Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 2 of 356
Found at i:407085 original size:16 final size:17
Alignment explanation
Indices: 407051--407091 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
407041 ATTATTTTAA
407051 ATTTT-ATTAAATCATAT
1 ATTTTAATTAAA-CATAT
407068 ATTTTAATTAAA-ATAT
1 ATTTTAATTAAACATAT
407084 A-TTTAATT
1 ATTTTAATT
407092 TTAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 5 0.22
18 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTAATTAAACATAT
Found at i:407162 original size:66 final size:65
Alignment explanation
Indices: 407092--407403 Score: 176
Period size: 61 Copynumber: 5.1 Consensus size: 65
407082 ATATTTAATT
407092 TTAATTATTTAAAATTATCTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAAT
1 TTAATTATTTAAAATTAT-TTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAAT
407157 A
65 A
* * * * **
407158 TTAATTA-TTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TTAAT
1 TTAATTATTTAA-AATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAAT
407211 A
65 A
* * *
407212 ATAATTATGTT-AATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAA
1 TTAATTAT-TTAAAATTAT-TTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAA
407276 TA
64 TA
* * * * * * * * **
407278 TTGATTA-TTAAGAATT-TTATTA-A--ATTATATATTTTAATTAT-AATATATTTA-ATAATTA
1 TTAATTATTTAA-AATTATTTTTATAGTATAATATATTATGATT-TGAGTAAATTCATATAAGAA
*
407336 TG
64 TA
*
407338 TT-A--ATTT---A-TA-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA
1 TTAATTATTTAAAATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATA
*
407395 TTGATTATT
1 TTAATTATT
407404 AAGAATTTTA
Statistics
Matches: 181, Mismatches: 37, Indels: 62
0.65 0.13 0.22
Matches are distributed among these distances:
53 5 0.03
54 15 0.08
55 7 0.04
56 27 0.15
57 12 0.07
58 4 0.02
59 11 0.06
60 19 0.10
61 30 0.17
62 2 0.01
63 4 0.02
64 11 0.06
65 11 0.06
66 23 0.13
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (65 bp):
TTAATTATTTAAAATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATA
Found at i:407174 original size:120 final size:119
Alignment explanation
Indices: 407050--407459 Score: 682
Period size: 120 Copynumber: 3.4 Consensus size: 119
407040 AATTATTTTA
* * *
407050 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATTTTAATTAT-TTAAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAA-TTTAATTATGTT-AATTTATATTT
* *
407114 TATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
407170 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAAT-TTAATTATGTTAATTTATATTTT
407235 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
65 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
407290 AATTTTATTAAATTATATATTTTAATTATAATATATTTAA--TAATTATGTTAATTTATATTTTA
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTTAATTATGTTAATTTATATTTTA
407353 TAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 TAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
407407 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAAATATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATT-TAATTATGTT
407460 TAAATATGAT
Statistics
Matches: 276, Mismatches: 9, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
117 116 0.42
119 1 0.00
120 157 0.57
121 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTTAATTATGTTAATTTATATTTTA
TAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:407210 original size:15 final size:15
Alignment explanation
Indices: 407175--407226 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
407165 TTAAGAATTT
*
407175 TATTAAATTAT-ATA
1 TATTTAATTATAATA
407189 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
407203 TATTTAATAATAAT-
1 TATTTAATTATAATA
407217 TATGTTAATT
1 TAT-TTAATT
407227 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:407442 original size:16 final size:16
Alignment explanation
Indices: 407408--407456 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
407398 ATTATTAAGA
407408 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
407425 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
407441 A-TTTAATTATAAATAT
1 ATTTTAATTA-AAATAT
407457 GTTTAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.27
16 11 0.37
17 5 0.17
18 6 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:407447 original size:15 final size:16
Alignment explanation
Indices: 407421--407462 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
407411 TTATTAAATT
407421 ATATATTTTAATTA-AA
1 ATATA-TTTAATTATAA
407437 ATATATTTAATTATAA
1 ATATATTTAATTATAA
*
407453 ATATGTTTAA
1 ATATATTTAA
407463 ATATGATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATATTTAATTATAA
Found at i:407672 original size:44 final size:45
Alignment explanation
Indices: 407607--407697 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
407597 ACCTCTATTC
* * *
407607 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
407651 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
407696 CA
1 CA
407698 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:407712 original size:17 final size:16
Alignment explanation
Indices: 407678--407730 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
407668 GATTAGCTAT
407678 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
407694 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
407711 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
407727 TACA
1 TACA
407731 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:412895 original size:5 final size:5
Alignment explanation
Indices: 412885--412913 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
412875 CAAATTAGGT
412885 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
412914 TTAATTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:417777 original size:23 final size:22
Alignment explanation
Indices: 417726--417777 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
417716 CCTCGTCTTT
*
417726 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
417748 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
417771 TTCTTTT
1 TTCTTTT
417778 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:420684 original size:21 final size:21
Alignment explanation
Indices: 420654--420695 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
420644 TTGCTGGACA
*
420654 AGAGCCGGAATGGGAGTGTTT
1 AGAGCCGGAATGAGAGTGTTT
*
420675 AGAGCTGGAATGAGAGTGTTT
1 AGAGCCGGAATGAGAGTGTTT
420696 GGTTGCTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.07, G:0.40, T:0.26
Consensus pattern (21 bp):
AGAGCCGGAATGAGAGTGTTT
Found at i:424477 original size:13 final size:13
Alignment explanation
Indices: 424458--424521 Score: 74
Period size: 13 Copynumber: 4.9 Consensus size: 13
424448 TAAACCAAAT
424458 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* * *
424471 TTCTCAAAAACAA
1 TTTTCAAAAGCAC
* *
424484 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
*
424497 TTTTCAAAAACAC
1 TTTTCAAAAGCAC
424510 TTTTCAAAAGCA
1 TTTTCAAAAGCA
424522 TTGCCAAACT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.41, C:0.25, G:0.05, T:0.30
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:424521 original size:26 final size:26
Alignment explanation
Indices: 424458--424521 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
424448 TAAACCAAAT
424458 TTTTCAAAAGCACTTCTCAAAAACAA
1 TTTTCAAAAGCACTTCTCAAAAACAA
* * * *
424484 TTTTCCACAGCACTTTTCAAAAACAC
1 TTTTCAAAAGCACTTCTCAAAAACAA
424510 TTTTCAAAAGCA
1 TTTTCAAAAGCA
424522 TTGCCAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.41, C:0.25, G:0.05, T:0.30
Consensus pattern (26 bp):
TTTTCAAAAGCACTTCTCAAAAACAA
Found at i:428943 original size:3 final size:3
Alignment explanation
Indices: 428935--428968 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
