Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 33 of 190
Found at i:9481771 original size:38 final size:39
Alignment explanation
Indices: 9481687--9481775 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 39
9481677 ACACACATAC
* * *
9481687 ATGAATAGTCACAACTTCTATAGCATTTAAGTTATGTAA
1 ATGAATAGTCACAACTCCTATACCATTTAAGTGATGTAA
*
9481726 ATGAATAGTCACAACTCCTATACCATTT-AGTGATGTAG
1 ATGAATAGTCACAACTCCTATACCATTTAAGTGATGTAA
9481764 ATGAATAGTCAC
1 ATGAATAGTCAC
9481776 TTACAACTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 20 0.43
39 26 0.57
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (39 bp):
ATGAATAGTCACAACTCCTATACCATTTAAGTGATGTAA
Found at i:9486183 original size:32 final size:32
Alignment explanation
Indices: 9486112--9486183 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
9486102 ATAAAATTTC
* * *
9486112 AAAAGTTAGAAATGTGAAGAGACTTGGATATG
1 AAAAGTTAGAAATGTGAAGAGACTTGAAGATA
* *
9486144 AAGAGTTAGTAATGTGAAGAGACTTGAAGATA
1 AAAAGTTAGAAATGTGAAGAGACTTGAAGATA
9486176 AAAAGTTA
1 AAAAGTTA
9486184 CACACATGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.46, C:0.03, G:0.26, T:0.25
Consensus pattern (32 bp):
AAAAGTTAGAAATGTGAAGAGACTTGAAGATA
Found at i:9486277 original size:38 final size:39
Alignment explanation
Indices: 9486196--9486281 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
9486186 CACATGCATA
*
9486196 AATAGTCACAACTCCTATAGCATTTAAGTTATGTAAATG
1 AATAGTCACAACTCCTATAGCATTTAAGTGATGTAAATG
* *
9486235 AATAGTTACAACTCCTATAGCATTT-AGTGATGTAGATG
1 AATAGTCACAACTCCTATAGCATTTAAGTGATGTAAATG
9486273 AATAGTCAC
1 AATAGTCAC
9486282 TTATAACTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 19 0.44
39 24 0.56
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (39 bp):
AATAGTCACAACTCCTATAGCATTTAAGTGATGTAAATG
Found at i:9493185 original size:91 final size:91
Alignment explanation
Indices: 9493035--9493242 Score: 308
Period size: 91 Copynumber: 2.3 Consensus size: 91
9493025 TTGATTTTAG
* * *
9493035 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATGATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATGATGATTAAATTAT
* * * **
9493100 ATTTAATATTAATTATTTTAACTTGTA
65 ATGTAATAATAATTATTTTAAATAATA
*
9493127 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATGATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATGATGATTAAATTATA
9493192 TGTAATAATAATTATTTTAAATAATA
66 TGTAATAATAATTATTTTAAATAATA
* *
9493218 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
9493243 GTTATAATTA
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 89 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATGATGATTAAATTATA
TGTAATAATAATTATTTTAAATAATA
Found at i:9493335 original size:59 final size:57
Alignment explanation
Indices: 9493269--9493577 Score: 157
Period size: 66 Copynumber: 5.2 Consensus size: 57
9493259 ATTTTATTAA
9493269 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * * ** * *
9493328 ATCATATATTATGATTTGAGTAAATTCGTATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
9493389 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
* * *** * *
9493448 ATCATATATTATGATTTGAGTAAATTCATACAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATA-TTTAATATTAATTATTTA-AATTATTTTTATAGT
* * * * *
9493509 ATTATATATTTTAATTATAATATATTTAATAATATTTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
9493568 ATCATATATT
1 ATCATATATT
9493578 ATGATTTGAG
Statistics
Matches: 180, Mismatches: 42, Indels: 56
0.65 0.15 0.20
Matches are distributed among these distances:
54 27 0.15
55 12 0.07
56 10 0.06
57 6 0.03
59 30 0.17
60 16 0.09
61 20 0.11
63 7 0.04
64 10 0.06
65 11 0.06
66 31 0.17
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.50
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:9493382 original size:120 final size:120
Alignment explanation
Indices: 9493258--9493670 Score: 729
Period size: 120 Copynumber: 3.4 Consensus size: 120
9493248 AATTATTTTA
* * * * *
9493258 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTT
*
9493322 TATAGTATCATATATTATGATTTGAGTAAATTCGTATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
9493378 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
9493443 ATAGTATCATATATTATGATTTGAGTAAATTCATACAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
9493498 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATATTTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
9493563 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
9493618 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
9493671 TAAATATGAT
Statistics
Matches: 281, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
120 279 0.99
121 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:9493398 original size:61 final size:60
Alignment explanation
Indices: 9493331--9493638 Score: 221
Period size: 61 Copynumber: 5.1 Consensus size: 60
9493321 TTATAGTATC
9493331 ATATATTATGATTTGAGTAAATTCGTATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTC-TATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * *
9493392 ATATATT-TTAATT-A-TAATATAT-T-TAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAA-AT-TCTATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
9493450 C
60 T
*
9493451 ATATATTATGATTTGAGTAAATTCATACAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTC-TATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * *
9493512 ATATATT-TTAATT-A-TAATATAT-T-TAATAATATTTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAA-AT-TCTATAAGAATA-TTA-ATT-ATTAAGAATTTTATTA-AAT
*
9493570 C
60 T
*
9493571 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTC-TATAAGAATATTAATTATTAAGAATTTTATTAAATT
9493632 ATATATT
1 ATATATT
9493639 TTAATTATAA
Statistics
Matches: 184, Mismatches: 35, Indels: 56
0.67 0.13 0.20
Matches are distributed among these distances:
57 12 0.07
58 19 0.10
59 40 0.22
60 36 0.20
61 47 0.26
62 18 0.10
63 12 0.07
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (60 bp):
ATATATTATGATTTGAGTAAATTCTATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:9493418 original size:15 final size:15
Alignment explanation
Indices: 9493383--9493434 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
9493373 TTAAGAATTT
*
9493383 TATTAAATTAT-ATA
1 TATTTAATTATAATA
9493397 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
9493411 TATTTAATAATAAT-
1 TATTTAATTATAATA
9493425 TATGTTAATT
1 TAT-TTAATT
9493435 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:9493653 original size:16 final size:16
Alignment explanation
Indices: 9493632--9493673 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
9493622 TTATTAAATT
*
9493632 ATATATTTTAATTATA
1 ATATATTTTAATAATA
9493648 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
9493663 AT-TATGTTTAA
1 ATATAT-TTTAA
9493674 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:9493658 original size:15 final size:15
Alignment explanation
Indices: 9493623--9493664 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9493613 TTAAGAATTT
*
9493623 TATTAAATTAT-ATA
1 TATTTAATTATAATA
9493637 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
9493651 TATTTAATAATAAT
1 TATTTAATTATAAT
9493665 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:9493908 original size:16 final size:16
Alignment explanation
Indices: 9493887--9493956 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 16
9493877 TTGATTTGTT
9493887 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
9493903 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
* * *
9493919 ATTACGCCTATATTCT
1 ATTACACCTCTATTCC
* *
9493935 ATTACGCTTCTATTCC
1 ATTACACCTCTATTCC
*
9493951 AATACA
1 ATTACA
9493957 GCGAACCAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.27, C:0.31, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:9494512 original size:64 final size:64
Alignment explanation
Indices: 9494410--9494530 Score: 190
Period size: 64 Copynumber: 1.9 Consensus size: 64
9494400 AAGAATCCAC
9494410 CAAAACTTTACACATGTCGAACATGTAGCATTAACGTTAGCACCT-ATCACTCCATTAAGACCCT
1 CAAAACTTTACACATGTCGAACATGTAGCATTAACGTTAGCACCTGA-CACTCCATTAAGACCCT
* * * *
9494474 CAAAACTTTACATATGTCGAACATGTGGCATTATCGTTAGGACCTGACACTCCATTA
1 CAAAACTTTACACATGTCGAACATGTAGCATTAACGTTAGCACCTGACACTCCATTA
9494531 CACGGCCACC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
64 51 0.98
65 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (64 bp):
CAAAACTTTACACATGTCGAACATGTAGCATTAACGTTAGCACCTGACACTCCATTAAGACCCT
Found at i:9496017 original size:18 final size:17
Alignment explanation
Indices: 9495983--9496041 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 17
9495973 CTGGAAACAT
9495983 ATTATGATTTAAAATTTTA
1 ATTAT-ATTT-AAATTTTA
9496002 ATTATATTATAAA-TTTA
1 ATTATATT-TAAATTTTA
*
9496019 GATTATATTTAATATTTTG
1 -ATTATATTTAA-ATTTTA
9496038 ATTA
1 ATTA
9496042 AATTGGTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 7 0.20
18 19 0.54
19 9 0.26
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
ATTATATTTAAATTTTA
Found at i:9498210 original size:15 final size:15
Alignment explanation
Indices: 9498160--9498212 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
9498150 ATTTTAAAAC
*
9498160 TTTTAT-TTTCAAGT
1 TTTTATATTTCAATT
9498174 TTTTA-ATTTTCACATAT
1 TTTTATA-TTTCA-AT-T
9498191 TTTTATATTTCAATT
1 TTTTATATTTCAATT
9498206 TTTTATA
1 TTTTATA
