Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold247
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: 4737410
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 14 of 29
Found at i:2038167 original size:3 final size:3
Alignment explanation
Indices: 2038159--2038194 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2038149 ACAAAGGTAA
2038159 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2038195 TCCTTTTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2042253 original size:1 final size:1
Alignment explanation
Indices: 2042247--2042337 Score: 74
Period size: 1 Copynumber: 91.0 Consensus size: 1
2042237 AAATCTTCAC
* * ** * * * **
2042247 TTTTTTTTTTGTTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
2042312 TTTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
2042338 CCAATTGCCA
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (1 bp):
T
Found at i:2042296 original size:33 final size:33
Alignment explanation
Indices: 2042247--2042336 Score: 155
Period size: 33 Copynumber: 2.7 Consensus size: 33
2042237 AAATCTTCAC
2042247 TTTTTT-TTTTGTTTTTTTTTTTTCTTTTTCCTT
1 TTTTTTGTTTTG-TTTTTTTTTTTCTTTTTCCTT
2042280 TTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCTT
1 TTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCTT
2042313 TTTTTTGTTTTGTTTTTTTCTTTT
1 TTTTTTGTTTTGTTTTTTT-TTTT
2042337 TCCAATTGCC
Statistics
Matches: 55, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
33 46 0.84
34 9 0.16
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.87
Consensus pattern (33 bp):
TTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCTT
Found at i:2054371 original size:22 final size:21
Alignment explanation
Indices: 2054305--2054372 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
2054295 ATTTCACATA
*
2054305 TAATCAATAAT-TAATTGATT
1 TAATAAATAATATAATTGATT
*
2054325 TAATAAATAATA-AAGTGATACT
1 TAATAAATAATATAATTGAT--T
*
2054347 TAATAAATAATATAACTTGGTT
1 TAATAAATAATATAA-TTGATT
2054369 TAAT
1 TAAT
2054373 TCCAAAAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 16 0.41
22 18 0.46
23 2 0.05
24 3 0.08
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (21 bp):
TAATAAATAATATAATTGATT
Found at i:2055716 original size:20 final size:21
Alignment explanation
Indices: 2055682--2055720 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2055672 AATAATATTT
*
2055682 AATTATTTATTATATTTTATG
1 AATTATTTATAATATTTTATG
2055703 AATT-TTTATAATATTTTA
1 AATTATTTATAATATTTTA
2055721 ATTTTATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
AATTATTTATAATATTTTATG
Found at i:2055723 original size:17 final size:17
Alignment explanation
Indices: 2055673--2055725 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
2055663 ACTTAACAAA
2055673 ATAATA-TTTAATTATTT
1 ATAATATTTTAATT-TTT
*
2055690 ATTATATTTTATGAATTTTT
1 ATAATA-TTT-T-AATTTTT
2055710 ATAATATTTTAATTTT
1 ATAATATTTTAATTTT
2055726 ATTGGCTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 5 0.17
20 9 0.30
21 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
ATAATATTTTAATTTTT
Found at i:2055874 original size:17 final size:18
Alignment explanation
Indices: 2055852--2055900 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
2055842 ACTTTTGTAT
2055852 ATTATTAATTATA-AA-TA
1 ATTATT-ATTATATAATTA
2055869 ATTATT-TTATATAATTA
1 ATTATTATTATATAATTA
*
2055886 ATTATTATTAAATAA
1 ATTATTATTATATAA
2055901 AAAAAAGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 2 0.07
17 14 0.50
18 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATTATTATATAATTA
Found at i:2057266 original size:11 final size:12
Alignment explanation
Indices: 2057242--2057290 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
2057232 GATATGTCAC
2057242 AAAAATAATATA
1 AAAAATAATATA
2057254 AAAAATAAT-TA
1 AAAAATAATATA
* * *
2057265 AAACATCATACA
1 AAAAATAATATA
2057277 AAAAATAACTATA
1 AAAAATAA-TATA
2057290 A
1 A
2057291 TATATTACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
11 9 0.31
12 16 0.55
13 4 0.14
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAATAATATA
Found at i:2057840 original size:28 final size:28
Alignment explanation
Indices: 2057783--2057840 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
2057773 GAAATCTACC
* * *
2057783 AAAATAATTATAACATTTACTTAAACTA
1 AAAATAATAATAACATTTACTAAAAATA
*
2057811 AAAATAATAATAACTTATTAC-AAAAATA
1 AAAATAATAATAACAT-TTACTAAAAATA
2057839 AA
1 AA
2057841 TTATAACACT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (28 bp):
AAAATAATAATAACATTTACTAAAAATA
Found at i:2058368 original size:34 final size:33
Alignment explanation
Indices: 2058315--2058535 Score: 255
Period size: 34 Copynumber: 6.5 Consensus size: 33
2058305 GGTAAAAAAC
* *
2058315 CACCATTTAATCAATAATGGCAA-CTTACCAAAT
1 CACCATTTAATCAACAATGGTAAGC-TACCAAAT
* *
2058348 CTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
2058382 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
** *
2058416 TTCTCATTTAATCAATAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAAT
* * * * *
2058450 CTCCCATTTAGTCAACAATGGCAAACCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
2058484 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
2058518 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
2058536 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
33 19 0.12
34 141 0.87
35 2 0.01
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAGCTACCAAAT
Found at i:2058459 original size:102 final size:101
Alignment explanation
Indices: 2058315--2058531 Score: 337
Period size: 102 Copynumber: 2.1 Consensus size: 101
2058305 GGTAAAAAAC
* *
2058315 CACCATTTAATCAATAATGGCAACTTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAATAATGGCAACTTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
2058380 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * *
2058416 TTCTCATTTAATCAATAATGGTAAGC-TACCAAATCTCCCATTTAGTCAACAATGGCAAACCACC
1 CAC-CATTTAATCAATAATGGCAA-CTTACCAAATCTACCATTTAGTCAACAATGGCAAACCACC
2058480 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
64 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
2058518 CACCATTTAATCAA
1 CACCATTTAATCAA
2058532 CAATTCTCCC
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
101 12 0.12
102 91 0.88
103 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAATAATGGCAACTTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:2062990 original size:34 final size:33
Alignment explanation
Indices: 2062942--2063160 Score: 226
Period size: 34 Copynumber: 6.5 Consensus size: 33
2062932 GGTAAAAAAC
*
2062942 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* * *
2062975 CTATCATTTAGTCAACAATAGTAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGGT-AACCTACCAAAT
* * **
2063009 CACCCATTTAATCAATAATGATAAGTTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
2063043 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
2063077 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
2063111 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
2063145 CACCATTTAATCAACA
1 CACCATTTAATCAACA
2063161 TATACCTCTA
Statistics
Matches: 152, Mismatches: 25, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
33 22 0.14
34 122 0.80
35 8 0.05
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:2063058 original size:68 final size:68
Alignment explanation
Indices: 2062944--2063160 Score: 274
Period size: 68 Copynumber: 3.2 Consensus size: 68
2062934 TAAAAAACCA
* * * * *
2062944 CCATTTAATCAACAATGGCAACCTACCAAATCTATCATTTAGTCAACAATAGTAAACCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAACTACCAAAT
2063009 CAC
66 CAC
* ** ** * *
2063012 CCATTTAATCAATAATGATAAGTTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAACTACCAAAT
*
2063077 CTC
66 CAC
* * * *
2063080 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAACTACCAAAT
2063145 CA-
66 CAC
2063147 CCATTTAATCAACA
1 CCATTTAATCAACA
2063161 TATACCTCTA
Statistics
Matches: 124, Mismatches: 25, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
67 13 0.10
68 111 0.90
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (68 bp):
CCATTTAATCAACAATGGCAAACTACCAAATCTCTCATTTAATCAACAATGGTAAACTACCAAAT
CAC
Found at i:2063121 original size:102 final size:101
Alignment explanation
Indices: 2062942--2063160 Score: 321
Period size: 102 Copynumber: 2.2 Consensus size: 101
2062932 GGTAAAAAAC
* *
2062942 CACCATTTAATCAACAATGGCAACCTACCAAATCTATCATTTAGTCAACAATAGTAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCAA
* **
2063007 ATCACCCATTTAATCAATAATGATAAGTTACCAAAT
66 ATCACCCATTTAATCAACAATGATAAACTACCAAAT
** * * * *
2063043 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCA
*
2063108 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGATAAACTACCAAAT
2063145 CACCATTTAATCAACA
1 CACCATTTAATCAACA
2063161 TATACCTCTA
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
101 14 0.14
102 89 0.86