428925 TTTTGCACAC
428935 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
428969 AGCAATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:438387 original size:94 final size:94
Alignment explanation
Indices: 438235--438423 Score: 351
Period size: 94 Copynumber: 2.0 Consensus size: 94
438225 CCATATCATA
438235 TTTCATATCCCTTGCTTTCATATGGGGTTGCACAGTTCAGTAGTCTTTAGGCTTTATATATGCCA
1 TTTCATATCCCTTGCTTTCATATGGGGTTGCACAGTTCAGTAGTCTTTAGGCTTTATATATGCCA
*
438300 TAAAGTTTCAACTCTCTTCTTTTTTATGC
66 TAAAGTTTCAACTCTCTTCCTTTTTATGC
*
438329 TTTCATATCCCTTGTTTTCATATGGGGTTGCACAGTTCAGTAGTCTTTAGGCTTTATATATGCCA
1 TTTCATATCCCTTGCTTTCATATGGGGTTGCACAGTTCAGTAGTCTTTAGGCTTTATATATGCCA
*
438394 TAAAGTTTCAGCTCTCTTCCTTTTTATGC
66 TAAAGTTTCAACTCTCTTCCTTTTTATGC
438423 T
1 T
438424 CTCCACTTAA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (94 bp):
TTTCATATCCCTTGCTTTCATATGGGGTTGCACAGTTCAGTAGTCTTTAGGCTTTATATATGCCA
TAAAGTTTCAACTCTCTTCCTTTTTATGC
Found at i:440154 original size:69 final size:70
Alignment explanation
Indices: 440053--440189 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 70
440043 GCGGCACCAA
440053 TAATTTTTTTTTAAAATCCATGTGGTAACGTCAACTAGTCAAACAGTATTGAAAAATATTATAGC
1 TAATTTTTTTTTAAAATCCATGTGGTAACGTCAACTAGTCAAACAGTATTGAAAAATATTATAGC
440118 AAAGT
66 AAAGT
*
440123 TAATTTTTTTTT-AAATCCATGTGGTATCGTCAACTAGTCAAACAGTATTGAAAAATATTATAGC
1 TAATTTTTTTTTAAAATCCATGTGGTAACGTCAACTAGTCAAACAGTATTGAAAAATATTATAGC
440187 AAA
66 AAA
440190 ATTTGTAGGG
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 54 0.82
70 12 0.18
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (70 bp):
TAATTTTTTTTTAAAATCCATGTGGTAACGTCAACTAGTCAAACAGTATTGAAAAATATTATAGC
AAAGT
Found at i:444582 original size:3 final size:3
Alignment explanation
Indices: 444564--444597 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
444554 TCTTCTTGGG
* *
444564 ATT AAT ATT CTT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
444598 CCAGAAGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:445864 original size:12 final size:12
Alignment explanation
Indices: 445849--445874 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
445839 ACATATTAAA
445849 TTAAAATTTATT
1 TTAAAATTTATT
445861 TTAAAATTTATT
1 TTAAAATTTATT
445873 TT
1 TT
445875 CGTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:447912 original size:3 final size:3
Alignment explanation
Indices: 447906--447930 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
447896 ACAACAACAA
447906 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
447931 TGCAAACAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:448665 original size:106 final size:105
Alignment explanation
Indices: 448476--448678 Score: 309
Period size: 106 Copynumber: 1.9 Consensus size: 105
448466 AATTCAAGAG
* * *
448476 GATATTTAGCAATTTGGCTAAACGTGAAATCGAAACCCAGCACCTTAGGGCACGTTTCTCGAATT
1 GATATTTAGCAATTTGGCTAAACGAGAAATCGAAACCCAACACCTTAGGGCACGTTCCTCGAATT
*
448541 TCTAAACGCAAAACATTGCCTTATTTTTGAAATTAAAAAAA
66 TCCAAACGCAAAACATTGCCTTA-TTTTGAAATTAAAAAAA
* * *
448582 GATATTTAGCTATTTGG-TCGAACGAGAAATCGAAACCCAATACCTTAGGGCACGTTCCTCGAAT
1 GATATTTAGCAATTTGGCT-AAACGAGAAATCGAAACCCAACACCTTAGGGCACGTTCCTCGAAT
*
448646 TTCCAAACGCAAAATATTGCCTTATTTTGAAAT
65 TTCCAAACGCAAAACATTGCCTTATTTTGAAAT
448679 ATTTTTTTTT
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
105 10 0.11
106 78 0.89
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (105 bp):
GATATTTAGCAATTTGGCTAAACGAGAAATCGAAACCCAACACCTTAGGGCACGTTCCTCGAATT
TCCAAACGCAAAACATTGCCTTATTTTGAAATTAAAAAAA
Found at i:448835 original size:12 final size:12
Alignment explanation
Indices: 448810--448862 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
448800 ATAAACAAAC
448810 TAAAGCATAAAAA
1 TAAA-CATAAAAA
*
448823 TAAACATATAAA
1 TAAACATAAAAA
* * *
448835 TAAATACATAAA
1 TAAACATAAAAA
*
448847 TGAACATAAAAA
1 TAAACATAAAAA
448859 TAAA
1 TAAA
448863 GGAAAATATA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
12 28 0.88
13 4 0.12
ACGTcount: A:0.68, C:0.08, G:0.04, T:0.21
Consensus pattern (12 bp):
TAAACATAAAAA
Found at i:448891 original size:9 final size:9
Alignment explanation
Indices: 448865--448897 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
448855 AAAATAAAGG
448865 AAAATATAT
1 AAAATATAT
*
448874 GAAAT-TAT
1 AAAATATAT
448882 AAAATATAT
1 AAAATATAT
448891 AAAATAT
1 AAAATAT
448898 GTATGTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAATATAT
Found at i:448966 original size:13 final size:13
Alignment explanation
Indices: 448948--449007 Score: 70
Period size: 13 Copynumber: 4.6 Consensus size: 13
448938 AATTATGAAA
448948 ATATATAAAATAT
1 ATATATAAAATAT
*
448961 ATATAT-AAGTAT
1 ATATATAAAATAT
*
448973 ATATTTTAAAAT-T
1 ATA-TATAAAATAT
448986 ACTATATAAAATAT
1 A-TATATAAAATAT
449000 ATATATAA
1 ATATATAA
449008 GTACGCATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 8 0.21
13 24 0.62
14 7 0.18
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (13 bp):
ATATATAAAATAT
Found at i:449243 original size:5 final size:6
Alignment explanation
Indices: 449228--449252 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
449218 TAAGTATATA
449228 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
449253 CACTCCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:452713 original size:44 final size:44
Alignment explanation
Indices: 452665--452884 Score: 157
Period size: 47 Copynumber: 4.9 Consensus size: 44
452655 AATATTAATT
*
452665 ATTTTAAATTATATAAATTCATATAAGAAAAATTATTATCAAGA
1 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGA
* * * * **
452709 ATTTTATGAAATTATATATCATT-AT-TAA-ATTATATTTAATATTAATT
1 A-TTT-T-AAATTATATA-AATTCATATAAGA--AAATTTATTATCAAGA
452756 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGA
1 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGA
* * * **
452800 ATTTTATGAAATTATATATTATT-AT-TAA-ATTATATTTAATAAT-AATT
1 A-TTT-T-AAATTATATA-AATTCATATAAGA--AAATTT-ATTATCAAGA
*
452847 ATTTTAAATTATACAAATTCATATAAGAAAATTTATTA
1 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTA
452885 GGTATAATTA
Statistics
Matches: 135, Mismatches: 22, Indels: 39
0.69 0.11 0.20
Matches are distributed among these distances:
43 9 0.07
44 41 0.30
45 16 0.12
46 16 0.12
47 43 0.32
48 10 0.07
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (44 bp):
ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGA
Found at i:452767 original size:101 final size:99
Alignment explanation
Indices: 452661--452959 Score: 302
Period size: 91 Copynumber: 3.1 Consensus size: 99
452651 ATTTAATATT
452661 AATTATTTTAAATTATATAAATTCATATAAGAAAAATTATTATCAAGAATTTTATGAAATTATAT
1 AATTATTTTAAATTATATAAATTCATATAAGAAAAATTATTATCAAGAATTTTATGAAATTATAT
452726 ATCATTATTAAAT-TA--T-AT-TTAA-TA--TT-
66 AT-ATTATTAAATATATTTAATATTAATTATTTTA
*
452752 AATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATAT
1 AATTATTTTAAATTATATAAATTCATATAAGAAAAATTATTATCAAGAATTTTATGAAATTATAT
*
452817 ATTATTATTAAATTATATTTAATAATAATTATTTTA
66 A-TATTATTAAA-TATATTTAATATTAATTATTTTA
** * * * * *
452853 AATTA-TACAAATTCATATAAGAAAATTTAT-TAGGTATAATTATTAT--A-AATTTTATTAAAT
1 AATTATTTTAAATT-ATAT----AAATTCATATAAGAAAAATTATTATCAAGAATTTTATGAAAT
* * *
452913 CATATATTTTAATTAAAATATATTTAATATTAATTATTTCA
61 TATATATATT-ATT-AAATATATTTAATATTAATTATTTTA
452954 AATTAT
1 AATTAT
452960 ATTTTATAGT
Statistics
Matches: 175, Mismatches: 14, Indels: 27
0.81 0.06 0.12
Matches are distributed among these distances:
91 74 0.42
92 2 0.01
93 2 0.01
95 1 0.01
96 2 0.01
97 3 0.02
98 2 0.01
100 11 0.06
101 55 0.31
102 4 0.02
104 12 0.07
105 7 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (99 bp):
AATTATTTTAAATTATATAAATTCATATAAGAAAAATTATTATCAAGAATTTTATGAAATTATAT
ATATTATTAAATATATTTAATATTAATTATTTTA