9498213 ATAATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
14 5 0.15
15 13 0.39
16 3 0.09
17 11 0.33
18 1 0.03
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTTATATTTCAATT
Found at i:9499861 original size:18 final size:18
Alignment explanation
Indices: 9499838--9499872 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9499828 GTCAAAAATT
9499838 TTAAATAATAATTATAAA
1 TTAAATAATAATTATAAA
*
9499856 TTAAATTATAATTATAA
1 TTAAATAATAATTATAA
9499873 TGATCACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATAATAATTATAAA
Found at i:9501047 original size:43 final size:43
Alignment explanation
Indices: 9500999--9501085 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
9500989 ACCACCACTG
9500999 ATTTGCAGATAAAAACTACCACTGGGTAGTGGATGCATAACAT
1 ATTTGCAGATAAAAACTACCACTGGGTAGTGGATGCATAACAT
*
9501042 ATTTGCAGATAAAAACTACCACTGGGTTGTGGATGCATAACAT
1 ATTTGCAGATAAAAACTACCACTGGGTAGTGGATGCATAACAT
9501085 A
1 A
9501086 CATATCATCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (43 bp):
ATTTGCAGATAAAAACTACCACTGGGTAGTGGATGCATAACAT
Found at i:9501186 original size:38 final size:38
Alignment explanation
Indices: 9501135--9501208 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 38
9501125 TGTAATAGAA
9501135 CAATTCAACACTAG-AAGTAGACATGCTTAACATGTATT
1 CAATTCAACACTAGCAA-TAGACATGCTTAACATGTATT
*
9501173 CAATTCAACACTAGCAATAGACATGCTTATCATGTA
1 CAATTCAACACTAGCAATAGACATGCTTAACATGTA
9501209 CTCTGTAGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 32 0.94
39 2 0.06
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (38 bp):
CAATTCAACACTAGCAATAGACATGCTTAACATGTATT
Found at i:9507399 original size:43 final size:43
Alignment explanation
Indices: 9507345--9507446 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 43
9507335 TACCACTTTG
**
9507345 CAGATAAAAACTACCACTGGGTTGTGGATGCACAACATATTTA
1 CAGATAAAAACTACCACTGGACTGTGGATGCACAACATATTTA
* *
9507388 TAGATAAAAACTGCCACTGGACTGTGGATGCACAACATATTTA
1 CAGATAAAAACTACCACTGGACTGTGGATGCACAACATATTTA
*
9507431 CA-A-ATAAACTACCACT
1 CAGATAAAAACTACCACT
9507447 CTTTTTCCGT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
41 11 0.21
42 1 0.02
43 40 0.77
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.25
Consensus pattern (43 bp):
CAGATAAAAACTACCACTGGACTGTGGATGCACAACATATTTA
Found at i:9509190 original size:20 final size:19
Alignment explanation
Indices: 9509153--9509195 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
9509143 TTTTTAAATG
* *
9509153 ATATTGATACATTTAAAAC
1 ATATTGATACAATTAAAAA
9509172 ATATTGATAACAATTAAAAA
1 ATATTGAT-ACAATTAAAAA
9509192 ATAT
1 ATAT
9509196 ATTATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (19 bp):
ATATTGATACAATTAAAAA
Found at i:9511191 original size:44 final size:43
Alignment explanation
Indices: 9511162--9511394 Score: 164
Period size: 44 Copynumber: 5.1 Consensus size: 43
9511152 CCTTTATTTT
*
9511162 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATT-TTAGCTTC
* * * *
9511206 AATCTGCTCCGCTGTAATCTCAGGAAGATAAGATTTCTAGCTTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTT-TAGCTTC
* * *
9511250 AATCTGACGTGATCTACTCTACTGTAA-CTTCAGAGAGATAGGATCCTTTA-TTTT
1 AATC---C--G--CT-C-C-ACTGTAATC-TCAGGGAGATAGGAT--TTTAGCTTC
* *
9511304 AATCCGCTCCACTGTAATCTCAGGGAGATAGTATTACTAGCTTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATT-TTAGCTTC
* * * * *
9511348 AATCTGCTCCGCTGTAATCTCAGGAAGATAAGATTTCTGGCTTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTT-TAGCTTC
9511392 AAT
1 AAT
9511395 TTGCTTCATT
Statistics
Matches: 147, Mismatches: 24, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 103 0.70
45 2 0.01
46 1 0.01
47 2 0.01
49 2 0.01
51 3 0.02
52 1 0.01
53 2 0.01
54 24 0.16
55 2 0.01
56 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (43 bp):
AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTTTAGCTTC
Found at i:9511303 original size:142 final size:142
Alignment explanation
Indices: 9511089--9511394 Score: 567
Period size: 142 Copynumber: 2.2 Consensus size: 142
9511079 AATATCGGGG
* *
9511089 AGATAAGATTTTTGGCTTCAATCTGACATGATCTACTCTACTGTAACTTCAGAGAGATATGATCC
1 AGATAAGATTTCTGGCTTCAATCTGACATGATCTACTCTACTGTAACTTCAGAGAGATAGGATCC
9511154 TTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCT
66 TTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCT
9511219 GTAATCTCAGGA
131 GTAATCTCAGGA
* *
9511231 AGATAAGATTTCTAGCTTCAATCTGACGTGATCTACTCTACTGTAACTTCAGAGAGATAGGATCC
1 AGATAAGATTTCTGGCTTCAATCTGACATGATCTACTCTACTGTAACTTCAGAGAGATAGGATCC
*
9511296 TTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGTATTACTAGCTTCAATCTGCTCCGCT
66 TTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCT
9511361 GTAATCTCAGGA
131 GTAATCTCAGGA
9511373 AGATAAGATTTCTGGCTTCAAT
1 AGATAAGATTTCTGGCTTCAAT
9511395 TTGCTTCATT
Statistics
Matches: 158, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 158 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (142 bp):
AGATAAGATTTCTGGCTTCAATCTGACATGATCTACTCTACTGTAACTTCAGAGAGATAGGATCC
TTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCT
GTAATCTCAGGA
Found at i:9523937 original size:20 final size:18
Alignment explanation
Indices: 9523888--9523937 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
9523878 TATGTATTTT
*
9523888 TTAAATAATATTGATACAT
1 TTAAA-AATATTGATACAA
9523907 TTAAAACATATTGATAACAA
1 TTAAAA-ATATTGAT-ACAA
9523927 TTAAGAAATAT
1 TTAA-AAATAT
9523938 ATTATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.04
19 13 0.48
20 11 0.41
21 2 0.07
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (18 bp):
TTAAAAATATTGATACAA
Found at i:9528479 original size:31 final size:30
Alignment explanation
Indices: 9528441--9528499 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
9528431 TTACAGAATG
*
9528441 AAAATACAAGGATAAAATTGATAACAAAAAT
1 AAAATACAAGGATAAAACTGATAA-AAAAAT
* *
9528472 AAAATACAAGGGTCAAACTGATAAAAAA
1 AAAATACAAGGATAAAACTGATAAAAAA
9528500 TTATACAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.63, C:0.08, G:0.12, T:0.17
Consensus pattern (30 bp):
AAAATACAAGGATAAAACTGATAAAAAAAT
Found at i:9529592 original size:2 final size:2
Alignment explanation
Indices: 9529587--9529626 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9529577 ATATATGCCA
9529587 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9529627 TTCATACTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9533549 original size:11 final size:11
Alignment explanation
Indices: 9533535--9533564 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
9533525 ACCTTTAATA
9533535 TATTTAAAATG
1 TATTTAAAATG
9533546 TATTTAAAATG
1 TATTTAAAATG
9533557 TATTTAAA
1 TATTTAAA
9533565 TATCTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTTAAAATG
Found at i:9535157 original size:11 final size:11
Alignment explanation
Indices: 9535141--9535167 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
9535131 TAGAAATTAG
9535141 TTTGTGAAACT
1 TTTGTGAAACT
9535152 TTTGTGAAACT
1 TTTGTGAAACT
9535163 TTTGT
1 TTTGT
9535168 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:9537171 original size:16 final size:18
Alignment explanation
Indices: 9537150--9537183 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
9537140 GAAAGAATGA
9537150 GTTTTAAA-AAA-TTTTT
1 GTTTTAAATAAACTTTTT
9537166 GTTTTAAATAAACTTTTT
1 GTTTTAAATAAACTTTTT
9537184 AAAACGGCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (18 bp):
GTTTTAAATAAACTTTTT
Found at i:9537568 original size:3 final size:3
Alignment explanation
Indices: 9537562--9537665 Score: 163
Period size: 3 Copynumber: 34.7 Consensus size: 3
9537552 TATCATCATC
*
9537562 ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
9537610 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT AAT ATT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
9537658 ATC ATT AT
1 ATT ATT AT
9537666 ATTTCCATTT
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:9538566 original size:110 final size:109
Alignment explanation
Indices: 9538350--9538647 Score: 424
Period size: 110 Copynumber: 2.7 Consensus size: 109
9538340 NNNNNNNNNN
* *
9538350 TTTAAAAATTTTAAAATAAGGCAATGTTTTGCG-TTGGAAAATTTGAGAAAAACATG-CCTAAGG
1 TTTAAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTTGAG--AAACGTGCCCTAAGG
9538413 TGCTGGGTGTCGA-TTTTCTCATTCAACCAAATGGCTAAATATCCT
64 TGCTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
*
9538458 TTTAAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAGAACGTGCCCTAAGGT
1 TTTAAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTTGAGA-AACGTGCCCTAAGGT
*
9538523 GCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCT
65 GCTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
* * ** * *
9538568 TTTAAAAAATTTTCGAAGTAAGATAATATTTTGCGTTT-GGAAATTTGAGAAACGTACCCTAAGG
1 TTT-AAAAATTTT-AAAATAAGGCAATGTTTTGCGTTTGGGAAATTTGAGAAACGTGCCCTAAGG
*
9538632 TGCTGGGTTTCGATTT
64 TGCTGGGTGTCGATTT
9538648 CTCGATTGAC
Statistics
Matches: 172, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
107 1 0.01
108 38 0.22
109 32 0.19
110 62 0.36
111 20 0.12
112 19 0.11
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (109 bp):
TTTAAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTTGAGAAACGTGCCCTAAGGTG
CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
Found at i:9539364 original size:47 final size:47