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATAGCAAACCACCAA
ATCACCCATTTAATCAACAATGATAAACTACCAAAT
Found at i:2068898 original size:2 final size:2
Alignment explanation
Indices: 2068886--2068922 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2068876 ATGATATAAA
*
2068886 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AA AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2068923 CTAAATTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2074021 original size:20 final size:21
Alignment explanation
Indices: 2073973--2074031 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
2073963 AAAGACCCAA
2073973 AATGTATCGATACAATTTGAAG
1 AATGTATCGATAC-ATTTGAAG
* **
2073995 CATGTATCGATACATTT-ATT
1 AATGTATCGATACATTTGAAG
2074015 AATGTATCGATACATTT
1 AATGTATCGATACATTT
2074032 CCTTAGTGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 17 0.52
21 4 0.12
22 12 0.36
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.39
Consensus pattern (21 bp):
AATGTATCGATACATTTGAAG
Found at i:2074984 original size:61 final size:61
Alignment explanation
Indices: 2074841--2074986 Score: 143
Period size: 61 Copynumber: 2.4 Consensus size: 61
2074831 GTCAGCGACG
* * ** * **
2074841 TTGGACTTAAGGATGCGAAGAATGATAAAGATGCCAATATGCTGATTCATGGCTAGTGATAT
1 TTGG-CTTAAAGATGCAAAGAATGATAAAGATGCCAATATGCTGATTCAAAGCCAACGATAT
* * * * *
2074903 TAGGCTTGAAGACG-AGAAGAATGATAAA-AGTGCCAATATGTTGATTTAAAGCCAACGATAT
1 TTGGCTTAAAGATGCA-AAGAATGATAAAGA-TGCCAATATGCTGATTCAAAGCCAACGATAT
2074964 TTGGCTTAAAGATGCAAAGAATG
1 TTGGCTTAAAGATGCAAAGAATG
2074987 CCAATGTGCT
Statistics
Matches: 66, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
60 1 0.02
61 61 0.92
62 4 0.06
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (61 bp):
TTGGCTTAAAGATGCAAAGAATGATAAAGATGCCAATATGCTGATTCAAAGCCAACGATAT
Found at i:2075325 original size:52 final size:52
Alignment explanation
Indices: 2074923--2076042 Score: 573
Period size: 52 Copynumber: 20.8 Consensus size: 52
2074913 GACGAGAAGA
* * * * * *
2074923 ATGATAAAAGTGCCAATATGTTGATTTAAAGCCAACGATATTTG-GCTTAAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATA-TTGAGCTTAAAG
* * * ** * *
2074975 ATG-CAAAGAATGCCAATGTGCTGATTCACGATCAGCCGACATT-AGACTTGAAG
1 ATGACAAAG-GTGCCAATATGCTGATTCAAGGCCAG-CGATATTGAG-CTTAAAG
* ** * * * * * * **
2075028 AT-AAAAAGAGCACCAATGTGCCGATTCAAGGTCAGTGACATTGACCTT-TGG
1 ATGACAAAG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGAGCTTAAAG
** * * * *
2075079 AATGTTAAAGGTGCTAATATACTGATTCAAGGCCAGCGATA-TCAGATTTAAAG
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAG-CTTAAAG
* * * * *
2075132 AAAGAAAAAGGTGCCAATGTGCTGATTCAAGGCCAACAATATTG-GACTTAAAG
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAG-CTTAAAG
* * * * * * ** *
2075185 ATGACAAAGATGCCAATGTGTTGATTTAAGGCTAGCAACATTAGAATTGAAAATAAGAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGC--GA-T---ATTG-AGCTTA-AAG
* * * *
2075245 AATGATAAAGGTGCCAATATACAGATTCAAGGCCAGCAATATTGAGCTTAAAG
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAGCTTAAAG
* * * *
2075298 ATGACAAATGTGCCAATGTGCTAATTCAAGGCCAACGATATTG-GACTTAAGAAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAG-CTT---AAAG
** * * **
2075353 AAAAATGGTAAAGGTGCCAATATGTTGATTCAAAGATAGCGATATT-AGGCTTAAAG
1 ----ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGA-GCTTAAAG
* * * *
2075409 ATGACAAAGGTGCTAATATGCTAATTCCAA-GCCAACGAGATTG-GACTTGAAGATGAG
1 ATGACAAAGGTGCCAATATGCTGATT-CAAGGCCAGCGATATTGAG-CTT--A-A--AG
* * *
2075466 AATAATGATAAAGATGCCAATATGCTGATTCAAGGCCGGCGATATT-AGGCTTAAAG
1 ----ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGA-GCTTAAAG
* * * * *
2075522 ATGACAAAGGTGCCAATGTGCTAATTCAAAGCCAGCGACATTAGACTTGAAGATGAGAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCG--A-T--A-TTG-AGCTTA-AAG
* ** * *
2075582 AATGATAAAGGTGCCAATATATTGATTTAAGGCTAGCGATATTGAGCTTTAAAG
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAGC-TTAAAG
* * * **
2075636 ATGACAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATT-AGATTTGAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAGCTTAAAG
* * * * * *
2075687 AAGGAAAAATGTGCCAATGTGCTAATTCAAGGACAGCGATATTG-GACTTAAAG
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAG-CTTAAAG
* * * * ** ** *
2075740 ATGACAAAAGTGCCAATATGTTGATTCCAGGCCAGTGATATCAAATTTAAGG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAGCTTAAAG
* * * * ** *
2075792 ATAACGAAGGTGCCAATATGCTAATTCTAGGCCAGCGATATCAAACTTAAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAGCTTAAAG
* ** * *
2075844 ATGAAAAATATGCCAATATGCTGATTCAAGGCCATCGATATTG-GACTTAAAA
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAG-CTTAAAG
* * * * *
2075896 AAGAAAAATGTGCCAATGTGCTGATTCAAGGCCAGCGACATTG-GACTTAAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAG-CTTAAAG
* * * *
2075948 ATGACAAATGTGCCAACATGCTGATTCAAGGCCTGCGATA-TCAGACTTAAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAG-CTTAAAG
* *
2076000 ATGACAAAGATGCCAATATGCTGATTCAAGGCCAGTGATATTG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
2076043 GACTTGGAAG
Statistics
Matches: 806, Mismatches: 198, Indels: 127
0.71 0.18 0.11
Matches are distributed among these distances:
51 13 0.02
52 470 0.58
53 130 0.16
54 12 0.01
55 16 0.02
56 7 0.01
57 3 0.00
58 9 0.01
59 43 0.05
60 11 0.01
61 91 0.11
62 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (52 bp):
ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAGCTTAAAG
Found at i:2075329 original size:113 final size:113
Alignment explanation
Indices: 2075129--2076042 Score: 692
Period size: 113 Copynumber: 8.4 Consensus size: 113
2075119 ATCAGATTTA
* * * * *
2075129 AAGAAAGAAAAAGGTGCCAATGTGCTGATTCAAGGCCAACAATATTG-GACTTAAAGATGACAAA
1 AAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAG-CTTAAAGATGACAAA
* * * * * * * *
2075193 GATGCCAATGTGTTGATTTAAGGCTAGCAACATTAGAATTGAAAATAAG
65 GGTGCCAATGTGCTAATTCAAGGCCAGCGACATTAGACTTGAAGATAAG
* * * *
2075242 AAGAATGATAAAGGTGCCAATATACAGATTCAAGGCCAGCAATATTGAGCTTAAAGATGACAAAT
1 AAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAGCTTAAAGATGACAAAG
* * *
2075307 GTGCCAATGTGCTAATTCAAGGCCAACGATATTGGACTT-AAGA-AAG
66 GTGCCAATGTGCTAATTCAAGGCCAGCGACATTAGACTTGAAGATAAG
* * * * **
2075353 AAAAATGGTAAAGGTGCCAATATGTTGATTCAAAGATAGCGATATT-AGGCTTAAAGATGACAAA
1 AAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGA-GCTTAAAGATGACAAA
* * * * * *
2075417 GGTGCTAATATGCTAATTCCAA-GCCAACGAGATTGGACTTGAAGATGAG
65 GGTGCCAATGTGCTAATT-CAAGGCCAGCGACATTAGACTTGAAGATAAG
* * *
2075466 AATAATGATAAAGATGCCAATATGCTGATTCAAGGCCGGCGATATT-AGGCTTAAAGATGACAAA
1 AAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGA-GCTTAAAGATGACAAA
* *
2075530 GGTGCCAATGTGCTAATTCAAAGCCAGCGACATTAGACTTGAAGATGAG
65 GGTGCCAATGTGCTAATTCAAGGCCAGCGACATTAGACTTGAAGATAAG
** * *
2075579 AAGAATGATAAAGGTGCCAATATATTGATTTAAGGCTAGCGATATTGAGCTTTAAAGATGACAAA
1 AAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAGC-TTAAAGATGACAAA
* *
2075644 GGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGATTTG-AG--AAG
65 GGTGCCAATGTGCTAATTCAAGGCCAGCGACATTAGACTTGAAGATAAG
* * * *
2075690 --G-A--A-AAATGTGCCAATGTGCTAATTCAAGGACAGCGATATTG-GACTTAAAGATGACAAA
1 AAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAG-CTTAAAGATGACAAA
* * * * * * * * *
2075748 AGTGCCAATATGTTGATTCCAGGCCAGTGATATCA-AATT-----TAAG
65 GGTGCCAATGTGCTAATTCAAGGCCAGCGACATTAGACTTGAAGATAAG
* ** * * ** * * *
2075791 --G-ATAACGAAGGTGCCAATATGCTAATTCTAGGCCAGCGATATCAAACTTAAAGATGAAAAAT
1 AAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAGCTTAAAGATGACAAAG
* * * * * *
2075853 ATGCCAATATGCTGATTCAAGGCCATCGATATTGGACTT--A-A-AA-
66 GTGCCAATGTGCTAATTCAAGGCCAGCGACATTAGACTTGAAGATAAG
* * *
2075896 AAG-A--A-AAATGTGCCAATGTGCTGATTCAAGGCCAGCGACATTG-GACTTAAAGATGACAAA
1 AAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAG-CTTAAAGATGACAAA
* ** * * * *
2075956 TGTGCCAACATGCTGATTCAAGGCCTGCGATATCAGAC-T-----T-A-
65 GGTGCCAATGTGCTAATTCAAGGCCAGCGACATTAGACTTGAAGATAAG
* * *
2075997 AAG-ATGACAAAGATGCCAATATGCTGATTCAAGGCCAGTGATATTG
1 AAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
2076043 GACTTGGAAG
Statistics
Matches: 666, Mismatches: 111, Indels: 57
0.80 0.13 0.07
Matches are distributed among these distances:
101 10 0.02
103 6 0.01
104 224 0.34
105 35 0.05
106 3 0.00
107 2 0.00
108 1 0.00
109 1 0.00
110 1 0.00
111 90 0.14
112 13 0.02
113 226 0.34
114 54 0.08
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (113 bp):
AAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGAGCTTAAAGATGACAAAG
GTGCCAATGTGCTAATTCAAGGCCAGCGACATTAGACTTGAAGATAAG
Found at i:2075385 original size:224 final size:226
Alignment explanation
Indices: 2075138--2075685 Score: 667
Period size: 224 Copynumber: 2.4 Consensus size: 226
2075128 AAAGAAAGAA
* * * * * *
2075138 AAAGGTGCCAATGTGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGACAAAGATGCCAATG
1 AAAGGTGCCAATATGTTGATTCAAGGCTAGCGATATTGGACTTAAAGATGACAAAGGTGCCAATG
* * * * *
2075203 TGTTGATTTAAGGCTAGCAACATTAGAATTGAAAATAAGAAGAATGATAAAGGTGCCAATATACA
66 TGCTGATTCAAGGCCAGCGACATTAGAATTGAAAATAAGAAGAATGATAAAGATGCCAATATACA
* *
2075268 GATTCAAGGCCAGCAATATT-GAGCTTAAAGATGACAAATGTGCCAATGTGCTAATTCAAGGCCA
131 GATTCAAGGCCAGCAATATTAG-GCTTAAAGATGACAAAGGTGCCAATGTGCTAATTCAAAGCCA
* * *
2075332 ACGATATTGGACTT-AAGA-AAGAAAAATGGT
195 ACGACATTAGACTTGAAGATAAGAAAAATGAT
* * *
2075362 AAAGGTGCCAATATGTTGATTCAAAGATAGCGATATTAGG-CTTAAAGATGACAAAGGTGCTAAT
1 AAAGGTGCCAATATGTTGATTCAAGGCTAGCGATATT-GGACTTAAAGATGACAAAGGTGCCAAT
* * * * * * * * * *
2075426 ATGCTAATTCCAA-GCCAACGAGATTGGACTTGAAGATGAGAATAATGATAAAGATGCCAATATG
65 GTGCTGATT-CAAGGCCAGCGACATTAGAATTGAAAATAAGAAGAATGATAAAGATGCCAATATA
* * *
2075490 CTGATTCAAGGCCGGCGATATTAGGCTTAAAGATGACAAAGGTGCCAATGTGCTAATTCAAAGCC
129 CAGATTCAAGGCCAGCAATATTAGGCTTAAAGATGACAAAGGTGCCAATGTGCTAATTCAAAGCC
* * *
2075555 AGCGACATTAGACTTGAAGATGAGAAGAATGAT
194 AACGACATTAGACTTGAAGATAAGAAAAATGAT
* *
2075588 AAAGGTGCCAATATATTGATTTAAGGCTAGCGATATT-GAGCTTTAAAGATGACAAAGGTGCCAA
1 AAAGGTGCCAATATGTTGATTCAAGGCTAGCGATATTGGA-C-TTAAAGATGACAAAGGTGCCAA
*
2075652 TGTGCTGATTCAAGGCCAGCGACATTAGATTTGA
64 TGTGCTGATTCAAGGCCAGCGACATTAGAATTGA
2075686 GAAGGAAAAA
Statistics
Matches: 269, Mismatches: 46, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
224 169 0.63
225 9 0.03
226 46 0.17
227 45 0.17
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.24
Consensus pattern (226 bp):
AAAGGTGCCAATATGTTGATTCAAGGCTAGCGATATTGGACTTAAAGATGACAAAGGTGCCAATG
TGCTGATTCAAGGCCAGCGACATTAGAATTGAAAATAAGAAGAATGATAAAGATGCCAATATACA
GATTCAAGGCCAGCAATATTAGGCTTAAAGATGACAAAGGTGCCAATGTGCTAATTCAAAGCCAA
CGACATTAGACTTGAAGATAAGAAAAATGAT
Found at i:2076101 original size:32 final size:33
Alignment explanation
Indices: 2076057--2076238 Score: 175
Period size: 32 Copynumber: 5.7 Consensus size: 33
2076047 TGGAAGGAGA
* *
2076057 TGCCACCAACTTGTGTGGGCTTTTCA-AAGAGT
1 TGCCACCGACTTGTGTGGGCTTTTGAGAAGAGT
*
2076089 TGCCACCGACTTGTGTGGGCTTTT--GAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAGAAGAGT
* * * * *
2076120 TACCATCGGCTTATGTGGGCTTTAGAGAA-AGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAGAAGA-GT
*
2076153 TGCCACC-AGCTTGTGTGGGC-TTTGAGAAGGGT
1 TGCCACCGA-CTTGTGTGGGCTTTTGAGAAGAGT
*
2076185 TGCCACC-AGCTTGTGTGGGC-TTTAAGAAG-GT
1 TGCCACCGA-CTTGTGTGGGCTTTTGAGAAGAGT
*
2076216 TACCACCGACTTGTGTGGGCTTT
1 TGCCACCGACTTGTGTGGGCTTT
2076239 GAAAAGGGTG
Statistics
Matches: 126, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
31 43 0.34
32 63 0.50
33 20 0.16
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (33 bp):
TGCCACCGACTTGTGTGGGCTTTTGAGAAGAGT
Found at i:2076140 original size:31 final size:32
Alignment explanation
Indices: 2076057--2076252 Score: 195
Period size: 31 Copynumber: 6.2 Consensus size: 32
2076047 TGGAAGGAGA
** * *
2076057 TGCCACCAACTTGTGTGGGCTTTTCA-AAGAGT
1 TGCCACCGGCTTGTGTGGGC-TTTAAGAAGGGT
* *
2076089 TGCCACCGACTTGTGTGGGCTTT-TGAAGGGT
1 TGCCACCGGCTTGTGTGGGCTTTAAGAAGGGT
* * * *
2076120 TACCATCGGCTTATGTGGGCTTTAGAGAAAGGT
1 TGCCACCGGCTTGTGTGGGCTTTA-AGAAGGGT
* *
2076153 TGCCACCAGCTTGTGTGGGCTTTGAGAAGGGT
1 TGCCACCGGCTTGTGTGGGCTTTAAGAAGGGT
*
2076185 TGCCACCAGCTTGTGTGGGCTTTAAGAA-GGT
1 TGCCACCGGCTTGTGTGGGCTTTAAGAAGGGT
* *
2076216 TACCACCGACTTGTGTGGGCTTTGAA-AAGGG-
1 TGCCACCGGCTTGTGTGGGCTTT-AAGAAGGGT
2076247 TGCCAC
1 TGCCAC
2076253 GGAGTTGTGA
Statistics
Matches: 139, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
31 57 0.41
32 57 0.41
33 25 0.18
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.29
Consensus pattern (32 bp):
TGCCACCGGCTTGTGTGGGCTTTAAGAAGGGT
Found at i:2076233 original size:96 final size:94
Alignment explanation
Indices: 2076057--2076252 Score: 254
Period size: 96 Copynumber: 2.1 Consensus size: 94
2076047 TGGAAGGAGA
*
2076057 TGCCACCAACTTGTGTGGGCTTTTCAAAGAGTTGCCACCGACTTGTGTGGGCTTTTGAAGGGTTA
1 TGCCACCAACTTGTGTGGGCTTTTCAAAGAGTTGCCACCGACTTGTGTGGGCTTTAGAAGGGTTA
* * *
2076122 CCATCGGCTTATGTGGGCTTTAGAGAAAGGT
66 CCACCGACTTATGTGGGCTTT-GA-AAAGGG
* * *
2076153 TGCCACCAGCTTGTGTGGGC-TTTGAGAAGGGTTGCCACC-AGCTTGTGTGGGCTTTAAGAA-GG
1 TGCCACCAACTTGTGTGGGCTTTTCA-AAGAGTTGCCACCGA-CTTGTGTGGGCTTT-AGAAGGG
*
2076215 TTACCACCGACTTGTGTGGGCTTTGAAAAGGG
63 TTACCACCGACTTATGTGGGCTTTGAAAAGGG
2076247 TGCCAC
1 TGCCAC
2076253 GGAGTTGTGA
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
94 11 0.12
95 7 0.08
96 68 0.76
97 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.29
Consensus pattern (94 bp):
TGCCACCAACTTGTGTGGGCTTTTCAAAGAGTTGCCACCGACTTGTGTGGGCTTTAGAAGGGTTA
CCACCGACTTATGTGGGCTTTGAAAAGGG
Found at i:2076343 original size:33 final size:32
Alignment explanation
Indices: 2076239--2076365 Score: 121
Period size: 33 Copynumber: 3.8 Consensus size: 32
2076229 TGTGGGCTTT
* * *
2076239 GAAAAGGGTGCCACGGAGTTGTGAACTCAAAAA
1 GAAAAAGGTGCCAC-GAGTTGTGGACTGAAAAA
* * *
2076272 GAAAAAGGTGCCACGAAATTGTTGACTTGAAAGA
1 GAAAAAGGTGCCACG-AGTTGTGGAC-TGAAAAA
*
2076306 -AAAAAGGTGCCACAGAGTCGTGGACTGAAAAA
1 GAAAAAGGTGCCAC-GAGTTGTGGACTGAAAAA
*
2076338 GAAAAAATGTGCCATCGAGTTGTGGACT
1 G-AAAAAGGTGCCA-CGAGTTGTGGACT
2076366 TTGAAAGGGA
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
32 7 0.09
33 40 0.53
34 28 0.37
35 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.28, T:0.18
Consensus pattern (32 bp):
GAAAAAGGTGCCACGAGTTGTGGACTGAAAAA
Found at i:2076397 original size:68 final size:66
Alignment explanation
Indices: 2076240--2076399 Score: 178
Period size: 68 Copynumber: 2.4 Consensus size: 66
2076230 GTGGGCTTTG
* * *
2076240 AAAAGGGTGCCACGGAGTTGTGAACTCAAAAAGAAAAAGGTGCCACGAAATTGTTGACTTGAAAG
1 AAAAGGGTGCCACAGAGTTGTGGACTCAAAAAGAAAAAGGTGCCACGAAATTGTGGACTTGAAAG
2076305 A
66 A
* * * * *
2076306 AAAAAGGTGCCACAGAGTCGTGGACTGAAAAAGAAAAAATGTGCCATCG-AGTTGTGGACTTTGA
1 AAAAGGGTGCCACAGAGTTGTGGACTCAAAAAG-AAAAAGGTGCCA-CGAAATTGTGGAC-TTGA
*
2076370 AAGG
63 AAGA
* * *
2076374 GAAAGGGTGCTACAGACTTGTGGACT
1 AAAAGGGTGCCACAGAGTTGTGGACT
2076400 TTAAAAAAGG
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
66 28 0.36
67 19 0.25
68 30 0.39
ACGTcount: A:0.38, C:0.14, G:0.29, T:0.19
Consensus pattern (66 bp):
AAAAGGGTGCCACAGAGTTGTGGACTCAAAAAGAAAAAGGTGCCACGAAATTGTGGACTTGAAAG
A
Found at i:2076447 original size:27 final size:28
Alignment explanation
Indices: 2076375--2076457 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 28
2076365 TTTGAAAGGG
* *
2076375 AAAGGGTGCTACAGACTTGTGGACTTTAAA
1 AAAGGGTGCCACAGAGTTGTGGAC-TT-AA
* * *
2076405 AAAGGATACCATAGAGTTGTGGACTT-A
1 AAAGGGTGCCACAGAGTTGTGGACTTAA
*
2076432 AAAGGGTGCCACAGAGTTGTCGACTT
1 AAAGGGTGCCACAGAGTTGTGGACTT
2076458 TGAAGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
27 23 0.52
29 2 0.05
30 19 0.43
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (28 bp):
AAAGGGTGCCACAGAGTTGTGGACTTAA
Found at i:2077745 original size:21 final size:21
Alignment explanation
Indices: 2077721--2077764 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2077711 TTTTTTGACT
*
2077721 TTTTG-TTGTTCCCTTTTTTTA
1 TTTTGCTT-TTCCATTTTTTTA
*
2077742 TTTTGCTTTTGCATTTTTTTA
1 TTTTGCTTTTCCATTTTTTTA
2077763 TT
1 TT
2077765 CTTTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.07, C:0.11, G:0.09, T:0.73
Consensus pattern (21 bp):
TTTTGCTTTTCCATTTTTTTA
Found at i:2077774 original size:15 final size:15
Alignment explanation
Indices: 2077756--2077791 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
2077746 GCTTTTGCAT
2077756 TTTTTTATTCTTTT-A
1 TTTTTTATT-TTTTCA
2077771 TTTTTTATTTTTTCA
1 TTTTTTATTTTTTCA
2077786 TTTTTT
1 TTTTTT
2077792 TGTGCTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTATTTTTTCA
Found at i:2077774 original size:23 final size:23
Alignment explanation
Indices: 2077748--2077792 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2077738 TTTATTTTGC
*
2077748 TTTTGCATTTTTTTATTCTTTTA
1 TTTTGCATTTTTTCATTCTTTTA
** *
2077771 TTTTTTATTTTTTCATTTTTTT
1 TTTTGCATTTTTTCATTCTTTT
2077793 GTGCTTTTGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.80
Consensus pattern (23 bp):
TTTTGCATTTTTTCATTCTTTTA
Found at i:2077781 original size:6 final size:7
Alignment explanation
Indices: 2077756--2077791 Score: 54
Period size: 8 Copynumber: 4.9 Consensus size: 7
2077746 GCTTTTGCAT
2077756 TTTTTTA
1 TTTTTTA
2077763 TTCTTTTA
1 TT-TTTTA
2077771 TTTTTTA
1 TTTTTTA
2077778 TTTTTTCA
1 TTTTTT-A
2077786 TTTTTT
1 TTTTTT
2077792 TGTGCTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 13 0.48
8 14 0.52
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTA
Found at i:2077814 original size:31 final size:31
Alignment explanation
Indices: 2077737--2077824 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 31
2077727 TGTTCCCTTT
* * *
2077737 TTTTA-TTTTG-CTTTTGCATTTTTTTATTC
1 TTTTACTTTTGACTTTTTCATTTTTTTGTGC
* * *
2077766 TTTTATTTTTTATTTTTTCATTTTTTTGTGC
1 TTTTACTTTTGACTTTTTCATTTTTTTGTGC
