Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 49 of 290
Found at i:16254879 original size:100 final size:100
Alignment explanation
Indices: 16254706--16254889 Score: 323
Period size: 100 Copynumber: 1.8 Consensus size: 100
16254696 TGTGAGGTCC
* * *
16254706 CGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAATTGGTCGCATGTGTAGTACTAAG
1 CGTGTGTAGTACTAAGTGCACGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACTAAG
16254771 TGCAGGCTACTATGCGTACTCGAAAACTGTGATCA
66 TGCAGGCTACTATGCGTACTCGAAAACTGTGATCA
* *
16254806 CGTGTGTAGTACTAAGTGCACGCTACTACGTGTACTAGATTATTGGTCGCATGTGTAGTACTAAG
1 CGTGTGTAGTACTAAGTGCACGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACTAAG
16254871 TGCAGGCTACTATGCGTAC
66 TGCAGGCTACTATGCGTAC
16254890 CAGATAGCTT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (100 bp):
CGTGTGTAGTACTAAGTGCACGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACTAAG
TGCAGGCTACTATGCGTACTCGAAAACTGTGATCA
Found at i:16260998 original size:38 final size:38
Alignment explanation
Indices: 16260955--16261115 Score: 223
Period size: 38 Copynumber: 4.2 Consensus size: 38
16260945 GTAGGCTATA
16260955 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTTG
1 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTTG
* *
16260993 CGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTTG
1 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTTG
* * *
16261031 TGCTGGTATTATATCCGGGTTAAATCCCGTAGGCCTAG
1 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTTG
** * *
16261069 TGCTGGTATTATATCTAAGCTTAAAGTCCCGCAGGTTTTG
1 TGCTGGTATTATATC-CGGGTTAAA-TCCCGCAGGCTTTG
16261109 TGCTGGT
1 TGCTGGT
16261116 TACTGGATTC
Statistics
Matches: 107, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 84 0.79
39 6 0.06
40 17 0.16
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (38 bp):
TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTTG
Found at i:16261038 original size:76 final size:78
Alignment explanation
Indices: 16260937--16261115 Score: 227
Period size: 76 Copynumber: 2.3 Consensus size: 78
16260927 ATCCGGGCTC
* * * * * *
16260937 AAAGACCCGTAGGCTATATGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTTGCGCTGGTAA
1 AAAGTCCCGCAGGCTTTGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAGCGCTGGTAA
** *
16261002 TATATC-CGGGTT
66 TATATCTAAGCTT
* * *
16261014 AAA-TCCCGCAGGCTTTGTGCTGGTATTATATCCGGGTTAAATCCCGTAGGCCTAGTGCTGGTAT
1 AAAGTCCCGCAGGCTTTGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAGCGCTGGTAA
16261078 TATATCTAAGCTT
66 TATATCTAAGCTT
*
16261091 AAAGTCCCGCAGGTTTTGTGCTGGT
1 AAAGTCCCGCAGGCTTTGTGCTGGT
16261116 TACTGGATTC
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
76 58 0.67
77 9 0.10
78 20 0.23
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (78 bp):
AAAGTCCCGCAGGCTTTGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAGCGCTGGTAA
TATATCTAAGCTT
Found at i:16269102 original size:27 final size:26
Alignment explanation
Indices: 16269072--16269131 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
16269062 TTAGTTTACC
*
16269072 AATTACAGAAATGCCCTCGACTTATAA
1 AATTACA-AAATACCCTCGACTTATAA
* * *
16269099 AATTACCAAAGTACCCTCGATTTATAG
1 AATTA-CAAAATACCCTCGACTTATAA
16269126 AATTAC
1 AATTAC
16269132 TATTTTACCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.04
27 25 0.89
28 2 0.07
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (26 bp):
AATTACAAAATACCCTCGACTTATAA
Found at i:16269140 original size:27 final size:27
Alignment explanation
Indices: 16269110--16269196 Score: 129
Period size: 27 Copynumber: 3.2 Consensus size: 27
16269100 ATTACCAAAG
*
16269110 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
16269137 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
16269164 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACTATTT
16269191 TACCCT
1 TACCCT
16269197 TGATGTGAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTATTT
Found at i:16269262 original size:27 final size:27
Alignment explanation
Indices: 16269232--16269330 Score: 128
Period size: 27 Copynumber: 3.7 Consensus size: 27
16269222 TATAGGGTAG
16269232 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * *
16269259 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
** *
16269286 AATTACTGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
16269313 AATTACCAAAATACCCCT
1 AATTACCAAAATACCCCT
16269331 GATTTACAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
26 3 0.05
27 52 0.88
28 4 0.07
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:16269272 original size:54 final size:54
Alignment explanation
Indices: 16269204--16269333 Score: 131
Period size: 54 Copynumber: 2.4 Consensus size: 54
16269194 CCTTGATGTG
** *
16269204 AAATTACTGAAATACCCCT-ATAGGGT-AGAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCCTGAT-GGGTGA-AATTACCAAAATACCCTC-AATTTGTA
* * ** **
16269258 AAATTACCAAAATACCACTGGTTTGTGAAATTACTGAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCCTGATGGGTGAAATTACCAAAATACCCTCAATTTGTA
16269312 AAATTACCAAAATACCCCTGAT
1 AAATTACCAAAATACCCCTGAT
16269334 TTACAAAATT
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
54 59 0.95
55 3 0.05
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTGATGGGTGAAATTACCAAAATACCCTCAATTTGTA
Found at i:16269335 original size:27 final size:27
Alignment explanation
Indices: 16269232--16269344 Score: 122
Period size: 27 Copynumber: 4.2 Consensus size: 27
16269222 TATAGGGTAG
16269232 AATTACCAAAATACCCCT-AGTTTGTAA
1 AATTACCAAAATACCCCTGA-TTTGTAA
* * *
16269259 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTGATTTGTAA
** *
16269286 AATTACTGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-GATTTGTAA
**
16269313 AATTACCAAAATACCCCTGATTTACAA
1 AATTACCAAAATACCCCTGATTTGTAA
16269340 AATTA
1 AATTA
16269345 TAGAAATACC
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
26 3 0.04
27 62 0.90
28 4 0.06
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGATTTGTAA
Found at i:16269342 original size:81 final size:79
Alignment explanation
Indices: 16269166--16269344 Score: 200
Period size: 81 Copynumber: 2.2 Consensus size: 79
16269156 TACTGTTTTA
*** * *
16269166 CCCTCGATTTACAAAATTACCATTTTACCCTTGATGTGAAATTACTGAAATACCCCTATAGGGTA
1 CCCT-GATTTACAAAATTACCAAAATACCCTGGATGTGAAATTACTGAAATACCCCAATAGGGTA
*
16269231 GAATTACCAAAATAC
65 AAATTACCAAAATAC
** * **
16269246 CCCT-AGTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACTGAAATACCCTCAAT-TT
1 CCCTGA-TTTACAAAATTACCAAAATACC-CTGG-ATGTGAAATTACTGAAATACCC-CAATAGG
16269309 GTAAAATTACCAAAATAC
62 GTAAAATTACCAAAATAC
16269327 CCCTGATTTACAAAATTA
1 CCCTGATTTACAAAATTA
16269345 TAGAAATACC
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
78 1 0.01
79 17 0.21
80 7 0.09
81 52 0.64
82 4 0.05
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (79 bp):
CCCTGATTTACAAAATTACCAAAATACCCTGGATGTGAAATTACTGAAATACCCCAATAGGGTAA
AATTACCAAAATAC
Found at i:16269343 original size:54 final size:54
Alignment explanation
Indices: 16269252--16269412 Score: 182
Period size: 54 Copynumber: 2.9 Consensus size: 54
16269242 ATACCCCTAG
***
16269252 TTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACTGAAATACCCTCAA
1 TTTGTAAAATTACCAAAATACCACTGGTTTACAAAATTACTGAAATACCCTCAA
* * * *
16269306 TTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTA-TAGAAATACCCTTGAC
1 TTTGTAAAATTACCAAAATACCACTGGTTTACAAAATTACT-GAAATACCC-TCAA
* * *
16269361 TTTCTAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCT
1 TTTGT-AAAATTACCA-AAATACCACTGGTTTACAAAATTACTGAAATACCCT
16269413 TGGTTTGTAG
Statistics
Matches: 90, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
53 1 0.01
54 43 0.48
55 8 0.09
56 37 0.41
57 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (54 bp):
TTTGTAAAATTACCAAAATACCACTGGTTTACAAAATTACTGAAATACCCTCAA
Found at i:16269418 original size:27 final size:27
Alignment explanation
Indices: 16269285--16269414 Score: 113
Period size: 27 Copynumber: 4.7 Consensus size: 27
16269275 CTGGTTTGTG
** **
16269285 AAATTACTGAAATACCCTCAATTTGTA
1 AAATTACTGAAATACCCTTGATTTACA
** *
16269312 AAATTACCAAAATACCCCTGATTTACA
1 AAATTACTGAAATACCCTTGATTTACA
16269339 AAATTA-TAGAAATACCCTTGACTTT-CTAA
1 AAATTACT-GAAATACCCTTGA-TTTAC--A
* *
16269368 AAATTA-TAGAAATACCATTGGTTTACA
1 AAATTACT-GAAATACCCTTGATTTACA
16269395 AAATTACTGAAATACCCTTG
1 AAATTACTGAAATACCCTTG
16269415 GTTTGTAGAT
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
27 56 0.67
28 7 0.08
29 21 0.25
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (27 bp):
AAATTACTGAAATACCCTTGATTTACA
Found at i:16269510 original size:27 final size:27
Alignment explanation
Indices: 16269435--16269536 Score: 73
Period size: 27 Copynumber: 3.8 Consensus size: 27
16269425 TTACCAAAAC
* * * * *
16269435 ACCCTTGTAGGATGAAATGACTAAAAT
1 ACCCCTGTAGGGTAAAATGACCATAAT
* * *
16269462 ACCCCTAATA-GGTAAAAAGACCGTAA-
1 ACCCCT-GTAGGGTAAAATGACCATAAT
* *
16269488 AGCCCTTGTAGGGTAAAGTGACCATAAT
1 A-CCCCTGTAGGGTAAAATGACCATAAT
*
16269516 ACCCCTGTATGGTAAAATGAC
1 ACCCCTGTAGGGTAAAATGAC
16269537 GAATATGCCC
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
26 3 0.05
27 49 0.89
28 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (27 bp):
ACCCCTGTAGGGTAAAATGACCATAAT
Found at i:16270384 original size:25 final size:25
Alignment explanation
Indices: 16270346--16270410 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
16270336 AGGAAGTGCT
* *
16270346 AAAAGGGCTATGCCCTAATTTACCG
1 AAAAGGGCTTTGCCCTAATTTACCA
* *
16270371 AAAAGGGCTTTGCCCTAGTTTATCA
1 AAAAGGGCTTTGCCCTAATTTACCA
*
16270396 AAAAAGGCTTTGCCC
1 AAAAGGGCTTTGCCC
16270411 CAGTTATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCTAATTTACCA
Found at i:16270417 original size:24 final size:24
Alignment explanation
Indices: 16270371--16270442 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
16270361 TAATTTACCG
* *
16270371 AAAAGGGCTTTGCCCTAGTTTATCA
1 AAAAAGGCTTTGCCCCAG-TTATCA
*
16270396 AAAAAGGCTTTGCCCCAGTTATTA
1 AAAAAGGCTTTGCCCCAGTTATCA
* **
16270420 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAAAGGCTTTGCC-CCAGTTAT
16270443 ATGATAAAGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.40
25 24 0.60
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (24 bp):
AAAAAGGCTTTGCCCCAGTTATCA
Found at i:16270671 original size:30 final size:30