Alignment explanation
Indices: 9539307--9539451 Score: 131
Period size: 47 Copynumber: 3.1 Consensus size: 47
9539297 ATAAGAACAT
* *
9539307 TTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTATA
** * *
9539354 TTTAATATTAATTA-TTT-T-AAATTGTATA-AATTCATATAAGA--AAA
1 TTTAATATTAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATTATA
* * *
9539398 TTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTATA
*
9539445 TGTAATA
1 TTTAATA
9539452 ATAATTATTT
Statistics
Matches: 74, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
43 3 0.04
44 23 0.31
45 8 0.11
46 8 0.11
47 29 0.39
48 3 0.04
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (47 bp):
TTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTATA
Found at i:9539414 original size:91 final size:91
Alignment explanation
Indices: 9539288--9539495 Score: 344
Period size: 91 Copynumber: 2.3 Consensus size: 91
9539278 ATGATTTTAG
* *
9539288 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
9539353 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
9539380 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
9539445 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
*
9539471 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
9539496 GNNNNNNNNN
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 93 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:9539464 original size:26 final size:28
Alignment explanation
Indices: 9539410--9539470 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
9539400 TATTATCAAG
* *
9539410 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
9539438 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
9539464 AATTATA
1 AATTATA
9539471 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:9539470 original size:44 final size:43
Alignment explanation
Indices: 9539328--9539470 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
9539318 GAATTTTATG
* *
9539328 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
9539372 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
9539419 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
9539463 AAATTATA
1 AAATTATA
9539471 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:9540833 original size:16 final size:16
Alignment explanation
Indices: 9540812--9540853 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
9540802 TTATTAAATT
*
9540812 ATATATTTTAATTATA
1 ATATATTTTAATAATA
9540828 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
9540843 AT-TATGTTTAA
1 ATATAT-TTTAA
9540854 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:9540838 original size:15 final size:15
Alignment explanation
Indices: 9540803--9540844 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9540793 TTAAGAATTT
*
9540803 TATTAAATTAT-ATA
1 TATTTAATTATAATA
9540817 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
9540831 TATTTAATAATAAT
1 TATTTAATTATAAT
9540845 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:9541086 original size:16 final size:16
Alignment explanation
Indices: 9541061--9541098 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
9541051 TTGATTTGCT
9541061 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
9541077 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
9541093 AATACA
1 ATTACA
9541099 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:9547902 original size:45 final size:45
Alignment explanation
Indices: 9547853--9547953 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 45
9547843 TATGGTGCGA
* * * *
9547853 ATAAACCACTAACCGGTGCAGATAAAATCTGTTAGTACGGTGTGG
1 ATAAACCACTAACCGATGCAGAGAAAATATGTTAATACGGTGTGG
***
9547898 ATAAACCACTATTTGATGCAGAGAAAATATGTTAATACGGTGTGG
1 ATAAACCACTAACCGATGCAGAGAAAATATGTTAATACGGTGTGG
9547943 ATAAACCACTA
1 ATAAACCACTA
9547954 TTCAATGTAG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.26
Consensus pattern (45 bp):
ATAAACCACTAACCGATGCAGAGAAAATATGTTAATACGGTGTGG
Found at i:9547954 original size:45 final size:45
Alignment explanation
Indices: 9547869--9547955 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
9547859 CACTAACCGG
* * *
9547869 TGCAGATAAAATCTGTTAGTACGGTGTGGATAAACCACTATTTGA
1 TGCAGAGAAAATATGTTAATACGGTGTGGATAAACCACTATTTGA
9547914 TGCAGAGAAAATATGTTAATACGGTGTGGATAAACCACTATT
1 TGCAGAGAAAATATGTTAATACGGTGTGGATAAACCACTATT
9547956 CAATGTAGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.30
Consensus pattern (45 bp):
TGCAGAGAAAATATGTTAATACGGTGTGGATAAACCACTATTTGA
Found at i:9557083 original size:8 final size:7
Alignment explanation
Indices: 9557051--9557082 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
9557041 ATTTATTGGG
9557051 TTTATTTT
1 TTTA-TTT
9557059 TTTATTT
1 TTTATTT
9557066 TTTATTT
1 TTTATTT
9557073 TTTATTT
1 TTTATTT
9557080 TTT
1 TTT
9557083 TGTCCTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTATTT
Found at i:9557309 original size:18 final size:19
Alignment explanation
Indices: 9557278--9557320 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
9557268 TTTCTAAAAT
9557278 TAAAAAGTCAAAAAATATA
1 TAAAAAGTCAAAAAATATA
*
9557297 TAAAAA-TCTAAAAATATA
1 TAAAAAGTCAAAAAATATA
9557315 TAAAAA
1 TAAAAA
9557321 AAATTACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (19 bp):
TAAAAAGTCAAAAAATATA
Found at i:9559511 original size:15 final size:16
Alignment explanation
Indices: 9559484--9559514 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9559474 ACCACTTTTT
9559484 TGGCCCGGGCCCGGCC
1 TGGCCCGGGCCCGGCC
9559500 TGGCCC-GGCCCGGCC
1 TGGCCCGGGCCCGGCC
9559515 CGAATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.00, C:0.52, G:0.42, T:0.06
Consensus pattern (16 bp):
TGGCCCGGGCCCGGCC
Found at i:9559803 original size:22 final size:23
Alignment explanation
Indices: 9559768--9559812 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
9559758 TGGCTAAATG
* **
9559768 TTTTCATTTAGTGATTAAATAGA
1 TTTTCATTAAGTGAAAAAATAGA
9559791 TTTTC-TTAAGTGAAAAAATAGA
1 TTTTCATTAAGTGAAAAAATAGA
9559813 AGTTGGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (23 bp):
TTTTCATTAAGTGAAAAAATAGA
Found at i:9561594 original size:6 final size:6
Alignment explanation
Indices: 9561583--9561609 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9561573 TTTTTTATAC
9561583 TTGAGT TTGAGT TTGAGT TTGAGT TTG
1 TTGAGT TTGAGT TTGAGT TTGAGT TTG
9561610 GTCATATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (6 bp):
TTGAGT
Found at i:9566505 original size:14 final size:15
Alignment explanation
Indices: 9566486--9566514 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9566476 CCCTAACTCA
9566486 CCACCTCC-CCCAAT
1 CCACCTCCACCCAAT
9566500 CCACCTCCACCCAAT
1 CCACCTCCACCCAAT
9566515 TCCAGAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.24, C:0.62, G:0.00, T:0.14
Consensus pattern (15 bp):
CCACCTCCACCCAAT
Found at i:9569693 original size:23 final size:23
Alignment explanation
Indices: 9569667--9569713 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
9569657 GGATGATTGG
9569667 ATGCGAGCTAAGGGATTTTCAAC
1 ATGCGAGCTAAGGGATTTTCAAC
9569690 ATGCGAGCTAAGGGATTTTCAAC
1 ATGCGAGCTAAGGGATTTTCAAC
9569713 A
1 A
9569714 GGTAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (23 bp):
ATGCGAGCTAAGGGATTTTCAAC
Found at i:9570212 original size:17 final size:17
Alignment explanation
Indices: 9570186--9570226 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
9570176 TGTTTACAAG
9570186 TAACAAAAATAAGAAAA
1 TAACAAAAATAAGAAAA
* *
9570203 TAACAGAAATAATAAAA
1 TAACAAAAATAAGAAAA
*
9570220 TTACAAA
1 TAACAAA
9570227 CAAGCATAAA
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:0.71, C:0.07, G:0.05, T:0.17
Consensus pattern (17 bp):
TAACAAAAATAAGAAAA
Found at i:9576063 original size:20 final size:19
Alignment explanation
Indices: 9576034--9576073 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
9576024 TATTAAGAGA
* *
9576034 TTTTAAAATATTATTATTT
1 TTTTAAAATAATATAATTT
9576053 TTTTAAAAATAATATAATTT
1 TTTT-AAAATAATATAATTT
9576073 T
1 T
9576074 ATGATAATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTAAAATAATATAATTT
Found at i:9584327 original size:66 final size:67
Alignment explanation
Indices: 9584206--9584336 Score: 165
Period size: 67 Copynumber: 2.0 Consensus size: 67
9584196 CCATTTTCTA
* * *
9584206 ATAATTGACAATTACCAGTCACGCAGAGTATACTCTTAAGAACTTCACACAGAATATGCTCAGAC
1 ATAATTGAAAATTACCAGTCAAGCAGAGTATACTCTTAAGAACTTCACACAGAATACGCTCAGAC
9584271 GG
66 GG
* * * * * * *
9584273 ATAATTGAAAATTACCGGTCAAGCGGAGTGTATTC-TAAGAACTTCATACTGAATACGTTCAGAC
1 ATAATTGAAAATTACCAGTCAAGCAGAGTATACTCTTAAGAACTTCACACAGAATACGCTCAGAC
9584337 TTCAGACAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
66 25 0.46
67 29 0.54
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (67 bp):
ATAATTGAAAATTACCAGTCAAGCAGAGTATACTCTTAAGAACTTCACACAGAATACGCTCAGAC
GG
Found at i:9593621 original size:44 final size:44
Alignment explanation
Indices: 9593556--9594167 Score: 461
Period size: 44 Copynumber: 13.6 Consensus size: 44
9593546 ACCGATATGG
* *
9593556 GAAGACAAGATCT-GTTGTCTTTGATCTACTTCACGCTAATACAT
1 GAAGACAAGATCTGGTT-TCTTTGATCTACTTCACGCCAGTACAT
* ** * * ***
9593600 GAATACAAGATCTACTTTCTTTGATCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTGGTTTCTTTGATCTACTTCA-CGCCAGTACAT
* * *
9593645 GGAGACAAGATCTGGTATCTTTGATCTACTTCACGCCACTACAT