Found at i:452781 original size:10 final size:9
Alignment explanation
Indices: 452623--452690 Score: 54
Period size: 10 Copynumber: 7.6 Consensus size: 9
452613 TGGTTAAATG
452623 TATAAATTA
1 TATAAATTA
452632 TATATAATTA
1 TATA-AATTA
452642 T-TAAATTA
1 TATAAATTA
452650 TAT---TTAA
1 TATAAATT-A
*
452657 TATTAATTA
1 TATAAATTA
*
452666 TTTTAAATTA
1 -TATAAATTA
452676 TATAAATTCA
1 TATAAATT-A
452686 TATAA
1 TATAA
452691 GAAAAATTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
6 2 0.04
7 4 0.08
8 6 0.12
9 15 0.31
10 21 0.44
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (9 bp):
TATAAATTA
Found at i:452903 original size:91 final size:91
Alignment explanation
Indices: 452626--452884 Score: 473
Period size: 91 Copynumber: 2.8 Consensus size: 91
452616 TTAAATGTAT
452626 AAATTATATATAATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATAATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
*
452691 GAAAAATTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
*
452717 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATAATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
452782 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
* * *
452808 AAATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATACAAATTCATATAA
1 AAATTATATATAATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
452873 GAAAATTTATTA
66 GAAAATTTATTA
452885 GGTATAATTA
Statistics
Matches: 163, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 163 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
AAATTATATATAATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
GAAAATTTATTATCAAGAATTTTATG
Found at i:453055 original size:16 final size:16
Alignment explanation
Indices: 453034--453075 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
453024 TTATTAAATT
*
453034 ATATATTTTAATTATA
1 ATATATTTTAATAATA
453050 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
453065 AT-TATGTTTAA
1 ATATAT-TTTAA
453076 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:453060 original size:15 final size:15
Alignment explanation
Indices: 453025--453066 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
453015 TTAAGAATTT
*
453025 TATTAAATTAT-ATA
1 TATTTAATTATAATA
453039 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
453053 TATTTAATAATAAT
1 TATTTAATTATAAT
453067 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:453311 original size:45 final size:44
Alignment explanation
Indices: 453220--453311 Score: 112
Period size: 45 Copynumber: 2.1 Consensus size: 44
453210 ACCTCTATTC
* * *
453220 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
*** *
453264 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTAATCCAATA
453309 CAT
1 CAT
453312 CTCTAATCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.30
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
Found at i:453315 original size:16 final size:16
Alignment explanation
Indices: 453291--453342 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
453281 GATTTGCTAT
453291 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
453307 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
453323 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
453339 TACA
1 TACA
453343 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:453798 original size:37 final size:37
Alignment explanation
Indices: 453708--453788 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
453698 TATACATTTG
* *
453708 AAAATGTTAGAAGTTAGATC-TTTGGGAGAAATTTTT
1 AAAATGTTAGAAATTAAATCTTTTGGGAGAAATTTTT
453744 AAAATGTTAGAAATTAAATCTTTTGGGAGAAATTTTT
1 AAAATGTTAGAAATTAAATCTTTTGGGAGAAATTTTT
*
453781 AAAGTGTT
1 AAAATGTT
453789 GTTTATTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 18 0.44
37 23 0.56
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.40
Consensus pattern (37 bp):
AAAATGTTAGAAATTAAATCTTTTGGGAGAAATTTTT
Found at i:459266 original size:15 final size:17
Alignment explanation
Indices: 459236--459268 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
459226 AAAATAAAAA
459236 AATTATATATATACATG
1 AATTATATATATACATG
459253 AATT-TATA-ATACATG
1 AATTATATATATACATG
459268 A
1 A
459269 TCCTCTATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (17 bp):
AATTATATATATACATG
Found at i:462089 original size:31 final size:31
Alignment explanation
Indices: 462029--462124 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
462019 ACTTAGCAAC
* *
462029 TCAGTGACTTAAATTAAAAA-ATGCAAATAGT
1 TCAGTGACTTAAA-TAAAAACTTTCAAATAGT
* ** **
462060 TTAGTGTTTTAAATAAAAACTTTTGAATAGT
1 TCAGTGACTTAAATAAAAACTTTCAAATAGT
*
462091 TCAGTGACTTAAATGAAAACTTTCAAATAGT
1 TCAGTGACTTAAATAAAAACTTTCAAATAGT
462122 TCA
1 TCA
462125 ATGATCATTT
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
30 6 0.12
31 45 0.88
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (31 bp):
TCAGTGACTTAAATAAAAACTTTCAAATAGT
Found at i:463623 original size:18 final size:18
Alignment explanation
Indices: 463600--463641 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
463590 TTTCTTTTTT
463600 AGTTGCAAAACAAGTTTC
1 AGTTGCAAAACAAGTTTC
463618 AGTTGCAAAACAAGTTTC
1 AGTTGCAAAACAAGTTTC
463636 AGTTGC
1 AGTTGC
463642 CACTTTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (18 bp):
AGTTGCAAAACAAGTTTC
Found at i:484262 original size:31 final size:31
Alignment explanation
Indices: 484227--484301 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
484217 TCAATTGATG
484227 CAATTATACATATAAAAAATTAA-TTTTACTT
1 CAATTATACATATAAAAAATTAATTTTTA-TT
***
484258 CAATTATACATATAAATTTTTAATTTTTATT
1 CAATTATACATATAAAAAATTAATTTTTATT
*
484289 TAATTATACATAT
1 CAATTATACATAT
484302 TTTAAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 34 0.87
32 5 0.13
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (31 bp):
CAATTATACATATAAAAAATTAATTTTTATT
Found at i:486543 original size:26 final size:24
Alignment explanation
Indices: 486512--486569 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
486502 GCTTTAGATG
* *
486512 TTTAAATTTAAGCTTAACTTATATTT
1 TTTAAATTTAA-CCTAAATT-TATTT
*
486538 TTTAAACTTTTACCTAAATTTATTT
1 TTTAAA-TTTAACCTAAATTTATTT
486563 TTTAAAT
1 TTTAAAT
486570 CTAATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.04
25 11 0.39
26 12 0.43
27 4 0.14
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTAAATTTAACCTAAATTTATTT
Found at i:489073 original size:20 final size:20
Alignment explanation
Indices: 489035--489074 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
489025 AAATATTTTA
*
489035 TTAACTAATAATTATAATTT
1 TTAACTAATAATTACAATTT
489055 TTAACTAAATAATT-CAATTT
1 TTAACT-AATAATTACAATTT
489075 AAAGGGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAACTAATAATTACAATTT
Found at i:499926 original size:111 final size:111
Alignment explanation
Indices: 499732--500065 Score: 596
Period size: 111 Copynumber: 3.0 Consensus size: 111
499722 CTCTTCGTTT
* *
499732 TAGTTACTGTGAAGCTTCATAAAAATTAAAATTTCTAACTTCCGTCTCATGAAAAAAAATTCTCT
1 TAGTTACTGTGGAGCTTCATAAAAATTAAAATTTCTAGCTTCCGTCTCATGAAAAAAAATTCTCT
*
499797 CCTTATTTGCAGTTTAACCCGACTTGACTCCCAAATGAATCGAATC
66 CCTTATTTGAAGTTTAACCCGACTTGACTCCCAAATGAATCGAATC
* *
499843 TAGTTACTGTGGAGCTTCATAAAAATTAAAATTTCTAGCTTCTGTCTCATGAAAAAAAATTATCT
1 TAGTTACTGTGGAGCTTCATAAAAATTAAAATTTCTAGCTTCCGTCTCATGAAAAAAAATTCTCT
* *
499908 CCTTATTTAAAGTTTAACCCGACTTGACTCCCAAATGAATCGAATG
66 CCTTATTTGAAGTTTAACCCGACTTGACTCCCAAATGAATCGAATC
499954 TAGTTACTGTGGAGCTTCATAAAAATTAAAATTTCTAGCTTCCGTCTCATGAAAAAAAATTCTCT
1 TAGTTACTGTGGAGCTTCATAAAAATTAAAATTTCTAGCTTCCGTCTCATGAAAAAAAATTCTCT
*
500019 CTTTATTTGAAGTTTAACCCGACTTGACTCCCAAATGAATCGAATC
66 CCTTATTTGAAGTTTAACCCGACTTGACTCCCAAATGAATCGAATC
500065 T
1 T
500066 GAATGCACCT
Statistics