Alignment explanation
Indices: 16270635--16270705 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 30
16270625 CGCTTACAGT
16270635 AAAGGCTTCGACCAGTGATATGATTTATGA
1 AAAGGCTTCGACCAGTGATATGATTTATGA
* *
16270665 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGC-TTCGACCAGTGATATGATTTATGA
*
16270696 AAAGGATTCG
1 AAAGGCTTCG
16270706 GCCCAGTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 9 0.25
31 27 0.75
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (30 bp):
AAAGGCTTCGACCAGTGATATGATTTATGA
Found at i:16270684 original size:31 final size:31
Alignment explanation
Indices: 16270646--16270717 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
16270636 AAGGCTTCGA
* *
16270646 CCAGTGATATGATTTATGAAAAGGCTTTGGC
1 CCAGTGATATGATTTATGAAAAGGATTCGGC
16270677 CCAGTGATATGATTTATGAAAAGGATTCGGC
1 CCAGTGATATGATTTATGAAAAGGATTCGGC
16270708 CCAGT-ATATG
1 CCAGTGATATG
16270718 TCGAAACTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 5 0.13
31 34 0.87
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (31 bp):
CCAGTGATATGATTTATGAAAAGGATTCGGC
Found at i:16272297 original size:38 final size:38
Alignment explanation
Indices: 16272250--16272385 Score: 141
Period size: 38 Copynumber: 3.5 Consensus size: 38
16272240 GGATTAAAGA
* *
16272250 CCCGAAGGCTATATGCTGGTATTATATCCAGGTTAAAT
1 CCCGCAGGCTATGTGCTGGTATTATATCCAGGTTAAAT
**
16272288 CCCGCAGGCT-TCGTGCTGGTATTATATCTGGGTTAAAT
1 CCCGCAGGCTAT-GTGCTGGTATTATATCCAGGTTAAAT
* *
16272326 CCCGCAGGCCTA-GTGCTGGTATTATATCTGAGCTTAAAGT
1 CCCGCAGG-CTATGTGCTGGTATTATATC-CAGGTTAAA-T
* * *
16272366 CCTGCAGGTTTTGTGCTGGT
1 CCCGCAGGCTATGTGCTGGT
16272386 GACTGGATTC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
37 1 0.01
38 56 0.68
39 9 0.11
40 16 0.20
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.33
Consensus pattern (38 bp):
CCCGCAGGCTATGTGCTGGTATTATATCCAGGTTAAAT
Found at i:16276948 original size:15 final size:15
Alignment explanation
Indices: 16276928--16276957 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16276918 TTACATGTTG
16276928 AACTAATTATGCATA
1 AACTAATTATGCATA
16276943 AACTAATTATGCATA
1 AACTAATTATGCATA
16276958 TCCTATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
AACTAATTATGCATA
Found at i:16289468 original size:17 final size:17
Alignment explanation
Indices: 16289446--16289481 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
16289436 TTAAAAAACA
16289446 AAAAATTACAAGCTTTC
1 AAAAATTACAAGCTTTC
16289463 AAAAATTACAAGCTTTC
1 AAAAATTACAAGCTTTC
16289480 AA
1 AA
16289482 CAATGACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (17 bp):
AAAAATTACAAGCTTTC
Found at i:16303553 original size:20 final size:20
Alignment explanation
Indices: 16303493--16303553 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
16303483 CTGGTGTGAG
*
16303493 ATTGCAACATTTGTGCCTCTG
1 ATTGC-ACATTTGTGCCTCTA
* * *
16303514 TTTCCAC-TTTGGTGCTTCTA
1 ATTGCACATTT-GTGCCTCTA
16303534 ATTGCACATTTGTGCCTCTA
1 ATTGCACATTTGTGCCTCTA
16303554 TTACGCATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
19 3 0.10
20 22 0.71
21 6 0.19
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.43
Consensus pattern (20 bp):
ATTGCACATTTGTGCCTCTA
Found at i:16303995 original size:21 final size:21
Alignment explanation
Indices: 16303966--16304042 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
16303956 TGTAGTCCGA
16303966 GGGACACGCCCGTGTGACCCT
1 GGGACACGCCCGTGTGACCCT
*
16303987 GGGATACGCCCGTGTGACCCT
1 GGGACACGCCCGTGTGACCCT
* *
16304008 GGGATATGCCCGTGTGACCCT
1 GGGACACGCCCGTGTGACCCT
* *
16304029 AGGACACACCCGTG
1 GGGACACGCCCGTG
16304043 CTACAGGTCG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.17, C:0.34, G:0.32, T:0.17
Consensus pattern (21 bp):
GGGACACGCCCGTGTGACCCT
Found at i:16305276 original size:21 final size:22
Alignment explanation
Indices: 16305224--16305276 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
16305214 AAATAAATTC
*
16305224 CATGTA-CAAATATCATCATCT
1 CATGTATCATATATCATCATCT
* *
16305245 CATGTTTTCATATATCAT-ATGT
1 CATG-TATCATATATCATCATCT
16305267 CATGTATCAT
1 CATGTATCAT
16305277 CATTTGCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.35
22 8 0.31
23 9 0.35
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.42
Consensus pattern (22 bp):
CATGTATCATATATCATCATCT
Found at i:16308397 original size:18 final size:18
Alignment explanation
Indices: 16308371--16308415 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
16308361 TCATAAAAAT
*
16308371 GGGCTCACATGCCCGTGC
1 GGGCCCACATGCCCGTGC
16308389 GGGCCCACATGCCCGTGC
1 GGGCCCACATGCCCGTGC
16308407 GGGCCCACA
1 GGGCCCACA
16308416 CGACCCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.42, G:0.33, T:0.11
Consensus pattern (18 bp):
GGGCCCACATGCCCGTGC
Found at i:16322175 original size:15 final size:16
Alignment explanation
Indices: 16322141--16322178 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
16322131 ATTGTTTTCT
*
16322141 TTTTTATTTAATTAAA
1 TTTTCATTTAATTAAA
*
16322157 TTTTCATTTAA-TAAC
1 TTTTCATTTAATTAAA
16322172 TTTTCAT
1 TTTTCAT
16322179 CATTTCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTCATTTAATTAAA
Found at i:16325046 original size:37 final size:37
Alignment explanation
Indices: 16325003--16325082 Score: 133
Period size: 37 Copynumber: 2.2 Consensus size: 37
16324993 ATACACTAGA
*
16325003 TATATTGAGGTTGTACATCTGTTGCGGACTATCGTGT
1 TATATTGAGGTCGTACATCTGTTGCGGACTATCGTGT
* *
16325040 TTTATTGAGGTCGTACATTTGTTGCGGACTATCGTGT
1 TATATTGAGGTCGTACATCTGTTGCGGACTATCGTGT
16325077 TATATT
1 TATATT
16325083 ATAGTGTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (37 bp):
TATATTGAGGTCGTACATCTGTTGCGGACTATCGTGT
Found at i:16327722 original size:21 final size:21
Alignment explanation
Indices: 16327670--16327732 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
16327660 CATGGTCTAC
*
16327670 TTACATGGGCATATGAAGTAG
1 TTACATGGGCATGTGAAGTAG
** *
16327691 TTACACAGGCATGTGCAGTAG
1 TTACATGGGCATGTGAAGTAG
* *
16327712 TTAGATGGGCATGTGGAGTAG
1 TTACATGGGCATGTGAAGTAG
16327733 CCACACGGCT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.27
Consensus pattern (21 bp):
TTACATGGGCATGTGAAGTAG
Found at i:16334028 original size:49 final size:47
Alignment explanation
Indices: 16333913--16334035 Score: 126
Period size: 49 Copynumber: 2.6 Consensus size: 47
16333903 TAATATCGAT
* * * *
16333913 GCCATGTCCCAGACATGGTCTTACACTGGCTTATCCATCAACTCAAT
1 GCCATGTCCTAGACATGGTCTTACACTGACTTATCAATCAACTCAAC
* *
16333960 GCCATGT-CTCAAACATGGTCTTACACTGAC-TATCGAAATCGAGGC-CAAC
1 GCCATGTCCT-AGACATGGTCTTACACTGACTTATC--AATC-A-ACTCAAC
16334009 GCCATGTCCTAGACATGGTCTTACACT
1 GCCATGTCCTAGACATGGTCTTACACT
16334036 AGCTCTCACA
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
46 5 0.08
47 25 0.40
48 3 0.05
49 27 0.43
50 3 0.05
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (47 bp):
GCCATGTCCTAGACATGGTCTTACACTGACTTATCAATCAACTCAAC
Found at i:16334123 original size:48 final size:51
Alignment explanation
Indices: 16334009--16334138 Score: 164
Period size: 48 Copynumber: 2.6 Consensus size: 51
16333999 CGAGGCCAAC
*
16334009 GCCATGTCCTAGACATGGTCTTACACT-AGC-TCTCACATATCTGTGTCGAT
1 GCCATGTCCTAGACATGGTCTTACACTGA-CACCTCACATATCTGTGTCGAT
* * *
16334059 GCCATGTCCCAAACATGGTCTTACACTGACACCTC-TATA-C-GTG-CTGAT
1 GCCATGTCCTAGACATGGTCTTACACTGACACCTCACATATCTGTGTC-GAT
16334107 GCCATGTCCTAGACATGGTCTTACACTGACAC
1 GCCATGTCCTAGACATGGTCTTACACTGACAC
16334139 ATCTCGTAAC
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
47 1 0.01
48 36 0.51
49 1 0.01
50 29 0.41
51 4 0.06
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (51 bp):
GCCATGTCCTAGACATGGTCTTACACTGACACCTCACATATCTGTGTCGAT
Found at i:16334276 original size:48 final size:47
Alignment explanation
Indices: 16333909--16334320 Score: 248
Period size: 46 Copynumber: 8.7 Consensus size: 47
16333899 GGTATAATAT
*
16333909 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT-T-ATC-CATCAAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAT--AC
* * * * ** **
16333955 TCAATGCCATGTCTCAAACATGGTCTTACACT-GACTATCGAAATCGAGGC
1 -CGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTC-ATCTC-ATAC
* * * * * **
16334005 CAACGCCATGTCCTAGACATGGTCTTACACTAGCTCTCACATATCTGTGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT--CATCTC-ATAC
* *
16334055 CGATGCCATGTCCCAAACATGGTCTTACACT-GACAC-C-TCT-ATAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTCATCTCATAC
* * * *
16334099 GTGCTGATGCCATGTCCTAGACATGGTCTTACACT-G-ACACATCTCGTAAC
1 ---C-GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAT-AC
* **
16334149 CGATG-CATGTCCCAGACAT-GTTTTACACTAGCT-TACATCTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATCTC-ATAC
*
16334195 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAATAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTC-ATAC
* *
16334241 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAT-GTAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-CTCATA-C
* *
16334289 CAATG-CATGTCCCAGACAT-GTATTACACTAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGC
16334321 ACACAAATAA
Statistics
Matches: 292, Mismatches: 46, Indels: 55
0.74 0.12 0.14
Matches are distributed among these distances:
44 10 0.03
45 14 0.05
46 72 0.25
47 65 0.22
48 56 0.19
49 33 0.11
50 39 0.13
51 2 0.01
52 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCATAC
Found at i:16334295 original size:94 final size:96
Alignment explanation
Indices: 16333911--16334320 Score: 313
Period size: 94 Copynumber: 4.3 Consensus size: 96
16333901 TATAATATCG
* * * *
16333911 ATGCCATGTCCCAGACATGGTCTTACACTGGCT-T-ATCCATC-AACTCAATGCCATGTCTCAAA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-C-TCGTAC-CGATGCCATGTCCCAAA
*
16333973 CATGGTCTTACACTGACTATCGA-AATCGAGGCCA
63 CATGGTCTTACACTGACTCTC-ATAATCGAGGCCA
* * * **
16334007 ACGCCATGTCCTAGACATGGTCTTACACTAGCTCTCACATATCTGTGTCGATGCCATGTCCCAAA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCT--CATCTC-GTACCGATGCCATGTCCCAAA
* * **
16334072 CATGGTCTTACACTGACACCTC-T-ATACG-TGCTG
63 CATGGTCTTACACTGAC-TCTCATAAT-CGAGGCCA
* * * *
16334105 ATGCCATGTCCTAGACATGGTCTTACACT-G-ACACATCTCGTAACCGATG-CATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCGT-ACCGATGCCATGTCCCAAACA
* * *
16334167 T-GTTTTACACT-AGCT-TACAT-CTCGAGGCCG
65 TGGTCTTACACTGA-CTCT-CATAATCGAGGCCA