1 GAAGACAAGATCTGGTTTCTTTGATCTACTTCACGCCAGTACAT
* * * * * * *
9593689 GAAGACAAGATATGTTTTCTTCGATCTACTCCACCACCAGTATAG
1 GAAGACAAGATCTGGTTTCTTTGATCTACTTCA-CGCCAGTACAT
* * * *
9593734 GAAGACAAGATCTAGTATCTCTGATTTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGGTTTCTTTGATCTACTTCACGCCAGTACAT
* * * * ***
9593778 GAAGACAAGATTTGCTTTCTTTGATCTGCTTCACCACCAGTATGG
1 GAAGACAAGATCTGGTTTCTTTGATCTACTTCA-CGCCAGTACAT
* * *
9593823 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGGTTTCTTTGATCTACTTCACGCCAGTACAT
* * * * * ***
9593867 GAAGACAAGATCTGCTTTTTCCTTCGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTG--GTTT-CTTTGATCTACTTC-ACGCCAGTACAT
* * * *
9593915 GAAGGCAAGATCTAGTATCTCTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGGTTTCTTTGATCTACTTCACGCCAGTACAT
* * * ***
9593959 GAAGACAAGATCTGCTTTCTTTGATCTGCTTCACCACCAGTATGG
1 GAAGACAAGATCTGGTTTCTTTGATCTACTTCA-CGCCAGTACAT
* * * *
9594004 GAAGGCAAGATCTGGTATCTCTGATCTACTTTACGCCAGTACAT
1 GAAGACAAGATCTGGTTTCTTTGATCTACTTCACGCCAGTACAT
* * * * * ***
9594048 GAAGACAAGATCTGCTTTTTCCTTCGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTG--GTTT-CTTTGATCTACTTC-ACGCCAGTACAT
* ** * *
9594096 GAAGGCAAGATCTAATATCTCTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGGTTTCTTTGATCTACTTCACGCCAGTACAT
* *
9594140 GAAGACAAGATCTGCTCTCTTTGATCTA
1 GAAGACAAGATCTGGTTTCTTTGATCTA
9594168 TTTCGCCACC
Statistics
Matches: 421, Mismatches: 134, Indels: 26
0.72 0.23 0.04
Matches are distributed among these distances:
44 198 0.47
45 156 0.37
46 8 0.02
47 21 0.05
48 38 0.09
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGGTTTCTTTGATCTACTTCACGCCAGTACAT
Found at i:9593978 original size:181 final size:181
Alignment explanation
Indices: 9593529--9594198 Score: 1035
Period size: 181 Copynumber: 3.7 Consensus size: 181
9593519 AGACTTGTAT
* *
9593529 CTTCGATCTACTTCGCCACC-GATATGGGAAGACAAGATCT-GTTGTCTTTGATCTACTTCACGC
1 CTTCGATCTACTTCGCCACCAG-TATGGGAAGACAAGATCTAG-TATCTCTGATCTACTTCACGC
* * * * * * *
9593592 TAATACATGAATACAAGATCTACTTTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATC
64 CAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATGGGAAGGCAAGATC
* * *
9593657 TGGTATCTTTGATCTACTTCACGCCACTACATGAAGACAAGATATG--TTTT-
129 TGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTC
* * * *
9593707 CTTCGATCTACTCCACCACCAGTATAGGAAGACAAGATCTAGTATCTCTGATTTACTTCACGCCA
1 CTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTACTTCACGCCA
* *
9593772 GTACATGAAGACAAGATTTGCTTTCTTTGATCTGCTTCACCACCAGTATGGGAAGGCAAGATCTG
66 GTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTG
9593837 GTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTC
131 GTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTC
* *
9593888 CTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATCTCTGATCTACTTCACGCCA
1 CTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTACTTCACGCCA
*
9593953 GTACATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCACCACCAGTATGGGAAGGCAAGATCTG
66 GTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTG
*
9594018 GTATCTCTGATCTACTTTACGCCAGTACATGAAGACAAGATCTGCTTTTTC
131 GTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTC
* * *
9594069 CTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAATATCTCTGATCTACTTCACGCCA
1 CTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTACTTCACGCCA
* * *
9594134 GTACATGAAGACAAGATCTGCTCTCTTTGATCTATTTCGCCACCAGTATGGGAAGGCAAGATCTG
66 GTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTG
9594199 CATCTTCGAT
Statistics
Matches: 456, Mismatches: 31, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
178 152 0.33
179 2 0.00
180 4 0.01
181 298 0.65
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (181 bp):
CTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTACTTCACGCCA
GTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGTATGGGAAGGCAAGATCTG
GTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTC
Found at i:9594042 original size:270 final size:268
Alignment explanation
Indices: 9593528--9594197 Score: 957
Period size: 270 Copynumber: 2.5 Consensus size: 268
9593518 AAGACTTGTA
* * * * *
9593528 TCTTCGATCTACTTCGCCACC-GATATGGGAAGACAAGATCTGTTGTCTTTGATCTACTTCACGC
1 TCTTCGATCTGCTTCGCCACCAG-TATGGGAAGGCAAGATCTGATATCTCTGATCTACTTCACGC
* * * * * * * *
9593592 TAATACATGAATACAAGATCTACTTTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATC
65 CAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGGCAAGATC
* * *
9593657 TGGTATCTTTGATCTACTTCACGCCACTACATGAAGACAAGATATGTTTTCTTCGATCTACTCCA
130 TAGTATCTCTGATCTACTTCACGCCACTACATGAAGACAAGATATGCTTTCTTCGATCTACTCCA
*
9593722 CCACCAGTATAGGAAGACAAGATCTAGTATCTCTGATTTACTTCACGCCAGTACATGAAGACAAG
195 CCACCAGTATAGGAAGACAAGATCTAGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAG
*
9593787 ATTTGC-TT
260 ATCTGCTTT
* * *
9593795 TCTTTGATCTGCTTCACCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCC
1 TCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGATATCTCTGATCTACTTCACGCC
* *
9593860 AGTACATGAAGACAAGATCTGCTTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGA
66 AGTACATGAAGACAAGATCTGC--TTT-CTTTGATCTACTTCGCCACCAGTATGGGAAGGCAAGA
* * * * *
9593925 TCTAGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTGCTT
128 TCTAGTATCTCTGATCTACTTCACGCCACTACATGAAGACAAGATATGCTTTCTTCGATCTACTC
* * * *
9593990 CACCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTTACGCCAGTACATGAAGACA
193 CACCACCAGTATAGGAAGACAAGATCTAGTATCTCTGATCTACTTCACGCCAGTACATGAAGACA
9594055 AGATCTGCTTTT
258 AGATCTGC-TTT
*
9594067 TCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAATATCTCTGATCTACTTCACGC
1 T-CTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGATATCTCTGATCTACTTCACGC
* *
9594132 CAGTACATGAAGACAAGATCTGCTCTCTTTGATCTATTTCGCCACCAGTATGGGAAGGCAAGATC
65 CAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGGCAAGATC
9594197 T
130 T
9594198 GCATCTTCGA
Statistics
Matches: 357, Mismatches: 39, Indels: 11
0.88 0.10 0.03
Matches are distributed among these distances:
267 74 0.21
268 1 0.00
269 3 0.01
270 192 0.54
271 2 0.01
272 3 0.01
273 82 0.23
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (268 bp):
TCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGATATCTCTGATCTACTTCACGCC
AGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCT
AGTATCTCTGATCTACTTCACGCCACTACATGAAGACAAGATATGCTTTCTTCGATCTACTCCAC
CACCAGTATAGGAAGACAAGATCTAGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGA
TCTGCTTT
Found at i:9594232 original size:44 final size:45
Alignment explanation
Indices: 9593526--9594249 Score: 198
Period size: 44 Copynumber: 16.1 Consensus size: 45
9593516 ATAAGACTTG
* *
9593526 TATCTTCGATCTACTTCGCCACC-G-ATATGGGAAGACAAGATCTGT
1 TATCTTCGATCCACTTCGCCACCAGCATA--GGAAGACAAGATCTGC
* * * * ** * *
9593571 TGTCTTTGATCTACTTCACGCTAATA-CAT--GAATACAAGATCTAC
1 TATCTTCGATCCACTT--CGCCACCAGCATAGGAAGACAAGATCTGC
* * * * * * * * *
9593615 TTTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGG
1 TATCTTCGATCCACTTCGCCACCAGCATAGGAAGACAAGATCTGC
* * * * *
9593660 TATCTTTGATCTACTTCACGCCACTA-CAT--GAAGACAAGATATGT
1 TATCTTCGATCCACTT--CGCCACCAGCATAGGAAGACAAGATCTGC
* * * * *
9593704 TTTCTTCGATCTACTCCACCACCAGTATAGGAAGACAAGATCTAG-
1 TATCTTCGATCCACTTCGCCACCAGCATAGGAAGACAAGATCT-GC
** * * * * * *
9593749 TATC-TCTGATTTACTTC-ACGCCAGTACATGAAGACAAGATTTGC
1 TATCTTC-GATCCACTTCGCCACCAGCATAGGAAGACAAGATCTGC
* * ** * * * * *
9593793 TTTCTTTGATCTGCTTCACCACCAGTATGGGAAGGCAAGATCTGG
1 TATCTTCGATCCACTTCGCCACCAGCATAGGAAGACAAGATCTGC
* * * * * *
9593838 TATC-TCTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGC
1 TATCTTC-GATCCACTTCGCCACCAGCATAGGAAGACAAGATCTGC
* ** * * *
9593882 TTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAG-
1 --TAT-CTTCGATCCACTTCGCCACCAGCATAGGAAGACAAGATCT-GC
* * * * * *
9593930 TATC-TCTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGC
1 TATCTTC-GATCCACTTCGCCACCAGCATAGGAAGACAAGATCTGC
* * ** * * * * *
9593974 TTTCTTTGATCTGCTTCACCACCAGTATGGGAAGGCAAGATCTGG
1 TATCTTCGATCCACTTCGCCACCAGCATAGGAAGACAAGATCTGC
* **
9594019 TATC-TCTGATCTACTTTACGCCAGTA-CAT--GAAGACAAGATCTGC
1 TATCTTC-GATCCAC-TT-CGCCACCAGCATAGGAAGACAAGATCTGC
* ** * * * **
9594063 TTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAA
1 --TAT-CTTCGATCCACTTCGCCACCAGCATAGGAAGACAAGATCTGC
* * * * * *
9594111 TATC-TCTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGC
1 TATCTTC-GATCCACTTCGCCACCAGCATAGGAAGACAAGATCTGC
* * * * * * *
9594155 TCTCTTTGATCTATTTCGCCACCAGTATGGGAAGGCAAGATCTGC
1 TATCTTCGATCCACTTCGCCACCAGCATAGGAAGACAAGATCTGC
* * *
9594200 -ATCTTCGATCCACTTCGCTACCAGCATAGGAAGACAGGATCTGT
1 TATCTTCGATCCACTTCGCCACCAGCATAGGAAGACAAGATCTGC
9594244 TATCTT
1 TATCTT
9594250 TCAACCTGCT
Statistics
Matches: 501, Mismatches: 136, Indels: 84
0.69 0.19 0.12
Matches are distributed among these distances:
42 10 0.02
43 6 0.01
44 219 0.44
45 177 0.35
46 19 0.04
47 32 0.06
48 37 0.07
49 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (45 bp):
TATCTTCGATCCACTTCGCCACCAGCATAGGAAGACAAGATCTGC
Found at i:9594250 original size:89 final size:89
Alignment explanation
Indices: 9593528--9594198 Score: 921
Period size: 89 Copynumber: 7.5 Consensus size: 89
9593518 AAGACTTGTA
* * * * * *
9593528 TCTTCGATCTACTTCGCCACC-GATATGGGAAGACAAGATCTGTTGTCTTTGATCTACTTCACGC
