGTATTGCTAATTA
31625194 TAGTATTGCTAATTA
1 TAGTATTGCTAATTA
31625209 AACTTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
TAGTATTGCTAATTA
Found at i:31636365 original size:20 final size:19
Alignment explanation
Indices: 31636342--31636399 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
31636332 TTAATTTTTA
31636342 TTTTAAAATATTAAAATAAT
1 TTTTAAAAT-TTAAAATAAT
*
31636362 TTTTAATATTTAATAATAA-
1 TTTTAAAATTTAA-AATAAT
*
31636381 ATTT-AAATTT-AAATAAT
1 TTTTAAAATTTAAAATAAT
31636398 TT
1 TT
31636400 AAATCAGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
18 5 0.16
19 7 0.22
20 13 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTAAAATTTAAAATAAT
Found at i:31636374 original size:19 final size:18
Alignment explanation
Indices: 31636341--31636399 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
31636331 TTTAATTTTT
*
31636341 ATTTTAAAATATTAAAATA
1 ATTTTTAAAT-TTAAAATA
31636360 ATTTTTAATATTTAATAATA
1 ATTTTTAA-ATTTAA-AATA
*
31636380 A-ATTTAAATTT-AAATA
1 ATTTTTAAATTTAAAATA
31636396 ATTT
1 ATTT
31636400 AAATCAGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 5 0.15
17 2 0.06
18 4 0.12
19 16 0.47
20 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTTAAATTTAAAATA
Found at i:31639834 original size:44 final size:44
Alignment explanation
Indices: 31639768--31639886 Score: 139
Period size: 44 Copynumber: 2.6 Consensus size: 44
31639758 GCATAAAGAA
*
31639768 AAGAAAAAGAAATGTGGAGAGTGTGGCGGTCAGGAGAGGAAGAAAG
1 AAGAAAAAGAAA-GTGG-GAGTGTGGCGGTCAGGAGAGGAACAAAG
* * * * **
31639814 AAGAAAAAGAACGTGGGAGTGTGTCAGTGAGGAGAGGAACCGAG
1 AAGAAAAAGAAAGTGGGAGTGTGGCGGTCAGGAGAGGAACAAAG
*
31639858 AAGAAAAGTGAAAGTGGGAGTGTGGCGGT
1 AAGAAAA-AGAAAGTGGGAGTGTGGCGGT
31639887 GGATTTAGGA
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
44 29 0.48
45 21 0.34
46 11 0.18
ACGTcount: A:0.39, C:0.06, G:0.42, T:0.13
Consensus pattern (44 bp):
AAGAAAAAGAAAGTGGGAGTGTGGCGGTCAGGAGAGGAACAAAG
Found at i:31646549 original size:25 final size:25
Alignment explanation
Indices: 31646521--31646575 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
31646511 GAATCGCTGG
31646521 TACTACCCATGATTGTATTAGCTTT
1 TACTACCCATGATTGTATTAGCTTT
*
31646546 TACTACCCATGATTGTATTGGCTTT
1 TACTACCCATGATTGTATTAGCTTT
31646571 T-CTAC
1 TACTAC
31646576 TTTCTGAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (25 bp):
TACTACCCATGATTGTATTAGCTTT
Found at i:31651250 original size:21 final size:21
Alignment explanation
Indices: 31651226--31651296 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
31651216 ATATTAATAT
*
31651226 TTATAAATTATTTAAATTTAA
1 TTATAAATTATTTAAATTAAA
**
31651247 TTATAATAAAATTTAAATTAAA
1 TTATAA-ATTATTTAAATTAAA
* *
31651269 TTTTATTATTA-TTAAATTAAA
1 TTATA-AATTATTTAAATTAAA
31651290 TT-TAAAT
1 TTATAAAT
31651297 ATAAATAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.05
20 2 0.05
21 18 0.45
22 18 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATAAATTATTTAAATTAAA
Found at i:31651269 original size:11 final size:11
Alignment explanation
Indices: 31651235--31651302 Score: 52
Period size: 11 Copynumber: 6.2 Consensus size: 11
31651225 TTTATAAATT
*
31651235 ATTTAAATTTA
1 ATTTAAATTAA
*
31651246 A-TTATAATAAA
1 ATTTA-AATTAA
31651257 ATTTAAATTAA
1 ATTTAAATTAA
*
31651268 ATTT-TATT-A
1 ATTTAAATTAA
*
31651277 TTATTAAATTAA
1 AT-TTAAATTAA
31651289 ATTTAAATATAA
1 ATTTAAAT-TAA
31651301 AT
1 AT
31651303 AATTTAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
9 2 0.05
10 8 0.18
11 24 0.55
12 10 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:31651276 original size:27 final size:27
Alignment explanation
Indices: 31651235--31651296 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
31651225 TTTATAAATT
31651235 ATTTAAATTTAATTATAATAAAATTTAA
1 ATTTAAATTTAATTATAATAAAA-TTAA
* * *
31651263 A-TTAAATTTTATTATTATTAAATTAA
1 ATTTAAATTTAATTATAATAAAATTAA
31651289 ATTTAAAT
1 ATTTAAAT
31651297 ATAAATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 5 0.17
27 24 0.80
28 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTTAAATTTAATTATAATAAAATTAA
Found at i:31651309 original size:21 final size:21
Alignment explanation
Indices: 31651227--31651313 Score: 52
Period size: 21 Copynumber: 3.9 Consensus size: 21
31651217 TATTAATATT
* *
31651227 TATAAATTATTTAAATTTAAT
1 TATAAATAATTTAAATTTAAA
*
31651248 TATAATAAAATTTAAA-TTAAA
1 TATAA-ATAATTTAAATTTAAA
* *
31651269 TTTTATTATTATTAAATTAAATTTAAA
1 ---TA-TA--AATAATTTAAATTTAAA
