Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 5 of 206
Found at i:1440192 original size:19 final size:20
Alignment explanation
Indices: 1440163--1440200 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1440153 TTTTTGTCAA
1440163 AATTGGTCCCTAAATTTAAC
1 AATTGGTCCCTAAATTTAAC
1440183 AATT-GTCCCTAAATTTAA
1 AATTGGTCCCTAAATTTAA
1440201 AAATCAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (20 bp):
AATTGGTCCCTAAATTTAAC
Found at i:1446069 original size:150 final size:150
Alignment explanation
Indices: 1445798--1446096 Score: 589
Period size: 150 Copynumber: 2.0 Consensus size: 150
1445788 GTGTGGGATG
1445798 CCAGAATTGGCTATGCTTTGGGATCTTTTTTTTGAGTTCGTTTTTGAATTTCATGTATTAATAGA
1 CCAGAATTGGCTATGCTTTGGGATCTTTTTTTTGAGTTCGTTTTTGAATTTCATGTATTAATAGA
*
1445863 ACTATTTTGCTTTTCAAAATATATTCTGCCATATAGTGTTGCATGCTGTATTTATTACAAACATT
66 ACTATTTTGCTTTTCAAAATATAATCTGCCATATAGTGTTGCATGCTGTATTTATTACAAACATT
1445928 CAGATCTCTTGCTAGTGATA
131 CAGATCTCTTGCTAGTGATA
1445948 CCAGAATTGGCTATGCTTTGGGATCTTTTTTTTGAGTTCGTTTTTGAATTTCATGTATTAATAGA
1 CCAGAATTGGCTATGCTTTGGGATCTTTTTTTTGAGTTCGTTTTTGAATTTCATGTATTAATAGA
1446013 ACTATTTTGCTTTTCAAAATATAATCTGCCATATAGTGTTGCATGCTGTATTTATTACAAACATT
66 ACTATTTTGCTTTTCAAAATATAATCTGCCATATAGTGTTGCATGCTGTATTTATTACAAACATT
1446078 CAGATCTCTTGCTAGTGAT
131 CAGATCTCTTGCTAGTGAT
1446097 TGCTCTTCTT
Statistics
Matches: 148, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 148 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.44
Consensus pattern (150 bp):
CCAGAATTGGCTATGCTTTGGGATCTTTTTTTTGAGTTCGTTTTTGAATTTCATGTATTAATAGA
ACTATTTTGCTTTTCAAAATATAATCTGCCATATAGTGTTGCATGCTGTATTTATTACAAACATT
CAGATCTCTTGCTAGTGATA
Found at i:1455256 original size:24 final size:22
Alignment explanation
Indices: 1455225--1455274 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
1455215 ATTTTTCAGC
* *
1455225 TTTTCTTGACTTTGGGTTTTCAT
1 TTTTCTTGAATTT-CGTTTTCAT
*
1455248 TTTTACTTGAATTTCTTTTTCAT
1 TTTT-CTTGAATTTCGTTTTCAT
1455271 TTTT
1 TTTT
1455275 TTTAAGGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.66
Consensus pattern (22 bp):
TTTTCTTGAATTTCGTTTTCAT
Found at i:1465168 original size:81 final size:79
Alignment explanation
Indices: 1464998--1465527 Score: 471
Period size: 80 Copynumber: 6.6 Consensus size: 79
1464988 AACATCATTG
* * * * * * * *
1464998 GTTTTTCCTCTTGAAAATTCTCAGAAAATTTTCACAGATTCACTCAAAGGAAATATAGAAAGAGC
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATT-ACTC-AAGGAAATACAGCAAGAAC
1465063 AAAAGGGTATCAGAATT
64 AAAAGGGTATCA-AATT
* *
1465080 GGTTTCCCTTCATGCAAATTCCAAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAACA
1 GTTTTCCC-TCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAAC-
* *
1465145 AAAAGGGCA-CAAACTA
64 AAAAGGGTATCAAA-TT
* * * * * *
1465161 GTTTTCCCTCAAGCGATTTCCCAGAAAATTTTCACAAATTACACAAGCAAATACAGCAAGAGCAA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAACAA
*
1465226 AAGGGAATCAAAAATT
66 AAGGGTATC--AAATT
** * **
1465242 GTTTTCCCTCATGCAAATTCCCAGAAAAAATTCACAGAGAACT-AAGGAAATACAGCAA-AAGCA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAA-CA
*
1465305 AAAGGATATCAAATT
65 AAAGGGTATCAAATT
* * * *
1465320 -TGGTCCCCTCTTGCAAATTCCCAGAAAATTTTCACAAATTACTAAAGGAAATACAGCAA-AAGC
1 GT-TTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAA-C
*
1465383 AAAAGGGTATCGAATT
64 AAAAGGGTATCAAATT
* * * * * *
1465399 GATTTCTCC-CATTCAAATTCCCAGAAAAAATTTCACAAATTACTCAAGCAAATACAACAAGAGC
1 GTTTTC-CCTCATGCAAATTCCCAG-AAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAAC
* * ***
1465463 AAAAGGATACCTAACCA
64 AAAAGGGTATC-AAATT
* * *
1465480 GTGTTCCCTCACT-CAAATTCCCAGAAAAAATTTCAGAAATTACTCAAG
1 GTTTTCCCTCA-TGCAAATTCCCAG-AAAATTTTCACAAATTACTCAAG
1465528 AAAAACTTAT
Statistics
Matches: 368, Mismatches: 64, Indels: 33
0.79 0.14 0.07
Matches are distributed among these distances:
77 1 0.00
78 38 0.10
79 57 0.15
80 120 0.33
81 103 0.28
82 22 0.06
83 27 0.07
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (79 bp):
GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAACAA
AAGGGTATCAAATT
Found at i:1465351 original size:159 final size:159
Alignment explanation
Indices: 1465004--1465555 Score: 535