1 TCTTTGATCTGCTTCGCCACCAG-TATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGC
* * * *
9593592 TAATACATGAATACAAGATCTACTT
65 CAGTACATGAAGACAAGATCTGCTT
* * * * * *
9593617 TCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGGTATCTTTGATCTACTTCACGCC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCC
* * *
9593682 ACTACATGAAGACAAGATATGTTT
66 AGTACATGAAGACAAGATCTGCTT
* * * * * * * *
9593706 TCTTCGATCTACTCCACCACCAGTATAGGAAGACAAGATCTAGTATCTCTGATTTACTTCACGCC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCC
*
9593771 AGTACATGAAGACAAGATTTGCTT
66 AGTACATGAAGACAAGATCTGCTT
*
9593795 TCTTTGATCTGCTTCACCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCC
9593860 AGTACATGAAGACAAGATCTGCTTTT
66 AGTACATGAAGACAAGATCTGC--TT
* *
9593886 TCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATCTCTGATCTACTTCACGC
1 T-CTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGC
9593951 CAGTACATGAAGACAAGATCTGCTT
65 CAGTACATGAAGACAAGATCTGCTT
* *
9593976 TCTTTGATCTGCTTCACCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTTACGCC
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCC
9594041 AGTACATGAAGACAAGATCTGCTTTT
66 AGTACATGAAGACAAGATCTGC--TT
* **
9594067 TCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAATATCTCTGATCTACTTCACGC
1 T-CTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGC
*
9594132 CAGTACATGAAGACAAGATCTGCTC
65 CAGTACATGAAGACAAGATCTGCTT
**
9594157 TCTTTGATCTATTTCGCCACCAGTATGGGAAGGCAAGATCTG
1 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTG
9594199 CATCTTCGAT
Statistics
Matches: 529, Mismatches: 46, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
89 353 0.67
90 6 0.01
91 6 0.01
92 164 0.31
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (89 bp):
TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCC
AGTACATGAAGACAAGATCTGCTT
Found at i:9600877 original size:19 final size:18
Alignment explanation
Indices: 9600854--9600895 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
9600844 TAATAACTAT
9600854 AATAATAAATAATATATA
1 AATAATAAATAATATATA
*
9600872 ACATAATGAATAATATATA
1 A-ATAATAAATAATATATA
9600891 AATAA
1 AATAA
9600896 AACTAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
AATAATAAATAATATATA
Found at i:9608598 original size:21 final size:21
Alignment explanation
Indices: 9608560--9608600 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9608550 GGATCAAATT
*
9608560 AATTTTACTATTAAATTGTTC
1 AATTTAACTATTAAATTGTTC
* *
9608581 AATTTAACTCTTATATTGTT
1 AATTTAACTATTAAATTGTT
9608601 AAAAATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.54
Consensus pattern (21 bp):
AATTTAACTATTAAATTGTTC
Found at i:9611942 original size:29 final size:29
Alignment explanation
Indices: 9611910--9611973 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
9611900 ATAAAAGAAC
*
9611910 CATTAAAAGAATCACAAGAAAAACTGATT
1 CATTAAAAGAATCAAAAGAAAAACTGATT
*
9611939 CATTAAAAGAATCAAAAGAAAACCTGATT
1 CATTAAAAGAATCAAAAGAAAAACTGATT
9611968 CATTAA
1 CATTAA
9611974 CCAAAGGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.22
Consensus pattern (29 bp):
CATTAAAAGAATCAAAAGAAAAACTGATT
Found at i:9617777 original size:59 final size:53
Alignment explanation
Indices: 9617671--9617779 Score: 137
Period size: 53 Copynumber: 1.9 Consensus size: 53
9617661 GCTAAATCCA
* *
9617671 TTTTCCACATATTCTTCGGGAGGCTATATCAAGATCACTCGTCCGGGCTAGAT
1 TTTTCCACACATTCTTCGGGAGGCTATATCAAGATCACCCGTCCGGGCTAGAT
*
9617724 TTTTTCACACATTCTTCGGGAGGGCTATATCAGGATAGGATCACCCGTCCGGGCTA
1 TTTTCCACACATTCTTCGGGA-GGCTATATC---A-A-GATCACCCGTCCGGGCTA
9617780 AATCCTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
53 19 0.40
54 9 0.19
57 1 0.02
58 1 0.02
59 17 0.36
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (53 bp):
TTTTCCACACATTCTTCGGGAGGCTATATCAAGATCACCCGTCCGGGCTAGAT
Found at i:9619058 original size:24 final size:24
Alignment explanation
Indices: 9619026--9619072 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
9619016 CTAAATTTAT
*
9619026 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTT-CTATCACTTTCTCTTC
*
9619050 AACATTTTCTATCACTTTCTCTT
1 AACACTTTCTATCACTTTCTCTT
9619073 ATTTCCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (24 bp):
AACACTTTCTATCACTTTCTCTTC
Found at i:9622287 original size:21 final size:21
Alignment explanation
Indices: 9622253--9622294 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9622243 TTCGTCTACT
**
9622253 AGTTAAAATTCAAAACCATTA
1 AGTTAAAAGACAAAACCATTA
*
9622274 AGTTAAAAGACAAAATCATTA
1 AGTTAAAAGACAAAACCATTA
9622295 TATTATTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (21 bp):
AGTTAAAAGACAAAACCATTA
Found at i:9622335 original size:82 final size:79
Alignment explanation
Indices: 9622173--9622341 Score: 241
Period size: 82 Copynumber: 2.1 Consensus size: 79
9622163 ACATTTCTAA
* * *
9622173 AGTTAAAAGTCAAAACCATTAAGTTAAAAGGCAAAACTATGTCGTTTTATGTAGTTAAATAATCT
1 AGTTAAAAGTCAAAACCATTAAGTTAAAAGACAAAACTATATC-TTTTATGTAATTAAATAATCT
9622238 TGCACTTCGTCTACT
65 TGCACTTCGTCTACT
*
9622253 AGTTAAAATTCAAAACCATTAAGTTAAAAGACAAAATCATTATAT-TATTTATGTAATTAAATAA
1 AGTTAAAAGTCAAAACCATTAAGTTAAAAGACAAAA-C--TATATCT-TTTATGTAATTAAATAA
*
9622317 TCTTGTACTTCGTCTACT
62 TCTTGCACTTCGTCTACT
9622335 AGTTAAA
1 AGTTAAA
9622342 TAATTGGTCC
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
80 34 0.43
81 2 0.03
82 40 0.50
83 4 0.05
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.36
Consensus pattern (79 bp):
AGTTAAAAGTCAAAACCATTAAGTTAAAAGACAAAACTATATCTTTTATGTAATTAAATAATCTT
GCACTTCGTCTACT
Found at i:9623033 original size:18 final size:18
Alignment explanation
Indices: 9622995--9623033 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
9622985 AATTCTGTAA
*
9622995 TTAGTTTAAATTTGATCT
1 TTAGTTTAAATTTAATCT
*
9623013 TTAGTTTAAATTTAATTT
1 TTAGTTTAAATTTAATCT
9623031 TTA
1 TTA
9623034 AAATTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (18 bp):
TTAGTTTAAATTTAATCT
Found at i:9628880 original size:9 final size:9
Alignment explanation
Indices: 9628866--9628896 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
9628856 GTTAAACGAA
9628866 TCGAGTTAT
1 TCGAGTTAT
*
9628875 TCGAGTTAA
1 TCGAGTTAT
9628884 TCGAGTTAT
1 TCGAGTTAT
9628893 TCGA
1 TCGA
9628897 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:9636861 original size:19 final size:20
Alignment explanation
Indices: 9636831--9636870 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
9636821 TGTCTTAGAT
9636831 GATATGCATGACTTGTAATG
1 GATATGCATGACTTGTAATG
9636851 GATAT-CATGACTTGTAATG
1 GATATGCATGACTTGTAATG
9636870 G
1 G
9636871 GTTGTAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (20 bp):
GATATGCATGACTTGTAATG
Found at i:9638004 original size:25 final size:25
Alignment explanation
Indices: 9637976--9638122 Score: 101
Period size: 24 Copynumber: 6.0 Consensus size: 25
9637966 GGACTCATCA
*
9637976 CGTATCATCTAGAAGGCCTTTGTGG
1 CGTATCATGTAGAAGGCCTTTGTGG
* * * *
9638001 CGTATCATCTGGAAGACCTTTATGG
1 CGTATCATGTAGAAGGCCTTTGTGG
*
9638026 C-TAAT-ATGT-GAAAAGCCTTTGTGG
1 CGT-ATCATGTAG-AAGGCCTTTGTGG
* * *
9638050 C-TAAT-TTGTGGAAAGCCTTTGTGG
1 CGT-ATCATGTAGAAGGCCTTTGTGG
*
9638074 CGTATCATGTAAAAGGCCTTTGTGG
1 CGTATCATGTAGAAGGCCTTTGTGG
* *
9638099 C-TAATC-TGCAGAAAGCCTTTGTGG
1 CGT-ATCATGTAGAAGGCCTTTGTGG
9638123 TTTATCAACT
Statistics
Matches: 101, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
23 1 0.01
24 54 0.53
25 46 0.46
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (25 bp):
CGTATCATGTAGAAGGCCTTTGTGG
Found at i:9638050 original size:24 final size:24
Alignment explanation
Indices: 9638017--9638171 Score: 127
Period size: 24 Copynumber: 6.4 Consensus size: 24
9638007 ATCTGGAAGA
*
9638017 CCTTTATGGCTAATATGTGAAAAG
1 CCTTTGTGGCTAATATGTGAAAAG
* *
9638041 CCTTTGTGGCTAATTTGTGGAAAG
1 CCTTTGTGGCTAATATGTGAAAAG
9638065 CCTTTGTGGCGT-ATCATGT-AAAAGG
1 CCTTTGTGGC-TAAT-ATGTGAAAA-G
* *
9638090 CCTTTGTGGCTAATCTG-CAGAAAG
1 CCTTTGTGGCTAATATGTGA-AAAG
* * ** *
9638114 CCTTTGTGGTTTATCAACTGGAAAG
1 CCTTTGTGGCTAAT-ATGTGAAAAG
* * *
9638139 CCTTTATGGCTAATTTGTGGAAAG
1 CCTTTGTGGCTAATATGTGAAAAG
9638163 CCTTTGTGG
1 CCTTTGTGG
9638172 TGTGTTATCT
Statistics
Matches: 103, Mismatches: 20, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
24 68 0.66
25 35 0.34
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (24 bp):
CCTTTGTGGCTAATATGTGAAAAG
Found at i:9638184 original size:49 final size:49
Alignment explanation
Indices: 9638037--9638187 Score: 187
Period size: 49 Copynumber: 3.1 Consensus size: 49
9638027 TAATATGTGA
* * *
9638037 AAAGCCTTTGTGGCTAATTTGTGGAAAGCCTTTGTGGCGTATCATGT-A
1 AAAGCCTTTGTGGCTAATTTGTGGAAAGCCTTTGTGGTGTATCATCTGG
* ** * *
9638085 AAAGGCCTTTGTGGCTAATCTGCAGAAAGCCTTTGTGGTTTATCAACTGG
1 AAA-GCCTTTGTGGCTAATTTGTGGAAAGCCTTTGTGGTGTATCATCTGG
* * *
9638135 AAAGCCTTTATGGCTAATTTGTGGAAAGCCTTTGTGGTGTGTTATCTGG
1 AAAGCCTTTGTGGCTAATTTGTGGAAAGCCTTTGTGGTGTATCATCTGG
9638184 AAAG
1 AAAG
9638188 TCTGTAGAGT
Statistics
Matches: 85, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
48 3 0.04
49 79 0.93
50 3 0.04
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (49 bp):
AAAGCCTTTGTGGCTAATTTGTGGAAAGCCTTTGTGGTGTATCATCTGG
Found at i:9638918 original size:9 final size:9
Alignment explanation
Indices: 9638904--9638945 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
9638894 TTTGGTTAAA