* * *
16334197 ATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAATACCGATGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTC-GTACCGATGCCATGTCCCAAACA
16334260 TGGTCTTACACT-AGCTCTCATAAT-GTA-GCCA
65 TGGTCTTACACTGA-CTCTCATAATCG-AGGCCA
*
16334291 ATG-CATGTCCCAGACAT-GTATTACACTAGC
1 ATGCCATGTCCCAGACATGGTCTTACACTAGC
16334321 ACACAAATAA
Statistics
Matches: 257, Mismatches: 35, Indels: 46
0.76 0.10 0.14
Matches are distributed among these distances:
90 11 0.04
91 18 0.07
92 31 0.12
93 30 0.12
94 59 0.23
95 3 0.01
96 31 0.12
97 2 0.01
98 34 0.13
99 34 0.13
100 4 0.02
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (96 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCGTACCGATGCCATGTCCCAAACAT
GGTCTTACACTGACTCTCATAATCGAGGCCA
Found at i:16335484 original size:25 final size:25
Alignment explanation
Indices: 16335446--16335500 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
16335436 AGCCAAACCA
16335446 AGCCTTTGTAGTGAATTATCTGAAG
1 AGCCTTTGTAGTGAATTATCTGAAG
* *
16335471 AGCCTTTTTGGTGAATTATCTGAAG
1 AGCCTTTGTAGTGAATTATCTGAAG
16335496 AGCCT
1 AGCCT
16335501 GTGTGATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (25 bp):
AGCCTTTGTAGTGAATTATCTGAAG
Found at i:16335513 original size:25 final size:25
Alignment explanation
Indices: 16335457--16335516 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
16335447 GCCTTTGTAG
* * *
16335457 TGAATTATCTGAAGAGCCTTTTTGG
1 TGAATTATCTGAAGAGCCTGTGTGA
16335482 TGAATTATCTGAAGAGCCTGTGTGA
1 TGAATTATCTGAAGAGCCTGTGTGA
*
16335507 TGTATTATCT
1 TGAATTATCT
16335517 AAAAAGTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (25 bp):
TGAATTATCTGAAGAGCCTGTGTGA
Found at i:16342010 original size:16 final size:16
Alignment explanation
Indices: 16341989--16342030 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
16341979 AGGTGATCAT
16341989 GGGCCGGGCCGGGTTC
1 GGGCCGGGCCGGGTTC
*
16342005 GGGCCGGGCTGGGTTC
1 GGGCCGGGCCGGGTTC
*
16342021 GGGCCAGGCC
1 GGGCCGGGCC
16342031 CATACAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.02, C:0.31, G:0.55, T:0.12
Consensus pattern (16 bp):
GGGCCGGGCCGGGTTC
Found at i:16342200 original size:25 final size:26
Alignment explanation
Indices: 16342172--16342222 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
16342162 TTTATTTCAT
*
16342172 TAAATAAAAAAT-TTTAAAAATATAA
1 TAAATAAAAAATATTTAAAAACATAA
* *
16342197 TAAATCAAATATATTTAAAAACATAA
1 TAAATAAAAAATATTTAAAAACATAA
16342223 AAACAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAATAAAAAATATTTAAAAACATAA
Found at i:16342214 original size:26 final size:24
Alignment explanation
Indices: 16342184--16342232 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
16342174 AATAAAAAAT
*
16342184 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
16342210 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
16342233 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:16342252 original size:21 final size:21
Alignment explanation
Indices: 16342203--16342261 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
16342193 ATAATAAATC
*
16342203 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
16342223 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
16342245 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
16342262 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:16342337 original size:15 final size:16
Alignment explanation
Indices: 16342307--16342339 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
16342297 AAACGGTTAT
16342307 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
16342324 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
16342339 A
1 A
16342340 AAAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:16345137 original size:6 final size:6
Alignment explanation
Indices: 16345111--16345157 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
16345101 ACAGTACCTA
* * *
16345111 AACAGT AATCAGA AACAGT AGCAGT AGCAGT AACAGT AACAGT AACA
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACA
16345158 ATATTCGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
6 31 0.86
7 5 0.14
ACGTcount: A:0.49, C:0.17, G:0.19, T:0.15
Consensus pattern (6 bp):
AACAGT
Found at i:16346226 original size:31 final size:29
Alignment explanation
Indices: 16346191--16346249 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
16346181 ATTATTTATC
16346191 TAATAAATATCTTTAACTTAAT-AATAATAAA
1 TAATAAATATC--T-ACTTAATAAATAATAAA
16346222 TAATAAATATCTACTTAATAAATAATAA
1 TAATAAATATCTACTTAATAAATAATAA
16346250 TTTTTATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 7 0.26
29 9 0.33
31 11 0.41
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (29 bp):
TAATAAATATCTACTTAATAAATAATAAA
Found at i:16352731 original size:18 final size:18
Alignment explanation
Indices: 16352710--16352746 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16352700 CAAAAAAGCA
16352710 ATTTGGGTATCAATATTG
1 ATTTGGGTATCAATATTG
* *
16352728 ATTTTGGTATCAATCTTG
1 ATTTGGGTATCAATATTG
16352746 A
1 A
16352747 AGGCCAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (18 bp):
ATTTGGGTATCAATATTG
Found at i:16352930 original size:11 final size:11
Alignment explanation
Indices: 16352914--16352938 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16352904 TATTGATTGA
16352914 AAATCATTTTT
1 AAATCATTTTT
16352925 AAATCATTTTT
1 AAATCATTTTT
16352936 AAA
1 AAA
16352939 CATACTCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATCATTTTT
Found at i:16354464 original size:10 final size:10
Alignment explanation
Indices: 16354424--16354469 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
16354414 AAAAAGGAAT
16354424 GAGCTGAAAC
1 GAGCTGAAAC
*
16354434 GAGCTAAAATC
1 GAGCTGAAA-C
* *
16354445 AAGCTCAAAC
1 GAGCTGAAAC
16354455 GAGCTGAAAC
1 GAGCTGAAAC
16354465 GAGCT
1 GAGCT
16354470 CAAGTGAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.13
Consensus pattern (10 bp):
GAGCTGAAAC
Found at i:16356971 original size:102 final size:102
Alignment explanation
Indices: 16356803--16356996 Score: 343
Period size: 102 Copynumber: 1.9 Consensus size: 102
16356793 TTCGCCTCCC
* *
16356803 TTGGGTGTGATCCTCGGAGTACTTACCTACTTTGTTGTAACTATATTACAACTTGACCTGTATAC
1 TTGGGTGTGATCCTCAGAGTACTTACCTAATTTGTTGTAACTATATTACAACTTGACCTGTATAC
* *
16356868 TTGCATAAACTGCCTAACTCTTATAATGGCGCCTTCA
66 TTGCAGAAACTACCTAACTCTTATAATGGCGCCTTCA
16356905 TTGGGTGTGATCCTCAGAGTACTTACCTAATTTGTTGTAACTATATTACAACTTGACCTGTATAC
1 TTGGGTGTGATCCTCAGAGTACTTACCTAATTTGTTGTAACTATATTACAACTTGACCTGTATAC
*
16356970 TTGCAGAAACTATCTAACTCTTATAAT
66 TTGCAGAAACTACCTAACTCTTATAAT
16356997 TGGCTATAGT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 87 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (102 bp):
TTGGGTGTGATCCTCAGAGTACTTACCTAATTTGTTGTAACTATATTACAACTTGACCTGTATAC
TTGCAGAAACTACCTAACTCTTATAATGGCGCCTTCA
Found at i:16366275 original size:17 final size:18
Alignment explanation
Indices: 16366241--16366282 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
16366231 AATATTAAGA
16366241 TAATTATTAGGATTA-TT
1 TAATTATTAGGATTATTT
*
16366258 TAATT-TTAGGTTTAATTT
1 TAATTATTAGGATT-ATTT
16366276 TAATTAT
1 TAATTAT
16366283 CTTTATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.33
17 6 0.29
18 7 0.33
19 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (18 bp):
TAATTATTAGGATTATTT
Found at i:16366292 original size:10 final size:10
Alignment explanation
Indices: 16366274--16366316 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
16366264 TAGGTTTAAT
16366274 TTTAATTATC
1 TTTAATTATC
*
16366284 TTTATTTATC
1 TTTAATTATC
**
16366294 TTTAATTAAA
1 TTTAATTATC
*
16366304 TGTAATTATC
1 TTTAATTATC
16366314 TTT
1 TTT
16366317 TTAGAATTTA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (10 bp):
TTTAATTATC
Found at i:16369948 original size:6 final size:6
Alignment explanation
Indices: 16369947--16370011 Score: 62
Period size: 6 Copynumber: 10.3 Consensus size: 6
16369937 ATTTTTATTT
*
16369947 TTTTTA TTTTTA TTTTTA TTTTTA -TTTTA TTTTATT TATTTTA TCTTATTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT-TA T-TTTTA T-TT-TTA
16369998 -TTTTA TTATTTA TT
1 TTTTTA TT-TTTA TT
16370012 ATTTTCAGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
5 8 0.16
6 24 0.48
7 12 0.24
8 6 0.12
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:16369956 original size:5 final size:5
Alignment explanation
Indices: 16369939--16370004 Score: 68
Period size: 5 Copynumber: 13.4 Consensus size: 5
16369929 GCAACCCAAT
16369939 TTTTA TTTT- TTTTA TTTTTA TTTTTA TTTTTA TTTTA TTTTA -TTTA
1 TTTTA TTTTA TTTTA -TTTTA -TTTTA -TTTTA TTTTA TTTTA TTTTA
*
16369985 TTTTA TCTTA --TTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TT
16370005 ATTTATTATT
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
3 3 0.05
4 8 0.15
5 27 0.49
6 17 0.31
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:16369975 original size:32 final size:33
Alignment explanation
Indices: 16369939--16370001 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
16369929 GCAACCCAAT
*
16369939 TTTTATTTTTTTTATTTTTAT-TT-TTATTTTTA
1 TTTTATTTTATTTA-TTTTATCTTATTATTTTTA
16369971 TTTTATTTTATTTATTTTATCTTATTATTTT
1 TTTTATTTTATTTATTTTATCTTATTATTTT
16370002 ATTATTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 6 0.21
32 15 0.54
33 7 0.25
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (33 bp):
TTTTATTTTATTTATTTTATCTTATTATTTTTA
Found at i:16369998 original size:27 final size:25
Alignment explanation
Indices: 16369937--16370011 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 25
16369927 AGGCAACCCA
16369937 ATTTTTATTTT-TTTTATTTTTATTTTT
1 ATTTTTATTTTATTTTA--TTTA-TTTT
16369964 ATTTTTATTTTATTTTATTTATTTT
1 ATTTTTATTTTATTTTATTTATTTT
16369989 ATCTTATTATTTTA--TTATTTATT
1 AT-TT-TTATTTTATTTTATTTATT
16370012 ATTTTCAGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
25 15 0.33
26 6 0.13
27 19 0.42
28 5 0.11
ACGTcount: A:0.20, C:0.01, G:0.00, T:0.79
Consensus pattern (25 bp):
ATTTTTATTTTATTTTATTTATTTT
Found at i:16370014 original size:32 final size:31
Alignment explanation
Indices: 16369941--16370015 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 31
16369931 AACCCAATTT
16369941 TTATTTTT-TTTATTTTTATTTTTATTTTTA
1 TTATTTTTATTTATTTTTATTTTTATTTTTA
*