Period size: 159 Copynumber: 3.4 Consensus size: 159
1464994 ATTGGTTTTT
* * * * * *
1465004 CCTCTTGAAAATTCTCAGAAAATTTTCACAGATTCACTCAAAGGAAATATAGAAAGAGCAAAAGG
1 CCTCTTGCAAATTCCCAGAAAATTTTCACAAATT-ACAC-AAGGAAATACAGCAAGAGCAAAAGG
* * **
1465069 GTATCAGAATTGGTTTCCCTTCATGCAAATTCCAAGAAAATTTTCACAAATTACTCAAGGAAATA
64 GTATCAGAATTGATTTCCC-TCATGCAAATTCCCAGAAAAAATTCACAAATTACTCAAGGAAATA
** * *
1465134 CAGCAAGAA-CAAAAAGGGCACAAACTAGTTTTC
128 CAGCAA-AAGC-AAAAGGATACAAACTAGTGTCC
** * * * *
1465167 CCTCAAGCGATTTCCCAGAAAATTTTCACAAATTACACAAGCAAATACAGCAAGAGCAAAAGGGA
1 CCTCTTGCAAATTCCCAGAAAATTTTCACAAATTACACAAGGAAATACAGCAAGAGCAAAAGGGT
* * * **
1465232 ATCAAAAATTGTTTTCCCTCATGCAAATTCCCAGAAAAAATTCACAGAGAACT-AAGGAAATACA
66 ATC-AGAATTGATTTCCCTCATGCAAATTCCCAGAAAAAATTCACAAATTACTCAAGGAAATACA
* *
1465296 GCAAAAGCAAAAGGATATCAAATTTG-GTCC
130 GCAAAAGCAAAAGGATA-CAAACTAGTGTCC
*
1465326 CCTCTTGCAAATTCCCAGAAAATTTTCACAAATTACTA-AAGGAAATACAGCAAAAGCAAAAGGG
1 CCTCTTGCAAATTCCCAGAAAATTTTCACAAATTAC-ACAAGGAAATACAGCAAGAGCAAAAGGG
* *
1465390 TATC-GAATTGATTTCTCC-CATTCAAATTCCCAGAAAAAATTTCACAAATTACTCAAGCAAATA
65 TATCAGAATTGATTTC-CCTCATGCAAATTCCCAGAAAAAA-TTCACAAATTACTCAAGGAAATA
* * * * *
1465453 CAACAAGAGCAAAAGGATACCTAACCAGTGTTC
128 CAGCAAAAGCAAAAGGATA-CAAACTAGTGTCC
* * * * * *
1465486 CCTCACT-CAAATTCCCAGAAAAAATTTCAGAAATTACTCAA-GAAAAACTTATCAAGAGCAAAA
1 CCTC-TTGCAAATTCCCAG-AAAATTTTCACAAATTACACAAGGAAATAC--AGCAAGAGC-AAA
1465549 AGGGTAT
61 AGGGTAT
1465556 TGAAAATCAA
Statistics
Matches: 320, Mismatches: 55, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
157 29 0.09
158 12 0.04
159 99 0.31
160 47 0.15
161 74 0.23
162 22 0.07
163 37 0.12
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.22
Consensus pattern (159 bp):
CCTCTTGCAAATTCCCAGAAAATTTTCACAAATTACACAAGGAAATACAGCAAGAGCAAAAGGGT
ATCAGAATTGATTTCCCTCATGCAAATTCCCAGAAAAAATTCACAAATTACTCAAGGAAATACAG
CAAAAGCAAAAGGATACAAACTAGTGTCC
Found at i:1473558 original size:153 final size:152
Alignment explanation
Indices: 1473423--1474019 Score: 424
Period size: 153 Copynumber: 3.8 Consensus size: 152
1473413 GAAGATTACT
* ** * * ** *
1473423 AAAGATTCAA-TGCTCAAGCTAATAATGAA-AAAACAAAGGTTTTGAG-TGAATTTGAGATAGGA
1 AAAGA-TCAAGTGCTCAAGCGAATAACCAATAAAACAAAGATTTTCAGCAAAATTAGAGATAGGA
*
1473485 AGTAACAAAAAACAAGGCAATTAGAGTGAAGGGTATCGAAATAAAATTGAAAAAAAAAAAAACAC
65 AGT--CAAAAAACAAGGCAATTAGAGTAAAGGGTATCGAAATAAAATTGAAAAAAAAAAAAACA-
1473550 AAAAACCCAGAGTCAAGAACACCATG
127 AAAAACCCAGAGTCAAGAACACCATG
* * *
1473576 AAAGATCAAGTGCTCTAGCGAATAACCAATAAAACAGAGATTTTCAGCAAAATTAGAGATATGAA
1 AAAGATCAAGTGCTCAAGCGAATAACCAATAAAACAAAGATTTTCAGCAAAATTAGAGATAGGAA
* * * * **
1473641 GTTAAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTGAAAAGAAAAAAAAC--CTA
66 GTCAAAAAACAAGGCAATTAGAGTAAAGGGTATCGAAATAAAATTGAAAAAAAAAAAAACAAAAA
* *
1473704 ACTCAGAGCCAAGAACACCATG
131 ACCCAGAGTCAAGAACACCATG
* * * * * *
1473726 AAAGATAAATTGCTCAAACGAACAACCAATATATATATAACAATGATTTTCAGCAAAA-TCGAGC
1 AAAGATCAAGTGCTCAAGCGAATAACC---A-ATA-A-AACAAAGATTTTCAGCAAAATTAGAG-
* * * * * *
1473790 A-AGGAAGTTTAAAAAAAAAAAAACCAAGGCAATTAGACTAAAGAGTATTGAGATAAATTTGAAA
59 ATAGGAAG--T------CAAAAAA-CAAGGCAATTAGAGTAAAGGGTATCGAAATAAAATTGAAA
*** * * *
1473854 AGAAAAAAAAA-ACCTAACCCAGTGCCAAAAACACCATG
115 A-AAAAAAAAACAAAAAACCCAGAGTCAAGAACACCATG
* * * * *
1473892 AAAGATCAAATGCTCAAGCGAATAACCAATAAAA-AAATTATTTTCAGCGAAA-TCGA-ACTAAG
1 AAAGATCAAGTGCTCAAGCGAATAACCAATAAAACAAA-GATTTTCAGCAAAATTAGAGA-TAGG
* * * * *
1473954 AAGTAAAAAAAAAAAAAAAGGGCAATTAGAGTAAAGGGTATTGGAATAAATTTGAAAAAAAAAAA
64 AAGT-----CAAAAAACAA-GGCAATTAGAGTAAAGGGTATCGAAATAAAATTGAAAAAAAAAAA
1474019 A
123 A
1474020 CCCAGAGCCA
Statistics
Matches: 368, Mismatches: 50, Indels: 49
0.79 0.11 0.10
Matches are distributed among these distances:
150 43 0.12
152 4 0.01
153 74 0.20
154 17 0.05
155 25 0.07
156 29 0.08
157 47 0.13
158 2 0.01
159 2 0.01
160 23 0.06
161 1 0.00
162 3 0.01
163 7 0.02
164 38 0.10
165 8 0.02
166 45 0.12
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (152 bp):
AAAGATCAAGTGCTCAAGCGAATAACCAATAAAACAAAGATTTTCAGCAAAATTAGAGATAGGAA
GTCAAAAAACAAGGCAATTAGAGTAAAGGGTATCGAAATAAAATTGAAAAAAAAAAAAACAAAAA
ACCCAGAGTCAAGAACACCATG
Found at i:1473852 original size:164 final size:155