Matches: 211, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 211 1.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (111 bp):
TAGTTACTGTGGAGCTTCATAAAAATTAAAATTTCTAGCTTCCGTCTCATGAAAAAAAATTCTCT
CCTTATTTGAAGTTTAACCCGACTTGACTCCCAAATGAATCGAATC
Found at i:517183 original size:14 final size:14
Alignment explanation
Indices: 517164--517191 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
517154 TATTATATAG
517164 TATATAGATATAAA
1 TATATAGATATAAA
517178 TATATAGATATAAA
1 TATATAGATATAAA
517192 ATAAATAAAA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
TATATAGATATAAA
Found at i:518457 original size:15 final size:16
Alignment explanation
Indices: 518431--518460 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
518421 TAGTGTTTAG
518431 GTGGGTTATTGGGTTT
1 GTGGGTTATTGGGTTT
518447 GTGGG-TATTGGGTT
1 GTGGGTTATTGGGTT
518461 CTTTTGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.00, G:0.47, T:0.47
Consensus pattern (16 bp):
GTGGGTTATTGGGTTT
Found at i:519131 original size:87 final size:87
Alignment explanation
Indices: 519015--519176 Score: 220
Period size: 87 Copynumber: 1.9 Consensus size: 87
519005 AGACTTGATG
* * * *
519015 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAACT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTC-TGACTTCAATCCGCTCCACTGTAACT
519079 TCAGGGAGATAGGATAGTGTCTT
65 TCAGGGAGATAGGATAGTGTCTT
* * * *
519102 CGATCTGCTCCGCTGTAATCTCA-AGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACT
1 CGATCTACTCCGCTGTAACCTCAGA-GAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACT
519166 TCAGGGAGATA
65 TCAGGGAGATA
519177 AGATCCAAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
86 1 0.02
87 63 0.97
88 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (87 bp):
CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACTT
CAGGGAGATAGGATAGTGTCTT
Found at i:519174 original size:44 final size:44
Alignment explanation
Indices: 519060--519181 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 44
519050 CCTTTATTTT
* * * *
519060 AATCCGCTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTC
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTGGCTTC
* * * *
519103 GATCTGCTCCGCTGTAA-TCTCAAGGAGATAAGATCTCTGGCTTC
1 AATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTGGCTTC
519147 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATC
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATC
519182 CAAATTCTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
42 1 0.02
43 27 0.42
44 36 0.55
45 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (44 bp):
AATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTGGCTTC
Found at i:531697 original size:20 final size:20
Alignment explanation
Indices: 531660--531720 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
531650 TATGCACGTG
* **
531660 TATTATATTGTAGGTATAAA
1 TATTATATAGTATATATAAA
*
531680 TATTATATAGTATATATATA
1 TATTATATAGTATATATAAA
*
531700 TAAATATATAG-ATAT-TAAA
1 T-ATTATATAGTATATATAAA
531719 TA
1 TA
531721 AATAAAAAGC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 1 0.03
19 4 0.12
20 21 0.62
21 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (20 bp):
TATTATATAGTATATATAAA
Found at i:531698 original size:16 final size:16
Alignment explanation
Indices: 531673--531720 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
531663 TATATTGTAG
*
531673 GTATAAATATTATATA
1 GTATAAATATTAAATA
*
531689 GTATATATATATAAATA
1 GTATAAATAT-TAAATA
*
531706 -TATAGATATTAAATA
1 GTATAAATATTAAATA
531721 AATAAAAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.21
16 17 0.61
17 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
GTATAAATATTAAATA
Found at i:531721 original size:19 final size:21
Alignment explanation
Indices: 531674--531724 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
531664 ATATTGTAGG
*
531674 TATAAAT-ATTATATAGTATA
1 TATAAATAAATATATAGTATA
*
531694 TATATATAAATATATAG-ATA
1 TATAAATAAATATATAGTATA
531714 T-TAAATAAATA
1 TATAAATAAATA
531725 AAAAGCAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.33
20 10 0.37
21 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
TATAAATAAATATATAGTATA
Found at i:532974 original size:15 final size:16
Alignment explanation
Indices: 532948--532977 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
532938 TAGTGTTTAG
532948 GTGGGTTATTGGGTTT
1 GTGGGTTATTGGGTTT
532964 GTGGG-TATTGGGTT
1 GTGGGTTATTGGGTT
532978 CTTTTGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.00, G:0.47, T:0.47
Consensus pattern (16 bp):
GTGGGTTATTGGGTTT
Found at i:546336 original size:17 final size:17
Alignment explanation
Indices: 546305--546338 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
546295 CATGGTAAAT
* *
546305 AATAAAAAGTTAACAAA
1 AATAAAAAATAAACAAA
546322 AATAAAAAATAAACAAA
1 AATAAAAAATAAACAAA
546339 CAAGAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (17 bp):
AATAAAAAATAAACAAA
Found at i:546644 original size:14 final size:14
Alignment explanation
Indices: 546625--546652 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
546615 TATTATATAG
546625 TATATAGATATAAA
1 TATATAGATATAAA
546639 TATATAGATATAAA
1 TATATAGATATAAA
546653 ATAAATAAAA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
TATATAGATATAAA
Found at i:547921 original size:15 final size:16
Alignment explanation
Indices: 547895--547924 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
547885 TAGTGTTTAG
547895 GTGGGTTATTGGGTTT
1 GTGGGTTATTGGGTTT
547911 GTGGG-TATTGGGTT
1 GTGGGTTATTGGGTT
547925 CTTTTGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.00, G:0.47, T:0.47
Consensus pattern (16 bp):
GTGGGTTATTGGGTTT
Found at i:549693 original size:14 final size:15
Alignment explanation
Indices: 549668--549711 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
549658 ATTATTTTAT
*
549668 AATTTTTTAAAATTA
1 AATTTATTAAAATTA
*
549683 AA-TTATTAAAATAA
1 AATTTATTAAAATTA
549697 AATTTATTAATAATT
1 AATTTATTAA-AATT
549712 TAATAGTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 12 0.50
15 9 0.38
16 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTATTAAAATTA
Found at i:556604 original size:18 final size:17
Alignment explanation
Indices: 556565--556614 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
556555 TCAAAAAATA
556565 TATTTTTATACTAA-ATT
1 TATTTTTATAC-AATATT
*
556582 TATTTTTATGCAATATT
1 TATTTTTATACAATATT
556599 TGATTTTTATACAATA
1 T-ATTTTTATACAATA
556615 AAATATCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 2 0.07
17 14 0.48
18 13 0.45
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (17 bp):
TATTTTTATACAATATT
Found at i:559225 original size:31 final size:32
Alignment explanation
Indices: 559179--559238 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
559169 TTTATATTTA
*
559179 TATTTATAG-TGTTTTTAAATTTTAAAATGTG
1 TATTTAGAGTTGTTTTTAAATTTTAAAATGTG
* *
559210 TATTTAGAGTTTTTTTTTAATTTTAAAAT
1 TATTTAGAGTTGTTTTTAAATTTTAAAAT
559239 TTCATATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 8 0.32
32 17 0.68
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (32 bp):
TATTTAGAGTTGTTTTTAAATTTTAAAATGTG
Found at i:566828 original size:18 final size:16
Alignment explanation
Indices: 566789--566838 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
566779 GTAATGAGCG
*
566789 TAAAAATATAATTAATA
1 TAAAAATAT-ATTAAAA
566806 TAAAAATATATTAAAA
1 TAAAAATATATTAAAA
*
566822 TGAAAAACTCTATTAAA
1 T-AAAAA-TATATTAAA
566839 CTTGTGAGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.24
17 14 0.48
18 8 0.28
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (16 bp):
TAAAAATATATTAAAA
Found at i:584789 original size:23 final size:24
Alignment explanation
Indices: 584745--584789 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
584735 AAATACAATG