16369971 TTTTATTTTATTTA-TTTTATCTTATTA-TTTTA
1 TTAT-TTTTATTTATTTTTAT-TT-TTATTTTTA
16370003 TTATTTATTATTT
1 TTATTT-TTATTT
16370016 TCAGATATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 3 0.08
31 12 0.32
32 20 0.53
33 3 0.08
ACGTcount: A:0.20, C:0.01, G:0.00, T:0.79
Consensus pattern (31 bp):
TTATTTTTATTTATTTTTATTTTTATTTTTA
Found at i:16371665 original size:27 final size:26
Alignment explanation
Indices: 16371605--16371666 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
16371595 ATAAGACTGC
16371605 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * * *
16371631 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
16371659 ATTTTATT
1 ATTTTATT
16371667 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 14 0.48
28 13 0.45
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:16371681 original size:10 final size:10
Alignment explanation
Indices: 16371662--16371708 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
16371652 TTTTAGGATT
16371662 TTAT-TTTAA
1 TTATCTTTAA
16371671 TTATCTTTAA
1 TTATCTTTAA
16371681 TTATCTTTAA
1 TTATCTTTAA
** *
16371691 TTAAATGTAA
1 TTATCTTTAA
16371701 TTATCTTT
1 TTATCTTT
16371709 TTAGAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
9 4 0.13
10 27 0.87
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:16373553 original size:17 final size:17
Alignment explanation
Indices: 16373531--16373578 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
16373521 GATAAGTATA
16373531 CATTGTCATTGCATTTT
1 CATTGTCATTGCATTTT
* *
16373548 CATTGTCATTCCATATT
1 CATTGTCATTGCATTTT
*
16373565 CA-TGTCAGTGCATT
1 CATTGTCATTGCATT
16373579 GGGGATAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (17 bp):
CATTGTCATTGCATTTT
Found at i:16377533 original size:6 final size:6
Alignment explanation
Indices: 16377507--16377553 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
16377497 ACAGTACCTA
* * *
16377507 AACAGT AATCAGA AACAGT AGCAGT AGCAGT AACAGT AACAGT AACA
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACA
16377554 ATATTCGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
6 31 0.86
7 5 0.14
ACGTcount: A:0.49, C:0.17, G:0.19, T:0.15
Consensus pattern (6 bp):
AACAGT
Found at i:16378622 original size:31 final size:29
Alignment explanation
Indices: 16378587--16378645 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
16378577 ATTATTTATC
16378587 TAATAAATATCTTTAACTTAAT-AATAATAAA
1 TAATAAATATC--T-ACTTAATAAATAATAAA
16378618 TAATAAATATCTACTTAATAAATAATAA
1 TAATAAATATCTACTTAATAAATAATAA
16378646 TTTTTATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 7 0.26
29 9 0.33
31 11 0.41
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (29 bp):
TAATAAATATCTACTTAATAAATAATAAA
Found at i:16385127 original size:18 final size:18
Alignment explanation
Indices: 16385106--16385142 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16385096 CAAAAAAGCA
16385106 ATTTGGGTATCAATATTG
1 ATTTGGGTATCAATATTG
* *
16385124 ATTTTGGTATCAATCTTG
1 ATTTGGGTATCAATATTG
16385142 A
1 A
16385143 AGGCCAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (18 bp):
ATTTGGGTATCAATATTG
Found at i:16385326 original size:11 final size:11
Alignment explanation
Indices: 16385310--16385334 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16385300 TATTGATTGA
16385310 AAATCATTTTT
1 AAATCATTTTT
16385321 AAATCATTTTT
1 AAATCATTTTT
16385332 AAA
1 AAA
16385335 CATACTCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATCATTTTT
Found at i:16386860 original size:10 final size:10
Alignment explanation
Indices: 16386820--16386865 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
16386810 AAAAAGGAAT
16386820 GAGCTGAAAC
1 GAGCTGAAAC
*
16386830 GAGCTAAAATC
1 GAGCTGAAA-C
* *
16386841 AAGCTCAAAC
1 GAGCTGAAAC
16386851 GAGCTGAAAC
1 GAGCTGAAAC
16386861 GAGCT
1 GAGCT
16386866 CAAGTGAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.13
Consensus pattern (10 bp):
GAGCTGAAAC
Found at i:16387683 original size:20 final size:19
Alignment explanation
Indices: 16387658--16387709 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
16387648 ACAAATAATT
16387658 ATTATATTTTAATAAATATA
1 ATTATA-TTTAATAAATATA
*
16387678 ATTATA-TTAATTAATATA
1 ATTATATTTAATAAATATA
*
16387696 TTTATAATTTAATA
1 ATTAT-ATTTAATA
16387710 TATTTGAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 15 0.56
19 1 0.04
20 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTATATTTAATAAATATA
Found at i:16388810 original size:19 final size:18
Alignment explanation
Indices: 16388786--16388823 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
16388776 TTAGTTATAA
*
16388786 TTAATTAATTAGTTTAATT
1 TTAATTAATT-GTTAAATT
16388805 TTAATTAATTGTTAAATT
1 TTAATTAATTGTTAAATT
16388823 T
1 T
16388824 ATTTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
TTAATTAATTGTTAAATT
Found at i:16391172 original size:42 final size:43
Alignment explanation
Indices: 16391072--16391184 Score: 122
Period size: 43 Copynumber: 2.6 Consensus size: 43
16391062 AATGCCGACA
* * * * **
16391072 TCCCAGACGTGGTCTTACATGTAACCAAATATCGATGTCACTG
1 TCCCAGACATGGTCTTACACGAAATCAAATATCGATACCACTG
* *
16391115 TCCCAGGCAGGGTCTTACACGAAATCAAATA-CGATACCGA-TG
1 TCCCAGACATGGTCTTACACGAAATCAAATATCGATACC-ACTG
16391157 TCCCAGACATGGTCTTACACGTAAATCA
1 TCCCAGACATGGTCTTACACG-AAATCA
16391185 TAAGTCGATG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
42 26 0.45
43 32 0.55
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGAAATCAAATATCGATACCACTG
Found at i:16395012 original size:31 final size:31
Alignment explanation
Indices: 16394974--16395032 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
16394964 TAACAGCCAA
16394974 TGACTTAAATAAAAACTTTTAAATAGTTCAG
1 TGACTTAAATAAAAACTTTTAAATAGTTCAG
* *
16395005 TGACTTAAATGAAAACTTTTGAATAGTT
1 TGACTTAAATAAAAACTTTTAAATAGTT
16395033 TAATGACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.37
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTAAATAGTTCAG
Found at i:16398166 original size:33 final size:33
Alignment explanation
Indices: 16398124--16398191 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
16398114 TATCAAAATG
16398124 GTATGCCAGTACGATTAAACACTAAAATATTAT
1 GTATGCCAGTACGATTAAACACTAAAATATTAT
16398157 GTATGCCAGTACGATTAAACACTAAAATATTAT
1 GTATGCCAGTACGATTAAACACTAAAATATTAT
16398190 GT
1 GT
16398192 CGGTGGGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (33 bp):
GTATGCCAGTACGATTAAACACTAAAATATTAT
Found at i:16398710 original size:25 final size:26
Alignment explanation
Indices: 16398664--16398712 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
16398654 GTTTTTAATT
*
16398664 TATTCTAAAGTTATTTTGTTAGTTAC
1 TATTATAAAGTTATTTTGTTAGTTAC
16398690 TATTATAAA-TTA-TTTGTTTAGTT
1 TATTATAAAGTTATTTTG-TTAGTT
16398713 TGATGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 9 0.43
26 8 0.38
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (26 bp):
TATTATAAAGTTATTTTGTTAGTTAC
Found at i:16402477 original size:11 final size:12
Alignment explanation
Indices: 16402450--16402479 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16402440 CATGAGTAAC
*
16402450 AAAAAACACAGT
1 AAAAAACACAAT
16402462 AAAAAACACAAT
1 AAAAAACACAAT
16402474 AAAAAA
1 AAAAAA
16402480 TCTCATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.77, C:0.13, G:0.03, T:0.07
Consensus pattern (12 bp):
AAAAAACACAAT
Found at i:16403103 original size:208 final size:207
Alignment explanation
Indices: 16402745--16403293 Score: 700
Period size: 208 Copynumber: 2.6 Consensus size: 207
16402735 TAATACATGT
* * * *
16402745 TAAACTAAACA-AAAAAATTATAACCTAATTATAAATTAC-TAAAAAAAACTTTAAAATAATTTA
1 TAAACTAAACACAAACAA-TATAACCTAATTATAAATTACTTCAAAATAACTTTAAAATAATTAA
* * * * *
16402808 AAAACACAAAAAAAATTACATTTATAACAAGTCACAATAAAAACTAAACTAAATACAAACAATTT
65 AAAACA-AAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTT
* * * * *
16402873 ATAACCTAATCATAAATTACT-AACAAAATAACTTTAAAATAATTAAAAAATTTACATTCATAAA
129 ATAACCTAACCATAAATTACTAAAAAAAATAACTTAAAAATAAATAAAAAAATTACATTCATAAA
16402937 AAATCACAATAAACAC
194 AAATCAC-A-AAACAC
* *
16402953 TAAACTAAACACGAAC-A-A-AACCTAATTATAAATTACTTGCAAAATAACTTTCAAATAATTAA
1 TAAACTAAACACAAACAATATAACCTAATTATAAATTACTT-CAAAATAACTTTAAAATAATTAA
* * *
16403015 AAAAAATAAAAAAAACTTACATTCATAAAAAATTACAATAAACATTAAACTAAACACAAACAATT
65 AAAACA-AAAAAAAA-TTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATT
* *
16403080 AATAACCTAACCATAAATTACTAAAAAAAATGACTTAAAAATAAATAAAAAAATTACATTCATAA
128 TATAACCTAACCATAAATTACTAAAAAAAATAACTTAAAAATAAATAAAAAAATTACATTCATAA
*
16403145 AAAATTACAAAACAC
193 AAAATCACAAAACAC
* * * * *
16403160 TAAACTAAACACAAACAATTTATAACGTAATCAGAAATTACTAACAAAATAACTATAAAATAATT
1 TAAACTAAACACAAACAA--TATAACCTAATTATAAATTACT-TCAAAATAACTTTAAAATAA-T
16403225 TAAAAAACAAAAAAAAATTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAAT
62 TAAAAAACAAAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAAT
16403288 TTATAA
127 TTATAA
16403294 ATTAAAAAAA
Statistics
Matches: 295, Mismatches: 34, Indels: 23
0.84 0.10 0.07
Matches are distributed among these distances:
205 18 0.06
206 2 0.01
207 53 0.18
208 76 0.26
209 75 0.25
210 1 0.00
211 20 0.07
212 41 0.14
213 9 0.03
ACGTcount: A:0.60, C:0.14, G:0.01, T:0.24
Consensus pattern (207 bp):
TAAACTAAACACAAACAATATAACCTAATTATAAATTACTTCAAAATAACTTTAAAATAATTAAA
AAACAAAAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTAT
AACCTAACCATAAATTACTAAAAAAAATAACTTAAAAATAAATAAAAAAATTACATTCATAAAAA
ATCACAAAACAC
Found at i:16403276 original size:73 final size:74
Alignment explanation
Indices: 16403199--16403362 Score: 192
Period size: 73 Copynumber: 2.2 Consensus size: 74
16403189 ATCAGAAATT
*
16403199 ACTAACA-AAATAA-CTATAAAATAATTTAAAAAACAAAAAAAAATTACATTCATAAAAAATCAC
1 ACTAACACAAACAATCTATAAAATAA---AAAAAACAAAAAAAAATTACATTCATAAAAAATCAC
16403262 -A-AAACACTAA
63 AATAAACACTAA
* * * * *
16403272 ACTAAACACAAACAATTTATAAATTAAAAAAAATAAAAAAAACTTACATTCATAAAAAATTACAA
1 ACT-AACACAAACAATCTATAAAATAAAAAAAACAAAAAAAAATTACATTCATAAAAAATCACAA
*
16403337 TAAACATTAA
65 TAAACACTAA
16403347 ACTAAACACAAACAAT
1 ACT-AACACAAACAAT
16403363 TAATAACCTA
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
73 36 0.46
74 5 0.06
75 29 0.37
76 9 0.11
ACGTcount: A:0.65, C:0.14, G:0.00, T:0.21
Consensus pattern (74 bp):
ACTAACACAAACAATCTATAAAATAAAAAAAACAAAAAAAAATTACATTCATAAAAAATCACAAT