Alignment explanation
Indices: 1473491--1474241 Score: 602
Period size: 149 Copynumber: 4.9 Consensus size: 155
1473481 AGGAAGTAAC
* * * * * *
1473491 AAAAAACAAGGCAATTAGAGTGAAGGGTATCGAAATAAAATTGAAAAAAAAAAAAACACAAAAAC
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAGATAAATTTGAAAAGAAAAAAAAC-C--TAAC
* * * * * * *
1473556 CCAGAGTCAAGAACACCATGAAAGATCAAGTGCTCTAGCGAATAACCAATAAAACAGA-GATTTT
63 CCAGAGCCAAAAACACCATGAAAGATCAAATGCTCAAACGAACAACCAATAAAA-AAATGATTTT
* * *
1473620 CAGCAAAATTAGAGA-TATGAAGT------T
127 CAGCAAAA-TCGA-ACTAAGAAGTAAAAAAA
* *
1473644 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTGAAAAGAAAAAAAACCTAACTCA
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAGATAAATTTGAAAAGAAAAAAAACCTAACCCA
*
1473709 GAGCCAAGAACACCATGAAAGAT-AAATTGCTCAAACGAACAACCAATATATATATAACAATGAT
66 GAGCCAAAAACACCATGAAAGATCAAA-TGCTCAAACGAACAACC-A-ATA-A-A-AA-AATGAT
*
1473773 TTTCAGCAAAATCGAGC-AAGGAAGTTTAAAAAAA
124 TTTCAGCAAAATCGAACTAA-GAAG--TAAAAAAA
* *
1473807 AAAAAACCAAGGCAATTAGACTAAAGAGTATTGAGATAAATTTGAAAAGAAAAAAAAAACCTAAC
1 AAAAAA-CAAGGCAATTAGAGTAAAGGGTATTGAGATAAATTTGAAAAG--AAAAAAAACCTAAC
* * * *
1473872 CCAGTGCCAAAAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAAAAATTATTTTC
63 CCAGAGCCAAAAACACCATGAAAGATCAAATGCTCAAACGAACAACCAATAAAAAAATGATTTTC
*
1473937 AGCGAAATCGAACTAAGAAGTAAAAAAA
128 AGCAAAATCGAACTAAGAAGTAAAAAAA
1473965 AAAAAA-AAGGGCAATTAGAGTAAAGGGTATTG-GAATAAATTTG--AA-AAAAAAAA---AACC
1 AAAAAACAA-GGCAATTAGAGTAAAGGGTATTGAG-ATAAATTTGAAAAGAAAAAAAACCTAACC
* * *** * * **
1474022 CAGAGCCAAGAATC-TCACCCAAGCTCGAATGCTCAAACGAACAACCAATAAATCAATGATTTTC
64 CAGAGCCAA-AAACACCATGAAAGATCAAATGCTCAAACGAACAACCAATAAAAAAATGATTTTC
* * *
1474086 AGCAAATTCGAGCTAAGAAGT--TAAAA
128 AGCAAAATCGAACTAAGAAGTAAAAAAA
* * * * * * * *
1474112 AAAAAACAAGGCAATTATACTAAAGGGAATTGAAATAAAATCG--AA-AAAACACA-CTAACCCA
1 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAGATAAATTTGAAAAGAAAAAAAACCTAACCCA
* * * ** * *
1474173 AAGCCAAGAATC-TCACCAAAGCTCAAATGCTCTAACGAACAACCAA-AAACAACAATGATTTTC
66 GAGCCAA-AAACACCATGAAAGATCAAATGCTCAAACGAACAACCAATAAA-AA-AATGATTTTC
1474236 AGCAAA
128 AGCAAA
1474242 TTCTAGCTGG
Statistics
Matches: 506, Mismatches: 60, Indels: 67
0.80 0.09 0.11
Matches are distributed among these distances:
147 45 0.09
148 5 0.01
149 119 0.24
150 60 0.12
151 1 0.00
152 12 0.02
153 54 0.11
154 3 0.01
155 11 0.02
156 17 0.03
157 31 0.06
158 14 0.03
160 24 0.05
161 4 0.01
162 1 0.00
163 7 0.01
164 42 0.08
165 1 0.00
166 52 0.10
167 3 0.01
ACGTcount: A:0.52, C:0.16, G:0.15, T:0.17
Consensus pattern (155 bp):
AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAGATAAATTTGAAAAGAAAAAAAACCTAACCCA
GAGCCAAAAACACCATGAAAGATCAAATGCTCAAACGAACAACCAATAAAAAAATGATTTTCAGC
AAAATCGAACTAAGAAGTAAAAAAA
Found at i:1475196 original size:31 final size:31
Alignment explanation
Indices: 1475161--1475221 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
1475151 GTAATTATAC
* * *
1475161 ACATGATATTTTAATTTTGGTTCAAATGTAT
1 ACATGAAACTTTAATTTTGATTCAAATGTAT
* *
1475192 ACATGAAACTTTGATTTTGATTCAATTGTA
1 ACATGAAACTTTAATTTTGATTCAAATGTA
1475222 CATATTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (31 bp):
ACATGAAACTTTAATTTTGATTCAAATGTAT
Found at i:1478565 original size:16 final size:17
Alignment explanation
Indices: 1478534--1478567 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1478524 TTTACTATTT
1478534 TAAAAAATAATTTTATAA
1 TAAAAAATAA-TTTATAA
1478552 TAAAAAATAA-TTATAA
1 TAAAAAATAATTTATAA
1478568 AATGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAAATAATTTATAA
Found at i:1480964 original size:60 final size:60
Alignment explanation
Indices: 1480893--1481020 Score: 202
Period size: 60 Copynumber: 2.1 Consensus size: 60
1480883 ACAAAATTGA
* *
1480893 ATAGTTAGGTGACCAAAAAATAAATGTACTAATAGTTGAGTGACCATTTTGTAACTTTTC
1 ATAGTTGGGTGACCAAAAAAGAAATGTACTAATAGTTGAGTGACCATTTTGTAACTTTTC
* * * *
1480953 ATAGTTGGGTGATCAAAGAAGAAATTTACTAATAGTTGAGTGACTATTTTGTAACTTTTC
1 ATAGTTGGGTGACCAAAAAAGAAATGTACTAATAGTTGAGTGACCATTTTGTAACTTTTC
1481013 ATAGTTGG
1 ATAGTTGG
1481021 ATGAAAAAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (60 bp):
ATAGTTGGGTGACCAAAAAAGAAATGTACTAATAGTTGAGTGACCATTTTGTAACTTTTC