31651296 TATAAATAATTT-AATTTA
1 TATAAATAATTTAAATTTA
31651314 TTTATCAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 17
0.67 0.11 0.23
Matches are distributed among these distances:
20 6 0.12
21 15 0.30
22 8 0.16
23 2 0.04
24 4 0.08
25 2 0.04
26 7 0.14
27 6 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATAAATAATTTAAATTTAAA
Found at i:31652897 original size:19 final size:19
Alignment explanation
Indices: 31652854--31652898 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
31652844 AAGAGATTAA
* *
31652854 AAAAAGATTATTTTTATAGT
1 AAAAA-ATTATTTTTAAAAT
*
31652874 GAAAAATTATTTTTAAAAT
1 AAAAAATTATTTTTAAAAT
31652893 AAAAAA
1 AAAAAA
31652899 GTAATATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (19 bp):
AAAAAATTATTTTTAAAAT
Found at i:31656047 original size:36 final size:36
Alignment explanation
Indices: 31655999--31656071 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
31655989 TATTTTATTA
31655999 TTAAAAAGAACCTAACTAAGATTGGAATGTTTCTTT
1 TTAAAAAGAACCTAACTAAGATTGGAATGTTTCTTT
* *
31656035 TTAAAAATAACCTAACTAAGGTTGGAATGTTTCTTT
1 TTAAAAAGAACCTAACTAAGATTGGAATGTTTCTTT
31656071 T
1 T
31656072 CTGTCTCAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (36 bp):
TTAAAAAGAACCTAACTAAGATTGGAATGTTTCTTT
Found at i:31660465 original size:15 final size:15
Alignment explanation
Indices: 31660434--31660472 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
31660424 TCTTTTTTTC
*
31660434 TTTTTTTTCCTTCCT
1 TTTTTTTTCCTACCT
*
31660449 TTTTTTTTCCTAGCT
1 TTTTTTTTCCTACCT
31660464 TTTTCTTTT
1 TTTT-TTTT
31660473 AAAATGCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTTTTTCCTACCT
Found at i:31661116 original size:2 final size:2
Alignment explanation
Indices: 31661109--31661140 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
31661099 TGAATTCCTT
31661109 TA TA TA TA TA TA -A TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31661141 CAAAAGGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31661127 original size:13 final size:13
Alignment explanation
Indices: 31661109--31661133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31661099 TGAATTCCTT
31661109 TATATATATATAA
1 TATATATATATAA
31661122 TATATATATATA
1 TATATATATATA
31661134 TATTATACAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:31661127 original size:15 final size:15
Alignment explanation
Indices: 31661109--31661140 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31661099 TGAATTCCTT
31661109 TATATATATATAATA
1 TATATATATATAATA
*
31661124 TATATATATATATTA
1 TATATATATATAATA
31661139 TA
1 TA
31661141 CAAAAGGCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATATATATAATA
Found at i:31664025 original size:20 final size:19
Alignment explanation
Indices: 31663983--31664035 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
31663973 CGGATTTAAA
*
31663983 TATTTAAATGATATAATACT
1 TATTT-AATAATATAATACT
* *
31664003 TATTTAATTATATATATATT
1 TATTTAATAATATA-ATACT
*
31664023 TATATAATAATAT
1 TATTTAATAATAT
31664036 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TATTTAATAATATAATACT
Found at i:31674891 original size:2 final size:2
Alignment explanation
Indices: 31674886--31674928 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
31674876 ACACACACAG
* *
31674886 AT AT AT AT AA AT AT TT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31674927 AT
1 AT
31674929 TTTAGTGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:31678093 original size:172 final size:172
Alignment explanation
Indices: 31677807--31678149 Score: 659
Period size: 172 Copynumber: 2.0 Consensus size: 172
31677797 ACAACCTGCA
*
31677807 GCAAATGATAAATGGATAAAGGAAAAAAACGGTTAGGAGTATATGATCTAGTCATAGGGCAGTGC
1 GCAAATGATAAATGGATAAAGGAAAAAAACGGTTAGGAGTATATGATCTAGTCATAGGACAGTGC
*
31677872 AATTTTAGTTAAAATATAATCCAGCCCTTTCAGGGATTGAATAGTTATGCTGATCAGAAAAAAAG
66 AATTTTAGTTAAAATATAATCCAGCCCATTCAGGGATTGAATAGTTATGCTGATCAGAAAAAAAG
31677937 GGAAATTTTTGTAAAGAAGATACAAATGGGCCACTCACCAAC
131 GGAAATTTTTGTAAAGAAGATACAAATGGGCCACTCACCAAC
31677979 GCAAATGATAAATGGATAAAGGAAAAAAACGGTTAGGAGTATATGATCTAGTCATAGGACAGTGC
1 GCAAATGATAAATGGATAAAGGAAAAAAACGGTTAGGAGTATATGATCTAGTCATAGGACAGTGC
*
31678044 AATTTTAGTTAAAATATAATCCAGCCCATTCTGGGATTGAATAGTTATGCTGATCAGAAAAAAAG
66 AATTTTAGTTAAAATATAATCCAGCCCATTCAGGGATTGAATAGTTATGCTGATCAGAAAAAAAG
31678109 GGAAATTTTTGTAAAGAAGATACAAATGGGCCACTCACCAA
131 GGAAATTTTTGTAAAGAAGATACAAATGGGCCACTCACCAA
31678150 TTTAAAAATT