AAACACTAA
Found at i:16403358 original size:75 final size:73
Alignment explanation
Indices: 16403226--16403368 Score: 223
Period size: 73 Copynumber: 1.9 Consensus size: 73
16403216 AAAATAATTT
*
16403226 AAAAAACAAAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTA
1 AAAAAACAAAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTAA
16403291 TAAATTAA
66 TAAATTAA
* * * *
16403299 AAAAAATAAAAAAAACTTACATTCATAAAAAATTACAATAAACATTAAACTAAACACAAACAATT
1 AAAAAACAAAAAAAAATTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATT
16403364 AATAA
64 AATAA
16403369 CCTAACCATA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 33 0.52
74 1 0.02
75 29 0.46
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (73 bp):
AAAAAACAAAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTAA
TAAATTAA
Found at i:16403495 original size:102 final size:102
Alignment explanation
Indices: 16403295--16403482 Score: 251
Period size: 100 Copynumber: 1.9 Consensus size: 102
16403285 AATTTATAAA
*
16403295 TTAAAAAAAATAAAAAAAACTTACATTCATAAAAAATTACAATAAACATTAAACTAAACACAAAC
1 TTAAAAAAAATAAAAAAAACTTACATTCATAAAAAATTACAATAAACACTAAACTAAACACAAAC
* ** *
16403360 AATTAATAACCTAACCATAAATTACTAAAAAAAATGAC
66 AATTAATAA-CTAACAATAAAAAACAAAAAAAAATGAC
16403398 TTAAAAATAAAT-AAAAAAA-TTACATTCATAAAAAATTAC-A-AAACACTAAACTAAACACAAA
1 TTAAAAA-AAATAAAAAAAACTTACATTCATAAAAAATTACAATAAACACTAAACTAAACACAAA
* *
16403459 CAATTTATAA-TAATTAATAAAAAA
65 CAATTAATAACTAA-CAATAAAAAA
16403483 ACAACATAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
98 3 0.04
99 6 0.08
100 29 0.38
101 1 0.01
102 20 0.26
103 14 0.18
104 4 0.05
ACGTcount: A:0.63, C:0.13, G:0.01, T:0.23
Consensus pattern (102 bp):
TTAAAAAAAATAAAAAAAACTTACATTCATAAAAAATTACAATAAACACTAAACTAAACACAAAC
AATTAATAACTAACAATAAAAAACAAAAAAAAATGAC
Found at i:16405155 original size:50 final size:49
Alignment explanation
Indices: 16404902--16405224 Score: 234
Period size: 46 Copynumber: 6.8 Consensus size: 49
16404892 TCACTTATGT
* * * *
16404902 GAGCTAGTGTAAGAAATGTCTAGGACAT-GCATCGGC-CAC-AATATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCACTCGAAGATGA
* * * * * *
16404948 GAGCCAGTGTAAGACCATGTCTGGAACATGACATCGGTA-TTGAA-ACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCACTCGAAGATGA
* * *
16404996 GTGCTAGTGTAAAACATGTCTGGGACAT-GCATCGGC-CTCG-AGACGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCACTCGAAGATG-A
* *
16405043 -AGCCAGTGTAAGACATGTTTGGGACAT-GCATCGG--CT-GCAAGAT--
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCACTCG-AAGATGA
* * * * *
16405086 GTG-TAAGTGTAAGACCATGTCTGTGACATAGCATCGGCACGGT-TATG-TGA
1 GAGCT-AGTGTAAGA-CATGTCTGGGACATGGCATCGGCAC--TCGAAGATGA
*
16405136 GAGCTAGTGTAAGATCATGTCAGGGACATGGCATCGGC-CTCGAAGATGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCACTCGAAGATGA
*
16405185 TAGCTAGTGTAAGACTATGTCTGGGACATGGCATCGGCAC
1 GAGCTAGTGTAAGAC-ATGTCTGGGACATGGCATCGGCAC
16405225 CTTACCCATG
Statistics
Matches: 217, Mismatches: 36, Indels: 44
0.73 0.12 0.15
Matches are distributed among these distances:
44 11 0.05
45 15 0.07
46 64 0.29
47 26 0.12
48 25 0.12
49 42 0.19
50 33 0.15
51 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (49 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCACTCGAAGATGA
Found at i:16405205 original size:99 final size:94
Alignment explanation
Indices: 16405047--16405224 Score: 234
Period size: 99 Copynumber: 1.8 Consensus size: 94
16405037 GACGTAAGCC
** *
16405047 AGTGTAAGACATGTTTGGGACATGCATCGGCTGCAAGATGTGTAAGTGTAAGACCATGTCTGTGA
1 AGTGTAAGACATGTCAGGGACATGCATCGGCTGCAAGATGTGTAAGTGTAAGACCATGTCTGGGA
16405112 CATAGCATCGGCACGGTTATGTGAGAGCT
66 CATAGCATCGGCACGGTTATGTGAGAGCT
*
16405141 AGTGTAAGATCATGTCAGGGACATGGCATCGGCCT-CGAAGATGATAGCT-AGTGTAAGACTATG
1 AGTGTAAGA-CATGTCAGGGACAT-GCATCGG-CTGC-AAGATG-T-G-TAAGTGTAAGACCATG
*
16405204 TCTGGGACATGGCATCGGCAC
59 TCTGGGACATAGCATCGGCAC
16405225 CTTACCCATG
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
94 9 0.12
95 12 0.17
96 8 0.11
97 8 0.11
98 1 0.01
99 33 0.46
100 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (94 bp):
AGTGTAAGACATGTCAGGGACATGCATCGGCTGCAAGATGTGTAAGTGTAAGACCATGTCTGGGA
CATAGCATCGGCACGGTTATGTGAGAGCT
Found at i:16410072 original size:14 final size:14
Alignment explanation
Indices: 16410053--16410085 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
16410043 AAATTGGAAC
16410053 AAATTTTGTAATAT
1 AAATTTTGTAATAT
*
16410067 AAATTTTGTTATAT
1 AAATTTTGTAATAT
16410081 AAATT
1 AAATT
16410086 AAATATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
AAATTTTGTAATAT
Found at i:16410109 original size:62 final size:62
Alignment explanation
Indices: 16409974--16410194 Score: 300
Period size: 62 Copynumber: 3.5 Consensus size: 62
16409964 ATTAAACAAC
* * * * *
16409974 TAAAACTTGTAACAAACTTTATAATATAACTTTTGTTTATAATATAAATTAAATACATTACATCA
1 TAAAAATTGGAACAAACTTTGTAATATAAATTTTG--T-T-ATATAAATTAAATACATTACAACA
*
16410039 C
62 T
* *
16410040 TAAAAATTGGAACAAATTTTGTAATATAAATTTTGTTATATAAATTAAATATATTACAACAT
1 TAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACATTACAACAT
* * *
16410102 TAAAAATTGGAACAAACTTTGCAATATAAATTTTTTTATATAAATTAAATACATTATAACAT
1 TAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACATTACAACAT
16410164 T-AAAATTGGAACAAACTTTGTAATATAAATT
1 TAAAAATTGGAACAAACTTTGTAATATAAATT
16410195 AGGTACATTG
Statistics
Matches: 141, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
61 29 0.21
62 80 0.57
63 1 0.01
64 1 0.01
66 30 0.21
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (62 bp):
TAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACATTACAACAT
Found at i:16413122 original size:10 final size:10
Alignment explanation
Indices: 16413109--16413141 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
16413099 TTTCTAATAT
*
16413109 AAAAACTTTA
1 AAAAATTTTA
16413119 AAAAATTTTA
1 AAAAATTTTA
16413129 AAAAATTTTA
1 AAAAATTTTA
16413139 AAA
1 AAA
16413142 CATAACATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:16413750 original size:4 final size:4
Alignment explanation
Indices: 16413741--16413785 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
16413731 AATACATGCC
16413741 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
16413786 CGTATTTTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:16424254 original size:74 final size:73
Alignment explanation
Indices: 16424151--16424300 Score: 210
Period size: 74 Copynumber: 2.0 Consensus size: 73
16424141 CGAGAAATTA
* * * *
16424151 AAATTAAATAAAATCTGCTTCAAGCTTTATTCTCGCTTTTTAACAAGATTTTATTCGATTTTAAT
1 AAATTAAATAAAATCTGCTTCAAGATTTATTCCCGCTATTTAACAAGATTTTATTCGATATTAA-
16424216 TTTGTTTCC
65 TTTGTTTCC
* * ** *
16424225 AAATTAAATAAAATTTGTTTTGAGATTTATTCCCGCTATTTAACAAGATTTTATTCGATATTGAT
1 AAATTAAATAAAATCTGCTTCAAGATTTATTCCCGCTATTTAACAAGATTTTATTCGATATTAAT
16424290 TTGTTTCC
66 TTGTTTCC
16424298 AAA
1 AAA
16424301 CGAAGACTTA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
73 12 0.18
74 55 0.82
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (73 bp):
AAATTAAATAAAATCTGCTTCAAGATTTATTCCCGCTATTTAACAAGATTTTATTCGATATTAAT
TTGTTTCC
Found at i:16424472 original size:87 final size:87
Alignment explanation
Indices: 16424360--16424549 Score: 229
Period size: 87 Copynumber: 2.2 Consensus size: 87
16424350 ACAGACTTTA
* * * * * * * *
16424360 TTTCGGGATTTATTCCTGCCATTCAACGAATTTTATTCCTTTTTTTATTTTATT-TCTAAACGAG
1 TTTCGAGATTTATTCCAGCCATTCAACGAATTTTATT-ATATTTTGATTTTATTGCCAAAACAAG
*
16424424 AAATTAAAGTTAAATAAAATCTG
65 AAATTAAAATTAAATAAAATCTG
* * * * * *
16424447 TTTTGAGATTTATTCCAGTCGTTCAATGGATTTTATTATATTTTGATTTTGTTGCCAAAACAAGA
1 TTTCGAGATTTATTCCAGCCATTCAACGAATTTTATTATATTTTGATTTTATTGCCAAAACAAGA
16424512 AATTAAAATTAAATAAAATCTG
66 AATTAAAATTAAATAAAATCTG
16424534 TTTCGAGATTTATTCC
1 TTTCGAGATTTATTCC
16424550 CGCCGTTTAA
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
86 12 0.14
87 74 0.86
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (87 bp):
TTTCGAGATTTATTCCAGCCATTCAACGAATTTTATTATATTTTGATTTTATTGCCAAAACAAGA
AATTAAAATTAAATAAAATCTG
Found at i:16424585 original size:87 final size:87
Alignment explanation
Indices: 16424417--16424592 Score: 221
Period size: 87 Copynumber: 2.0 Consensus size: 87
16424407 TTTTATTTCT
* * * * **
16424417 AAACGAGAAATTAAAGTTAAATAAAATCTGTTTTGAGATTTATTCCAGTCGTTCAATGGATTTTA
1 AAACAAGAAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCAGCCGTTCAAAAGATTTTA
* *
16424482 TTATATTTTGATTTTGTTGCCA
66 TTATATATTGAATTTGTTGCCA
* *
16424504 AAACAAGAAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCCGCCGTTTAACAAGATTTT
1 AAACAAGAAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCAGCCGTTCAA-AAGATTTT
*
16424569 ATT-TGATATT-AATTTGTTTCCA
65 ATTAT-ATATTGAATTTGTTGCCA
16424591 AA
1 AA
16424593 TGAAGATTTA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
87 63 0.83
88 13 0.17
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (87 bp):
AAACAAGAAATTAAAATTAAATAAAATCTGTTTCGAGATTTATTCCAGCCGTTCAAAAGATTTTA
TTATATATTGAATTTGTTGCCA
Found at i:16424751 original size:292 final size:291
Alignment explanation
Indices: 16424225--16424946 Score: 1049
Period size: 292 Copynumber: 2.5 Consensus size: 291
16424215 TTTTGTTTCC
* * *
16424225 AAATTAAATAAAATTTGTTTTGAGATTTATTCCCGCTATTTAACAAGATTTTATTCGATATTGAT
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGCCATTTAACAAGATTTTATTCGATATTGAT
* *
16424290 TTGTTTCCAAACGAAGACTTAATCAAATAATTCTATTTCAGGATTTATTCTCACCGTTTAACAGA
66 TTGTTTCCAAACGAAGACTTAATCAAATAATTCTGTTTTAGGATTTATT-TCACCGTTTAACAGA
* *
16424355 CTTTATTTCGGGATTTATTCCTGCCATTCAACGAATTTTATTCCTTTTTTTATTTTATTTCTAAA
130 CTTTATTTCGGGATTTATTCCTGCCATTCAACGAATTTTATTCCTTTTTTTACTTTATTTCCAAA
* * * * *
16424420 CGAGAAATTAAAGTTAAATAAAATCTGTTTTGAGATTTATT-CCAGTCGTTCAATGGATTTTATT
195 CGAGAAATTAAAGTTAAATAAAATCTATTTCGAGATTTATTCCCA-CCATTCAACGGATTTTATT
*
16424484 ATATTTTGATTTTGTTGCCAAAACAAGAAATTA
259 ATATTTTGATTTTGTTACCAAAACAAGAAATTA
* * *
16424517 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGCCGTTTAACAAGATTTTATTTGATATTAAT
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGCCATTTAACAAGATTTTATTCGATATTGAT
* * *
16424582 TTGTTTCCAAATGAAGATTTAATCAAATAATTTTGTTTTAGGATTTATTTCACCCGTTTAACAGA
66 TTGTTTCCAAACGAAGACTTAATCAAATAATTCTGTTTTAGGATTTATTTCA-CCGTTTAACAGA
* *