** *
584745 AAAAATGTTAATTTATTTTTGAAA
1 AAAAATGTTAATCCATTGTTGAAA
584769 AAAAATGTTAATCCA-TGTTGA
1 AAAAATGTTAATCCATTGTTGA
584790 GTGTAATGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.40
Consensus pattern (24 bp):
AAAAATGTTAATCCATTGTTGAAA
Found at i:589860 original size:27 final size:26
Alignment explanation
Indices: 589830--589881 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
589820 CACATCCGTC
589830 ATTTTAA-AAAAATTTATATTATATATT
1 ATTTTAATAAAAA--TATATTATATATT
589857 ATTTTAATTAAAAATATATTATATA
1 ATTTTAA-TAAAAATATATTATATA
589882 ACATATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
27 18 0.78
29 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTTAATAAAAATATATTATATATT
Found at i:590333 original size:16 final size:16
Alignment explanation
Indices: 590299--590333 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
590289 TAGCAATGAC
590299 ATTTAAAATTTTTATA
1 ATTTAAAATTTTTATA
590315 ATTTATAAATTTTTA-A
1 ATTTA-AAATTTTTATA
590331 ATT
1 ATT
590334 AGTAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTAAAATTTTTATA
Found at i:590384 original size:8 final size:9
Alignment explanation
Indices: 590357--590386 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
590347 TTACACTTTT
*
590357 AATTTTAAA
1 AATTATAAA
590366 AATTATAAA
1 AATTATAAA
590375 AATTATAAA
1 AATTATAAA
590384 AAT
1 AAT
590387 ATTTAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AATTATAAA
Found at i:596303 original size:31 final size:31
Alignment explanation
Indices: 596235--596305 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
596225 TTTACCCTTT
* *
596235 ATTTT-AATTTGGTACTTGTGTTTTGTTTTA
1 ATTTTCAATTTGGTACATGAGTTTTGTTTTA
* * *
596265 ATATTCAATTTGGTACATGAGTTTTTTTTTC
1 ATTTTCAATTTGGTACATGAGTTTTGTTTTA
*
596296 TTTTTCAATT
1 ATTTTCAATT
596306 AAGTGTTTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.61
Consensus pattern (31 bp):
ATTTTCAATTTGGTACATGAGTTTTGTTTTA
Found at i:597810 original size:14 final size:14
Alignment explanation
Indices: 597791--597823 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
597781 TTATAGGTGT
597791 AAAGGTGAAGTTAA
1 AAAGGTGAAGTTAA
597805 AAAGGTGAAGTTAA
1 AAAGGTGAAGTTAA
597819 AAAGG
1 AAAGG
597824 GGAAATTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.30, T:0.18
Consensus pattern (14 bp):
AAAGGTGAAGTTAA
Found at i:606267 original size:33 final size:33
Alignment explanation
Indices: 606179--606331 Score: 165
Period size: 33 Copynumber: 4.8 Consensus size: 33
606169 TTGTTGTGAT
* * *
606179 GGTGGTGGGTACTGCGGAGGCTGCTGTAGAGCA
1 GGTGGTGGGTACTGCGGTGGCTGTTGTTGAGCA
* *
606212 GGTAGTGGGTACTGCGGAGGCTGTTGTTGAGCA
1 GGTGGTGGGTACTGCGGTGGCTGTTGTTGAGCA
* * *
606245 GGTGGTGGGTATTGCCGTGGCTGTTGCTGAGCA
1 GGTGGTGGGTACTGCGGTGGCTGTTGTTGAGCA
*
606278 GGTGGT-GG---T-C-GTGGCTGTTGCTGAGCA
1 GGTGGTGGGTACTGCGGTGGCTGTTGTTGAGCA
* *
606305 GGTGGTGGGTATTGCGGTGGTTGTTGT
1 GGTGGTGGGTACTGCGGTGGCTGTTGT
606332 GGCGGGAATT
Statistics
Matches: 104, Mismatches: 10, Indels: 12
0.83 0.08 0.10
Matches are distributed among these distances:
27 23 0.22
28 3 0.03
29 1 0.01
31 1 0.01
32 3 0.03
33 73 0.70
ACGTcount: A:0.10, C:0.12, G:0.48, T:0.29
Consensus pattern (33 bp):
GGTGGTGGGTACTGCGGTGGCTGTTGTTGAGCA
Found at i:606296 original size:27 final size:27
Alignment explanation
Indices: 606260--606312 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
606250 TGGGTATTGC
606260 CGTGGCTGTTGCTGAGCAGGTGGTGGT
1 CGTGGCTGTTGCTGAGCAGGTGGTGGT
606287 CGTGGCTGTTGCTGAGCAGGTGGTGG
1 CGTGGCTGTTGCTGAGCAGGTGGTGG
606313 GTATTGCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.08, C:0.15, G:0.49, T:0.28
Consensus pattern (27 bp):
CGTGGCTGTTGCTGAGCAGGTGGTGGT
Found at i:606333 original size:24 final size:24
Alignment explanation
Indices: 606306--606354 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
606296 TGCTGAGCAG
* * *
606306 GTGGTGGGTATTGCGGTGGTTGTT
1 GTGGCGGGAATTGAGGTGGTTGTT
*
606330 GTGGCGGGAATTGAGGTTGTTGTT
1 GTGGCGGGAATTGAGGTGGTTGTT
606354 G
1 G
606355 GCCTTGTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.08, C:0.04, G:0.49, T:0.39
Consensus pattern (24 bp):
GTGGCGGGAATTGAGGTGGTTGTT
Found at i:617938 original size:13 final size:13
Alignment explanation
Indices: 617920--617944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
617910 CGAAAATCGA
617920 AAAAAGGAAGAGC
1 AAAAAGGAAGAGC
617933 AAAAAGGAAGAG
1 AAAAAGGAAGAG
617945 TAGAATTATG
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:0.64, C:0.04, G:0.32, T:0.00
Consensus pattern (13 bp):
AAAAAGGAAGAGC
Found at i:622375 original size:55 final size:55
Alignment explanation
Indices: 622291--622403 Score: 226
Period size: 55 Copynumber: 2.1 Consensus size: 55
622281 CTCACGGAAG
622291 TAAGTAAATATATGATTTCACTATCAATATGTTTGATTTATTGTTTCTCAGACAT
1 TAAGTAAATATATGATTTCACTATCAATATGTTTGATTTATTGTTTCTCAGACAT
622346 TAAGTAAATATATGATTTCACTATCAATATGTTTGATTTATTGTTTCTCAGACAT
1 TAAGTAAATATATGATTTCACTATCAATATGTTTGATTTATTGTTTCTCAGACAT
622401 TAA
1 TAA
622404 AACCGGAAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (55 bp):
TAAGTAAATATATGATTTCACTATCAATATGTTTGATTTATTGTTTCTCAGACAT
Found at i:631943 original size:35 final size:35
Alignment explanation
Indices: 631904--631977 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
631894 CGTAAATAAC
*
631904 CATGCATTTCCATGTGTTTTAGCTTTTGTATTTGG
1 CATGCATTTCCATGTGTTTTAGCTTTTGGATTTGG
631939 CATGCATTTCCATGTGTTTTAGCTTTTGGATTTGG
1 CATGCATTTCCATGTGTTTTAGCTTTTGGATTTGG
631974 CATG
1 CATG
631978 TATCTTGTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.49
Consensus pattern (35 bp):
CATGCATTTCCATGTGTTTTAGCTTTTGGATTTGG
Found at i:635138 original size:4 final size:4
Alignment explanation
Indices: 635129--635183 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
635119 TATATACATA
* * * * * *
635129 TATG TATG TATG TATC TATG CATG TATA TATA TAGG TATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
635177 TATG TAT
1 TATG TAT
635184 ATGTGCTGAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:635155 original size:20 final size:20
Alignment explanation
Indices: 635130--635183 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
635120 ATATACATAT
635130 ATGTATGTATGTATCTATGC
1 ATGTATGTATGTATCTATGC
* * **
635150 ATGTATATATATAGGTATGC
1 ATGTATGTATGTATCTATGC
635170 ATGTATGTATGTAT
1 ATGTATGTATGTAT
635184 ATGTGCTGAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (20 bp):
ATGTATGTATGTATCTATGC
Found at i:635167 original size:28 final size:28
Alignment explanation
Indices: 635126--635185 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
635116 ACATATATAC
* * *
635126 ATATATGTATGTATGTATCTATGCATGT
1 ATATATATAGGTATGCATCTATGCATGT
* *
635154 ATATATATAGGTATGCATGTATGTATGT
1 ATATATATAGGTATGCATCTATGCATGT
635182 ATAT
1 ATAT
635186 GTGCTGATAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (28 bp):
ATATATATAGGTATGCATCTATGCATGT
Found at i:635168 original size:32 final size:32
Alignment explanation
Indices: 635112--635185 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
635102 GTGACTGAAA
* * *
635112 CTATACATATATACATATATGTATGTATGTAT
1 CTATGCATATATACATATAGGTATGCATGTAT
* *
635144 CTATGCATGTATATATATAGGTATGCATGTAT
1 CTATGCATATATACATATAGGTATGCATGTAT
* *
635176 GTATGTATAT
1 CTATGCATAT
635186 GTGCTGATAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (32 bp):
CTATGCATATATACATATAGGTATGCATGTAT
Found at i:637064 original size:31 final size:30
Alignment explanation
Indices: 637006--637067 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
636996 GGATTGTACC
*
637006 TAAATTAATTTCAAATTAAATATTTAAGTT
1 TAAATTAATTTCAAATTAAATACTTAAGTT
*
637036 TAAATTTAATGTTC-AATTTAATACTTAAGTT
1 TAAA-TTAAT-TTCAAATTAAATACTTAAGTT
637067 T
1 T
637068 TTTTTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 21 0.75