Found at i:1481019 original size:29 final size:29
Alignment explanation
Indices: 1480924--1481019 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
1480914 AAATGTACTA
*
1480924 ATAGTTGAGTGACCATTTTGTAACTTTTC
1 ATAGTTGAGTGACAATTTTGTAACTTTTC
* **** * *
1480953 ATAGTTGGGTGATCAAAGAAG-AAATTTACTA
1 ATAGTTGAGTGA-CAATTTTGTAACTTT--TC
*
1480984 ATAGTTGAGTGACTATTTTGTAACTTTTC
1 ATAGTTGAGTGACAATTTTGTAACTTTTC
1481013 ATAGTTG
1 ATAGTTG
1481020 GATGAAAAAA
Statistics
Matches: 47, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
29 24 0.51
30 6 0.13
31 17 0.36
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (29 bp):
ATAGTTGAGTGACAATTTTGTAACTTTTC
Found at i:1481048 original size:60 final size:59
Alignment explanation
Indices: 1480923--1481057 Score: 155
Period size: 60 Copynumber: 2.3 Consensus size: 59
1480913 TAAATGTACT
* ** * ***
1480923 AATAGTTGAGTGACCATTTTGTAACTTTTCATAGTTGGGTGATCAAAGAAGAAATTTAC
1 AATAGTTGAGTGACCATTTTGTAACTTTTCATAGTTGGATGAAAAAAGAAAAAAAAAAC
*
1480982 TAATAGTTGAGTGACTATTTTGTAACTTTTCATAGTTGGATGAAAAAAGGAAAAAAGAAAAC
1 -AATAGTTGAGTGACCATTTTGTAACTTTTCATAGTTGGATGAAAAAA-GAAAAAA-AAAAC
*
1481044 -ATAGTTGGGTGACC
1 AATAGTTGAGTGACC
1481058 TCTACCATAG
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
60 55 0.87
61 6 0.10
62 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (59 bp):
AATAGTTGAGTGACCATTTTGTAACTTTTCATAGTTGGATGAAAAAAGAAAAAAAAAAC
Found at i:1484372 original size:11 final size:11
Alignment explanation
Indices: 1484356--1484448 Score: 58
Period size: 11 Copynumber: 8.9 Consensus size: 11
1484346 ACCAAAAATT
1484356 TATTTTAAAAA
1 TATTTTAAAAA
1484367 TATTTT--AAA
1 TATTTTAAAAA
*
1484376 -A-TTAAAAAA
1 TATTTTAAAAA
1484385 GTATTTTAAAAA
1 -TATTTTAAAAA
1484397 TATTTT--AAA
1 TATTTTAAAAA
*
1484406 -A-TTAAAAAA
1 TATTTTAAAAA
*
1484415 AATTTTAAAAAA
1 TATTTT-AAAAA
* *
1484427 GTATCTTAAAAG
1 -TATTTTAAAAA
1484439 TATTTTAAAA
1 TATTTTAAAA
1484449 TTAAAAAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 22
0.68 0.09 0.24
Matches are distributed among these distances:
7 4 0.06
8 2 0.03
9 12 0.19
10 1 0.02
11 24 0.38
12 16 0.25
13 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:1484426 original size:30 final size:30
Alignment explanation
Indices: 1484357--1484425 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
1484347 CCAAAAATTT
*
1484357 ATTTTAAAAATATTTTAAAATTAAAAAAGT
1 ATTTTAAAAATATTTTAAAATTAAAAAAGA
1484387 ATTTTAAAAATATTTTAAAATTAAAAAA-A
1 ATTTTAAAAATATTTTAAAATTAAAAAAGA
1484416 ATTTTAAAAA
1 ATTTTAAAAA
1484426 AGTATCTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 10 0.26
30 28 0.74
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
ATTTTAAAAATATTTTAAAATTAAAAAAGA
Found at i:1484436 original size:42 final size:42
Alignment explanation
Indices: 1484377--1484456 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
1484367 TATTTTAAAA
*
1484377 TTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATT
1 TTAAAAAAGTATCTTAAAAATATTTTAAAATTAAAAAAAATT
*
1484419 TTAAAAAAGTATCTTAAAAGTATTTTAAAATTAAAAAA
1 TTAAAAAAGTATCTTAAAAATATTTTAAAATTAAAAAA
1484457 TAAAAATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (42 bp):
TTAAAAAAGTATCTTAAAAATATTTTAAAATTAAAAAAAATT
Found at i:1485219 original size:30 final size:28
Alignment explanation
Indices: 1485170--1485228 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
1485160 AAAGTGATTT
*
1485170 AAATGAAATAATTAGGGCTAAAATGATA
1 AAATGAAAAAATTAGGGCTAAAATGATA
*
1485198 AAATGAAAAATATTAGAGGCTAAAATTATA
1 AAATGAAAAA-ATTAG-GGCTAAAATGATA
1485228 A
1 A
1485229 TTAAGCATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 9 0.33
29 5 0.19
30 13 0.48
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.25
Consensus pattern (28 bp):
AAATGAAAAAATTAGGGCTAAAATGATA
Found at i:1489902 original size:2 final size:2
Alignment explanation
Indices: 1489895--1489936 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1489885 TATGAAGCAT
1489895 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1489937 ATGTCTAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1491758 original size:29 final size:30
Alignment explanation