16424647 CTTTATTTCGGGATTTATT-CTCGCCATTCAACGGATTTTTTTTCC-TTTTTTACTTTATTTCCA
130 CTTTATTTCGGGATTTATTCCT-GCCATTCAAC-GAATTTTATTCCTTTTTTTACTTTATTTCCA
* *
16424710 AACGAGAAATTAAAGTTAAATAAAATTTATTTCGGGATTTATTCCCACCATTCAACGGATTTTAT
193 AACGAGAAATTAAAGTTAAATAAAATCTATTTCGAGATTTATTCCCACCATTCAACGGATTTTAT
* *
16424775 TATATTTTGATTTTTTTACCAAAACGAGAAATTA
258 TATATTTTGATTTTGTTACCAAAACAAGAAATTA
* * *
16424809 AAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCATTTAACAAGATTTTATTCAATACTGAT
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGCCATTTAACAAGATTTTATTCGATATTGAT
* * * *
16424874 TTGTTTCTAAACGAAGACTTAATCAAATAATTCTG-TTTCGTGATTTA-TTCATGTCGTTTAATA
66 TTGTTTCCAAACGAAGACTTAATCAAATAATTCTGTTTTAG-GATTTATTTCA--CCGTTTAACA
16424937 GACTTTATTT
128 GACTTTATTT
16424947 TGATTTAATT
Statistics
Matches: 385, Mismatches: 39, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
291 13 0.03
292 359 0.93
293 13 0.03
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (291 bp):
AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGCCATTTAACAAGATTTTATTCGATATTGAT
TTGTTTCCAAACGAAGACTTAATCAAATAATTCTGTTTTAGGATTTATTTCACCGTTTAACAGAC
TTTATTTCGGGATTTATTCCTGCCATTCAACGAATTTTATTCCTTTTTTTACTTTATTTCCAAAC
GAGAAATTAAAGTTAAATAAAATCTATTTCGAGATTTATTCCCACCATTCAACGGATTTTATTAT
ATTTTGATTTTGTTACCAAAACAAGAAATTA
Found at i:16424800 original size:87 final size:87
Alignment explanation
Indices: 16424648--16424863 Score: 276
Period size: 87 Copynumber: 2.5 Consensus size: 87
16424638 TTTAACAGAC
* * * *
16424648 TTTATTTCGGGATTTATTCTCGCCATTCAACGGATTTT-TTTTCCTTTTTTACTTTATTTCCAAA
1 TTTATTTCGGGATTTATTCCCGCCATTCAACGGATTTTATTAT-CATTTTGACTTTATTTCCAAA
*
16424712 CGAGAAATTAAAGTTAAATAAAA
65 CGAGAAATTAAAATTAAATAAAA
* *
16424735 TTTATTTCGGGATTTATTCCCACCATTCAACGGATTTTATTAT-ATTTTGA-TTTTTTTACCAAA
1 TTTATTTCGGGATTTATTCCCGCCATTCAACGGATTTTATTATCATTTTGACTTTATTT-CC-AA
16424798 ACGAGAAATTAAAATTAAATAAAA
64 ACGAGAAATTAAAATTAAATAAAA
* * * *
16424822 TCTGTTTCGGGATTTATTCCCGCCATTTAACAAGATTTTATT
1 TTTATTTCGGGATTTATTCCCGCCATTCAAC-GGATTTTATT
16424864 CAATACTGAT
Statistics
Matches: 113, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
85 6 0.05
86 7 0.06
87 88 0.78
88 12 0.11
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (87 bp):
TTTATTTCGGGATTTATTCCCGCCATTCAACGGATTTTATTATCATTTTGACTTTATTTCCAAAC
GAGAAATTAAAATTAAATAAAA
Found at i:16437872 original size:11 final size:10
Alignment explanation
Indices: 16437852--16437893 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
16437842 TGAACGTTGA
*
16437852 TTCTATATTT
1 TTCTTTATTT
*
16437862 TTCTTTAATT
1 TTCTTTATTT
16437872 TT-TTTATTT
1 TTCTTTATTT
16437881 TTCTTTGATTT
1 TTCTTT-ATTT
16437892 TT
1 TT
16437894 TGGAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 8 0.30
10 13 0.48
11 6 0.22
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.76
Consensus pattern (10 bp):
TTCTTTATTT
Found at i:16437881 original size:19 final size:19
Alignment explanation
Indices: 16437857--16437894 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16437847 GTTGATTCTA
16437857 TATTTTTCTTTAATTTTTT
1 TATTTTTCTTTAATTTTTT
*
16437876 TATTTTTCTTTGATTTTTT
1 TATTTTTCTTTAATTTTTT
16437895 GGAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (19 bp):
TATTTTTCTTTAATTTTTT
Found at i:16439497 original size:15 final size:15
Alignment explanation
Indices: 16439477--16439505 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16439467 TTGATGGTTA
16439477 TGTTCTTTTTTTTTT
1 TGTTCTTTTTTTTTT
16439492 TGTTCTTTTTTTTT
1 TGTTCTTTTTTTTT
16439506 CATGTAGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (15 bp):
TGTTCTTTTTTTTTT
Found at i:16441834 original size:6 final size:6
Alignment explanation
Indices: 16441825--16441856 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
16441815 GCTCTGGCTT
16441825 TGGCAC TGGCAC TGGCAC TGGCAC TGGCAC TG
1 TGGCAC TGGCAC TGGCAC TGGCAC TGGCAC TG
16441857 TAATCCTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.31, G:0.34, T:0.19
Consensus pattern (6 bp):
TGGCAC
Found at i:16442749 original size:30 final size:30
Alignment explanation
Indices: 16442707--16442764 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
16442697 GGTTGGGATG
*
16442707 GAAGGGAGTAAAAGTTTTAGAGGGAAAGTGA
1 GAAGGGAGTAAAAGTTTT-GAAGGAAAGTGA
16442738 GAAGGG-GTAAAAGTTTTGAAGGAAAGT
1 GAAGGGAGTAAAAGTTTTGAAGGAAAGT
16442765 AAAAATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 9 0.35
30 11 0.42
31 6 0.23
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (30 bp):
GAAGGGAGTAAAAGTTTTGAAGGAAAGTGA
Found at i:16450885 original size:11 final size:11
Alignment explanation
Indices: 16450869--16450896 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
16450859 CCCAACTATA
16450869 GTTGAATATTG
1 GTTGAATATTG
16450880 GTTGAATATTG
1 GTTGAATATTG
16450891 GTTGAA
1 GTTGAA
16450897 GGCCACAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (11 bp):
GTTGAATATTG
Found at i:16456840 original size:20 final size:20
Alignment explanation
Indices: 16456817--16456858 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
16456807 TTTGGGTAAA
* *
16456817 TTTTGGACTATTTGGACATT
1 TTTTGGACTATCTAGACATT
16456837 TTTTGGACTATCTAGACATT
1 TTTTGGACTATCTAGACATT
16456857 TT
1 TT
16456859 GGTTGTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (20 bp):
TTTTGGACTATCTAGACATT
Found at i:16465150 original size:40 final size:39
Alignment explanation
Indices: 16465084--16465177 Score: 93
Period size: 40 Copynumber: 2.4 Consensus size: 39
16465074 CCATCTCTGT
* *
16465084 CCAACCCA-ACACACC-ATGTGGAGATAAGATCAACCTAC
1 CCAA-CCATACACACCAATGTGGAGATAAAATCAACCCAC
* * * *
16465122 CCAGCCATACACACCAAGTGTGGGGATAAAATTAACCCAT
1 CCAACCATACACACCAA-TGTGGAGATAAAATCAACCCAC
*
16465162 CCAACCCTACACACCA
1 CCAACCATACACACCA
16465178 CATGGTACCG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
37 3 0.07
38 10 0.22
39 1 0.02
40 31 0.69
ACGTcount: A:0.38, C:0.35, G:0.13, T:0.14
Consensus pattern (39 bp):
CCAACCATACACACCAATGTGGAGATAAAATCAACCCAC
Found at i:16467327 original size:31 final size:31
Alignment explanation
Indices: 16467292--16467358 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
16467282 CCAAGTCTCG
* * *
16467292 TACAAAGATATAA-TCAATACAAGACAAACTA
1 TACAAAAATATAAGT-AATACAAGAAAAACCA
16467323 TACAAAAATATAAGTAATACAAGAAAAACCA
1 TACAAAAATATAAGTAATACAAGAAAAACCA
16467354 TACAA
1 TACAA
16467359 GACAAATATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.61, C:0.15, G:0.06, T:0.18
Consensus pattern (31 bp):
TACAAAAATATAAGTAATACAAGAAAAACCA
Found at i:16472282 original size:11 final size:11
Alignment explanation
Indices: 16472248--16472285 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16472238 AACTTATAGA
16472248 ATTTTATAAAT
1 ATTTTATAAAT
*
16472259 ATATTT-TATAT
1 AT-TTTATAAAT
16472270 ATTTTATAAAT
1 ATTTTATAAAT
16472281 ATTTT
1 ATTTT
16472286 CATTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.13
11 17 0.74
12 3 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTTATAAAT
Found at i:16475845 original size:40 final size:40
Alignment explanation
Indices: 16475780--16475875 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
16475770 GATTATGTTC
* * * *
16475780 GACACTAAGTATGCGATTTGAAATAGCTTCGGCTATAAAT-A
1 GACACTAAGTGTGTGAATTGAAATAGCTTCAGCTAT--ATGA
*
16475821 G-CACTAAGTGTGTGAATTGGAATAGCTTCAGCTATATGA
1 GACACTAAGTGTGTGAATTGAAATAGCTTCAGCTATATGA
16475860 GACACTAAGTGTGTGA
1 GACACTAAGTGTGTGA
16475876 TACCGAGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
38 2 0.04
39 2 0.04
40 43 0.90
41 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (40 bp):
GACACTAAGTGTGTGAATTGAAATAGCTTCAGCTATATGA
Found at i:16480867 original size:27 final size:27
Alignment explanation
Indices: 16480836--16481013 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
16480826 TAAATTGTAC
16480836 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
16480863 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
16480889 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
16480917 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
16480945 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
16480972 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
16480999 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
16481014 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:16480950 original size:82 final size:81
Alignment explanation
Indices: 16480837--16480992 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16480827 AAATTGTACA
* *
16480837 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
16480901 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
16480918 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
16480983 TGCGAGTTGA
65 TGCGAATTGA
16480993 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:16481004 original size:82 final size:81
Alignment explanation
Indices: 16480833--16481013 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
16480823 GATTAAATTG
* *
16480833 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
16480898 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
16480914 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
16480978 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
16480996 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
16481014 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:16495830 original size:827 final size:825
Alignment explanation
Indices: 16494220--16495872 Score: 2031
Period size: 827 Copynumber: 2.0 Consensus size: 825
16494210 TGATGATAAT
* * * *
16494220 CCGTAATTTATACATATTTTTATCCCATGCTTAGCGCATTTACGGATGATTTCTCCTTAGATTTG
1 CCGTAATTTATACATATTTTTACCCCATGCTTAACACATTTACGGATGATTTCTCCTTAGAATTG
*
16494285 GTGAATTCGATGCTTCTAATCATTTAATTTCATGTTCTATACTTAGGTGAGCATAAGAGAGTAAA
66 GTGAATTCGATGCTCCTAATCATTTAATTTCATGTTCTATACTTAGGTGAGCATAAGAGAGTAAA
* * * * *
16494350 AAAGAGCGAGAAACGGGCCGAAAATGGAGAAAATAGAACTACATGGGAAAACAACACGGCCTGGA
131 AAAGAACGAGAAACGGGCCAAAAACGGAGAAAATAGAACCACATGGCAAAACAACACGGCCTGGA
** * * * * *
16494415 CTTCCTCACACGGGCATGTGACACGGCTGTGTCAATTTGGCAGGATCGAAGCACAACTTACACGG
196 CTTCCTCACACGGGCATGCCACACGACTGTGTCAATTTGGCAGAATCGAAGCACAACTCAAACGA
* * * *
16494480 GTAGATCACACACCCATGCCCATTTAATAGCCTTGACCACGACCTTAAGTAATCGCACACGGGCC
261 GTAAAACACACACCCATGCCCATTTAAAAG-CTTGACCACGACCTGAAGTAATCGCACACGGGCC