Statistics
Matches: 168, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
172 168 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (172 bp):
GCAAATGATAAATGGATAAAGGAAAAAAACGGTTAGGAGTATATGATCTAGTCATAGGACAGTGC
AATTTTAGTTAAAATATAATCCAGCCCATTCAGGGATTGAATAGTTATGCTGATCAGAAAAAAAG
GGAAATTTTTGTAAAGAAGATACAAATGGGCCACTCACCAAC
Found at i:31698987 original size:2 final size:2
Alignment explanation
Indices: 31698982--31699010 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31698972 ACACATGTAC
31698982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31699011 AAGAACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31704738 original size:22 final size:22
Alignment explanation
Indices: 31704713--31704754 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
31704703 AATAATAGTT
*
31704713 TTTAAATTTTAAATTAATTAAA
1 TTTAAATTTTAAAATAATTAAA
**
31704735 TTTATTTTTTAAAATAATTA
1 TTTAAATTTTAAAATAATTA
31704755 TATGAATAAA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAAATTTTAAAATAATTAAA
Found at i:31707529 original size:17 final size:17
Alignment explanation
Indices: 31707488--31707530 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
31707478 ATTCAAACTC
*
31707488 AAATTAAAATATTTTAT
1 AAATTAAAATATATTAT
*
31707505 TAATTAAAATATATTA-
1 AAATTAAAATATATTAT
31707521 AAATATAAAA
1 AAAT-TAAAA
31707531 ATTCAATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTAAAATATATTAT
Found at i:31709122 original size:18 final size:17
Alignment explanation
Indices: 31709099--31709133 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
31709089 CACACATCAG
*
31709099 AATTATTAATTAATAAAA
1 AATTATCAA-TAATAAAA
31709117 AATTATCAATAATAAAA
1 AATTATCAATAATAAAA
31709134 TTTTTAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTATCAATAATAAAA
Found at i:31724966 original size:12 final size:12
Alignment explanation
Indices: 31724949--31724978 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
31724939 TATTTAAATG
31724949 TTTAAACTATTA
1 TTTAAACTATTA
31724961 TTTAAACTATTA
1 TTTAAACTATTA
31724973 TTTAAA
1 TTTAAA
31724979 TAATATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTAAACTATTA
Found at i:31726336 original size:29 final size:29
Alignment explanation
Indices: 31726304--31726359 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
31726294 AAAATTATTT
31726304 AAATTATTAATATTTTATTAT-AATTAATC
1 AAATTATTAATATTTTATT-TCAATTAATC
* * *
31726333 AAATTCTTTATCTTTTATTTCAATTAA
1 AAATTATTAATATTTTATTTCAATTAA
31726360 ATTAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.04
29 22 0.96
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (29 bp):
AAATTATTAATATTTTATTTCAATTAATC
Found at i:31727232 original size:16 final size:17
Alignment explanation
Indices: 31727204--31727236 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
31727194 AATATTATAA
31727204 AAATTTAAAATTGATTT
1 AAATTTAAAATTGATTT
31727221 AAATTT-AAATTGATTT
1 AAATTTAAAATTGATTT
31727237 TTTTATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
AAATTTAAAATTGATTT
Found at i:31727339 original size:20 final size:22
Alignment explanation
Indices: 31727294--31727346 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
31727284 TAAAATTTTG
*
31727294 TTTTTATATTATTTAATATAAAA
1 TTTTAATA-TATTTAATATAAAA
31727317 TTTTAATATATTTAA-AT-AAA
1 TTTTAATATATTTAATATAAAA
*
31727337 TTTTGATATA
1 TTTTAATATA
31727347 AAATTATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 12 0.43
21 2 0.07
22 7 0.25
23 7 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTTAATATATTTAATATAAAA
Found at i:31729889 original size:6 final size:6
Alignment explanation
Indices: 31729878--31729911 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
31729868 AACCAGCAAG
* *
31729878 AACCCA AACCCA AACCCA AATCCA AATCCA AACC
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACC
31729912 GTCTGATTTA
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:0.50, C:0.44, G:0.00, T:0.06
Consensus pattern (6 bp):
AACCCA
Found at i:31737716 original size:16 final size:17
Alignment explanation
Indices: 31737685--31737718 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
31737675 CGCCATGGTT
31737685 TTTGAAAAAATAAAAAG
1 TTTGAAAAAATAAAAAG
31737702 TTTGAAAAAATAAAAAG
1 TTTGAAAAAATAAAAAG
31737719 CTCACGATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (17 bp):
TTTGAAAAAATAAAAAG
Found at i:31740415 original size:2 final size:2
Alignment explanation