9638904 AATTAACCG
1 AATTAACCG
9638913 AATTAACCG
1 AATTAACCG
* *
9638922 AATCACCCG
1 AATTAACCG
9638931 AATT-ACCAG
1 AATTAACC-G
9638940 AATTAA
1 AATTAA
9638946 ATCATTACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 2 0.07
9 24 0.89
10 1 0.04
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.21
Consensus pattern (9 bp):
AATTAACCG
Found at i:9638986 original size:37 final size:37
Alignment explanation
Indices: 9638945--9639016 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
9638935 ACCAGAATTA
* * *
9638945 AATCATTACTTAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
9638982 AATCACTACATAATTAAAAACATTACATAATTCTT
1 AATCACTACATAATTAAAAACATTACATAAGTCTT
9639017 GAAATTAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.38
Consensus pattern (37 bp):
AATCACTACATAATTAAAAACATTACATAAGTCTTTG
Found at i:9639225 original size:39 final size:39
Alignment explanation
Indices: 9639143--9639259 Score: 209
Period size: 39 Copynumber: 3.0 Consensus size: 39
9639133 TACTCAGAAT
* *
9639143 TAGACTTTAGTTTTATTTTTATTGAGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
9639181 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
9639220 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
9639259 T
1 T
9639260 TGGGTTGGAT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
38 26 0.34
39 50 0.66
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:9639258 original size:13 final size:13
Alignment explanation
Indices: 9639240--9639264 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9639230 TTTTAGTTTT
9639240 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
9639253 ATTGGGTTGGGT
1 ATTGGGTTGGGT
9639265 TGGATAATTT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:9640301 original size:13 final size:13
Alignment explanation
Indices: 9640279--9640312 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
9640269 ATTTGACTCG
9640279 TAAATATTTTT-A
1 TAAATATTTTTAA
9640291 TAAATATTTTTAA
1 TAAATATTTTTAA
9640304 TAAATATTT
1 TAAATATTT
9640313 ATGAAGCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTTTTAA
Found at i:9640912 original size:12 final size:12
Alignment explanation
Indices: 9640895--9640919 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9640885 GTGAAAAAGG
9640895 AATAAATTGTAA
1 AATAAATTGTAA
9640907 AATAAATTGTAA
1 AATAAATTGTAA
9640919 A
1 A
9640920 TTTTGAGTAA
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
AATAAATTGTAA
Found at i:9644265 original size:22 final size:22
Alignment explanation
Indices: 9644237--9644369 Score: 108
Period size: 22 Copynumber: 6.0 Consensus size: 22
9644227 TACACCACAC
*
9644237 CAGTAGGCACCATAGTGTAAAT
1 CAGTAGGCACCATAGTGCAAAT
*
9644259 CAGTAGGCACCAAAGTGC-AAT
1 CAGTAGGCACCATAGTGCAAAT
* *
9644280 ACAGTAGGCACCGTAGTACAAAT
1 -CAGTAGGCACCATAGTGCAAAT
** * *
9644303 CAAAAGGCACTATAGTACAGAAT
1 CAGTAGGCACCATAGTGCA-AAT
* **
9644326 -AGTAGACACTGTAGTGCAAAT
1 CAGTAGGCACCATAGTGCAAAT
* * *
9644347 CAGTAGGCATCAAATTGCAAAT
1 CAGTAGGCACCATAGTGCAAAT
9644369 C
1 C
9644370 CCATACACGC
Statistics
Matches: 87, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
21 6 0.07
22 75 0.86
23 6 0.07
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.20
Consensus pattern (22 bp):
CAGTAGGCACCATAGTGCAAAT
Found at i:9644303 original size:44 final size:43
Alignment explanation
Indices: 9644237--9644367 Score: 127
Period size: 44 Copynumber: 3.0 Consensus size: 43
9644227 TACACCACAC
* *
9644237 CAGTAGGCACCATAGTGTAAATCAGTAGGCACCAAAGTGCAATA
1 CAGTAGGCACCGTAGTGCAAATCAGTAGGCACCAAAGTGCAA-A
* ** * * *
9644281 CAGTAGGCACCGTAGTACAAATCAAAAGGCACTATAGTACAGAA
1 CAGTAGGCACCGTAGTGCAAATCAGTAGGCACCAAAGTGCA-AA
* * * * *
9644325 TAGTAGACACTGTAGTGCAAATCAGTAGGCATCAAATTGCAAA
1 CAGTAGGCACCGTAGTGCAAATCAGTAGGCACCAAAGTGCAAA
9644368 TCCCATACAC
Statistics
Matches: 67, Mismatches: 19, Indels: 3
0.75 0.21 0.03
Matches are distributed among these distances:
43 2 0.03
44 64 0.96
45 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (43 bp):
CAGTAGGCACCGTAGTGCAAATCAGTAGGCACCAAAGTGCAAA
Found at i:9647946 original size:33 final size:34
Alignment explanation
Indices: 9647904--9647972 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 34
9647894 TTCCACAAAC
9647904 AACTTTTAAAAATTGCACGTCTCT-CTTTTTTAA
1 AACTTTTAAAAATTGCACGTCTCTACTTTTTTAA
* *
9647937 AACTTTTAAAAATTGCACGTGTCTATTTTTTTAA
1 AACTTTTAAAAATTGCACGTCTCTACTTTTTTAA
9647971 AA
1 AA
9647973 ATATTTTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 23 0.70
34 10 0.30
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.45
Consensus pattern (34 bp):
AACTTTTAAAAATTGCACGTCTCTACTTTTTTAA
Found at i:9648138 original size:14 final size:13
Alignment explanation
Indices: 9648115--9648144 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
9648105 AACAATTACA
9648115 ATTTAGAAAATTT
1 ATTTAGAAAATTT
9648128 ATTTAAGAAAATTT
1 ATTT-AGAAAATTT
9648142 ATT
1 ATT
9648145 CAATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (13 bp):
ATTTAGAAAATTT
Found at i:9649790 original size:19 final size:18
Alignment explanation
Indices: 9649768--9649816 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
9649758 CTATTTCCTA
*
9649768 AAATAAATATTATTTAATC
1 AAATAAATATT-CTTAATC
* *
9649787 AAATTAATATTCTTAATT
1 AAATAAATATTCTTAATC
9649805 AAATAAAT-TTCT
1 AAATAAATATTCT
9649817 CAACTCAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 4 0.15
18 12 0.46
19 10 0.38
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATAAATATTCTTAATC
Found at i:9654017 original size:2 final size:2
Alignment explanation
Indices: 9654012--9654048 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9654002 TATATATATA
9654012 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
9654049 TAGTCAATGT
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:9654820 original size:41 final size:41
Alignment explanation
Indices: 9654775--9655001 Score: 357
Period size: 41 Copynumber: 5.5 Consensus size: 41
9654765 GACTTTAAGT
*
9654775 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
9654816 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
* * *
9654857 CTAGCAGGCTAAGTGTCGATGATCTGAACTAGGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
* *
9654898 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
* * *
9654939 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTAT-AAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAA-C
9654980 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
9655002 ATATGTTAAA
Statistics
Matches: 173, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 2 0.01
41 171 0.99
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
Found at i:9657149 original size:12 final size:12
Alignment explanation
Indices: 9657132--9657160 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
9657122 CTCGTGCACC
9657132 TGCCAGAGCATA
1 TGCCAGAGCATA
9657144 TGCCAGAGCATA
1 TGCCAGAGCATA
9657156 TGCCA
1 TGCCA
9657161 TCTGTGCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.17
Consensus pattern (12 bp):
TGCCAGAGCATA
Found at i:9660771 original size:2 final size:2
Alignment explanation
Indices: 9660766--9660802 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9660756 TATATATATA
9660766 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
9660803 TAGTCAATGT
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:9661574 original size:41 final size:41
Alignment explanation
Indices: 9661529--9661796 Score: 421
Period size: 41 Copynumber: 6.5 Consensus size: 41
9661519 GACTTTAAGT
*
9661529 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
*
9661570 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGATTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
* *
9661611 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
*
9661652 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
* * *
9661693 CTAGCAAGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
* * *
9661734 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTAT-AAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAA-C
9661775 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
9661797 ATATGTTAAA
Statistics
Matches: 210, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 2 0.01
41 208 0.99
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
Found at i:9661706 original size:123 final size:123
Alignment explanation
Indices: 9661529--9661796 Score: 464
Period size: 123 Copynumber: 2.2 Consensus size: 123
9661519 GACTTTAAGT
*
9661529 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAACCTAGCAGGCTAAGTGCCGGTGATC
1 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAACCTAGCAAGCTAAGTGCCGGTGATC
* *
9661594 TGAACCAGATTATGAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
66 TGAACCAGATTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
9661652 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAACCTAGCAAGCTAAGTGCCGGTGATC
1 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAACCTAGCAAGCTAAGTGCCGGTGATC
* * * *
9661717 TGAATCAGGTTATAAACCTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAGC
66 TGAACCAGATTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
*
9661775 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTACGTGCCGGTGA
9661797 ATATGTTAAA
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 137 1.00