32 3 0.11
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (30 bp):
TAAATTAATTTCAAATTAAATACTTAAGTT
Found at i:643119 original size:11 final size:11
Alignment explanation
Indices: 643103--643127 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
643093 TATAGATTTC
643103 ATTAATAAAAA
1 ATTAATAAAAA
643114 ATTAATAAAAA
1 ATTAATAAAAA
643125 ATT
1 ATT
643128 TCTGCACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATTAATAAAAA
Found at i:643167 original size:4 final size:4
Alignment explanation
Indices: 643158--643182 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
643148 TTCTATGAAA
643158 GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
643183 CGTGAGTGCA
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:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:651271 original size:18 final size:18
Alignment explanation
Indices: 651248--651290 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
651238 TCAATTTTAA
*
651248 AAATTATAAAATATTATT
1 AAATTATAAAATATAATT
651266 AAATTATAAAATATAATT
1 AAATTATAAAATATAATT
651284 AAATTAT
1 AAATTAT
651291 TCAAATGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTATAAAATATAATT
Found at i:660173 original size:21 final size:23
Alignment explanation
Indices: 660147--660189 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
660137 CACTAAATTA
660147 TTTTTATAT-TG-AATATATAAT
1 TTTTTATATATGCAATATATAAT
660168 TTTTTATATATGCAATATATAA
1 TTTTTATATATGCAATATATAA
660190 ACATAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (23 bp):
TTTTTATATATGCAATATATAAT
Found at i:661404 original size:31 final size:32
Alignment explanation
Indices: 661363--661430 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 32
661353 TTAATATAAT
* *
661363 ATTTGGTACTTGAACCTGATA-TTTTTTCTTA
1 ATTTGATACTTAAACCTGATACTTTTTTCTTA
** *
661394 ATTTGATACTTAAATTTGATACTTTTTTTTTA
1 ATTTGATACTTAAACCTGATACTTTTTTCTTA
661426 ATTTG
1 ATTTG
661431 GTACCTAAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 17 0.55
32 14 0.45
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.56
Consensus pattern (32 bp):
ATTTGATACTTAAACCTGATACTTTTTTCTTA
Found at i:661411 original size:13 final size:13
Alignment explanation
Indices: 661393--661417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
661383 ATTTTTTCTT
661393 AATTTGATACTTA
1 AATTTGATACTTA
661406 AATTTGATACTT
1 AATTTGATACTT
661418 TTTTTTTAAT
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:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
AATTTGATACTTA
Found at i:661944 original size:31 final size:30
Alignment explanation
Indices: 661870--661979 Score: 114
Period size: 31 Copynumber: 3.6 Consensus size: 30
661860 GACCCTCTAA
* * *
661870 AAATTTAAGTATCAACTTAAAAAAAATGTC
1 AAATTTAAGTACCAAATTAAAAAAAATATC
* *
661900 AAGTTT-AGATACCAAATTAAGAGAAAATATC
1 AAATTTAAG-TACCAAATTAA-AAAAAATATC
*
661931 AAATTTAAGTACCAAATTAAAAAATATATATT
1 AAATTTAAGTACCAAATTAAAAAA-A-ATATC
*
661963 AAATTTAAATACCAAAT
1 AAATTTAAGTACCAAAT
661980 ATTATATTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
29 2 0.03
30 17 0.26
31 25 0.38
32 22 0.33
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (30 bp):
AAATTTAAGTACCAAATTAAAAAAAATATC
Found at i:671594 original size:16 final size:17
Alignment explanation
Indices: 671573--671606 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
671563 AATTAGAGAA
671573 TTCTATTTAA-TTCTAT
1 TTCTATTTAATTTCTAT
671589 TTCTATTTAATTTCTAT
1 TTCTATTTAATTTCTAT
671606 T
1 T
671607 AAATCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTATTTAATTTCTAT
Found at i:675685 original size:11 final size:11
Alignment explanation
Indices: 675658--675724 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
675648 AAACATTATA
*
675658 ATTAATTTAAAT
1 ATTAA-TTAATT
675670 A-TAATTAATT
1 ATTAATTAATT
675680 ATTAATTAATT
1 ATTAATTAATT
*
675691 A-TAA-CAATT
1 ATTAATTAATT
*
675700 ATAAATCTATATT
1 ATTAAT-TA-ATT
*
675713 ATTATTTAATT
1 ATTAATTAATT
675724 A
1 A
675725 GTGTCATAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
9 5 0.11
10 11 0.25
11 17 0.39
12 4 0.09
13 7 0.16
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTAATTAATT
Found at i:675692 original size:36 final size:37
Alignment explanation
Indices: 675652--675724 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
675642 ATAAAAAAAC
*
675652 ATTATAATTAATT-TAAATATA-ATTAATTA-TTAATTA
1 ATTATAA-CAATTATAAATATATATT-ATTATTTAATTA
*
675688 ATTATAACAATTATAAATCTATATTATTATTTAATTA
1 ATTATAACAATTATAAATATATATTATTATTTAATTA
675725 GTGTCATAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 4 0.12
36 18 0.56
37 10 0.31
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTATAACAATTATAAATATATATTATTATTTAATTA
Found at i:681716 original size:7 final size:7
Alignment explanation
Indices: 681704--681761 Score: 62
Period size: 7 Copynumber: 8.3 Consensus size: 7
681694 CTAAAACTAC
681704 CACTTAT
1 CACTTAT
681711 CACTTAT
1 CACTTAT
681718 CACTTAT
1 CACTTAT
*
681725 CACTTGT
1 CACTTAT
* *
681732 CGCTTGT
1 CACTTAT
* *
681739 CGCTTGT
1 CACTTAT
681746 CACTTAT
1 CACTTAT
*
681753 CACTGAT
1 CACTTAT
681760 CA
1 CA
681762 GATAAGTGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.21, C:0.29, G:0.10, T:0.40
Consensus pattern (7 bp):
CACTTAT
Found at i:692395 original size:52 final size:53
Alignment explanation
Indices: 692322--692466 Score: 204
Period size: 52 Copynumber: 2.7 Consensus size: 53
692312 CTTACACGGT
* *
692322 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
692377 -CACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
**
692429 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTA
692467 AACAGGCACA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
51 1 0.01
52 41 0.49
53 36 0.43
54 5 0.06
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:694995 original size:7 final size:7
Alignment explanation
Indices: 694983--695040 Score: 71
Period size: 7 Copynumber: 8.3 Consensus size: 7
694973 CTAAAACTAC
694983 CACTTAT
1 CACTTAT
694990 CACTTAT
1 CACTTAT
694997 CACTTAT
1 CACTTAT
*
695004 CACTTGT
1 CACTTAT
*
695011 CGCTTAT
1 CACTTAT
* *
695018 CGCTTGT
1 CACTTAT
695025 CACTTAT
1 CACTTAT
*
695032 CACTGAT
1 CACTTAT
695039 CA
1 CA
695041 GATAAGTGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.22, C:0.29, G:0.09, T:0.40
Consensus pattern (7 bp):
CACTTAT
Found at i:719136 original size:7 final size:7
Alignment explanation
Indices: 719124--719149 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
719114 ACAGTTGTGG
719124 ACCTTCC
1 ACCTTCC
719131 ACCTTCC
1 ACCTTCC
719138 ACCTTCC
1 ACCTTCC
719145 ACCTT
1 ACCTT
719150 TTCTTTCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
ACCTTCC
Found at i:722450 original size:31 final size:30
Alignment explanation
Indices: 722415--722472 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
722405 TTATAAGTTG
722415 TTATATTTTTTAAAAATTAAAAATTTAATTT
1 TTATATTTTTT-AAAATTAAAAATTTAATTT
* *
722446 TTATATTTTTTAAATTTTAAAATTTAA
1 TTATATTTTTTAAAATTAAAAATTTAA
722473 GTTGAATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TTATATTTTTTAAAATTAAAAATTTAATTT
Found at i:722598 original size:29 final size:28
Alignment explanation
Indices: 722565--722632 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
722555 ATATTTTTTT
722565 AATTTTAAAATATCA-CACGAATAAACTTA
1 AATTTTAAAATATCACCAC-AA-AAACTTA
* *
722594 AA-TTTAACAATATTATCCACCAAAACTTA
1 AATTTTAA-AATATCA-CCACAAAAACTTA
722623 AATTTTAAAA
1 AATTTTAAAA
722633 CTAAAAGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
28 5 0.15
29 19 0.58
30 6 0.18
31 3 0.09
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.32
Consensus pattern (28 bp):
AATTTTAAAATATCACCACAAAAACTTA
Found at i:726236 original size:28 final size:28