* * *
2077797 TTTTGCTTTTGACTTTTTCGTTATTTTG
1 TTTTACTTTTGACTTTTTCATTTTTTTG
2077825 AAGGGAACTT
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 5 0.11
30 4 0.09
31 37 0.80
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.73
Consensus pattern (31 bp):
TTTTACTTTTGACTTTTTCATTTTTTTGTGC
Found at i:2085154 original size:20 final size:21
Alignment explanation
Indices: 2085111--2085162 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2085101 AGGGTGGTTT
*
2085111 TGTATCGATACATTTCAGGCA
1 TGTATCGATACATTTCACGCA
**
2085132 TGTATCGATACA-TTCACTTA
1 TGTATCGATACATTTCACGCA
2085152 TGTATCGATAC
1 TGTATCGATAC
2085163 CTTTACTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (21 bp):
TGTATCGATACATTTCACGCA
Found at i:2093234 original size:20 final size:20
Alignment explanation
Indices: 2093209--2093247 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2093199 CGATACAAAC
2093209 AGTGAATGTATCAATACATA
1 AGTGAATGTATCAATACATA
2093229 AGTGAATGTATCAATACAT
1 AGTGAATGTATCAATACAT
2093248 GTCTGAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (20 bp):
AGTGAATGTATCAATACATA
Found at i:2095203 original size:13 final size:13
Alignment explanation
Indices: 2095185--2095210 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2095175 CAATTTTTTG
2095185 TGTATCGATACAT
1 TGTATCGATACAT
2095198 TGTATCGATACAT
1 TGTATCGATACAT
2095211 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2097771 original size:13 final size:13
Alignment explanation
Indices: 2097753--2097778 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2097743 ATAATCACCC
2097753 TGTATCGATACAA
1 TGTATCGATACAA
2097766 TGTATCGATACAA
1 TGTATCGATACAA
2097779 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2099877 original size:15 final size:15
Alignment explanation
Indices: 2099857--2099887 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2099847 ATTTCGTTTG
*
2099857 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2099872 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2099887 G
1 G
2099888 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2101720 original size:21 final size:21
Alignment explanation
Indices: 2101691--2101735 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2101681 AAGTTTTCAT
*
2101691 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2101711 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2101733 TTT
1 TTT
2101736 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2103972 original size:13 final size:13
Alignment explanation
Indices: 2103954--2103979 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2103944 CAATTTTTTG
2103954 TGTATCGATACAT
1 TGTATCGATACAT
2103967 TGTATCGATACAT
1 TGTATCGATACAT
2103980 ACTTGCTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2104536 original size:15 final size:13
Alignment explanation
Indices: 2104504--2104529 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2104494 CAGGGTAGTT
2104504 TTGTATCGATATA
1 TTGTATCGATATA
2104517 TTGTATCGATATA
1 TTGTATCGATATA
2104530 AATTGTAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TTGTATCGATATA
Found at i:2105587 original size:13 final size:13
Alignment explanation
Indices: 2105569--2105593 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2105559 AATTTTTTGC
2105569 GTATCGATACATT
1 GTATCGATACATT
2105582 GTATCGATACAT
1 GTATCGATACAT
2105594 ACTTTGTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2105610 original size:32 final size:33
Alignment explanation
Indices: 2105548--2105611 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2105538 TACAAGCCAA
**
2105548 TGTATCGATACAATTTTTTGCGTATCGATACAT
1 TGTATCGATACAATACTTTGCGTATCGATACAT
*
2105581 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGCGTATCGATACA
2105612 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGCGTATCGATACAT
Found at i:2108182 original size:13 final size:13
Alignment explanation
Indices: 2108166--2108197 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2108156 TCCCTATATT
2108166 GATACAGTGTATC
1 GATACAGTGTATC
*
2108179 GATACATTGTATC
1 GATACAGTGTATC
2108192 GATACA
1 GATACA
2108198 AAGAAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (13 bp):
GATACAGTGTATC
Found at i:2110295 original size:15 final size:15
Alignment explanation
Indices: 2110275--2110305 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2110265 ATTTCGTTTG
*
2110275 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2110290 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2110305 G
1 G
2110306 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2114387 original size:13 final size:13
Alignment explanation
Indices: 2114369--2114394 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2114359 CAATTTTTTG
2114369 TGTATCGATACAT
1 TGTATCGATACAT
2114382 TGTATCGATACAT
1 TGTATCGATACAT
2114395 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2114406 original size:32 final size:33
Alignment explanation
Indices: 2114349--2114412 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2114339 TACAAGCCAA
**
2114349 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
2114382 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
2114413 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:2115822 original size:154 final size:153
Alignment explanation
Indices: 2115292--2115823 Score: 502
Period size: 155 Copynumber: 3.4 Consensus size: 153
2115282 GCATTATCCC
* * * * * *
2115292 AAGTCCTTTAGGGGTATCAAGTACTTTTACGTCAAAGGTATTGCTGAGGGGCATTTTCATAATTT
1 AAGTCCTCTAGGGGTATCAAGTACTTTTACGTCGAAGGTATTCCTAAGGAGCATTTTCGTAATTT
* * *
2115357 TTCAGAACTGAGTCCTAGGTTG-ACCTCAGTCCGCTTTTATGCCAAAAGATAGATATTGAGGATC
66 TTCAGAACCGAGTCCTAGGTTGTAAC-CAGTCCGCTTTTATGCCAAAAG-TAGATATT-AGGATA
*
2115421 GGTTCATCTCATCTATTATCTTTTTT
128 GGTTCATCTCATCTATTATCCTTTTT
* * * * *
2115447 AAGTCCTCTAGGGGTATCGAGTACTTTTATGTCGAAGATATCCCCTAAGG-GCATTTTTGTAATT
1 AAGTCCTCTAGGGGTATCAAGTACTTTTACGTCGAAGGTAT-TCCTAAGGAGCATTTTCGTAATT
* * * * * *
2115511 TTAT-AAAATCGAGTCCTAGGTTGTCACCGAGTCCACTTTTATGCCGAAGGTAGATATTTAGGAT
65 TT-TCAGAACCGAGTCCTAGGTTGTAACC-AGTCCGCTTTTATGCCAAAAGTAGATA-TTAGGAT
* *
2115575 AGGTTCATCTCATGTATTATTCTTTTT
127 AGGTTCATCTCATCTATTATCCTTTTT
* * ** *
2115602 AAGTCCTCTAGGGGTATCAAGTACTTTTACATCGAAAGTATTCTCTAA-GAATATTTTCTTAATT
1 AAGTCCTCTAGGGGTATCAAGTACTTTTACGTCGAAGGTATTC-CTAAGGAGCATTTTCGTAATT
* * ** * **
2115666 TTTCAGAACCAACTCCTAGGTTGTTGCCATGTCCGCTTTTATGCCAAAAGTGGGCAGTTAGGATA
65 TTTCAGAACCGAGTCCTAGGTTGTAACCA-GTCCGCTTTTATGCCAAAAGTAGATA-TTAGGATA
* * * *
2115731 GGTTCATCCCAT-T-TCAAACCTTTTA
128 GGTTCATCTCATCTAT-TATCCTTTTT
* * * ** *
2115756 AAGGCTTTTAGGGGTATCGGGTACTTTTACGTCGAAGGTATCTCCT-AGGATCATTTTCGTAATT
1 AAGTCCTCTAGGGGTATCAAGTACTTTTACGTCGAAGGTAT-TCCTAAGGAGCATTTTCGTAATT
2115820 TTTC
65 TTTC
2115824 TACAAAACTA
Statistics
Matches: 305, Mismatches: 60, Indels: 25
0.78 0.15 0.06
Matches are distributed among these distances:
153 2 0.01
154 64 0.21
155 212 0.70
156 27 0.09
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (153 bp):
AAGTCCTCTAGGGGTATCAAGTACTTTTACGTCGAAGGTATTCCTAAGGAGCATTTTCGTAATTT
TTCAGAACCGAGTCCTAGGTTGTAACCAGTCCGCTTTTATGCCAAAAGTAGATATTAGGATAGGT
TCATCTCATCTATTATCCTTTTT
Found at i:2120937 original size:19 final size:19
Alignment explanation
Indices: 2120913--2120960 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2120903 CCATGAGATG
*
2120913 AAGAAAAACA-GAAAAAGC
1 AAGAAAAAAATGAAAAAGC
*
2120931 AAAGAAAAAAATGAAAAATC
1 -AAGAAAAAAATGAAAAAGC
2120951 AAGAAAAAAA
1 AAGAAAAAAA
2120961 AAGAAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.77, C:0.06, G:0.12, T:0.04
Consensus pattern (19 bp):
AAGAAAAAAATGAAAAAGC
Found at i:2122844 original size:52 final size:54
Alignment explanation
Indices: 2122726--2122837 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
2122716 TCTCAAAAAG
* * * * *
2122726 GATACTCCAATCTCATTTTCACTTCCGAAATATCAAATTTTTTTCACCATCGGA
1 GATACTCCAACCCCGTTTTCACTTCCAAAATATCAAATTTTTTTCACCAACGGA
* *
2122780 GATACTCCAACCCCGTTTTCACTTCTAAAATATCAAA-TTTTTT-ACCAACGGG
1 GATACTCCAACCCCGTTTTCACTTCCAAAATATCAAATTTTTTTCACCAACGGA
2122832 GATACT
1 GATACT
2122838 TTAACCCTGT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 13 0.25
53 6 0.12
54 32 0.63
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (54 bp):
GATACTCCAACCCCGTTTTCACTTCCAAAATATCAAATTTTTTTCACCAACGGA
Found at i:2122997 original size:81 final size:80
Alignment explanation
Indices: 2122780--2123085 Score: 258
Period size: 80 Copynumber: 3.8 Consensus size: 80
2122770 CACCATCGGA
* * * * ** **
2122780 GATACTCCAACCCCGTTTTCACTTCTAAAATATCAAATTTTTTACCAACGGGGATACTTTAACCC
1 GATACTCCAACCCCATTTTCACTTCAAAAACATCAAATTTTTCACCATTGGGGATACTCCAACCC
* * ***
2122845 TG-TTATTTTTGAGGG
66 -GATCATCTCAAAGGG
* * * * * * * *
2122860 GATATTCCAACACCGTTTTTACTTCCAAAACATCAAAATTTTCACCATTAGGGATACTCCGACCT
1 GATACTCCAACCCCATTTTCACTTCAAAAACATCAAATTTTTCACCATTGGGGATACTCCAACC-