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.22
Consensus pattern (123 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAACCTAGCAAGCTAAGTGCCGGTGATC
TGAACCAGATTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
Found at i:9664583 original size:19 final size:18
Alignment explanation
Indices: 9664541--9664585 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
9664531 ATTTTATTTT
9664541 TTATTTTTTAATTTCATA
1 TTATTTTTTAATTTCATA
*
9664559 TAATTTTTTAAATTTTC-TA
1 TTATTTTTT-AA-TTTCATA
9664578 TTATTTTT
1 TTATTTTT
9664586 GAATAATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 11 0.48
20 4 0.17
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTTTTAATTTCATA
Found at i:9664631 original size:17 final size:18
Alignment explanation
Indices: 9664611--9664659 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
9664601 TTTTTTTGTA
9664611 ATTTTATATTTTTCCA-T
1 ATTTTATATTTTTCCACT
*
9664628 ATTTTATAATTTTTGCACT
1 ATTTTAT-ATTTTTCCACT
9664647 -TTTCTATATTTTT
1 ATTT-TATATTTTT
9664660 ATAACATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.25
18 17 0.61
19 4 0.14
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTATATTTTTCCACT
Found at i:9667051 original size:20 final size:18
Alignment explanation
Indices: 9667028--9667112 Score: 61
Period size: 18 Copynumber: 4.7 Consensus size: 18
9667018 AAGAAACTAG
*
9667028 AAAATTATTAAAGTTATTAT
1 AAAATTA-TAAAATT-TTAT
9667048 AAAATTATAAAATTTTAT
1 AAAATTATAAAATTTTAT
*
9667066 -AAA-TAAAAAATTCTT-T
1 AAAATTATAAAATT-TTAT
**
9667082 AAAA-TATTAAAAAGTTAT
1 AAAATTA-TAAAATTTTAT
9667100 AAAATTTATAAAA
1 AAAA-TTATAAAA
9667113 AAAATAAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
16 9 0.17
17 12 0.22
18 13 0.24
19 11 0.20
20 9 0.17
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATTATAAAATTTTAT
Found at i:9667548 original size:18 final size:20
Alignment explanation
Indices: 9667525--9667562 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9667515 CAAAAAAGTG
9667525 TAGTAA-TTT-TTAAATTTT
1 TAGTAAGTTTGTTAAATTTT
9667543 TAGTAAGTTTGTTAAATTTT
1 TAGTAAGTTTGTTAAATTTT
9667563 ATATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (20 bp):
TAGTAAGTTTGTTAAATTTT
Found at i:9682581 original size:2 final size:2
Alignment explanation
Indices: 9682574--9682613 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9682564 TCATTTGTGT
9682574 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9682614 ATTTGATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9683984 original size:48 final size:49
Alignment explanation
Indices: 9683889--9683985 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 49
9683879 TGAGGGAATT
** * * **
9683889 CTGTTGAATCTTTTATCGTTGCAAGATTAGGCTGACTTAGGTGTTTTTA
1 CTGTTGAATCCGTTATCATTGCAAGATTAGGCTAACTTAGGCATTTTTA
*
9683938 CTGTTGAATCCGTTATCATTGCGAG-TTAGGCTAACTTAGGCATTTTTA
1 CTGTTGAATCCGTTATCATTGCAAGATTAGGCTAACTTAGGCATTTTTA
9683986 AGCAAAGAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
48 20 0.49
49 21 0.51
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (49 bp):
CTGTTGAATCCGTTATCATTGCAAGATTAGGCTAACTTAGGCATTTTTA
Found at i:9690559 original size:10 final size:11
Alignment explanation
Indices: 9690533--9690558 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9690523 GAAAATGTTT
9690533 AAAAACTTCAA
1 AAAAACTTCAA
9690544 AAAAACTTCAA
1 AAAAACTTCAA
9690555 AAAA
1 AAAA
9690559 CAGGCTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAACTTCAA
Found at i:9700848 original size:24 final size:24
Alignment explanation
Indices: 9700821--9700902 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 24
9700811 GTCATTAGGG
*
9700821 TTACCGATTTCAGCTCATATGAGC
1 TTACCGATTTCAGCTCATAAGAGC
*
9700845 TTACC-ATTATTCAGCTCAGAAGAGC
1 TTACCGA-T-TTCAGCTCATAAGAGC
**
9700870 TTACCG-TTTACAGCTTGTAAGAGC
1 TTACCGATTT-CAGCTCATAAGAGC
*
9700894 ATACCGATT
1 TTACCGATT
9700903 CAGAGCTCGT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
23 3 0.06
24 23 0.49
25 21 0.45
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (24 bp):
TTACCGATTTCAGCTCATAAGAGC
Found at i:9704220 original size:31 final size:32
Alignment explanation
Indices: 9704153--9704218 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
9704143 ATCCTTTAAA
9704153 TTTTAAAAAATAAAAAAAATTAATAAAAATAT
1 TTTTAAAAAATAAAAAAAATTAATAAAAATAT
*
9704185 TTTTAAAAATTAAAAAAACA-T-A-AAAAATAT
1 TTTTAAAAAATAAAAAAA-ATTAATAAAAATAT
9704215 TTTT
1 TTTT
9704219 TATTAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 12 0.38
31 1 0.03
32 18 0.56
33 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTTAAAAAATAAAAAAAATTAATAAAAATAT
Found at i:9711536 original size:32 final size:32
Alignment explanation
Indices: 9711499--9711562 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
9711489 CTACTAAGAC
9711499 ACCTGCATTTTTCCCCTTTGACAATCCTCCAA
1 ACCTGCATTTTTCCCCTTTGACAATCCTCCAA
9711531 ACCTGCATTTTTCCCCTTTGACAATCCTCCAA
1 ACCTGCATTTTTCCCCTTTGACAATCCTCCAA
9711563 TGTACTTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.38, G:0.06, T:0.34
Consensus pattern (32 bp):
ACCTGCATTTTTCCCCTTTGACAATCCTCCAA
Found at i:9713773 original size:16 final size:16
Alignment explanation
Indices: 9713736--9713775 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
9713726 TTGATAAAAT
* *
9713736 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
9713752 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
9713768 TAAAATTA
1 TAAAATTA
9713776 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:9714010 original size:16 final size:16
Alignment explanation
Indices: 9713989--9714022 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
9713979 TATATATTTT
9713989 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
9714005 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
9714021 AA
1 AA
9714023 CTAGTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.18
Consensus pattern (16 bp):
AAACATAAAAAACTTA
Found at i:9715265 original size:24 final size:24
Alignment explanation
Indices: 9715223--9715268 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
9715213 CTTGAAACCA
* * *
9715223 TTTCCACAGCTCTTTTCTTCACCC
1 TTTCCACAACTCCTCTCTTCACCC
9715247 TTTCCACAACTCCTCTCTTCAC
1 TTTCCACAACTCCTCTCTTCAC
9715269 TCTCTTCACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.15, C:0.43, G:0.02, T:0.39
Consensus pattern (24 bp):
TTTCCACAACTCCTCTCTTCACCC
Found at i:9715310 original size:14 final size:14
Alignment explanation
Indices: 9715291--9715320 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9715281 ATCGATTGCA
9715291 GCCTCATCATCTCT
1 GCCTCATCATCTCT
*
9715305 GCCTCATCTTCTCT
1 GCCTCATCATCTCT
9715319 GC
1 GC
9715321 TAATTTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.43, G:0.10, T:0.37
Consensus pattern (14 bp):
GCCTCATCATCTCT
Found at i:9715803 original size:27 final size:27
Alignment explanation
Indices: 9715747--9715804 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
9715737 AAAATTGCAG
*
9715747 CCTTAACACCAATACAGTAGCATCTTA
1 CCTTAACACCAATACAGTAACATCTTA
9715774 CCTTAACACCAATACAGTAACAT-TTGA
1 CCTTAACACCAATACAGTAACATCTT-A
9715801 CCTT
1 CCTT
9715805 CAAAGCTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.28
Consensus pattern (27 bp):
CCTTAACACCAATACAGTAACATCTTA
Found at i:9717179 original size:17 final size:15
Alignment explanation
Indices: 9717145--9717187 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
9717135 AATAGCATGG
*
9717145 CATTTGTTTTTGAAA
1 CATTTGTTTTTCAAA
9717160 CATTTGTTTCATTCAAA
1 CATTTGTTT--TTCAAA
9717177 CATTTGTTTTT
1 CATTTGTTTTT
9717188 ATATATACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 11 0.44
17 14 0.56
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (15 bp):
CATTTGTTTTTCAAA
Found at i:9718118 original size:15 final size:15
Alignment explanation
Indices: 9718098--9718128 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9718088 AAAATATTAA
*
9718098 CATCATCAGTCACAT
1 CATCATCAATCACAT
9718113 CATCATCAATCACAT
1 CATCATCAATCACAT
9718128 C
1 C
9718129 CTTGGCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.35, G:0.03, T:0.26
Consensus pattern (15 bp):
CATCATCAATCACAT
Found at i:9718313 original size:20 final size:20
Alignment explanation
Indices: 9718249--9718325 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
9718239 AAATCATTGC
*
9718249 AATATATGTAAAAATAATTT
1 AATATATGTAAAAACAATTT
* ** *
9718269 AA-A-ATATAAAAATTTATTA
1 AATATATGTAAAAA-CAATTT
9718288 ATATATATGTAAAAACAATTT
1 A-ATATATGTAAAAACAATTT
9718309 AATATATGTAAAAACAA
1 AATATATGTAAAAACAA
9718326 CTTTTCCGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
18 8 0.17
19 6 0.13
20 19 0.41
21 5 0.11
22 8 0.17
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (20 bp):
AATATATGTAAAAACAATTT
Found at i:9718437 original size:20 final size:20
Alignment explanation
Indices: 9718412--9718451 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9718402 AATATTTTCC
*
9718412 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
9718432 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
9718452 TCATTTTCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:9718458 original size:14 final size:14
Alignment explanation
Indices: 9718435--9718472 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