Alignment explanation
Indices: 726198--726253 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
726188 AACCTAAAGA
*
726198 AAAACAGGATTAATTTCCAGAAGCACAG
1 AAAACAGGATTAATTTCCAAAAGCACAG
726226 AAAACAGGATTAATTTCCAAAAGCACAG
1 AAAACAGGATTAATTTCCAAAAGCACAG
726254 CCTTTACTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.18
Consensus pattern (28 bp):
AAAACAGGATTAATTTCCAAAAGCACAG
Found at i:731696 original size:31 final size:32
Alignment explanation
Indices: 731651--731713 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
731641 TTTCTTAATT
**
731651 AATTTGAAAAAAATACGAA-TTAGACATAAAAA
1 AATTTGAAAAAAATAAAAAGTTAGA-ATAAAAA
*
731683 AATTT-AAAGAAATAAAAAGTTAGAATAAAAA
1 AATTTGAAAAAAATAAAAAGTTAGAATAAAAA
731714 TAAGATGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.65, C:0.03, G:0.10, T:0.22
Consensus pattern (32 bp):
AATTTGAAAAAAATAAAAAGTTAGAATAAAAA
Found at i:732813 original size:21 final size:22
Alignment explanation
Indices: 732788--732835 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
732778 TTTAATTAGG
732788 AAATATATT-TTTAA-ATTATAA
1 AAATATATTATTTAATATT-TAA
732809 AAATATATTATTTAATATTTAA
1 AAATATATTATTTAATATTTAA
732831 AAATA
1 AAATA
732836 ATAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 9 0.36
22 13 0.52
23 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATATATTATTTAATATTTAA
Found at i:738389 original size:26 final size:24
Alignment explanation
Indices: 738359--738406 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
738349 AATAAAAAAA
*
738359 TTAAAAATATAATAAATCAAATATAT
1 TTAAAAACATAA-AAA-CAAATATAT
738385 TTAAAAACATAAAAACAAATAT
1 TTAAAAACATAAAAACAAATAT
738407 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 3 0.14
26 11 0.52
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (24 bp):
TTAAAAACATAAAAACAAATATAT
Found at i:739014 original size:21 final size:22
Alignment explanation
Indices: 738990--739037 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
738980 AAAAATATTT
* *
738990 AAATTTTATATAAACT-TAAAA
1 AAATTTCAAATAAACTATAAAA
*
739011 AAA-TTCAAATAAATTATAAAA
1 AAATTTCAAATAAACTATAAAA
739032 AAATTT
1 AAATTT
739038 ATGATAGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 9 0.41
21 11 0.50
22 2 0.09
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATTTCAAATAAACTATAAAA
Found at i:739718 original size:21 final size:20
Alignment explanation
Indices: 739694--739733 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
739684 TTTAACCAAA
*
739694 AATTATAATTAATTAAAATTT
1 AATTAT-ATTAAATAAAATTT
739715 AATTATATTAAATAAAATT
1 AATTATATTAAATAAAATT
739734 ATTAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTATATTAAATAAAATTT
Found at i:739719 original size:15 final size:17
Alignment explanation
Indices: 739692--739726 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
739682 TATTTAACCA
739692 AAAATTATAATTA-ATT
1 AAAATTATAATTATATT
739708 AAAATT-TAATTATATT
1 AAAATTATAATTATATT
739724 AAA
1 AAA
739727 TAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTATAATTATATT
Found at i:748225 original size:2 final size:2
Alignment explanation
Indices: 748218--748242 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
748208 TAATACCATG
748218 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 A
748243 AAGAGTAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:752752 original size:20 final size:20
Alignment explanation
Indices: 752727--752776 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
752717 TGGCTTAAAA
752727 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
752747 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
752764 GTGGTAGTGGATT
1 TTGGTAGTGGATT
752777 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:757391 original size:20 final size:20
Alignment explanation
Indices: 757366--757415 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
757356 TGGCTTAAAA
757366 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
757386 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
757403 GTGGTAGTGGATT
1 TTGGTAGTGGATT
757416 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:764026 original size:21 final size:22
Alignment explanation
Indices: 763994--764044 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
763984 TTTTAAACGA
763994 CTTAAA-TTTTACTCAAA-C-T
1 CTTAAATTTTTACTCAAATCTT
764013 CTTAATATTTTTACTCAAATCTT
1 CTTAA-ATTTTTACTCAAATCTT
764036 CTTAAATTT
1 CTTAAATTT
764045 CTAAAGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.18
20 1 0.04
21 11 0.39
22 5 0.18
23 6 0.21
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (22 bp):
CTTAAATTTTTACTCAAATCTT
Found at i:766798 original size:16 final size:16
Alignment explanation
Indices: 766764--766810 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
766754 TCAACTGTCC
*
766764 AAATTTAAAAAAA-AA
1 AAATATAAAAAAATAA
* *
766779 AAATCTAAAAAAATAT
1 AAATATAAAAAAATAA
*
766795 AAATATAAACAAATAA
1 AAATATAAAAAAATAA
766811 CAATTTTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATATAAAAAAATAA
Found at i:776552 original size:33 final size:32
Alignment explanation
Indices: 776510--776576 Score: 116
Period size: 33 Copynumber: 2.1 Consensus size: 32
776500 AGAAATTTCT
776510 CAAAAAGACAACCACAAACCCAAACATAAAAA
1 CAAAAAGACAACCACAAACCCAAACATAAAAA
*
776542 CAAAGAAGACAACCACAAACCCGAACATAAAAA
1 CAAA-AAGACAACCACAAACCCAAACATAAAAA
776575 CA
1 CA
776577 CGAAGGATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.63, C:0.28, G:0.06, T:0.03
Consensus pattern (32 bp):
CAAAAAGACAACCACAAACCCAAACATAAAAA
Found at i:795981 original size:21 final size:21
Alignment explanation
Indices: 795955--795995 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
795945 AGACGAGCAA
* *
795955 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
795976 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
795996 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:830386 original size:43 final size:43
Alignment explanation
Indices: 830338--830424 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
830328 GTTCCTTGCC
830338 TTAGAACCAAAGATTCAAGCTTGTTAAAATGCTTGCAACCTGG
1 TTAGAACCAAAGATTCAAGCTTGTTAAAATGCTTGCAACCTGG
830381 TTAGAACCAAAGATTCAAGCTTGTTAAAATGCTTGCAACCTGG
1 TTAGAACCAAAGATTCAAGCTTGTTAAAATGCTTGCAACCTGG
830424 T
1 T
830425 CTGAATTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (43 bp):
TTAGAACCAAAGATTCAAGCTTGTTAAAATGCTTGCAACCTGG
Found at i:834513 original size:48 final size:48
Alignment explanation
Indices: 834359--834506 Score: 224
Period size: 48 Copynumber: 3.1 Consensus size: 48
834349 ATATATACAC
* **
834359 ATCTCATACATATTTCACATTAGCCATTTGGCTTTACCACATATGCAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
** * *
834407 GGCTCATACATATTTCACATTAGCCTTTCGACTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
*
834455 ATCTCATACATATTTTACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
834503 ATCT
1 ATCT
834507 TGTACATCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
Found at i:838319 original size:42 final size:42
Alignment explanation
Indices: 838256--838382 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
838246 CTTCCTTTTC
** * *
838256 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
838299 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
838340 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
838381 TC
1 TC
838383 TCACTGATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.13
42 64 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:838444 original size:47 final size:46
Alignment explanation
Indices: 838341--838464 Score: 167
Period size: 47 Copynumber: 2.7 Consensus size: 46
838331 ATTCATATAT
* * * * *
838341 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