Indices: 1491725--1491794 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
1491715 CTTATCATTA
**
1491725 TAAAATAAATATAATTCATGCAAAAAAT-T
1 TAAAATAAATATAATTCATAAAAAAAATGT
* * *
1491754 TAAAATATACATTATTCATAAAAAAAATGT
1 TAAAATAAATATAATTCATAAAAAAAATGT
1491784 TAAAATGAAAT
1 TAAAAT-AAAT
1491795 TTGTTGATTG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
29 23 0.72
30 7 0.22
31 2 0.06
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (30 bp):
TAAAATAAATATAATTCATAAAAAAAATGT
Found at i:1494049 original size:239 final size:237
Alignment explanation
Indices: 1493620--1494147 Score: 744
Period size: 239 Copynumber: 2.2 Consensus size: 237
1493610 AGACTACCCC
* * * *
1493620 TTCAAGATTTTGTTGTCCATGGATAACCATGTATTTAGCCTTTATTTATTCCACCTATATAATAG
1 TTCAAGATTTTGTTGTCCAAGTATAACCATGAATTTAGCCTTTATTTATTCCACCTATATAATAA
* * *
1493685 AATTGGTCAAATTTCACGGAAAGTCCCTCTATTATTTTTTTTTCACAAATTTAGCCTCTCTACTA
66 AATTGGTCAAATTTCACAGAAACTCCCTCTATTATTTTTTTTTCACAAATTTAACCTCTCTACTA
* * * * *
1493750 TAATTTAGTCAATTTTTGGGTGATTGGAGAGTACCGAGTTAATTTAAAGTTCAAGAGAGTGGGAT
131 TAATTTAGTCAATTTTTGGGTGAGTAGAGAGTACCGAGTGAAGTTAAAGTACAAGAGAGTGGGAT
* *
1493815 TCTATCAACAAAGTTTGAATAATGGTCATTGAAAGTG-CCTT
196 TATATCAACAAAGTTTGAATAATGATCATTGAAAGTGTCCTT
*
1493856 TTCAAGATTTTGTTGTCCAAGTATAACCATGAATTTAGCCATTATTTA-TCC-CCGTATATAATA
1 TTCAAGATTTTGTTGTCCAAGTATAACCATGAATTTAGCCTTTATTTATTCCACC-TATATAATA
* *
1493919 AAATTGGTCAAATTTCATAGAAACTCCCTCTATTATTTATTTTTTTCCCACAAATTTAATCTCTC
65 AAATTGGTCAAATTTCACAGAAACTCCCTCTATTA-TT-TTTTTTT--CACAAATTTAACCTCTC
*
1493984 TACTATAATTT-GATC-ATTTCTTGGGTGAGTAGAGAGTACCGAGTGAAGTTACAA-TACAGGAG
126 TACTATAATTTAG-TCAATTT-TTGGGTGAGTAGAGAGTACCGAGTGAAGTTA-AAGTACAAGAG
*
1494046 AGTGGGATTATATCAACAAAGTTTGAATAATGATCATTGAGAGTGTCCTT
188 AGTGGGATTATATCAACAAAGTTTGAATAATGATCATTGAAAGTGTCCTT
* * *
1494096 TTCAAGATTTTCTTGTCCAAATATAACCATGAATTTAGCCTTTATTTGTTCC
1 TTCAAGATTTTGTTGTCCAAGTATAACCATGAATTTAGCCTTTATTTATTCC
1494148 CTCTAAAATT
Statistics
Matches: 259, Mismatches: 23, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
234 2 0.01
235 43 0.17
236 46 0.18
237 7 0.03
238 5 0.02
239 103 0.40
240 50 0.19
241 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (237 bp):
TTCAAGATTTTGTTGTCCAAGTATAACCATGAATTTAGCCTTTATTTATTCCACCTATATAATAA
AATTGGTCAAATTTCACAGAAACTCCCTCTATTATTTTTTTTTCACAAATTTAACCTCTCTACTA
TAATTTAGTCAATTTTTGGGTGAGTAGAGAGTACCGAGTGAAGTTAAAGTACAAGAGAGTGGGAT
TATATCAACAAAGTTTGAATAATGATCATTGAAAGTGTCCTT
Found at i:1501991 original size:18 final size:18
Alignment explanation
Indices: 1501968--1502008 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1501958 TTTAAGTCTA
1501968 ATTTATATATATATATAT
1 ATTTATATATATATATAT
* * *
1501986 ATTTATTTATTTATTTAT
1 ATTTATATATATATATAT
1502004 ATTTA
1 ATTTA
1502009 AATAGTGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTATATATATATATAT
Found at i:1504420 original size:14 final size:14
Alignment explanation
Indices: 1504401--1504428 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1504391 AAAGAAATTG
1504401 ATTTGATAATTGAT
1 ATTTGATAATTGAT
1504415 ATTTGATAATTGAT
1 ATTTGATAATTGAT
1504429 TTAACAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (14 bp):
ATTTGATAATTGAT
Found at i:1505346 original size:21 final size:20
Alignment explanation
Indices: 1505320--1505360 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1505310 CGTAAAATGA
*
1505320 TTTCTGGAAAAATGCTTTACT
1 TTTCT-GAAAAATGATTTACT
*
1505341 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
1505361 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:1515845 original size:26 final size:26
Alignment explanation
Indices: 1515806--1515860 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
1515796 AAACACTTAA
1515806 ATTTTTCAAAAGCACTTCTT-AAAAAC
1 ATTTTTCAAAAGCACTT-TTCAAAAAC
* *
1515832 ATTTTTCTACAGCACTTTTCAAAAAC
1 ATTTTTCAAAAGCACTTTTCAAAAAC
1515858 ATT
1 ATT
1515861 GCCAAATTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (26 bp):
ATTTTTCAAAAGCACTTTTCAAAAAC
Found at i:1516002 original size:22 final size:25
Alignment explanation
Indices: 1515961--1516009 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
1515951 TTTGAATCAG
1515961 TTTTCTCTAATTTTTAATAA-TTAT