Indices: 31740408--31740441 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
31740398 ATGATCAATG
*
31740408 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31740442 GTGGAACTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31741387 original size:3 final size:3
Alignment explanation
Indices: 31741381--31741411 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31741371 ATTGTTGTTG
31741381 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
31741412 ATATATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31747885 original size:29 final size:31
Alignment explanation
Indices: 31747844--31747901 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
31747834 GTTGTTTGGT
*
31747844 AAATTAAATAAATTTAATATTGAAAAATTAA
1 AAATTAAATAAATTTAATATTAAAAAATTAA
*
31747875 AAATT-AA-AAATTTAATTTTAAAAAATT
1 AAATTAAATAAATTTAATATTAAAAAATT
31747902 TCAATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.72
30 2 0.08
31 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
AAATTAAATAAATTTAATATTAAAAAATTAA
Found at i:31747895 original size:14 final size:14
Alignment explanation
Indices: 31747853--31747928 Score: 68
Period size: 15 Copynumber: 5.4 Consensus size: 14
31747843 TAAATTAAAT
31747853 AAATTTAATATTGAA
1 AAATTTAATATT-AA
* *
31747868 AAATTAAAAATTAA
1 AAATTTAATATTAA
*
31747882 AAATTTAATTTTAAA
1 AAATTTAATATT-AA
31747897 AAATTTCAATATT--
1 AAATTT-AATATTAA
31747910 AAATTT-ATAATTAA
1 AAATTTAAT-ATTAA
31747924 AAATT
1 AAATT
31747929 ATTTGGTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
11 2 0.04
12 3 0.06
13 6 0.12
14 16 0.32
15 18 0.36
16 5 0.10
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (14 bp):
AAATTTAATATTAA
Found at i:31747898 original size:15 final size:15
Alignment explanation
Indices: 31747846--31747912 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
31747836 TGTTTGGTAA
31747846 ATTAAATAAATTTAAT
1 ATTAAA-AAATTTAAT
* * *
31747862 ATTGAAAAATTAAAA
1 ATTAAAAAATTTAAT
31747877 ATT-AAAAATTTAAT
1 ATTAAAAAATTTAAT
*
31747891 TTTAAAAAATTTCAAT
1 ATTAAAAAATTT-AAT
31747907 ATTAAA
1 ATTAAA
31747913 TTTATAATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
14 11 0.26
15 18 0.43
16 13 0.31
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (15 bp):
ATTAAAAAATTTAAT
Found at i:31755776 original size:69 final size:69
Alignment explanation
Indices: 31755665--31755810 Score: 211
Period size: 69 Copynumber: 2.1 Consensus size: 69
31755655 TTTGAGATAT
* * * * *
31755665 CTTGACCCCTTAAATACTCCTCTCGAAACATTACCAGAGACAATTGGTCATCTGTGCAATTTGCA
1 CTTGACCTCTCAAACACTCATCTCCAAACATTACCAGAGACAATTGGTCATCTGTGCAATTTGCA
*
31755730 AACG
66 AACA
* * *
31755734 CTTGACCTCTCAAACACTCATCTCCAAACATTACCGGGGACAATTGGTCGTCTGTGCAATTTGCA
1 CTTGACCTCTCAAACACTCATCTCCAAACATTACCAGAGACAATTGGTCATCTGTGCAATTTGCA
31755799 AACA
66 AACA
31755803 CTTGACCT
1 CTTGACCT
31755811 TTCAGGATGC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (69 bp):
CTTGACCTCTCAAACACTCATCTCCAAACATTACCAGAGACAATTGGTCATCTGTGCAATTTGCA
AACA
Found at i:31785510 original size:84 final size:84
Alignment explanation
Indices: 31785369--31785532 Score: 240
Period size: 84 Copynumber: 2.0 Consensus size: 84
31785359 TATATTTCAG
* * * * * * *
31785369 AATACATTAATATCTGATAAGGTATGTCACGTGAATGTTTATATGAATAACTTATATTTTTTACA
1 AATACATTAATATATGATAAGATATGTCACATGAATGCTTACATGAATAACCTATATTTTTGACA
31785434 TGTA-AGATAATAATTACAA
66 TGTACA-ATAATAATTACAA
*
31785453 AATACATTAATGTATGATAAGATATGTCACATGAATGCTTACATGAATAACCTATATTTTTGACA
1 AATACATTAATATATGATAAGATATGTCACATGAATGCTTACATGAATAACCTATATTTTTGACA
31785518 TGTACAATAATAATT
66 TGTACAATAATAATT
31785533 GAATTTAAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 70 0.99
85 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.38
Consensus pattern (84 bp):
AATACATTAATATATGATAAGATATGTCACATGAATGCTTACATGAATAACCTATATTTTTGACA
TGTACAATAATAATTACAA
Found at i:31788188 original size:71 final size:71
Alignment explanation
Indices: 31788095--31788236 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
31788085 GCTACTCAAA
31788095 CTCAAGCTCAACTCGATAATAATCGAACTGAATTCGAGTTTTATTCGAATCGAACTCAAGTAGCT
1 CTCAAGCTCAACTCGATAATAATCGAACTGAATTCGAGTTTTATTCGAATCGAACTCAAGTAGCT
31788160 TGTGAG
66 TGTGAG
31788166 CTCAAGCTCAACTCGATAATAATCGAACTGAATTCGAGTTTTATTCGAATCGAACTCAAGTAGCT
1 CTCAAGCTCAACTCGATAATAATCGAACTGAATTCGAGTTTTATTCGAATCGAACTCAAGTAGCT
31788231 TGTGAG
66 TGTGAG
31788237 TACTAATATA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (71 bp):