* * *
16494545 GTGTCCTTGCTGAACCCAAGTTTAGTCCAATTTAGAAAAGGCCAATTTTGAGGGCTCTTAGCATT
325 GTGTCCCTGCTGAACCCAA---TAGTCCAATTGAGAAAAGGCCAATTTTGAGGACTCTTAGCATT
* * * * * ** *
16494610 CCAAAGCCTATTTAAACACTTGAGGAGGCACTTAGGAAGGGGGACGCAGAGTAGGAAGCAAGGAA
387 CCAAAGCC-ATTAAAACACCTGAGAAGGCA--TAGGAAAGAGGAAACAGAGAAGGAAGCAAGGAA
* * *
16494675 TTACTCAAGGAAAGCCGATTGATCCATCTCAAGAGCCGGATTCATCATCAAGACTGAAGATCTCC
449 CTACTCAAGGAAAGCCGATTGATCCATCTCAAGAGCCGAATTCACCATCAAGACTGAAGATCTCC
* * * * *
16494740 CTTCAAGTTCCTTTAGGAGTTTTGGGTTTTCTTATGTTTTGTTATCTTTATGCTTTTAAGGTGTT
514 CCTCAAGTTCCTTTAGGAGTTTTGGGTTTTCTTATGTTTTGTTATCATCATGCTTCTAAGATGTT
*
16494805 TTCTTTCATAAGTATGAACTAAATCCCTAAATACCTAAGGGGAATGAAACCTAATACATATCTTG
579 TTCTTT-ATAAGTATGAACTAAATCCCTAAATACCTAAGGGGAATGAAACCTAAGACATATCTTG
*
16494870 TTATTATTATCTAAATTATATGATAAATATTTGACTTGTTCTTAATTATGTGTTCTTAATTCTTG
643 TTATTATTATCTAAATTATATGATAAATATTTAACTTGTTCTTAATTATGTGTTCTTAATTCTTG
* * * *
16494935 TTTTGATATTCCAAGATATTGATTCAAGTTAAGCTCTTATTCAGAGGAGGAGTAAACCCTGTCTA
708 TTTTGATATTCCAAGATACTGATTCAAGATAAGCTCTTATTCAGAGGAGGAATAAACCCTGCCTA
*
16495000 AGAGTAAATTTGTCATAATTAAGCGGAGTTGATTGCGCGCCTAGAGTTATAGA
773 AGAGTAAATTTGTCATAATTAAGCAGAGTTGATTGCGCGCCTAGAGTTATAGA
* * *
16495053 CCGTAATTTATACATATTTTTACCCCATGCTTAACACATTTTATGGATGATTTTTCTTTAGAATT
1 CCGTAATTTATACATATTTTTACCCCATGCTTAACACA-TTTACGGATGATTTCTCCTTAGAATT
* * * *
16495118 GGTGAATTCGATGCTCCTATTGC-TTTAATTTCATGTTTTATACTTAGGTGAGCATAGGAGAG-C
65 GGTGAATTCGATGCTCCTAAT-CATTTAATTTCATGTTCTATACTTAGGTGAGCATAAGAGAGTA
* * * *
16495181 GAAAGGAACGAGAAACGGGCCAAAAACGGAGAAAAT-GAGCCA-ATGTTCAAAATCAACACGGCC
129 AAAAAGAACGAGAAACGGGCCAAAAACGGAGAAAATAGAACCACATG-GCAAAA-CAACACGGCC
* *
16495244 TGGACTTCCTTACACGGG-A-GACCACACGACTGTGTCAATTTGGCAGAATCGAAGCACGACTCA
192 TGGACTTCCTCACACGGGCATG-CCACACGACTGTGTCAATTTGGCAGAATCGAAGCACAACTCA
* * * * * *
16495307 AACGAGTAAAACACACGCCCGTG-CCGTTCTAACAAG-TTCGAGCAC-AGCCTGAAGTAGTCGTA
256 AACGAGTAAAACACACACCCATGCCCATT-TAA-AAGCTT-GACCACGA-CCTGAAGTAATCGCA
* * *
16495369 CACGGG-CGTGTCCCTGCTGAGCCC-A-AGTCCAATTCGA-AAAAGGCTAATTTTGAGGACTTTT
317 CACGGGCCGTGTCCCTGCTGAACCCAATAGTCCAATT-GAGAAAAGGCCAATTTTGAGGACTCTT
*
16495430 AGGCATTCTAAAGCC-TTAAATACACCCT-A-AAGG-A-AGAGAAAGAGGAAACAGAGAAAAGGA
381 A-GCATTCCAAAGCCATTAAA-ACA-CCTGAGAAGGCATAG-GAAAGAGGAAACAGAG--AAGGA
* * * * *
16495490 GGCAGGGAACTGCTCAA-GAGAAGCCGATTGATCCATCTC-AGAAGCCGAATTCACCATTAAGAT
440 AGCAAGGAACTACTCAAGGA-AAGCCGATTGATCCATCTCAAG-AGCCGAATTCACCATCAAGAC
*
16495553 TGAAGATCTCCCCTCAATTTCCCTTTAGGAGTTTTGGGTTTTCTTTATGTTTTG-TATTCATCAT
503 TGAAGATCTCCCCTCAAGTT-CCTTTAGGAGTTTTGGGTTTTC-TTATGTTTTGTTA-TCATCAT
* * * * *
16495617 TCTTCTGATATGTTTTCCTTT-TTAGCTATGAACTAAATCCCTTAAATACTTAAGGGGAATGAAA
565 GCTTCTAAGATGTTTT-CTTTATAAG-TATGAACTAAATCCC-TAAATACCTAAGGGGAATGAAA
* * * *
16495681 CCTAAGACGA-ATCTTGTTGTTATTTTCTGAATTGTATGATAAATATTTAACTTGTTCTTAATTA
627 CCTAAGAC-ATATCTTGTTATTATTATCTAAATTATATGATAAATATTTAACTTGTTCTTAATTA
16495745 TGTGTTCTTAATTCTTGTTTTGATA-TCTCAAGATACTGATTCAAGATAAGCTCTTATTCAGAGG
691 TGTGTTCTTAATTCTTGTTTTGATATTC-CAAGATACTGATTCAAGATAAGCTCTTATTCAGAGG
* * * *
16495809 AGGAATAGACCCTGCCTAAGAGTACATTTTTCATAATTAAGCAGAGTTGATTGCGCGCTTAGAG
755 AGGAATAAACCCTGCCTAAGAGTAAATTTGTCATAATTAAGCAGAGTTGATTGCGCGCCTAGAG
16495873 ATAGGGTGAC
Statistics
Matches: 705, Mismatches: 89, Indels: 58
0.83 0.10 0.07
Matches are distributed among these distances:
821 2 0.00
822 12 0.02
823 4 0.01
824 72 0.10
825 34 0.05
826 78 0.11
827 212 0.30
828 1 0.00
830 1 0.00
831 27 0.04
832 88 0.12
833 95 0.13
834 78 0.11
835 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (825 bp):
CCGTAATTTATACATATTTTTACCCCATGCTTAACACATTTACGGATGATTTCTCCTTAGAATTG
GTGAATTCGATGCTCCTAATCATTTAATTTCATGTTCTATACTTAGGTGAGCATAAGAGAGTAAA
AAAGAACGAGAAACGGGCCAAAAACGGAGAAAATAGAACCACATGGCAAAACAACACGGCCTGGA
CTTCCTCACACGGGCATGCCACACGACTGTGTCAATTTGGCAGAATCGAAGCACAACTCAAACGA
GTAAAACACACACCCATGCCCATTTAAAAGCTTGACCACGACCTGAAGTAATCGCACACGGGCCG
TGTCCCTGCTGAACCCAATAGTCCAATTGAGAAAAGGCCAATTTTGAGGACTCTTAGCATTCCAA
AGCCATTAAAACACCTGAGAAGGCATAGGAAAGAGGAAACAGAGAAGGAAGCAAGGAACTACTCA
AGGAAAGCCGATTGATCCATCTCAAGAGCCGAATTCACCATCAAGACTGAAGATCTCCCCTCAAG
TTCCTTTAGGAGTTTTGGGTTTTCTTATGTTTTGTTATCATCATGCTTCTAAGATGTTTTCTTTA
TAAGTATGAACTAAATCCCTAAATACCTAAGGGGAATGAAACCTAAGACATATCTTGTTATTATT
ATCTAAATTATATGATAAATATTTAACTTGTTCTTAATTATGTGTTCTTAATTCTTGTTTTGATA
TTCCAAGATACTGATTCAAGATAAGCTCTTATTCAGAGGAGGAATAAACCCTGCCTAAGAGTAAA
TTTGTCATAATTAAGCAGAGTTGATTGCGCGCCTAGAGTTATAGA
Found at i:16505378 original size:45 final size:45
Alignment explanation
Indices: 16505323--16505413 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
16505313 GGTGAAACCT
* *
16505323 AATAAGGGAATCCATAGATTGAGTTAATGTAATTCTAGGGTGTTA
1 AATAAAGGAATCCATAGATTGAGTTAATGCAATTCTAGGGTGTTA
16505368 AATAAAGGAATCCATAGATTGAGTTAATGCAATTCTAGGGTGTTA
1 AATAAAGGAATCCATAGATTGAGTTAATGCAATTCTAGGGTGTTA
16505413 A
1 A
16505414 TTAGAAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (45 bp):
AATAAAGGAATCCATAGATTGAGTTAATGCAATTCTAGGGTGTTA
Found at i:16509913 original size:12 final size:12
Alignment explanation
Indices: 16509896--16509925 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16509886 ATCGTCAGAC
16509896 CGTGGGCATTGA
1 CGTGGGCATTGA
16509908 CGTGGGCATTGA
1 CGTGGGCATTGA
*
16509920 TGTGGG
1 CGTGGG
16509926 GGCTCTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.47, T:0.27
Consensus pattern (12 bp):
CGTGGGCATTGA
Found at i:16510943 original size:20 final size:23
Alignment explanation
Indices: 16510898--16510947 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 23
16510888 ATTTTTTTAC
16510898 TTTTATTCTATTTTAAGACTACT
1 TTTTATTCTATTTTAAGACTACT
16510921 TTTTATT-T-TTTTAAG-CTTA-T
1 TTTTATTCTATTTTAAGAC-TACT
16510941 TTTTATT
1 TTTTATT
16510948 AGGTTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.35
21 9 0.35
22 1 0.04
23 7 0.27
ACGTcount: A:0.22, C:0.08, G:0.04, T:0.66
Consensus pattern (23 bp):
TTTTATTCTATTTTAAGACTACT
Found at i:16517585 original size:40 final size:40
Alignment explanation
Indices: 16517536--16517686 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 40
16517526 CGAAATTTAA
** *
16517536 CCGGATATAGCT-ACTCGTTCAAATGCCTTCAGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCAGGACATAAC
* * *
16517576 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCAGGACATAAC
* * * * *
16517616 CCGGATTTAGTAACTCACACCAATGCCTTC--GAGCTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCAGGA-CATAAC
*
16517655 CC-GAAATTAGTAACTCGCACAAATGCCTTCAG
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCAG
16517687 ATCTTAGTCC
Statistics
Matches: 91, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
38 4 0.04
39 29 0.32
40 58 0.64
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCAGGACATAAC
Found at i:16517680 original size:39 final size:39
Alignment explanation
Indices: 16517583--16517693 Score: 141
Period size: 39 Copynumber: 2.8 Consensus size: 39
16517573 AGCCCGGTTA
* * * *
16517583 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGAG-CTTAGCCCGAAAT
* *
16517623 TAGTAACTCACACCAATGCCTTCGAGCTTAGCCCGAAAT
1 TAGTAACTCGCACAAATGCCTTCGAGCTTAGCCCGAAAT
*
16517662 TAGTAACTCGCACAAATGCCTTCAGATCTTAG
1 TAGTAACTCGCACAAATGCCTTC-GAGCTTAG
16517694 TCCGGATATG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 31 0.51
40 30 0.49
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (39 bp):
TAGTAACTCGCACAAATGCCTTCGAGCTTAGCCCGAAAT
Found at i:16518522 original size:59 final size:59
Alignment explanation
Indices: 16518451--16518570 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
16518441 AAGACACCAT
16518451 TTACCCTTATATTTACCATAGCCGAAAACCTTACTCATTCCAAAAATTCAAATCTCAAG
1 TTACCCTTATATTTACCATAGCCGAAAACCTTACTCATTCCAAAAATTCAAATCTCAAG
16518510 TTACCCTTATATTTACCATAGCCGAAAACCTTACTCATTCCAAAAATTCAAATCTCAAG
1 TTACCCTTATATTTACCATAGCCGAAAACCTTACTCATTCCAAAAATTCAAATCTCAAG
16518569 TT
1 TT
16518571 GGTCACAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.32
Consensus pattern (59 bp):
TTACCCTTATATTTACCATAGCCGAAAACCTTACTCATTCCAAAAATTCAAATCTCAAG
Found at i:16519086 original size:85 final size:85
Alignment explanation
Indices: 16518954--16519220 Score: 534
Period size: 85 Copynumber: 3.1 Consensus size: 85
16518944 TAATATTTTA
16518954 CCACCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCTACATGTTTATGACATGT
1 CCACCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCTACATGTTTATGACATGT
16519019 TTTTAGCCATAACATCTTGT
66 TTTTAGCCATAACATCTTGT
16519039 CCACCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCTACATGTTTATGACATGT
1 CCACCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCTACATGTTTATGACATGT
16519104 TTTTAGCCATAACATCTTGT
66 TTTTAGCCATAACATCTTGT
16519124 CCACCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCTACATGTTTATGACATGT
1 CCACCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCTACATGTTTATGACATGT
16519189 TTTTAGCCATAACATCTTGT
66 TTTTAGCCATAACATCTTGT
16519209 CCACCCATGCTC
1 CCACCCATGCTC
16519221 ATGGCCGGCC
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 182 1.00
ACGTcount: A:0.25, C:0.27, G:0.08, T:0.39
Consensus pattern (85 bp):
CCACCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCTACATGTTTATGACATGT
TTTTAGCCATAACATCTTGT
Found at i:16521913 original size:56 final size:56
Alignment explanation
Indices: 16521827--16521942 Score: 223
Period size: 56 Copynumber: 2.1 Consensus size: 56
16521817 GGGATGATGT
16521827 GCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGG
1 GCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGG
*
16521883 GCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGG
1 GCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGG
16521939 GCAA
1 GCAA
16521943 TAAACTAATA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.22
Consensus pattern (56 bp):
GCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGG
Found at i:16523346 original size:40 final size:40
Alignment explanation
Indices: 16523068--16523332 Score: 331
Period size: 40 Copynumber: 6.7 Consensus size: 40
16523058 TCGAATGATG
* * * * *
16523068 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
16523108 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
16523148 TTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