* *
2122925 CGCT-ATCTCCAAGGG
65 CGATCATCTCAAAGGG
*
2122940 GATACTCCAACCCCATTTTCACTTTCAAAAACATCGAATTTTTCACCATTGGGGATACTCCAACC
1 GATACTCCAACCCCATTTTCAC-TTCAAAAACATCAAATTTTTCACCATTGGGGATACTCCAACC
* *
2123005 CTATCATTTCAAAGGG
65 CGATCATCTCAAAGGG
* * * * * * *
2123021 GATACTTCGA-CCCATTTTCACTTCTAAAATATCAAATTTTTTTATCATCGGGGATACTCCAACC
1 GATACTCCAACCCCATTTTCACTTCAAAAACATCAAA-TTTTTCACCATTGGGGATACTCCAACC
2123085 C
65 C
2123086 CGTTTTTACT
Statistics
Matches: 183, Mismatches: 38, Indels: 10
0.79 0.16 0.04
Matches are distributed among these distances:
79 12 0.07
80 115 0.63
81 56 0.31
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (80 bp):
GATACTCCAACCCCATTTTCACTTCAAAAACATCAAATTTTTCACCATTGGGGATACTCCAACCC
GATCATCTCAAAGGG
Found at i:2123077 original size:161 final size:160
Alignment explanation
Indices: 2122780--2123080 Score: 345
Period size: 161 Copynumber: 1.9 Consensus size: 160
2122770 CACCATCGGA
* * * * **
2122780 GATACTCCAACCCCGTTTTCACTTCTAAAATATCAAATTTTTTACCAACGGGGATACTTTAACCC
1 GATACTCCAACCCCATTTTCACTTCAAAAACATCAAATTTTTCACCAACGGGGATACTCCAACCC
* * *** * * *
2122845 TGTTATTTTTGAGGGGATATTCCAACACCGTTTTTACTTCCAAAACATCAAAATTTTCACCATTA
66 TATCATTTCAAAGGGGATATTCCAACACCATTTTCACTTCCAAAACATCAAAATTTTCACCATCA
2122910 GGGATACTCCGACCTCGCTATCTCCAAGGG
131 GGGATACTCCGACCTCGCTATCTCCAAGGG
* **
2122940 GATACTCCAACCCCATTTTCACTTTCAAAAACATCGAATTTTTCACCATTGGGGATACTCCAACC
1 GATACTCCAACCCCATTTTCAC-TTCAAAAACATCAAATTTTTCACCAACGGGGATACTCCAACC
* * * * * *
2123005 CTATCATTTCAAAGGGGATACTT-CGAC-CCATTTTCACTTCTAAAATATCAAATTTTTTTATCA
65 CTATCATTTCAAAGGGGATA-TTCCAACACCATTTTCACTTCCAAAACATCAAA-ATTTTCACCA
*
2123068 TCGGGGATACTCC
128 TCAGGGATACTCC
2123081 AACCCCGTTT
Statistics
Matches: 114, Mismatches: 24, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
160 42 0.37
161 70 0.61
162 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (160 bp):
GATACTCCAACCCCATTTTCACTTCAAAAACATCAAATTTTTCACCAACGGGGATACTCCAACCC
TATCATTTCAAAGGGGATATTCCAACACCATTTTCACTTCCAAAACATCAAAATTTTCACCATCA
GGGATACTCCGACCTCGCTATCTCCAAGGG
Found at i:2123113 original size:133 final size:134
Alignment explanation
Indices: 2122937--2123221 Score: 346
Period size: 133 Copynumber: 2.1 Consensus size: 134
2122927 CTATCTCCAA
* **
2122937 GGGGATACTCCAACCCCATTTTCACTTTCAAAAACATCGAATTTTTCACCATTGGGGATACTCCA
1 GGGGATACTCCAACCCCATTTTCACTTTCAAAAACATCAAATTTTTCACCATCAGGGATACTCCA
* * * * * * *
2123002 ACCCTATCATTTC-AAAGGGGATACTTCGACCC-ATTTTCACTTCTAAAATATCAAATTTTTTTA
66 ACCCCATCAATTCTAAA-GGGATACTCCAACCCTATTTTCACTTCTAAAACATCAAATTTCTTCA
2123065 TCATC-
130 TC-TCT
* * *
2123070 GGGGATACTCCAACCCCGTTTTTACTTTC-AAAATATCAAAATTTTTCACCATCAGGGATACTCC
1 GGGGATACTCCAACCCCATTTTCACTTTCAAAAACATC-AAATTTTTCACCATCAGGGATACTCC
* * * **
2123134 AACCCCATCAATTCTGAAGGGATACTCCAACCCTGTTTTTACTTCTAAAACATTGAATTTCTTCA
65 AACCCCATCAATTCTAAAGGGATACTCCAACCCTATTTTCACTTCTAAAACATCAAATTTCTTCA
2123199 TCTCT
130 TCTCT
2123204 GGGG-TACTCCAACCCCAT
1 GGGGATACTCCAACCCCAT
2123222 ATTTTGAGGG
Statistics
Matches: 129, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
132 7 0.05
133 90 0.70
134 32 0.25
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (134 bp):
GGGGATACTCCAACCCCATTTTCACTTTCAAAAACATCAAATTTTTCACCATCAGGGATACTCCA
ACCCCATCAATTCTAAAGGGATACTCCAACCCTATTTTCACTTCTAAAACATCAAATTTCTTCAT
CTCT
Found at i:2125667 original size:19 final size:20
Alignment explanation
Indices: 2125630--2125667 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2125620 TACAATGTCA
*
2125630 AAAAACTCAAACAGTAATTG
1 AAAAACTCAAACAGAAATTG
*
2125650 AAAAATTCAAACA-AAATT
1 AAAAACTCAAACAGAAATT
2125668 CCAAAAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.61, C:0.13, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAAACTCAAACAGAAATTG
Found at i:2128905 original size:18 final size:18
Alignment explanation
Indices: 2128882--2128918 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2128872 TTGGCACATA
2128882 ATTTAAACATGCAAAACC
1 ATTTAAACATGCAAAACC
* *
2128900 ATTTAAATATGTAAAACC
1 ATTTAAACATGCAAAACC
2128918 A
1 A
2128919 ATGCATGCAG
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:0.51, C:0.16, G:0.05, T:0.27
Consensus pattern (18 bp):
ATTTAAACATGCAAAACC
Found at i:2131399 original size:19 final size:20
Alignment explanation
Indices: 2131357--2131407 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2131347 GCCAGTTTCG
*
2131357 TGTATCGATACAATTATCCA
1 TGTATCGATACAATGATCCA
*
2131377 TGTATCGATACAATGA-GCA
1 TGTATCGATACAATGATCCA
*
2131396 TGTATCAATACA
1 TGTATCGATACA
2131408 TTCAAGGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (20 bp):
TGTATCGATACAATGATCCA
Found at i:2133400 original size:20 final size:22
Alignment explanation
Indices: 2133359--2133401 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
2133349 GCAGTCGGTG
*
2133359 TGGGAGCTGCCTGATTGCGACC
1 TGGGAGCTGCCTGATCGCGACC
2133381 TGGGAG-TGCC-GATCGCGACC
1 TGGGAGCTGCCTGATCGCGACC
2133401 T
1 T
2133402 AGAGATGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.21
Consensus pattern (22 bp):
TGGGAGCTGCCTGATCGCGACC
Found at i:2135948 original size:16 final size:16
Alignment explanation
Indices: 2135923--2135962 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2135913 TGTTCATCAA
2135923 CTTC-TTTTGGAGC-TT
1 CTTCATTTTGGA-CATT
2135938 CTTCATTTTGGACATT
1 CTTCATTTTGGACATT
2135954 -TTCATTTTG
1 CTTCATTTTG
2135963 CTCCTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.17, G:0.15, T:0.55
Consensus pattern (16 bp):
CTTCATTTTGGACATT
Found at i:2140027 original size:20 final size:20
Alignment explanation
Indices: 2140002--2140055 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
2139992 GTTACAAGCA
2140002 ATGTATCGATACAAT-TCAT
1 ATGTATCGATACAATGTCAT
*
2140021 CATGTATCGATACAATGTCCT
1 -ATGTATCGATACAATGTCAT
2140042 ATGTATCGATACAA
1 ATGTATCGATACAA
2140056 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.91
21 3 0.09
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTCAT
Found at i:2140109 original size:20 final size:20
Alignment explanation
Indices: 2140084--2140143 Score: 77
Period size: 19 Copynumber: 3.0 Consensus size: 20
2140074 CTGCCCGTTT
2140084 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
* **
2140104 CATGTATCGATATAA-TGAG
1 CATGTATCGATACAATTGTC
2140123 CATGTATCGATACAATGTGTC
1 CATGTATCGATACAAT-TGTC
2140144 GATACAAAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 16 0.50
20 14 0.44
21 2 0.06
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTC
Found at i:2140794 original size:20 final size:20
Alignment explanation
Indices: 2140771--2140843 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2140761 ACAATTCAAA
2140771 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2140791 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2140812 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2140832 GTATCGATACAT
1 GTATCGATACAT
2140844 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2140815 original size:21 final size:21
Alignment explanation
Indices: 2140789--2140864 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2140779 ACATGTTGCA
2140789 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2140810 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2140830 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
2140851 ATGTATCGATACAT
1 ATGTATCGATACAT
2140865 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2140822 original size:41 final size:41
Alignment explanation
Indices: 2140771--2140864 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2140761 ACAATTCAAA
*
2140771 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2140812 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2140853 GTATCGATACAT
1 GTATCGATACAT
2140865 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2140921 original size:13 final size:13
Alignment explanation
Indices: 2140903--2140928 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2140893 TACAGCAAGT
2140903 ATGTATCGATACA
1 ATGTATCGATACA
2140916 ATGTATCGATACA
1 ATGTATCGATACA
2140929 TAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2145010 original size:15 final size:15
Alignment explanation
Indices: 2144990--2145028 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2144980 TAAAAATGTC
*
2144990 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2145005 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
2145020 CCAAATGAA
1 CAAAATGAA
2145029 ATTGATGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2147113 original size:20 final size:21
Alignment explanation
Indices: 2147034--2147112 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
2147024 AATGTCCAAA
*
2147034 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
2147054 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
2147079 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