CTCAAGCTCAACTCGATAATAATCGAACTGAATTCGAGTTTTATTCGAATCGAACTCAAGTAGCT
TGTGAG
Found at i:31789023 original size:9 final size:8
Alignment explanation
Indices: 31789004--31789039 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
31788994 CTCAACACAC
31789004 TTTTTTAT
1 TTTTTTAT
*
31789012 TTTTTAAT
1 TTTTTTAT
31789020 TTTTTTAT
1 TTTTTTAT
31789028 TTTTTTAT
1 TTTTTTAT
31789036 TTTT
1 TTTT
31789040 GAAAAAGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTAT
Found at i:31789178 original size:43 final size:41
Alignment explanation
Indices: 31789119--31789342 Score: 157
Period size: 41 Copynumber: 5.4 Consensus size: 41
31789109 GAGGCATAAC
*
31789119 AACTTTGAAAAAATAAAATGCTTC-TTTAAACAAAGGCACCGT
1 AACTTTG-AAAAATAAAATGC-TCATTTAAACAAAGGCACCAT
* * *
31789161 AACTTTTGAAAGAATAAATTGCTCATTTAAATAAAGGTACCAT
1 AAC-TTTGAAA-AATAAAATGCTCATTTAAACAAAGGCACCAT
* ** * * * *
31789204 AACTTTGAAAAATAAATTATTCCTCTAAACAGAA-GCACTAC
1 AACTTTGAAAAATAAAATGCTCATTTAAACA-AAGGCACCAT
* * * * * ** *
31789245 AACTTTGAAAAATAAATTGCTCCTCTAAATAGAGATACCAC
1 AACTTTGAAAAATAAAATGCTCATTTAAACAAAGGCACCAT
* * * * *
31789286 AACTTTGAAAAATAAATTACT-TTTCTAAACAGAGGCACCGT
1 AACTTTGAAAAATAAAATGCTCATT-TAAACAAAGGCACCAT
31789327 AACTTTGAAAAATAAA
1 AACTTTGAAAAATAAA
31789343 TTATTCATCA
Statistics
Matches: 149, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
40 2 0.01
41 99 0.66
42 17 0.11
43 31 0.21
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (41 bp):
AACTTTGAAAAATAAAATGCTCATTTAAACAAAGGCACCAT
Found at i:31789249 original size:41 final size:41
Alignment explanation
Indices: 31789199--31789348 Score: 178
Period size: 41 Copynumber: 3.7 Consensus size: 41
31789189 AAATAAAGGT
*
31789199 ACCATAACTTTGAAAAATAAATTATTCCTCTAAACAGAAGC
1 ACCACAACTTTGAAAAATAAATTATTCCTCTAAACAGAAGC
* ** * *
31789240 ACTACAACTTTGAAAAATAAATTGCTCCTCTAAATAG-AGAT
1 ACCACAACTTTGAAAAATAAATTATTCCTCTAAACAGAAG-C
* *
31789281 ACCACAACTTTGAAAAATAAATTACTT-TTCTAAACAGAGGC
1 ACCACAACTTTGAAAAATAAATTA-TTCCTCTAAACAGAAGC
**
31789322 ACCGTAACTTTGAAAAATAAATTATTC
1 ACCACAACTTTGAAAAATAAATTATTC
31789349 ATCAACAATC
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
40 4 0.04
41 84 0.93
42 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.29
Consensus pattern (41 bp):
ACCACAACTTTGAAAAATAAATTATTCCTCTAAACAGAAGC
Found at i:31789284 original size:82 final size:82
Alignment explanation
Indices: 31789117--31789344 Score: 262
Period size: 82 Copynumber: 2.7 Consensus size: 82
31789107 CAGAGGCATA
* * * **
31789117 ACAACTTTGAAAAAATAAAATGCTTCTTTAAACA-AAGGCACCGTAACTTTTGAAAGAATAAATT
1 ACAACTTTG-AAAAATAAATTACTTCTCTAAACAGAA-GCACCACAAC-TTTGAAA-AATAAATT
* *
31789181 GCTCATTTAAATAAAGGTACC
62 GCTCATCTAAATAAAGATACC
* *
31789202 ATAACTTTGAAAAATAAATTA-TTCCTCTAAACAGAAGCACTACAACTTTGAAAAATAAATTGCT
1 ACAACTTTGAAAAATAAATTACTT-CTCTAAACAGAAGCACCACAACTTTGAAAAATAAATTGCT
* *
31789266 CCTCTAAATAGAGATACC
65 CATCTAAATAAAGATACC
* * **
31789284 ACAACTTTGAAAAATAAATTACTTTTCTAAACAGAGGCACCGTAACTTTGAAAAATAAATT
1 ACAACTTTGAAAAATAAATTACTTCTCTAAACAGAAGCACCACAACTTTGAAAAATAAATT
31789345 ATTCATCAAC
Statistics
Matches: 123, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
82 77 0.63
83 11 0.09
84 25 0.20
85 10 0.08
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (82 bp):
ACAACTTTGAAAAATAAATTACTTCTCTAAACAGAAGCACCACAACTTTGAAAAATAAATTGCTC
ATCTAAATAAAGATACC
Found at i:31790393 original size:7 final size:7
Alignment explanation
Indices: 31790381--31790424 Score: 61
Period size: 7 Copynumber: 5.9 Consensus size: 7
31790371 TCTTTATCAT
31790381 TTTTTTA
1 TTTTTTA
31790388 TTTTTTA
1 TTTTTTA
31790395 TTTTTTTTA
1 --TTTTTTA
31790404 TTTTTTA
1 TTTTTTA
31790411 TTTTTTAA
1 TTTTTT-A
31790419 TTTTTT
1 TTTTTT
31790425 TAAGCATAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 20 0.59
8 7 0.21
9 7 0.21
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:31790407 original size:23 final size:23
Alignment explanation
Indices: 31790381--31790426 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
31790371 TCTTTATCAT
*
31790381 TTTTTTATTTTTTATTTTTTTTA
1 TTTTTTATTTTTTAATTTTTTTA
31790404 TTTTTTATTTTTTAATTTTTTTA
1 TTTTTTATTTTTTAATTTTTTTA
31790427 AGCATAGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (23 bp):
TTTTTTATTTTTTAATTTTTTTA
Found at i:31790426 original size:16 final size:15
Alignment explanation
Indices: 31790379--31790424 Score: 74
Period size: 16 Copynumber: 3.0 Consensus size: 15