1 TTTTCTCTAATTTTTAATAATTTAT
*
1515985 TTTTCT-TTATTTTT-ATAATTTAT
1 TTTTCTCTAATTTTTAATAATTTAT
1516008 TT
1 TT
1516010 AATTAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 13 0.57
24 6 0.26
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTCTCTAATTTTTAATAATTTAT
Found at i:1519699 original size:13 final size:14
Alignment explanation
Indices: 1519683--1519716 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
1519673 AATAAATATA
1519683 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
1519696 TATTTTTTAATTTT
1 TATTTTTTAATTTT
1519710 TAATTTT
1 T-ATTTT
1519717 AAAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 6 0.32
15 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:1521082 original size:3 final size:3
Alignment explanation
Indices: 1521043--1521072 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1521033 ATAAGATTTT
1521043 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1521073 GGTATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1523423 original size:10 final size:10
Alignment explanation
Indices: 1523410--1523466 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
1523400 TTTTTTTTGA
1523410 ATTTTTAGTG
1 ATTTTTAGTG
1523420 ATTTTTAGTG
1 ATTTTTAGTG
1523430 AATTTTTAGTG
1 -ATTTTTAGTG
* *
1523441 CTTTTAAGTG
1 ATTTTTAGTG
**
1523451 ATAGTTAGTG
1 ATTTTTAGTG
1523461 ATTTTT
1 ATTTTT
1523467 TTTTTTGAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
10 28 0.74
11 10 0.26
ACGTcount: A:0.23, C:0.02, G:0.19, T:0.56
Consensus pattern (10 bp):
ATTTTTAGTG
Found at i:1523424 original size:21 final size:21
Alignment explanation
Indices: 1523407--1523466 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1523397 TTATTTTTTT
1523407 TGAATTTTTAGTGATTTTTAG
1 TGAATTTTTAGTGATTTTTAG
* *
1523428 TGAATTTTTAGTGCTTTTAAG
1 TGAATTTTTAGTGATTTTTAG
**
1523449 TG-ATAGTTAGTGATTTTT
1 TGAATTTTTAGTGATTTTT
1523467 TTTTTTGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 12 0.36
21 21 0.64
ACGTcount: A:0.23, C:0.02, G:0.20, T:0.55
Consensus pattern (21 bp):
TGAATTTTTAGTGATTTTTAG
Found at i:1528238 original size:12 final size:12
Alignment explanation
Indices: 1528222--1528256 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1528212 ATTATTTGGT
1528222 ATTTAAT-TTTA
1 ATTTAATATTTA
1528233 ACTTTAATATTTA
1 A-TTTAATATTTA
1528246 ATTTAATATTT
1 ATTTAATATTT
1528257 GAAGTCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 16 0.73
13 5 0.23
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTTAATATTTA
Found at i:1528712 original size:3 final size:3
Alignment explanation
Indices: 1528706--1528750 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
1528696 AAAAAAAAGT
1528706 AGA AGA AGA AGA AGA AGA AGAA AGAA AGA A-A AGA A-A AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AG-A AG-A AGA AGA AGA AGA AGA AGA AGA
1528750 A
1 A
1528751 AAATATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.16
3 25 0.66
4 7 0.18
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1528732 original size:4 final size:5
Alignment explanation
Indices: 1528706--1528752 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
1528696 AAAAAAAAGT
1528706 AGAAGA AGAAGA AGAAGA AG-AA AG-AA AGAAA AGAAA AGAAA AGAAA
1 AGAA-A AGAA-A AGAA-A AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
1528752 A
1 A
1528753 ATATAATAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 7 0.17
5 19 0.47
6 14 0.35
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:1531577 original size:57 final size:57
Alignment explanation
Indices: 1531509--1531623 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
1531499 GAATGGAACT
1531509 TAAACTGCTTACCAATGGTTTAAGGCATAATCAATATCGAAACAATATTGATTACCA
1 TAAACTGCTTACCAATGGTTTAAGGCATAATCAATATCGAAACAATATTGATTACCA
1531566 TAAACTGCTTACCAATGGTTTAAGGCATAATCAATATCGAAACAATATTGATTACCA
1 TAAACTGCTTACCAATGGTTTAAGGCATAATCAATATCGAAACAATATTGATTACCA
1531623 T
1 T
1531624 GGTTCTAATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (57 bp):
TAAACTGCTTACCAATGGTTTAAGGCATAATCAATATCGAAACAATATTGATTACCA
Found at i:1533856 original size:21 final size:22
Alignment explanation
Indices: 1533814--1533856 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1533804 GAATGGTAGC