838387 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
838434 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
838465 GAAATCACTT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 27 0.40
47 41 0.60
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:838524 original size:31 final size:31
Alignment explanation
Indices: 838489--838668 Score: 288
Period size: 31 Copynumber: 5.8 Consensus size: 31
838479 CTTGCCACTT
*
838489 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
838520 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
838551 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
838582 GTAGCCGGAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
838613 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
838644 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
838669 TGTCATTTGT
Statistics
Matches: 140, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 140 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:838750 original size:50 final size:50
Alignment explanation
Indices: 838644--838820 Score: 257
Period size: 50 Copynumber: 3.5 Consensus size: 50
838634 CACTGATCAG
* * * * *
838644 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTATCCTTGATCAGATAAGT
838695 GTAGCCGAAGCTATCACTTATCACTTTCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCA-TTTATCCTTGATCAGATAAGT
* * *
838745 GTAGCCGAAGCTATTATTTATCACTTTAATTTATCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTATCCTTGATCAGATAAGT
838795 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
838821 GTTGCCATTG
Statistics
Matches: 115, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
49 3 0.03
50 86 0.75
51 26 0.23
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTATCCTTGATCAGATAAGT
Found at i:844021 original size:40 final size:39
Alignment explanation
Indices: 843971--844095 Score: 115
Period size: 39 Copynumber: 3.2 Consensus size: 39
843961 CCCGAGTCCA
* * *
843971 ATTTCTAGCACAAAGCCTACGGGACTTTAAGCCCGGATAT
1 ATTTCCAGCACAAAGCCTAC-GGACCTCAAGCCCGGATAT
** * *
844011 ATTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGGATAT
1 ATTTCCAGCACAAAGCCTACGGACCTCAAGCCCGGATAT
* ** * * *
844050 GTTTCCAGCACGTAGCCTGCGGACCTCAAGTCTGGATAT
1 ATTTCCAGCACAAAGCCTACGGACCTCAAGCCCGGATAT
*
844089 GTTTCCA
1 ATTTCCA
844096 AGTATCATGC
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
39 60 0.79
40 16 0.21
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (39 bp):
ATTTCCAGCACAAAGCCTACGGACCTCAAGCCCGGATAT
Found at i:844055 original size:39 final size:39
Alignment explanation
Indices: 844003--844095 Score: 168
Period size: 39 Copynumber: 2.4 Consensus size: 39
843993 GACTTTAAGC
*
844003 CCGGATATATTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATGTTTCCAGCACGTAGCCTGCGGACCTCAAGT
844042 CCGGATATGTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATGTTTCCAGCACGTAGCCTGCGGACCTCAAGT
*
844081 CTGGATATGTTTCCA
1 CCGGATATGTTTCCA
844096 AGTATCATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.26
Consensus pattern (39 bp):
CCGGATATGTTTCCAGCACGTAGCCTGCGGACCTCAAGT
Found at i:851920 original size:39 final size:39
Alignment explanation
Indices: 851866--851996 Score: 217
Period size: 39 Copynumber: 3.4 Consensus size: 39
851856 ACTTTAAGCT
* *
851866 CGGATATATTTCCAGCACATAGCCTGCGGACCTCAAGTC
1 CGGATATGTTTCCAGCACGTAGCCTGCGGACCTCAAGTC
*
851905 CTGATATGTTTCCAGCACGTAGCCTGCGGACCTCAAGTC
1 CGGATATGTTTCCAGCACGTAGCCTGCGGACCTCAAGTC
* *
851944 CGGATATGTTTCCAGCATGTAACCTGCGGACCTCAAGTC
1 CGGATATGTTTCCAGCACGTAGCCTGCGGACCTCAAGTC
851983 CGGATATGTTTCCA
1 CGGATATGTTTCCA
851997 AGTATCATGC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 86 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (39 bp):
CGGATATGTTTCCAGCACGTAGCCTGCGGACCTCAAGTC
Found at i:862017 original size:34 final size:35
Alignment explanation
Indices: 861962--862028 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
861952 CAAACACCAG
*
861962 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
861997 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
862029 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:870485 original size:28 final size:26
Alignment explanation
Indices: 870430--870489 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
870420 TGAATATTTT
*
870430 TTATAATATAAAAATTAAATAAATAA
1 TTATAATATAAAAATTAAATAAAAAA
*
870456 TTATAATATATAACATTGATAA-AAAAAA
1 TTATAATATA-AAAATT-A-AATAAAAAA
870484 TTATAA
1 TTATAA
870490 ATTACTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 10 0.34
27 5 0.17
28 12 0.41
29 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (26 bp):
TTATAATATAAAAATTAAATAAAAAA
Found at i:878271 original size:15 final size:15
Alignment explanation
Indices: 878248--878278 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
878238 GGGTAGTAGT
878248 CTAGAAGCGGCGGCA
1 CTAGAAGCGGCGGCA
*
878263 CTAGCAGCGGCGGCA
1 CTAGAAGCGGCGGCA
878278 C
1 C
878279 GAATATCAGT
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:0.23, C:0.32, G:0.39, T:0.06
Consensus pattern (15 bp):
CTAGAAGCGGCGGCA
Found at i:883061 original size:29 final size:28
Alignment explanation
Indices: 883029--883088 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
883019 AGAATTGATT
*
883029 CAAACCAAAATTGAATGTATAAAATTACA
1 CAAACCAAAATT-AATGTATAAAAATACA
* * *
883058 CAAAATCAAAGTTCATGTATAAAAATACA
1 C-AAACCAAAATTAATGTATAAAAATACA
883087 CA
1 CA
883089 TTAAACTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.04
29 16 0.62
30 9 0.35
ACGTcount: A:0.55, C:0.15, G:0.07, T:0.23
Consensus pattern (28 bp):
CAAACCAAAATTAATGTATAAAAATACA
Found at i:883110 original size:31 final size:29
Alignment explanation
Indices: 883030--883110 Score: 74
Period size: 31 Copynumber: 2.7 Consensus size: 29
883020 GAATTGATTC
* * *
883030 AAACCAAAATTGAATGTATAAAATTACACA
1 AAACTAAAATTCAA-GTATAAAAATACACA
* *
883060 AAA-TCAAAGTTCATGTATAAAAATACACA
1 AAACT-AAAATTCAAGTATAAAAATACACA
883089 TTAAACTAAAATTCAAGTATAA
1 --AAACTAAAATTCAAGTATAA
883111 TTTTAAGATT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
29 14 0.35
30 9 0.22
31 16 0.40
32 1 0.03
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (29 bp):
AAACTAAAATTCAAGTATAAAAATACACA
Found at i:897273 original size:24 final size:27
Alignment explanation
Indices: 897230--897283 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
897220 TATATTTTCT
*
897230 TTTTTTAAGATATATCATTTATAA-TA
1 TTTTTTAAGATATATCATTTAAAATTA
*
897256 TTTTTTAATATA-AT-ATTTAAAATTA
1 TTTTTTAAGATATATCATTTAAAATTA
897281 TTT
1 TTT
897284 ATAATTCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 7 0.28
26 11 0.44
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTTTAAGATATATCATTTAAAATTA
Found at i:902528 original size:2 final size:2
Alignment explanation
Indices: 902523--902547 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
902513 ACAAAAAAAA
902523 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
902548 ACATAATCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:904916 original size:19 final size:20
Alignment explanation
Indices: 904874--904917 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
904864 TTTTTATTTG
* *
904874 TAAAAAATTTATAATATAAT
1 TAAAAAATTCATAAAATAAT
904894 TAAAAAATTCATAAAATAA-
1 TAAAAAATTCATAAAATAAT
904913 TAAAA
1 TAAAA
904918 GTACTAATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAAAATTCATAAAATAAT
Found at i:905527 original size:22 final size:22
Alignment explanation
Indices: 905501--905546 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
905491 ATGATGTTAA
* *
905501 TATTTTGATAATTT-AATTACAT
1 TATTTT-AAAATTTAAATTAAAT
905523 TATTTTAAAATTTAAATTAAAT
1 TATTTTAAAATTTAAATTAAAT
905545 TA
1 TA
905547 AAATGTGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTTTAAAATTTAAATTAAAT
Done.