2147099 TTGTATCGATACAT
1 ATGTATCGATACAT
2147113 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:2147117 original size:13 final size:13
Alignment explanation
Indices: 2147099--2147137 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2147089 ACATTTTTCT
2147099 TTGTATCGATACA
1 TTGTATCGATACA
2147112 TTGTATCGATACA
1 TTGTATCGATACA
*
2147125 CTGTATCGATACA
1 TTGTATCGATACA
2147138 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2149587 original size:20 final size:20
Alignment explanation
Indices: 2149564--2149636 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2149554 ACAATTCAAA
2149564 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2149584 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2149605 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2149625 GTATCGATACAT
1 GTATCGATACAT
2149637 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2149608 original size:21 final size:21
Alignment explanation
Indices: 2149582--2149657 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2149572 ACATGTTGCA
2149582 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2149603 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2149623 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
2149644 ATGTATCGATACAT
1 ATGTATCGATACAT
2149658 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2149615 original size:41 final size:41
Alignment explanation
Indices: 2149564--2149657 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2149554 ACAATTCAAA
*
2149564 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2149605 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2149646 GTATCGATACAT
1 GTATCGATACAT
2149658 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2149714 original size:13 final size:13
Alignment explanation
Indices: 2149696--2149721 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2149686 TACAGCAAGT
2149696 ATGTATCGATACA
1 ATGTATCGATACA
2149709 ATGTATCGATACA
1 ATGTATCGATACA
2149722 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2150990 original size:35 final size:35
Alignment explanation
Indices: 2150951--2151049 Score: 89
Period size: 34 Copynumber: 2.9 Consensus size: 35
2150941 CTGATTTGGC
2150951 AAGATTTAGAACCATACCATTGAAGAAACTTAATA
1 AAGATTTAGAACCATACCATTGAAGAAACTTAATA
* * * * * *
2150986 AAGATTTTGCAGCAGTTAGCC----CAGAAACCTAATG
1 AAGATTTAGAACCA--TA-CCATTGAAGAAACTTAATA
2151020 AAGATTTAGAACCATACCATTGAAGAAACT
1 AAGATTTAGAACCATACCATTGAAGAAACT
2151050 CATACACCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 14
0.65 0.15 0.20
Matches are distributed among these distances:
31 2 0.04
32 2 0.04
34 21 0.46
35 17 0.37
37 2 0.04
38 2 0.04
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.24
Consensus pattern (35 bp):
AAGATTTAGAACCATACCATTGAAGAAACTTAATA
Found at i:2152227 original size:21 final size:21
Alignment explanation
Indices: 2152201--2152252 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
2152191 TCATCATCAT
*
2152201 TTGTTGTTGTTGATATTGCTG
1 TTGTTGTTGATGATATTGCTG
2152222 TTGTTGTTGATGATATTGCTG
1 TTGTTGTTGATGATATTGCTG
*
2152243 CTGTTGTTGA
1 TTGTTGTTGA
2152253 GCCAATAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.12, C:0.06, G:0.29, T:0.54
Consensus pattern (21 bp):
TTGTTGTTGATGATATTGCTG
Found at i:2157097 original size:2 final size:2
Alignment explanation
Indices: 2157090--2157117 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2157080 ACAAAACAAC
2157090 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2157118 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2157122 original size:2 final size:2
Alignment explanation
Indices: 2157117--2157149 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2157107 ATATATATAT
2157117 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2157150 AGAAGAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2159001 original size:19 final size:18
Alignment explanation
Indices: 2158965--2159017 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
2158955 TTCAATACAA
*
2158965 ATTTTAAGATTAAAATCG
1 ATTTCAAGATTAAAATCG
2158983 ATTTCAAGATTAGAAATCG
1 ATTTCAAGATTA-AAATCG
2159002 ATTTCAA-ATTTAAAAT
1 ATTTCAAGA-TTAAAAT
2159018 TAAATTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (18 bp):
ATTTCAAGATTAAAATCG
Found at i:2162541 original size:10 final size:10
Alignment explanation
Indices: 2162505--2162534 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2162495 GCTTGGTAAG
2162505 ATGAAAAA-A
1 ATGAAAAATA
2162514 ATGAAAAATA
1 ATGAAAAATA
2162524 ATGAAAAATA
1 ATGAAAAATA
2162534 A
1 A
2162535 GAGAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (10 bp):
ATGAAAAATA
Found at i:2163337 original size:29 final size:29
Alignment explanation
Indices: 2163282--2163350 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
2163272 ATTTGAAATA
*
2163282 TTTATAT-ATTCATATTTTATTCATATTAT
1 TTTATATCATTCATATTTTAAT-ATATTAT
*
2163311 TTTATATCATATCATATTTTAAT-TATTTT
1 TTTATATCAT-TCATATTTTAATATATTAT
*
2163340 TTTGTATCATT
1 TTTATATCATT
2163351 TTCATATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 1 0.03
29 21 0.60
30 2 0.06
31 11 0.31
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.62
Consensus pattern (29 bp):
TTTATATCATTCATATTTTAATATATTAT
Found at i:2164657 original size:9 final size:9
Alignment explanation
Indices: 2164643--2164685 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
2164633 ACTATGAATT
2164643 AAAAAAGAG
1 AAAAAAGAG
2164652 AAAAAAGAG
1 AAAAAAGAG
2164661 AAAAAAGAG
1 AAAAAAGAG
*
2164670 AAAGAAGAG
1 AAAAAAGAG
2164679 AAAAAAG
1 AAAAAAG
2164686 TAATTTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:2165118 original size:13 final size:13
Alignment explanation
Indices: 2165100--2165126 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2165090 CCATGACATT
2165100 ACCTTCCCCTCCA
1 ACCTTCCCCTCCA
2165113 ACCTTCCCCTCCA
1 ACCTTCCCCTCCA
2165126 A
1 A
2165127 AAGGTCCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.59, G:0.00, T:0.22
Consensus pattern (13 bp):
ACCTTCCCCTCCA
Found at i:2169652 original size:19 final size:20
Alignment explanation
Indices: 2169628--2169674 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2169618 CGATACAATA
* *
2169628 TATCGATACAT-GTTCATTG
1 TATCGATACATGGATAATTG
2169647 TATCGATACATGGATAATTG
1 TATCGATACATGGATAATTG
2169667 TATCGATA
1 TATCGATA
2169675 TATGAAACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (20 bp):
TATCGATACATGGATAATTG
Found at i:2169653 original size:32 final size:33
Alignment explanation
Indices: 2169595--2169656 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
2169585 CCCTTGAATG
*
2169595 TATCGATACATTATGCTTTGTATCGATACAATA
1 TATCGATACATTATGCATTGTATCGATACAATA
2169628 TATCGATACATGT-T-CATTGTATCGATACA
1 TATCGATACAT-TATGCATTGTATCGATACA
2169657 TGGATAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 14 0.52
33 12 0.44
34 1 0.04
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (33 bp):
TATCGATACATTATGCATTGTATCGATACAATA
Found at i:2169744 original size:13 final size:13
Alignment explanation
Indices: 2169723--2169775 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
2169713 CGATACATGG
*
2169723 TACAATGTATCGA
1 TACATTGTATCGA
2169736 TACATTGTATCGA
1 TACATTGTATCGA
2169749 TACA-TG-AT-G-
1 TACATTGTATCGA
2169758 -A-ATTGTATCGA
1 TACATTGTATCGA
2169769 TACATTG
1 TACATTG
2169776 CTTGTAACAG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:2169752 original size:33 final size:33
Alignment explanation
Indices: 2169710--2169775 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2169700 CCACTGTTTA
*
2169710 TATCGATACATGGT-ACAATGTATCGATACATTG
1 TATCGATACATGATGA-AATGTATCGATACATTG
*
2169743 TATCGATACATGATGAATTGTATCGATACATTG
1 TATCGATACATGATGAAATGTATCGATACATTG
2169776 CTTGTAACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (33 bp):
TATCGATACATGATGAAATGTATCGATACATTG
Found at i:2172899 original size:267 final size:267
Alignment explanation
Indices: 2172424--2172959 Score: 1054
Period size: 267 Copynumber: 2.0 Consensus size: 267
2172414 TTGATCCTTG
* *
2172424 TTTTTGTAGGAGGTGGAGCATTGCTACAAAGTACGGGAATCAAAGAAGAATTTTTGGTACCTTGA
1 TTTTTGTAGGAGGTGGAGCATTGCTACAAAGTAAGGCAATCAAAGAAGAATTTTTGGTACCTTGA
2172489 TAGTGGATGCTCAAGGCACATGACCGGAGATAAAAGCTTATTCTCAAAAATCAAATCAAAAGAAG
66 TAGTGGATGCTCAAGGCACATGACCGGAGATAAAAGCTTATTCTCAAAAATCAAATCAAAAGAAG
2172554 GTGGATGTGTCACCTTTGGTGATAACTCGAAAAGAAAAATCAAAGGAATCGATACCATTGGTAAC
131 GTGGATGTGTCACCTTTGGTGATAACTCGAAAAGAAAAATCAAAGGAATCGATACCATTGGTAAC
2172619 ATCTCTTCATTTTGTATTGAAAATGTTTTATATGTCAATGGTCTTAAGCATAACCTCCTTAGCAT
196 ATCTCTTCATTTTGTATTGAAAATGTTTTATATGTCAATGGTCTTAAGCATAACCTCCTTAGCAT
2172684 TAGCCAA
261 TAGCCAA
2172691 TTTTTGTAGGAGGTGGAGCATTGCTACAAAGTAAGGCAATCAAAGAAGAATTTTTGGTACCTTGA
1 TTTTTGTAGGAGGTGGAGCATTGCTACAAAGTAAGGCAATCAAAGAAGAATTTTTGGTACCTTGA
2172756 TAGTGGATGCTCAAGGCACATGACCGGAGATAAAAGCTTATTCTCAAAAATCAAATCAAAAGAAG