*
1533814 AAAACAGTGGCAAAAAAGCAAG
1 AAAACAGTGGCAAAAAAACAAG
1533836 AAAACA-TGG-AAAAACAACAAG
1 AAAACAGTGGCAAAAA-AACAAG
1533857 GGTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 8 0.42
22 6 0.32
ACGTcount: A:0.63, C:0.14, G:0.19, T:0.05
Consensus pattern (22 bp):
AAAACAGTGGCAAAAAAACAAG
Found at i:1534645 original size:31 final size:28
Alignment explanation
Indices: 1534600--1534661 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 28
1534590 AAATATGTTG
*
1534600 TTAGTACTTGTATTTATATAGAATTTAAGAT
1 TTAGTACTTGTATTT-TA-A-AATTTAAAAT
* *
1534631 TTAGTCCTTTTATTTTAAAATTTAAAAT
1 TTAGTACTTGTATTTTAAAATTTAAAAT
1534659 TTA
1 TTA
1534662 ATTCCTTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.43
29 1 0.04
30 2 0.07
31 13 0.46
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52
Consensus pattern (28 bp):
TTAGTACTTGTATTTTAAAATTTAAAAT
Found at i:1535881 original size:58 final size:58
Alignment explanation
Indices: 1535798--1535907 Score: 184
Period size: 58 Copynumber: 1.9 Consensus size: 58
1535788 TTTTAATAGG
* *
1535798 ATTATTATTAAAAATAATTTGATAAAAATAATAAATAATTTAATCATATTTTAACGTA
1 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATAATATTTTAACGTA
* *
1535856 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTTT
1 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATAATATTTT
1535908 TAATATATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATAATATTTTAACGTA
Found at i:1541510 original size:18 final size:19
Alignment explanation
Indices: 1541471--1541511 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
1541461 ATTGATTGGA
*
1541471 TATTGTATAATTTTTGTTT
1 TATTGTATAATTTTTGTAT
1541490 TATTGT-TAATTTTAT-TAT
1 TATTGTATAATTTT-TGTAT
1541508 TATT
1 TATT
1541512 TTAGAGGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (19 bp):
TATTGTATAATTTTTGTAT
Found at i:1555652 original size:10 final size:10
Alignment explanation
Indices: 1555637--1555663 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1555627 CATTAACTGA
1555637 ATTTTTTTAT
1 ATTTTTTTAT
1555647 ATTTTTTTAT
1 ATTTTTTTAT
1555657 ATTTTTT
1 ATTTTTT
1555664 AGATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
ATTTTTTTAT
Found at i:1559573 original size:23 final size:22
Alignment explanation
Indices: 1559547--1559590 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1559537 TTTAAAAAAT
*
1559547 AAAATATGAAATTAATTTATTAG
1 AAAAGATG-AATTAATTTATTAG
**
1559570 AAAAGATGCGTTAATTTATTA
1 AAAAGATGAATTAATTTATTA
1559591 ATAAAACAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (22 bp):
AAAAGATGAATTAATTTATTAG
Found at i:1564538 original size:29 final size:30
Alignment explanation
Indices: 1564487--1564552 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
1564477 TAGGAATTGT
* * *
1564487 ATCAAATTAGTCCCTCTATTATTAA-ATGA
1 ATCAAATTAGTCCCTATACTATTAACAAGA
* *
1564516 ATCAATTTAGTCCTTATACTATTAACAAGA
1 ATCAAATTAGTCCCTATACTATTAACAAGA
1564546 ATCAAAT
1 ATCAAAT
1564553 AATATCAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (30 bp):
ATCAAATTAGTCCCTATACTATTAACAAGA
Found at i:1568077 original size:17 final size:17
Alignment explanation
Indices: 1568055--1568088 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1568045 CATTTGTAAT
1568055 TTGTACTATATCTATAA
1 TTGTACTATATCTATAA
1568072 TTGTACTATATCTATAA
1 TTGTACTATATCTATAA
1568089 CACATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (17 bp):
TTGTACTATATCTATAA
Found at i:1571144 original size:25 final size:27
Alignment explanation
Indices: 1571094--1571146 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
1571084 TTTAAAATAC
* *
1571094 TTTTAAAATATATATTTTTATTTTTAT
1 TTTTAAAATATATATTTTAATGTTTAT
1571121 TTTTAAAATA-AT-TTTTAATGTTTAT
1 TTTTAAAATATATATTTTAATGTTTAT
1571146 T
1 T
1571147 AAAAAATGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 12 0.50
26 2 0.08
27 10 0.42
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTTAAAATATATATTTTAATGTTTAT
Found at i:1574221 original size:32 final size:32
Alignment explanation
Indices: 1574180--1574248 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
1574170 ACCCTCCAAA
* *
1574180 TTTTTGAAAATTTTCATTATGC-CTTTTAATTT