31790369 CATCTTTATC
31790379 ATTTTTTTATTTTTT
1 ATTTTTTTATTTTTT
31790394 ATTTTTTTTATTTTTT
1 A-TTTTTTTATTTTTT
*
31790410 ATTTTTTAATTTTTT
1 ATTTTTTTATTTTTT
31790425 TAAGCATAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 14 0.48
16 15 0.52
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (15 bp):
ATTTTTTTATTTTTT
Found at i:31801348 original size:15 final size:15
Alignment explanation
Indices: 31801330--31801358 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31801320 ATTTCAAATT
31801330 TTTTATATTTTTATG
1 TTTTATATTTTTATG
31801345 TTTTATATTTTTAT
1 TTTTATATTTTTAT
31801359 ACTTTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTATATTTTTATG
Found at i:31801575 original size:20 final size:20
Alignment explanation
Indices: 31801539--31801576 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31801529 AAATATTTTA
*
31801539 TTTTTTATTGTTTTTTTAAT
1 TTTTTTATTGTTCTTTTAAT
31801559 TTTTTTAATT-TTCTTTTA
1 TTTTTT-ATTGTTCTTTTA
31801577 CAAAAAATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTTTATTGTTCTTTTAAT
Found at i:31801912 original size:17 final size:18
Alignment explanation
Indices: 31801892--31801927 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
31801882 TTCTCATCCC
31801892 TTTTCTCTCTC-CTCTTT
1 TTTTCTCTCTCTCTCTTT
31801909 TTTTCTCTCTCTCTCTTT
1 TTTTCTCTCTCTCTCTTT
31801927 T
1 T
31801928 CTAACTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCTCTCTCTCTCTTT
Found at i:31803886 original size:239 final size:235
Alignment explanation
Indices: 31803516--31804378 Score: 807
Period size: 239 Copynumber: 3.7 Consensus size: 235
31803506 TTTTACTATT
* * *
31803516 AAATTTATTTGGTGGGAAATATTTTTGTGATGTTTTTTTTTTTAATTTTAGGTGACATTATAATT
1 AAATTTATTTGGT-GAAAATATTTTTGTGA--CTTTTTTTTTT-ATTTTAGGTAACATTATAATT
* * * * * *
31803581 TTGTCACCAATTTAAAATTT-TCTATGACAAATTTTTTCTTATAGATTTTAAGTAACGTTATTAA
62 TTATCACCAATTTAAAATTTAT-TTTGACGAATTTTTTCTTGTAGATTTTAGGTGACGTTATTAA
* * * **
31803645 TTTTTGTCACAAATTGAACACTTTAGTCAACTATTATTGACATGGCAATTTTGTTGCATCAATGT
126 TTTTTGTCACAAATTGAACACTTT-GTTAACTATTAATAACATGGCAATTTTGTCACATCAATGT
* * *
31803710 ATGGTGTTATATGATGAAACCATAAATGTCACAAATTTTTACT-GCC
190 ATGATGTTATATGATGAAAACATAAATGTCACAAACTTTTA-TAGCC
* * *
31803756 AAATTTATTTGGTGAAAATTTTTTTTGTGACTTTTTTTTTTATTTTAGGTAACGTTCTAATTTTA
1 AAATTTATTTGGTGAAAA-TATTTTTGTGACTTTTTTTTTTATTTTAGGTAACATTATAATTTTA
* * * *
31803821 CCACCAATTTAAAATTTTATTTGTGATGAATTTTTTCTTGTAAATTTTGGGTGACGTTATTAATT
65 TCACCAATTTAAAA-TTTATTT-TGACGAATTTTTTCTTGTAGATTTTAGGTGACGTTATTAATT
* * * * *
31803886 TTTATCACAAATTGAACACTTTTGTTAATTATTAATAATATTGCAATTTTGTCACGTCAATGTAT
128 TTTGTCACAAATTGAACAC-TTTGTTAACTATTAATAACATGGCAATTTTGTCACATCAATGTAT
31803951 GATGTTATATGATGAAAACATAAATGTCACAAACTTTTATAGCC
192 GATGTTATATGATGAAAACATAAATGTCACAAACTTTTATAGCC
* * * * *
31803995 AAATTTATTTGGTGAAAAAAATTTTTGGGAC---ATTTTTTGTTTTAGGTACCATTATAATTTTA
1 AAATTTATTTGGTG-AAAATATTTTTGTGACTTTTTTTTTTATTTTAGGTAACATTATAATTTTA
* * *
31804057 TCACCAATTTTAAAATTTATCTTTGACGAATTGTTT-TGGATAGATTTTAGGTGATGTTATTAAT
65 TCACCAA-TTTAAAATTTAT-TTTGACGAATTTTTTCTTG-TAGATTTTAGGTGACGTTATTAAT
* * *
31804121 TTTTGTCACAAATTGAATACTGTTGTTAAC---T-AT----T---AATTTCGTCACATTAATGTA
127 TTTTGTCACAAATTGAACACT-TTGTTAACTATTAATAACATGGCAATTTTGTCACATCAATGTA
* * * * *
31804175 TGATGTTATATGAT-AATAATATAAATGTTACGAACTTTTACCA-TC
191 TGATGTTATATGATGAA-AACATAAATGTCACAAACTTTTA-TAGCC
* * ** *
31804220 AAATTTATTTGGTGAGAAATATTTTTGTGA--TATTTTTTTATTTTAGGTGATGTTATAATTTTG
1 AAATTTATTTGGTGA-AAATATTTTTGTGACTTTTTTTTTTATTTTAGGTAACATTATAATTTTA
* * * * ** * * * *
31804283 TCACTAATTTAAAATTTTATCTATGA-TAAATTTTTCTAATAGATTTTAAGTAATGTTATTAAAT
65 TCACCAATTTAAAA-TTTAT-TTTGACGAATTTTTTCTTGTAGATTTTAGGTGACGTTATTAATT
* * *
31804347 TTTGTCATAAATTGAATACTATAGTTAACTAT
128 TTTGTCACAAATTGAACACT-TTGTTAACTAT
31804379 CAATGAAGTT
Statistics
Matches: 525, Mismatches: 77, Indels: 54
0.80 0.12 0.08
Matches are distributed among these distances:
224 3 0.01
225 139 0.26
226 42 0.08
228 1 0.00
232 2 0.00
233 1 0.00
235 3 0.01
236 94 0.18
237 42 0.08
238 15 0.03
239 153 0.29
240 30 0.06
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.47
Consensus pattern (235 bp):
AAATTTATTTGGTGAAAATATTTTTGTGACTTTTTTTTTTATTTTAGGTAACATTATAATTTTAT
CACCAATTTAAAATTTATTTTGACGAATTTTTTCTTGTAGATTTTAGGTGACGTTATTAATTTTT
GTCACAAATTGAACACTTTGTTAACTATTAATAACATGGCAATTTTGTCACATCAATGTATGATG
TTATATGATGAAAACATAAATGTCACAAACTTTTATAGCC
Found at i:31807137 original size:15 final size:14