16523187 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
16523227 TTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
16523267 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
16523308 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
16523333 AACGAGTAGC
Statistics
Matches: 199, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
39 33 0.17
40 156 0.78
41 10 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:16528908 original size:40 final size:40
Alignment explanation
Indices: 16528859--16529007 Score: 142
Period size: 40 Copynumber: 3.8 Consensus size: 40
16528849 CGGAATTTAA
** *
16528859 CCGGATATAGCT-ACTCGTTCAAATGCCTTCAGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCAGGACATAAC
* * *
16528899 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCAGGACATAAC
* * * * * *
16528939 CCGGATTTAGTAACTCACACCAATGCCTTC-GGGCTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCAGGACATAAC
*
16528978 CTGGA-ATTAGTAACTCGCACAAATGCCTTC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTC
16529008 GGATCTTAGT
Statistics
Matches: 91, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
39 33 0.36
40 58 0.64
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCAGGACATAAC
Found at i:16528978 original size:79 final size:79
Alignment explanation
Indices: 16528880--16529062 Score: 201
Period size: 79 Copynumber: 2.3 Consensus size: 79
16528870 TACTCGTTCA
* * *
16528880 AATGCCTTCAGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTC-GGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
*
16528943 ATTTAGTAACTCA-CACC
63 ATATAGTAACTCAGCA-C
* **
16528960 AATGCCTTCGGGCTTAGCCTGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATA
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATA
* * *
16529025 TGGTCACTTAGCAC
66 TAGTAACTCAGCAC
*
16529039 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGG-CTTAGCCCGGA
16529063 CATCATTCGA
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 62 0.71
80 22 0.25
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATA
TAGTAACTCAGCAC
Found at i:16529003 original size:39 final size:40
Alignment explanation
Indices: 16528878--16529062 Score: 164
Period size: 40 Copynumber: 4.7 Consensus size: 40
16528868 GCTACTCGTT
* * * *
16528878 CAAATGCCTTCAGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAAT-TAGTAACTCGCA
* *
16528918 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
* * *
16528958 CCAATGCCTTCGGG-CTTAGCCTGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
** * * *
16528997 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAAT-TAGTAAC-TCGCA
*
16529038 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
16529063 CATCATTCGA
Statistics
Matches: 122, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 74 0.61
41 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
Found at i:16533056 original size:17 final size:17
Alignment explanation
Indices: 16533030--16533062 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16533020 CTGCCAGAAG
16533030 TAAATAAAAG-AAAAAT
1 TAAATAAAAGCAAAAAT
16533046 TAAACTAAAAGCAAAAA
1 TAAA-TAAAAGCAAAAA
16533063 GTGAATTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (17 bp):
TAAATAAAAGCAAAAAT
Found at i:16541973 original size:17 final size:16
Alignment explanation
Indices: 16541937--16541980 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
16541927 AAAACCTGCC
*
16541937 AAAAGTAAATAAAAGG
1 AAAAGTAAATAAAAGA
*
16541953 AAAATTAAACTAAAAGAA
1 AAAAGTAAA-TAAAAG-A
16541971 AAAAGTAAAT
1 AAAAGTAAAT
16541981 TGCAATAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 7 0.30
18 8 0.35
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.16
Consensus pattern (16 bp):
AAAAGTAAATAAAAGA
Found at i:16553870 original size:41 final size:41
Alignment explanation
Indices: 16553790--16553870 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
16553780 AGCTTGTATC
* * *
16553790 ATACACCGGCACAAAGCCTGCTAGACTCAAAGTCTGATTTT
1 ATACACCGGCACAAAGCCTACTAGACTCAAAGCCCGATTTT
*
16553831 ATACACCGGCA-ATAAGCCTACTAGGCAT-AAAGCCCGATTT
1 ATACACCGGCACA-AAGCCTACTAGAC-TCAAAGCCCGATTT
16553871 AACTCACCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
40 1 0.03
41 32 0.94
42 1 0.03
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (41 bp):
ATACACCGGCACAAAGCCTACTAGACTCAAAGCCCGATTTT
Found at i:16557712 original size:21 final size:21
Alignment explanation
Indices: 16557687--16557736 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
16557677 TTATATGCTC
*
16557687 AGTATGATCTGTAATATGACA
1 AGTATGATCTATAATATGACA
* *
16557708 TGTATGATCTATAATATGATA
1 AGTATGATCTATAATATGACA
16557729 AGTATGAT
1 AGTATGAT
16557737 ATGTTATTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (21 bp):
AGTATGATCTATAATATGACA
Found at i:16557766 original size:20 final size:21
Alignment explanation
Indices: 16557727--16557766 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16557717 TATAATATGA
*
16557727 TAAGTATGATATGTTATTTGG
1 TAAGCATGATATGTTATTTGG
*
16557748 TAAGCATGATCTG-TATTTG
1 TAAGCATGATATGTTATTTG
16557767 TTGTAAAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.45
Consensus pattern (21 bp):
TAAGCATGATATGTTATTTGG
Found at i:16559895 original size:29 final size:29
Alignment explanation
Indices: 16559850--16559958 Score: 132
Period size: 29 Copynumber: 3.8 Consensus size: 29
16559840 GTGTGACTAT
* *
16559850 ACATGGTCTGGCACACGCCCATGTGTTCC
1 ACATGGCCTGACACACGCCCATGTGTTCC
* *
16559879 ACACGGCCTGAGACACGCCC--GTGTTCC
1 ACATGGCCTGACACACGCCCATGTGTTCC
* * **
16559906 ACATGGTCTGACACAAGCTTATGTGTTCC
1 ACATGGCCTGACACACGCCCATGTGTTCC
16559935 ACATGGCCTGACACACGCCCATGT
1 ACATGGCCTGACACACGCCCATGT
16559959 CACTTGCTTG
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
27 21 0.33
29 43 0.67
ACGTcount: A:0.21, C:0.34, G:0.23, T:0.22
Consensus pattern (29 bp):
ACATGGCCTGACACACGCCCATGTGTTCC
Found at i:16566206 original size:27 final size:27
Alignment explanation
Indices: 16566176--16566353 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
16566166 ATATTGAGTC
* * * *
16566176 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
16566203 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16566230 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
16566258 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
16566285 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
16566312 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16566339 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16566354 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:16566315 original size:82 final size:81
Alignment explanation
Indices: 16566197--16566352 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16566187 TGCTATATAA
* *
16566197 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16566262 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
16566279 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16566343 CACTTAGTGC
65 CACTTAGTGC
16566353 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:16587195 original size:28 final size:29
Alignment explanation
Indices: 16587150--16587204 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
16587140 AAAAAAGTAT
*
16587150 TTTATGTATATATTTATT-ATTTAAATGG
1 TTTATGTATATATTTATTGATTAAAATGG
*
16587178 TTTATTTATAT-TTATATTGATTAAAAT
1 TTTATGTATATATT-TATTGATTAAAAT
16587205 ACAATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 14 0.61
29 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (29 bp):
TTTATGTATATATTTATTGATTAAAATGG
Found at i:16587677 original size:7 final size:7
Alignment explanation
Indices: 16587659--16587755 Score: 50
Period size: 7 Copynumber: 13.4 Consensus size: 7
16587649 AGGGATTAGT
*
16587659 GGGTAAA
1 GGGTTAA
16587666 GGGTTAA
1 GGGTTAA
*
16587673 GGGTTAT
1 GGGTTAA
* *
16587680 GGATTAT
1 GGGTTAA
16587687 GGGTTTAA
1 GGG-TTAA
* *
16587695 TGATTAA
1 GGGTTAA
*
16587702 GGGTTAT
1 GGGTTAA
*
16587709 GGGTTAC
1 GGGTTAA
16587716 GGGTTTAA
1 GGG-TTAA
*
16587724 TGGTTAAA
1 GGGTT-AA
* *
16587732 GGGATAG
1 GGGTTAA
*
16587739 GGGTTAG
1 GGGTTAA
*
16587746 GGGTTGA
1 GGGTTAA
16587753 GGG
1 GGG
16587756 CCGGTTTAAT
Statistics
Matches: 68, Mismatches: 19, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
7 54 0.79
8 14 0.21
ACGTcount: A:0.25, C:0.01, G:0.42, T:0.32
Consensus pattern (7 bp):
GGGTTAA
Found at i:16587683 original size:29 final size:29
Alignment explanation
Indices: 16587651--16587720 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
16587641 TAAAGTTTAG
*
16587651 GGATTAGTGGG-TAAAGGGTTAAGGGTTAT
1 GGATTA-TGGGTTAAAGGATTAAGGGTTAT
* *
16587680 GGATTATGGGTTTAATGATTAAGGGTTAT
1 GGATTATGGGTTAAAGGATTAAGGGTTAT
* *
16587709 GGGTTACGGGTT
1 GGATTATGGGTT
16587721 TAATGGTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 4 0.11
29 31 0.89
ACGTcount: A:0.24, C:0.01, G:0.39, T:0.36
Consensus pattern (29 bp):
GGATTATGGGTTAAAGGATTAAGGGTTAT
Found at i:16587721 original size:29 final size:29
Alignment explanation
Indices: 16587669--16587750 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
16587659 GGGTAAAGGG
* *
16587669 TTAAGGGTTATGGATTATGGGTTTAATGA
1 TTAAGGGTTATGGGTTACGGGTTTAATGA
*
16587698 TTAAGGGTTATGGGTTACGGGTTTAATGG
1 TTAAGGGTTATGGGTTACGGGTTTAATGA
* * *
16587727 TTAAAGGGATAGGGGTTAGGGGTT
1 TT-AAGGGTTATGGGTTACGGGTT
16587751 GAGGGCCGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 28 0.61
30 18 0.39
ACGTcount: A:0.24, C:0.01, G:0.38, T:0.37
Consensus pattern (29 bp):
TTAAGGGTTATGGGTTACGGGTTTAATGA
Found at i:16589736 original size:89 final size:89
Alignment explanation
Indices: 16589585--16589759 Score: 350
Period size: 89 Copynumber: 2.0 Consensus size: 89
16589575 GGGACATCAT
16589585 CAGGAATGTCCTCTAGATCCTCCTCATCAATGGCATGAGTGAGACGGTATTGAGGAGGATCGGTC
1 CAGGAATGTCCTCTAGATCCTCCTCATCAATGGCATGAGTGAGACGGTATTGAGGAGGATCGGTC
16589650 CCACGGCGGCGCTCAATCATCCTC
66 CCACGGCGGCGCTCAATCATCCTC
16589674 CAGGAATGTCCTCTAGATCCTCCTCATCAATGGCATGAGTGAGACGGTATTGAGGAGGATCGGTC
1 CAGGAATGTCCTCTAGATCCTCCTCATCAATGGCATGAGTGAGACGGTATTGAGGAGGATCGGTC
16589739 CCACGGCGGCGCTCAATCATC
66 CCACGGCGGCGCTCAATCATC
16589760 GTCCTGTGTA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.22
Consensus pattern (89 bp):
CAGGAATGTCCTCTAGATCCTCCTCATCAATGGCATGAGTGAGACGGTATTGAGGAGGATCGGTC
CCACGGCGGCGCTCAATCATCCTC
Done.