9718425 ACAGAAAAGT
9718435 AAAACATTTTCCAG
1 AAAACATTTTCCAG
* *
9718449 AAATCATTTTCCGG
1 AAAACATTTTCCAG
9718463 AAAACATTTT
1 AAAACATTTT
9718473 ACTCCCAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (14 bp):
AAAACATTTTCCAG
Found at i:9718642 original size:6 final size:6
Alignment explanation
Indices: 9718631--9718670 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
9718621 AACCCGCCAC
9718631 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
9718671 CAGCTTTGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:9724117 original size:31 final size:31
Alignment explanation
Indices: 9724081--9724143 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
9724071 AGGGGCTATT
9724081 GGATGGATGATTATCGACATAAAAGGGTTAA
1 GGATGGATGATTATCGACATAAAAGGGTTAA
9724112 GGATGGATGATTATCGACATAAAAGGGTTAA
1 GGATGGATGATTATCGACATAAAAGGGTTAA
9724143 G
1 G
9724144 TCCCTCAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.30, T:0.25
Consensus pattern (31 bp):
GGATGGATGATTATCGACATAAAAGGGTTAA
Found at i:9726384 original size:10 final size:10
Alignment explanation
Indices: 9726369--9726393 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9726359 CTCATATTCG
9726369 GTAAAAAGAT
1 GTAAAAAGAT
9726379 GTAAAAAGAT
1 GTAAAAAGAT
9726389 GTAAA
1 GTAAA
9726394 CCTTCCAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (10 bp):
GTAAAAAGAT
Found at i:9728479 original size:13 final size:13
Alignment explanation
Indices: 9728461--9728502 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
9728451 AATTTTAAAT
9728461 TATTTAGTGATAA
1 TATTTAGTGATAA
*
9728474 TATTTA--GA-AT
1 TATTTAGTGATAA
9728484 TATTTAGTGATAA
1 TATTTAGTGATAA
9728497 TATTTA
1 TATTTA
9728503 TGAAAAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 2 0.08
13 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:9728502 original size:23 final size:22
Alignment explanation
Indices: 9728454--9728502 Score: 89
Period size: 23 Copynumber: 2.2 Consensus size: 22
9728444 ATTTTTAAAT
9728454 TTTAAATTATTTAGTGATAATA
1 TTTAAATTATTTAGTGATAATA
9728476 TTTAGAATTATTTAGTGATAATA
1 TTTA-AATTATTTAGTGATAATA
9728499 TTTA
1 TTTA
9728503 TGAAAAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (22 bp):
TTTAAATTATTTAGTGATAATA
Found at i:9731239 original size:19 final size:19
Alignment explanation
Indices: 9731215--9731253 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
9731205 ATTTTAAAAT
9731215 TTTAAAGAAATAAAAATTA
1 TTTAAAGAAATAAAAATTA
** *
9731234 TTTAAATTATTAAAAATTA
1 TTTAAAGAAATAAAAATTA
9731253 T
1 T
9731254 AAAAATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TTTAAAGAAATAAAAATTA
Found at i:9731246 original size:27 final size:25
Alignment explanation
Indices: 9731202--9731263 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 25
9731192 ACAATTAAGT
9731202 AATATTTTAAAATTTTAAAGAA-ATAAA
1 AATA-TTT-AAATTTTAAA-AATATAAA
9731229 AATTATTTAAATTATTAAAAATTATAAA
1 AA-TATTTAAATT-TTAAAAA-TATAAA
9731257 AATATTT
1 AATATTT
9731264 TTATTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
26 7 0.23
27 15 0.48
28 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
AATATTTAAATTTTAAAAATATAAA
Found at i:9733053 original size:30 final size:30
Alignment explanation
Indices: 9733017--9733087 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
9733007 GCTGCAAGGG
* *
9733017 TCACACGGCCATGTGGCCGGACTGTGTGAT
1 TCACACGGCCATGTGGCCAGACCGTGTGAT
9733047 TCACACGGCCATGTGGCCAGACCGTGTGAT
1 TCACACGGCCATGTGGCCAGACCGTGTGAT
9733077 TCACACGGCCA
1 TCACACGGCCA
9733088 AGAGACACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.20, C:0.31, G:0.30, T:0.20
Consensus pattern (30 bp):
TCACACGGCCATGTGGCCAGACCGTGTGAT
Found at i:9734303 original size:25 final size:25
Alignment explanation
Indices: 9734244--9734356 Score: 95
Period size: 25 Copynumber: 4.5 Consensus size: 25
9734234 GTACATATAT
* * * *
9734244 GCTCATATGAGCTATGAATCGGTAT
1 GCTCATACGAGCTAAGAATCAGTAA
* *
9734269 GTTC-TCACGAGCTATGAATCAGTAA
1 GCTCAT-ACGAGCTAAGAATCAGTAA
* *
9734294 ACTCATACGAGTTAAGAATCAGTAA
1 GCTCATACGAGCTAAGAATCAGTAA
* **
9734319 GCTC-TCACGAGCTACGAATTGGTAA
1 GCTCAT-ACGAGCTAAGAATCAGTAA
9734344 GCTCATACGAGCT
1 GCTCATACGAGCT
9734357 GTGGTGTGTC
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
24 2 0.03
25 67 0.94
26 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTAAGAATCAGTAA
Found at i:9736672 original size:17 final size:18
Alignment explanation
Indices: 9736652--9736757 Score: 66
Period size: 18 Copynumber: 6.1 Consensus size: 18
9736642 AATAAATATA
* *
9736652 TTTATTTTTTAAAT-TTT
1 TTTAATTTTAAAATATTT
9736669 TTTAATTTTAAAATATTT
1 TTTAATTTTAAAATATTT
*
9736687 TTT--TATT-----ATTT
1 TTTAATTTTAAAATATTT
9736698 TTTAATTTTAAAATATTT
1 TTTAATTTTAAAATATTT
* * *
9736716 TTAAAATACTTTGTAAATTTTT
1 TT-TAAT--TTT-AAAATATTT
9736738 TTTAATTTTAAAATATTT
1 TTTAATTTTAAAATATTT
9736756 TT
1 TT
9736758 AAAATACTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 23
0.67 0.10 0.23
Matches are distributed among these distances:
11 7 0.10
13 3 0.04
16 3 0.04
17 12 0.18
18 21 0.31
19 6 0.09
21 6 0.09
22 9 0.13
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (18 bp):
TTTAATTTTAAAATATTT
Found at i:9736718 original size:40 final size:40
Alignment explanation
Indices: 9736674--9736778 Score: 158
Period size: 40 Copynumber: 2.6 Consensus size: 40
9736664 ATTTTTTTAA
9736674 TTTTAAAATA-TTTTTTTATTATTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTTTATT-TTTTTTAATTTTAAAATAT
* **
9736714 TTTTAAAATACTTTGTAAATTTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTTTATTTTTTTTAATTTTAAAATAT
*
9736754 TTTTAAAATACTTTTTTTAATTTTT
1 TTTTAAAATACTTTTTTTATTTTTT
9736779 ACAATAAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 50 0.88
41 7 0.12
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (40 bp):
TTTTAAAATACTTTTTTTATTTTTTTTAATTTTAAAATAT
Found at i:9736762 original size:29 final size:30
Alignment explanation
Indices: 9736714--9736777 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 30
9736704 TTTAAAATAT
9736714 TTTTAAAATACTTTGTAAAT-TTTTTTTAA
1 TTTTAAAATACTTTGTAAATATTTTTTTAA
*
9736743 TTTTAAAATA-TTTTTAAAATACTTTTTTTAA
1 TTTTAAAATACTTTGT-AAATA-TTTTTTTAA
9736774 TTTT
1 TTTT
9736778 TACAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 4 0.13
29 14 0.45
31 13 0.42
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTTAAAATACTTTGTAAATATTTTTTTAA
Found at i:9736790 original size:21 final size:21
Alignment explanation
Indices: 9736752--9736791 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9736742 ATTTTAAAAT
**
9736752 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
*
9736773 ATTTTTACAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
9736792 GGTATTTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:9739787 original size:34 final size:34
Alignment explanation
Indices: 9739744--9739811 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
9739734 TTACTGACGA
*
9739744 TTGTATTTTGTTTGGTGATGCGATAAAAAGAGGG
1 TTGTATTTTGTTTGGTGATGCGACAAAAAGAGGG
9739778 TTGTATTTTGTTTGGTGATGCGACAAAAAGAGGG
1 TTGTATTTTGTTTGGTGATGCGACAAAAAGAGGG
9739812 GCACATACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.26, C:0.04, G:0.32, T:0.37
Consensus pattern (34 bp):
TTGTATTTTGTTTGGTGATGCGACAAAAAGAGGG
Found at i:9742682 original size:31 final size:31
Alignment explanation
Indices: 9742613--9742682 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
9742603 TTTAAGCCCC
* * * *
9742613 TCAAAATTTTTAAAAGTTCTAATTTAAATCT
1 TCAAAAATATTAAAACTTCTAATTAAAATCT
** *
9742644 TTTAAAATATTAAAACTTTTAATTAAAATCT
1 TCAAAAATATTAAAACTTCTAATTAAAATCT
9742675 TCAAAAAT
1 TCAAAAAT
9742683 TTATGTAAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (31 bp):
TCAAAAATATTAAAACTTCTAATTAAAATCT
Found at i:9748345 original size:40 final size:39
Alignment explanation
Indices: 9748265--9748397 Score: 160
Period size: 40 Copynumber: 3.3 Consensus size: 39
9748255 AAACAGGCTT
* * *
9748265 TTAGCGGCGTTTGGACAAAAAACGCCACTAAAAATCGAGCA
1 TTAGCGGCGTTT-TAC-AAAAACGCCGCTAAAAATAGAGCA
**
9748306 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGGTAGAGCA
1 TTAGCGGCG-TTTTACAAAAACGCCGCTAAAAATAGAGCA
* *
9748346 TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAAATA-AGCA
1 TTAGCGGCG-TTTTACAAAAACGCCGCTAAAAATAGAGCA
9748385 TTAGCGGCGTTTT
1 TTAGCGGCGTTTT
9748398 CTGAAAAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
38 3 0.04
39 13 0.16
40 51 0.63
41 11 0.14
42 3 0.04
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (39 bp):
TTAGCGGCGTTTTACAAAAACGCCGCTAAAAATAGAGCA
Found at i:9748410 original size:39 final size:38
Alignment explanation
Indices: 9748282--9748416 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 38
9748272 CGTTTGGACA
* *
9748282 AAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTTAC-
1 AAAAACGCCGCTAAAAAT-AAGCATTAGCGGCG-TTTT-CT
** * *
9748322 AAAAACGCCGCTAAAGGTAGAGCATTAGCGGCGCTTCTCC
1 AAAAACGCCGCTAAAAATA-AGCATTAGCGGCG-TTTTCT
9748362 AAAAACGCCGCTAAAAATAAGCATTAGCGGCGTTTTCT
1 AAAAACGCCGCTAAAAATAAGCATTAGCGGCGTTTTCT
*
9748400 GAAAAGCGCCGC-AAAAA
1 -AAAAACGCCGCTAAAAA
9748417 GCCTAAGCCA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
38 9 0.11
39 24 0.29
40 49 0.60
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (38 bp):
AAAAACGCCGCTAAAAATAAGCATTAGCGGCGTTTTCT
Done.