Alignment explanation
Indices: 31807106--31807139 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31807096 TGGTAAAAAG
*
31807106 TTCTTTTTCTTTTC
1 TTCTTTTGCTTTTC
31807120 TTCTTTTGCTTGTTC
1 TTCTTTTGCTT-TTC
31807135 TTCTT
1 TTCTT
31807140 GATTCTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.00, C:0.21, G:0.06, T:0.74
Consensus pattern (14 bp):
TTCTTTTGCTTTTC
Found at i:31813631 original size:17 final size:17
Alignment explanation
Indices: 31813591--31813631 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
31813581 AAAAAAACTT
*
31813591 ACAAAATAAATATAATA
1 ACAAAATAAATAAAATA
*
31813608 ACTAAATAAATAAAATA
1 ACAAAATAAATAAAATA
*
31813625 CCAAAAT
1 ACAAAAT
31813632 GGCTCAGCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.22
Consensus pattern (17 bp):
ACAAAATAAATAAAATA
Found at i:31814090 original size:30 final size:31
Alignment explanation
Indices: 31814056--31814121 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
31814046 TGATGCTTGT
31814056 CAAAAAATTCAACCAACAT-AAAAAATTCAC
1 CAAAAAATTCAACCAACATCAAAAAATTCAC
* * * *
31814086 CAAAAAATTCAATCGACATCGAAAAATTCAT
1 CAAAAAATTCAACCAACATCAAAAAATTCAC
31814117 CAAAA
1 CAAAA
31814122 TCTGAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.58, C:0.21, G:0.03, T:0.18
Consensus pattern (31 bp):
CAAAAAATTCAACCAACATCAAAAAATTCAC
Found at i:31814128 original size:19 final size:19
Alignment explanation
Indices: 31814088--31814132 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
31814078 AAATTCACCA
* *
31814088 AAAAATTCAATCGACATCG
1 AAAAATTCAATCAAAATCG
31814107 AAAAATTC-ATCAAAATCTG
1 AAAAATTCAATCAAAATC-G
31814126 AAAAATT
1 AAAAATT
31814133 TTGTCGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24
Consensus pattern (19 bp):
AAAAATTCAATCAAAATCG
Found at i:31815870 original size:199 final size:200
Alignment explanation
Indices: 31815423--31815898 Score: 573
Period size: 199 Copynumber: 2.4 Consensus size: 200
31815413 TAGGATTTAA
** *
31815423 TGATGTTAATTGTGTCACCAATACTATGACGATTTACCTTTCGTCACTAATATATCAAATTTTAT
1 TGATGTTAATTGTGTCACCAATACTAAAACGATTTATCTTTCGTCACTAATATATCAAATTTTAT
* * ** *
31815488 CATTTATTTTGTGATGATTATAGCATTTAATAACATTTATTTTCATATGTAGCTGACAAAATCTA
66 CATTTATTTTATGATAATTATAGCATTTAATAACATTTATTTTCATAAATAACTGACAAAATCTA
* * * *
31815553 ATGTCACAAAAAAAGCATAAGATGGTGTTTAATTTTATTGTCATGTTTGACGTTATCTTACAATC
131 ACGTCACAAAAAAAGCATAAGATGATGTTTAATTTTATTGTCATATTTGACATTATCTTACAATC
* *
31815618 GTTTG
196 ATTAG
* * * * * * * *
31815623 TGACGTTAATTGTGCCACTAATGCTTAAATGGTTTATCTTTTGTCACTAATATAT-AAGATTTTA
1 TGATGTTAATTGTGTCACCAATACTAAAACGATTTATCTTTCGTCACTAATATATCAA-ATTTTA
* * *
31815687 TTATTTATTTTATGATAATTATAGCATTTAATGACATTT-TTTTCATAAATAACTTACAAAAAT-
65 TCATTTATTTTATGATAATTATAGCATTTAATAACATTTATTTTCATAAATAACTGAC-AAAATC
* * * * *
31815750 TAACGTCATAAAAAAATCATAAGGTGATGTTTGATTTTATTGTCATATTTGATATTATCTTACAA
129 TAACGTCACAAAAAAAGCATAAGATGATGTTTAATTTTATTGTCATATTTGACATTATCTTAC-A
31815815 AT-ATTAG
193 ATCATTAG
* * ** * *
31815822 TGATGATAATTATGTCACCAATACTGCAACGATTTATCATTCGTCACTAATTTATCAAATTTTAT
1 TGATGTTAATTGTGTCACCAATACTAAAACGATTTATCTTTCGTCACTAATATATCAAATTTTAT
31815887 CATTTATTTTAT
66 CATTTATTTTAT
31815899 AAGTTTTTTT
Statistics
Matches: 228, Mismatches: 44, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
199 133 0.58
200 95 0.42
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (200 bp):
TGATGTTAATTGTGTCACCAATACTAAAACGATTTATCTTTCGTCACTAATATATCAAATTTTAT
CATTTATTTTATGATAATTATAGCATTTAATAACATTTATTTTCATAAATAACTGACAAAATCTA
ACGTCACAAAAAAAGCATAAGATGATGTTTAATTTTATTGTCATATTTGACATTATCTTACAATC
ATTAG
Found at i:31816209 original size:20 final size:21
Alignment explanation
Indices: 31816162--31816210 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
31816152 GTGAGATAAG
*
31816162 ATAATTTATTTATTAATTAAA
1 ATAATTTATTTATAAATTAAA
* * *
31816183 ATTATTTTTTTA-AAATTAAT
1 ATAATTTATTTATAAATTAAA
31816203 ATAATTTA
1 ATAATTTA
31816211 AATTATTGAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATAATTTATTTATAAATTAAA
Found at i:31832883 original size:10 final size:10
Alignment explanation
Indices: 31832868--31832893 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
31832858 TAGACATGAA
31832868 CTTGAAAATT
1 CTTGAAAATT
31832878 CTTGAAAATT
1 CTTGAAAATT
31832888 CTTGAA
1 CTTGAA
31832894 GGCATCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (10 bp):
CTTGAAAATT
Found at i:31847437 original size:319 final size:319