66 TAGTGGATGCTCAAGGCACATGACCGGAGATAAAAGCTTATTCTCAAAAATCAAATCAAAAGAAG
2172821 GTGGATGTGTCACCTTTGGTGATAACTCGAAAAGAAAAATCAAAGGAATCGATACCATTGGTAAC
131 GTGGATGTGTCACCTTTGGTGATAACTCGAAAAGAAAAATCAAAGGAATCGATACCATTGGTAAC
2172886 ATCTCTTCATTTTGTATTGAAAATGTTTTATATGTCAATGGTCTTAAGCATAACCTCCTTAGCAT
196 ATCTCTTCATTTTGTATTGAAAATGTTTTATATGTCAATGGTCTTAAGCATAACCTCCTTAGCAT
2172951 TAGCCAA
261 TAGCCAA
2172958 TT
1 TT
2172960 ATGTGACAAA
Statistics
Matches: 267, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
267 267 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (267 bp):
TTTTTGTAGGAGGTGGAGCATTGCTACAAAGTAAGGCAATCAAAGAAGAATTTTTGGTACCTTGA
TAGTGGATGCTCAAGGCACATGACCGGAGATAAAAGCTTATTCTCAAAAATCAAATCAAAAGAAG
GTGGATGTGTCACCTTTGGTGATAACTCGAAAAGAAAAATCAAAGGAATCGATACCATTGGTAAC
ATCTCTTCATTTTGTATTGAAAATGTTTTATATGTCAATGGTCTTAAGCATAACCTCCTTAGCAT
TAGCCAA
Found at i:2176230 original size:13 final size:13
Alignment explanation
Indices: 2176212--2176248 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2176202 ACATTCCTTG
2176212 TATCGATACATTA
1 TATCGATACATTA
*
2176225 TATCGATACATTG
1 TATCGATACATTA
2176238 TATCGATACAT
1 TATCGATACAT
2176249 GGGTTACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:2178720 original size:13 final size:13
Alignment explanation
Indices: 2178702--2178728 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2178692 GCATTATGCT
2178702 TTGTATCGATACA
1 TTGTATCGATACA
2178715 TTGTATCGATACA
1 TTGTATCGATACA
2178728 T
1 T
2178729 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2178758 original size:20 final size:19
Alignment explanation
Indices: 2178712--2178768 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
2178702 TTGTATCGAT
*
2178712 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
2178731 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
2178750 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
2178769 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:2178852 original size:30 final size:30
Alignment explanation
Indices: 2178799--2178857 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2178789 ACCACTGTTC
*
2178799 GTATCGATACATGGTACAATGTATCGATAT
1 GTATCGATACATGATACAATGTATCGATAT
*
2178829 GTATCGATACATGATGA-ATTGTATCGATA
1 GTATCGATACATGAT-ACAATGTATCGATA
2178858 CATTGCTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (30 bp):
GTATCGATACATGATACAATGTATCGATAT
Found at i:2181399 original size:84 final size:84
Alignment explanation
Indices: 2181258--2181413 Score: 224
Period size: 84 Copynumber: 1.9 Consensus size: 84
2181248 ATTATTAATG
*
2181258 GCATTAGTAAGTTAGCCCATTTGTATCTCAAGGTTCCTTAAAAATGCTACTTGGTTCTAAACTAT
1 GCATTAGTAAGTTAGCCCATTTGTATCTCAAGGTTCCTTAAAAATGCTACTTGGTTCTAAACAAT
2181323 AGCTTCAGTTCTCTTAAAA
66 AGCTTCAGTTCTCTTAAAA
* * * * * * *
2181342 GCATTGGTAAGTTGGCCCATTT-TCATTTCAAGGTTCCTTAGAGATGCTGCTTGGTTCTAATCAA
1 GCATTAGTAAGTTAGCCCATTTGT-ATCTCAAGGTTCCTTAAAAATGCTACTTGGTTCTAAACAA
2181406 TAGCTTCA
65 TAGCTTCA
2181414 ATTTTGTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 1 0.02
84 62 0.98
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Consensus pattern (84 bp):
GCATTAGTAAGTTAGCCCATTTGTATCTCAAGGTTCCTTAAAAATGCTACTTGGTTCTAAACAAT
AGCTTCAGTTCTCTTAAAA
Found at i:2182862 original size:33 final size:33
Alignment explanation
Indices: 2182822--2182908 Score: 165
Period size: 33 Copynumber: 2.6 Consensus size: 33
2182812 ATATTGTAAG
2182822 ACACCTTGTAATGTATCGATAGATTGTATCGAT
1 ACACCTTGTAATGTATCGATAGATTGTATCGAT
2182855 ACACCTTGTAATGTATCGATAGATTGTATCGAT
1 ACACCTTGTAATGTATCGATAGATTGTATCGAT
*
2182888 ACACCTTGCAATGTATCGATA
1 ACACCTTGTAATGTATCGATA
2182909 CATTATGTGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (33 bp):
ACACCTTGTAATGTATCGATAGATTGTATCGAT
Found at i:2182871 original size:20 final size:19
Alignment explanation
Indices: 2182846--2182910 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
2182836 ATCGATAGAT
2182846 TGTATCGATACACCTTGTAA
1 TGTATCGATACACCTTG-AA
*
2182866 TGTATCGAT--A----GAT
1 TGTATCGATACACCTTGAA
2182879 TGTATCGATACACCTTGCAA
1 TGTATCGATACACCTTG-AA
2182899 TGTATCGATACA
1 TGTATCGATACA
2182911 TTATGTGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 22 0.61
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (19 bp):
TGTATCGATACACCTTGAA
Found at i:2185648 original size:50 final size:50
Alignment explanation
Indices: 2185584--2185684 Score: 148
Period size: 50 Copynumber: 2.0 Consensus size: 50
2185574 ATGCCTAGAA
* * *
2185584 AGGTAGTATTTGACAAAAGCTAATTTCTTGAGAGTTCATCGATAAGGAAC
1 AGGTAGTATTTGACAAAAGCAAATTGCTTGAGAGTTCATCGACAAGGAAC
* **
2185634 AGGTTGTATTTGACAAAAGCAAATTGCTTGAGAGTTTTTCGACAAGGAAC
1 AGGTAGTATTTGACAAAAGCAAATTGCTTGAGAGTTCATCGACAAGGAAC
2185684 A
1 A
2185685 AGTTTACTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (50 bp):
AGGTAGTATTTGACAAAAGCAAATTGCTTGAGAGTTCATCGACAAGGAAC
Found at i:2194273 original size:15 final size:15
Alignment explanation
Indices: 2194253--2194281 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2194243 AACTGATCTT
2194253 GTTCATCCACCACCC
1 GTTCATCCACCACCC
2194268 GTTCATCCACCACC
1 GTTCATCCACCACC
2194282 TATTTACCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.52, G:0.07, T:0.21
Consensus pattern (15 bp):
GTTCATCCACCACCC
Found at i:2194972 original size:16 final size:16
Alignment explanation
Indices: 2194941--2194974 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2194931 AACAACTTAA
* *
2194941 TATTTATTAGTTTAAT
1 TATTTATTAATATAAT
2194957 TATTTATTAATATAAT
1 TATTTATTAATATAAT
2194973 TA
1 TA
2194975 CTTAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TATTTATTAATATAAT
Found at i:2195241 original size:29 final size:29
Alignment explanation
Indices: 2195193--2195248 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2195183 GATAAAATAG
*
2195193 TATTATCTTGATAAAATATTTTAAAAAAA
1 TATTATCTTGATAAAATATTTCAAAAAAA
* **
2195222 TATTATTTTGATAATTTATTTCAAAAA
1 TATTATCTTGATAAAATATTTCAAAAA
2195249 TAAGGATAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (29 bp):
TATTATCTTGATAAAATATTTCAAAAAAA
Found at i:2203299 original size:2 final size:2
Alignment explanation
Indices: 2203281--2203323 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2203271 TTCAAAATAA
* *
2203281 AT AT AC AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2203323 A
1 A
2203324 AACACTTGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2203586 original size:37 final size:37
Alignment explanation
Indices: 2203545--2203622 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
2203535 ATATGTTAAC
* *
2203545 TGCTTTTTGACGGTCTTTAATCAAGCAATAAACCAGA
1 TGCTTTCTGAAGGTCTTTAATCAAGCAATAAACCAGA
* *
2203582 TGCTTTCTGAAGGTCTTTAATCGAGCCATAAACCAGA
1 TGCTTTCTGAAGGTCTTTAATCAAGCAATAAACCAGA
2203619 TGCT
1 TGCT
2203623 AATATGTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (37 bp):
TGCTTTCTGAAGGTCTTTAATCAAGCAATAAACCAGA
Found at i:2204866 original size:20 final size:20
Alignment explanation
Indices: 2204829--2204866 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2204819 ATATTAAATA
*
2204829 GTTATAGATAAATGATTTGT
1 GTTATAGATAAATCATTTGT
2204849 GTTATAAGAT-AATCATTT
1 GTTAT-AGATAAATCATTT
2204867 AGATAGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.45
Consensus pattern (20 bp):
GTTATAGATAAATCATTTGT
Found at i:2206110 original size:126 final size:123
Alignment explanation
Indices: 2205874--2206120 Score: 296
Period size: 126 Copynumber: 2.0 Consensus size: 123
2205864 AAAATACTAC
* * * * *
2205874 TTTTTTTCATATATATTTTAATGGTTGAATTTTTTTATATCGAATAAATAATTAAATATTTTTTA
1 TTTTTTTCATATATATTTTAATAGTTAAATTTTTTTACATCAAACAAATAATTAAATATTTTTTA
* ** * * * *
2205939 TTAATTAAAAACTTGCCGTGCATAATCCACAAAAATAAAATATAAAATATAACGATAA
66 TTAACTAAAAACTTAACATACATAATCCACAAAAATAAAACATAAAATACAACGATAA
2205997 TTTTTTTCAATATATATTTTAATAGTTAAATTTTTTTTTACATCAAACAAATAATTAAATATTTT
1 TTTTTTTC-ATATATATTTTAATAGTTAAA--TTTTTTTACATCAAACAAATAATTAAATATTTT
* * * ** * *
2206062 TTATTTACTCAAAACTTAACATACATGATTTACAAGAATAGAACATAAAATACAACGAT
63 TTATTAACTAAAAACTTAACATACATAATCCACAAAAATAAAACATAAAATACAACGAT
2206121 CGAATTAAAT
Statistics
Matches: 102, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
123 8 0.08
124 19 0.19
126 75 0.74
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.42
Consensus pattern (123 bp):
TTTTTTTCATATATATTTTAATAGTTAAATTTTTTTACATCAAACAAATAATTAAATATTTTTTA
TTAACTAAAAACTTAACATACATAATCCACAAAAATAAAACATAAAATACAACGATAA
Found at i:2208060 original size:2 final size:2
Alignment explanation
Indices: 2208053--2208089 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2208043 CTTAACATGC
2208053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2208090 CATCTTGATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2208958 original size:19 final size:19
Alignment explanation