Alignment explanation
Indices: 31846857--31847495 Score: 944
Period size: 319 Copynumber: 2.0 Consensus size: 319
31846847 TTGATAGTGA
* * *
31846857 AAATTTTTTTAGTGATCCGTAATTTTTTCGTCTACACTGGAAGGTTTTTCACGTAAATTTTGGTT
1 AAATTTTTTTAGTGATCCGTAATTTTTTCGTCTACACTGGAAGGTTTTTCACGTAAATCTTAGTG
* *
31846922 TGCTTTATTTTTTCTGTATTTTTTATTATTGATTATTGTCTATTGCTATGGGTTTATTACGATAT
66 TGCTTTATTTTTTCTATATTTTTTATTATTGATTATTGTCTATTGCTATGAGTTTATTACGATAT
*
31846987 ATTACTTCTGTATTATTGTAATTATTGCTTCAGGTGCAACAATTGGTATCAGAGCAATGATTATT
131 ATTACTTCTGTATTATTATAATTATTGCTTCAGGTGCAACAATTGGTATCAGAGCAATGATTATT
* * *
31847052 TTGAGACATCGATACAGAAACAACCCAAGACAGAAGTAAATTTTATTTGAGATCATGAAGGGTGA
196 TTAAGACATCGATACAGAAACAACCCAAGACAGAAGTAAATTCTATTTGAGATCATGAAAGGTGA
* *
31847117 TACAGGTTTCATGATAAAATTGACAGCATCGAATTATTCAATTTGGAAGCATATGATGG
261 TACAGGTTTCACGATAAAATTGACAGCATCGAATTATTCAATTTGAAAGCATATGATGG
* * *
31847176 AAATTTTTTTGGTGATCCGTGATTTTTTTC-TCTACACT-TAAGCGTTTTTCACGTAAATCTTAG
1 AAATTTTTTTAGTGATCCGT-AATTTTTTCGTCTACACTGGAAG-GTTTTTCACGTAAATCTTAG
* * *
31847239 TGTGCTTTATTTTTTTTATATTTTTTATTATTGATTGTTGTCTATTGCTATGAGTTTATTGCGAT
64 TGTGCTTTATTTTTTCTATATTTTTTATTATTGATTATTGTCTATTGCTATGAGTTTATTACGAT
* * * * *
31847304 ATATTGCTTCTGTATTGTTATGATTATTGCTTCAGGCT-CAATAATTGGTATCAGAGCGA-GAGT
129 ATATTACTTCTGTATTATTATAATTATTGCTTCAGG-TGCAACAATTGGTATCAGAGCAATGA-T
* * ** * *
31847367 TATTTTAAGATATTGATACAGAAGTAACCCAAGACAGAAGTAAATTCTGTTTGAGATCGTGAAAG
192 TATTTTAAGACATCGATACAGAAACAACCCAAGACAGAAGTAAATTCTATTTGAGATCATGAAAG
* *
31847432 GTGATACAGGTTTCACGATAAAATTGACAGTATCGAATTATTCAATTTGAAAGCTTATGATGG
257 GTGATACAGGTTTCACGATAAAATTGACAGCATCGAATTATTCAATTTGAAAGCATATGATGG
31847495 A
1 A
31847496 GGATCATCTA
Statistics
Matches: 286, Mismatches: 30, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
318 5 0.02
319 272 0.95
320 9 0.03
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (319 bp):
AAATTTTTTTAGTGATCCGTAATTTTTTCGTCTACACTGGAAGGTTTTTCACGTAAATCTTAGTG
TGCTTTATTTTTTCTATATTTTTTATTATTGATTATTGTCTATTGCTATGAGTTTATTACGATAT
ATTACTTCTGTATTATTATAATTATTGCTTCAGGTGCAACAATTGGTATCAGAGCAATGATTATT
TTAAGACATCGATACAGAAACAACCCAAGACAGAAGTAAATTCTATTTGAGATCATGAAAGGTGA
TACAGGTTTCACGATAAAATTGACAGCATCGAATTATTCAATTTGAAAGCATATGATGG
Found at i:31853563 original size:35 final size:35
Alignment explanation
Indices: 31853524--31853590 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
31853514 GAATTCAATG
31853524 TATAGCAATCGAGAATTGACAAGTTATAAATAATA
1 TATAGCAATCGAGAATTGACAAGTTATAAATAATA
31853559 TATAGCAATCGAGAATTGACAAGTTATAAATA
1 TATAGCAATCGAGAATTGACAAGTTATAAATA
31853591 CCAAGCTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (35 bp):
TATAGCAATCGAGAATTGACAAGTTATAAATAATA
Found at i:31877473 original size:27 final size:27
Alignment explanation
Indices: 31877438--31877496 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
31877428 AAATATAGTC
*
31877438 CATGACTTTTAGCACTCCATGTGATAG
1 CATGTCTTTTAGCACTCCATGTGATAG
31877465 CATGTCTTTTAGCACTCCATGTGATAG
1 CATGTCTTTTAGCACTCCATGTGATAG
31877492 CATGT
1 CATGT
31877497 TTGTCTTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (27 bp):
CATGTCTTTTAGCACTCCATGTGATAG
Found at i:31884400 original size:17 final size:18
Alignment explanation
Indices: 31884363--31884400 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
31884353 ATATTTTAAA
*
31884363 AAATTATATTAATAGTTT
1 AAATTATATTAAAAGTTT
*
31884381 AAATTATA-TAAAATTTT
1 AAATTATATTAAAAGTTT
31884398 AAA
1 AAA
31884401 AAATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
AAATTATATTAAAAGTTT
Found at i:31890736 original size:4 final size:4
Alignment explanation
Indices: 31890727--31890751 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
31890717 TTATTTTGAG
31890727 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
31890752 ATCTTTAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:31891435 original size:30 final size:29
Alignment explanation
Indices: 31891381--31891463 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 29
31891371 TTTAGTAATA
*
31891381 AAAATTTAATTAAAAAAGAAATAAATATTT
1 AAAATTTAATTAAATAA-AAATAAATATTT
31891411 AAAAGTTTAATTAAATAAAAATAAATATTT
1 AAAA-TTTAATTAAATAAAAATAAATATTT
* *
31891441 AAATATTTAATTAATTTAAAATA
1 AAA-ATTTAATTAAATAAAAATA
31891464 TGATTTATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
30 35 0.73
31 13 0.27
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (29 bp):
AAAATTTAATTAAATAAAAATAAATATTT
Done.