Indices: 2208931--2208968 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2208921 AATCAAATTA
*
2208931 TATATTAGATAAAT-TTTAT
1 TATAATAGA-AAATATTTAT
2208950 TATAATAGAAAATATTTAT
1 TATAATAGAAAATATTTAT
2208969 AATGACACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
TATAATAGAAAATATTTAT
Found at i:2209125 original size:19 final size:19
Alignment explanation
Indices: 2209090--2209126 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2209080 TGTTATTTTA
2209090 TTTATTTTTAAATAATAAC
1 TTTATTTTTAAATAATAAC
2209109 TTTATATTTTAAA-AATAA
1 TTTAT-TTTTAAATAATAA
2209127 GTAAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTATTTTTAAATAATAAC
Found at i:2210991 original size:3 final size:3
Alignment explanation
Indices: 2210977--2211015 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2210967 ACACGGAATT
*
2210977 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2211016 GAAAATCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2212178 original size:36 final size:39
Alignment explanation
Indices: 2212102--2212178 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
2212092 ATTATATTTT
2212102 TTTAACTAATATATTATGTATTATATTAAATATAAAATA
1 TTTAACTAATATATTATGTATTATATTAAATATAAAATA
* *
2212141 TTTAACTATTATATTAT-TATT-TA-TAAATATAATATA
1 TTTAACTAATATATTATGTATTATATTAAATATAAAATA
2212177 TT
1 TT
2212179 AAAATTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 14 0.39
37 2 0.06
38 4 0.11
39 16 0.44
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (39 bp):
TTTAACTAATATATTATGTATTATATTAAATATAAAATA
Found at i:2212185 original size:23 final size:24
Alignment explanation
Indices: 2212150--2212208 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
2212140 ATTTAACTAT
** *
2212150 TATATTATTATTTA-TAAATATAA
1 TATATTAAAATTTATTAAATAAAA
*
2212173 TATATTAAAATTTTATTTAATAAAA
1 TATATTAAAA-TTTATTAAATAAAA
2212198 TATATTAAAAT
1 TATATTAAAAT
2212209 ATCACATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 8 0.27
24 5 0.17
25 17 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATATTAAAATTTATTAAATAAAA
Found at i:2212218 original size:25 final size:25
Alignment explanation
Indices: 2212166--2212230 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
2212156 ATTATTTATA
* * * **
2212166 AATATAATATATTAAAATTTTATTT
1 AATAAAATATATTAAAATATCACAT
2212191 AATAAAATATATTAAAATATCACAT
1 AATAAAATATATTAAAATATCACAT
*
2212216 AAT-AAATATTTTAAA
1 AATAAAATATATTAAA
2212231 TATTATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 11 0.32
25 23 0.68
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (25 bp):
AATAAAATATATTAAAATATCACAT
Found at i:2212354 original size:21 final size:21
Alignment explanation
Indices: 2212328--2212368 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2212318 ATTATTATAA
2212328 TTATTTTA-TTTTATCAAAATT
1 TTATTTTATTTTTAT-AAAATT
2212349 TTATTTTATTTTTATAAAAT
1 TTATTTTATTTTTATAAAAT
2212369 AGTTATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTTTATTTTTATAAAATT
Found at i:2212374 original size:22 final size:21
Alignment explanation
Indices: 2212328--2212376 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2212318 ATTATTATAA
*
2212328 TTATTTTATTTTATCAAAATT
1 TTATTTTATTTTATCAAAATG
2212349 TTATTTTATTTTTAT-AAAATAG
1 TTATTTTA-TTTTATCAAAAT-G
2212371 TTATTT
1 TTATTT
2212377 CATTATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTATTTTATTTTATCAAAATG
Found at i:2215698 original size:16 final size:16
Alignment explanation
Indices: 2215674--2215720 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
2215664 GAATTGACCC
2215674 AAATTTAAAATAATTT
1 AAATTTAAAATAATTT
*
2215690 AAATATAAAATAATTT
1 AAATTTAAAATAATTT
2215706 AAATTTAAAATAATT
1 AAATTTAAAATAATT
2215721 CGAACTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTTAAAATAATTT
Found at i:2216031 original size:23 final size:25
Alignment explanation
Indices: 2215974--2216032 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
2215964 TATATGTGTC
*
2215974 TATTATAATAATTTTTAATATTTGAT
1 TATTATAA-AATTTTTAATAATTGAT
*
2216000 TAGTT-TAAATTTTTTAA-AATTG-T
1 TA-TTATAAAATTTTTAATAATTGAT
2216023 TATTATAAAA
1 TATTATAAAA
2216033 GAAAGAAGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 2 0.07
23 7 0.25
24 4 0.14
25 8 0.29
26 5 0.18
27 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (25 bp):
TATTATAAAATTTTTAATAATTGAT
Found at i:2216957 original size:16 final size:16
Alignment explanation
Indices: 2216923--2217012 Score: 85
Period size: 16 Copynumber: 5.6 Consensus size: 16
2216913 TTAAAATCAG
*
2216923 AACTTAAAATAACGT-A
1 AACTTAAAATAA-TTCA
*
2216939 AACTCAAAATAATTCA
1 AACTTAAAATAATTCA
* *
2216955 AACTTAAAATATTTTA
1 AACTTAAAATAATTCA
* *
2216971 AAATTAAAATAATTTA
1 AACTTAAAATAATTCA
*
2216987 AATTTAAAATTAATTC-
1 AACTTAAAA-TAATTCA
2217003 AACTTAAAAT
1 AACTTAAAAT
2217013 TATTTAGGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
15 2 0.03
16 55 0.89
17 5 0.08
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (16 bp):
AACTTAAAATAATTCA
Found at i:2219198 original size:30 final size:30
Alignment explanation
Indices: 2219141--2219198 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2219131 TTGGAAGATA
* * *
2219141 TAAATAAAAATATCAAATACCACTTGAACG
1 TAAATAAAAAAATCAAAGAACACTTGAACG
*
2219171 TAAATAAAAAAATCAAAGAACATTTGAA
1 TAAATAAAAAAATCAAAGAACACTTGAA
2219199 AGTGATTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.59, C:0.12, G:0.07, T:0.22
Consensus pattern (30 bp):
TAAATAAAAAAATCAAAGAACACTTGAACG
Found at i:2219326 original size:2 final size:2
Alignment explanation
Indices: 2219315--2219356 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2219305 CAGACAAATA
2219315 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2219356 A
1 A
2219357 AAATAAGGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2222556 original size:19 final size:20
Alignment explanation
Indices: 2222532--2222573 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2222522 AAATATACAC
* *
2222532 ATAAAATAATTGCTTTTT-T
1 ATAAAAAAATTGATTTTTAT
2222551 ATAAAAAAATTGATTTTTAT
1 ATAAAAAAATTGATTTTTAT
2222571 ATA
1 ATA
2222574 TTATTTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (20 bp):
ATAAAAAAATTGATTTTTAT
Found at i:2226203 original size:25 final size:25
Alignment explanation
Indices: 2226166--2226214 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2226156 TTATTTTATT
*
2226166 TTATTTTTATATTTTGTGTTGTGTG
1 TTATGTTTATATTTTGTGTTGTGTG
* * *
2226191 TTATGTTTGTATTTTTTTTTGTGT
1 TTATGTTTATATTTTGTGTTGTGT
2226215 TCGTATCTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.18, T:0.71
Consensus pattern (25 bp):
TTATGTTTATATTTTGTGTTGTGTG
Found at i:2229498 original size:13 final size:13
Alignment explanation
Indices: 2229480--2229504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2229470 ACCAAGATCA
2229480 TGTATCGATACAC
1 TGTATCGATACAC
2229493 TGTATCGATACA
1 TGTATCGATACA
2229505 AAGTAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:2229500 original size:32 final size:32
Alignment explanation
Indices: 2229461--2229523 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 32
2229451 ATAATTACTG
*
2229461 TGTATCGATACCAAG-ATCATGTATCGATACAC
1 TGTATCGATACAAAGAAT-ATGTATCGATACAC
2229493 TGTATCGATACAAAGTAATATGTATCGATAC
1 TGTATCGATACAAAG-AATATGTATCGATAC
2229524 TTTTGAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.50
33 12 0.43
34 2 0.07
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (32 bp):
TGTATCGATACAAAGAATATGTATCGATACAC
Found at i:2231017 original size:13 final size:13
Alignment explanation
Indices: 2230999--2231023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2230989 CATAAAATGT
2230999 TGTATCGATACAA
1 TGTATCGATACAA
2231012 TGTATCGATACA
1 TGTATCGATACA
2231024 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2231021 original size:33 final size:33
Alignment explanation
Indices: 2230979--2231048 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2230969 TTCAACGATT
2230979 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2231012 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2231045 TGTA
1 TGTA
2231049 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2231106 original size:13 final size:13
Alignment explanation
Indices: 2231088--2231112 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2231078 ATTACTCACA
2231088 TGTATCGATACAT
1 TGTATCGATACAT
2231101 TGTATCGATACA
1 TGTATCGATACA
2231113 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2231177 original size:52 final size:52
Alignment explanation
Indices: 2231121--2231245 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
2231111 CACTGATCTT
*
2231121 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
2231173 TGTATCGATACATGCAGGCAAATTTGTCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2231225 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
2231246 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Done.