1 TTTTTGAAAACTTTAATTATGCTC-TTTAATTT
1574212 TTTTTGAAAACTTTAATTATGCTCTTTAATTT
1 TTTTTGAAAACTTTAATTATGCTCTTTAATTT
1574244 TTTTT
1 TTTTT
1574249 TTGAAATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 33 0.97
33 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.61
Consensus pattern (32 bp):
TTTTTGAAAACTTTAATTATGCTCTTTAATTT
Found at i:1575413 original size:10 final size:10
Alignment explanation
Indices: 1575400--1575440 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
1575390 TACCTTACAT
*
1575400 ACATACATAT
1 ACATACATAC
1575410 ACATACATAC
1 ACATACATAC
**
1575420 ACACGCATAC
1 ACATACATAC
1575430 ACATACATAC
1 ACATACATAC
1575440 A
1 A
1575441 TGCTAATCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (10 bp):
ACATACATAC
Found at i:1584361 original size:23 final size:23
Alignment explanation
Indices: 1584317--1584385 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 23
1584307 TGAGATAAAG
*
1584317 AAAAACTCAAGTATCAAATTGAA
1 AAAAACTCAAGTACCAAATTGAA
* * *
1584340 AAAAATTCAGGTACCAATTTGAGACA
1 AAAAACTCAAGTACCAAATT--GA-A
1584366 AAAAACTCAAGTACCAAATT
1 AAAAACTCAAGTACCAAATT
1584386 AAACATTGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 16 0.44
25 2 0.06
26 18 0.50
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.22
Consensus pattern (23 bp):
AAAAACTCAAGTACCAAATTGAA
Found at i:1585118 original size:35 final size:36
Alignment explanation
Indices: 1585079--1585157 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 36
1585069 GGCCCGGCCC
1585079 AAATATAAT-AAATATATATTTTTTA-TTTTTA-TTTT
1 AAATATAATAAAATA-AT-TTTTTTATTTTTTATTTTT
**
1585114 AAATACTTTTAAAATAATTTTTTTATTTTTTATTTTT
1 AAATA-TAATAAAATAATTTTTTTATTTTTTATTTTT
1585151 AAA-ATAA
1 AAATATAA
1585158 ATTTTTAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
35 13 0.36
36 11 0.31
37 12 0.33
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (36 bp):
AAATATAATAAAATAATTTTTTTATTTTTTATTTTT
Found at i:1585150 original size:27 final size:26
Alignment explanation
Indices: 1585120--1585181 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
1585110 TTTTAAATAC
* * *
1585120 TTTTAAAATAATTTTTTTATTTTTTAT
1 TTTTAAAATAA-ATTTTTAATGTTTAT
1585147 TTTTAAAATAAATTTTTAATGTTTAT
1 TTTTAAAATAAATTTTTAATGTTTAT
*
1585173 TTTAAAAAT
1 TTTTAAAAT
1585182 GGGCAGGCCG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTAAAATAAATTTTTAATGTTTAT
Found at i:1589506 original size:4 final size:4
Alignment explanation
Indices: 1589489--1589518 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1589479 CATTATTTTC
*
1589489 AATT AATA AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
1589519 AACTAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (4 bp):
AATT
Found at i:1589747 original size:32 final size:32
Alignment explanation
Indices: 1589710--1589778 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
1589700 ACCCCCAAAA
* * *
1589710 AAGTTTTA-AGTACTAACTTAAGAAAAAGTGTC
1 AAGTTTTAGA-TACCAAATTAAGAAAAAATGTC
*
1589742 AAG-TTTAGATACCAAATTAGGAAAAAATGTC
1 AAGTTTTAGATACCAAATTAAGAAAAAATGTC
1589773 AAGTTT
1 AAGTTT
1589779 GGGGTACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (32 bp):
AAGTTTTAGATACCAAATTAAGAAAAAATGTC
Found at i:1589791 original size:31 final size:30
Alignment explanation
Indices: 1589714--1589792 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
1589704 CCAAAAAAGT
* * *
1589714 TTTAAGTACTAACTTAAGAAAAAGTGTCAAG
1 TTTAGGTACTAA-TTAGGAAAAAATGTCAAG
* *
1589745 TTTAGATACCAAATTAGGAAAAAATGTCAAG
1 TTTAGGTA-CTAATTAGGAAAAAATGTCAAG
*
1589776 TTTGGGGTACTAATTAG
1 TTT-AGGTACTAATTAG
1589793 ACTAAAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
31 32 0.84
32 6 0.16
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (30 bp):
TTTAGGTACTAATTAGGAAAAAATGTCAAG
Found at i:1590891 original size:312 final size:313
Alignment explanation
Indices: 1590162--1590919 Score: 904
Period size: 314 Copynumber: 2.4 Consensus size: 313
1590152 AAATTCAGGT
* * *
1590162 CCATACAAGTATTAGTCATACC-ATATCAATTAGGT-TCAATTATTAACACCATTAAAACGTACA
1 CCATACAAGTATTAATCACACCAATATCAATCAGGTCT-AATTATTAACACCATTAAAACGTACA
* *
1590225 AAGAGCACAGGGATTTGGGTATATTTTAATCTTTAAACAGGTTTTGTTTTTCTTCCTCAACTCCA
65 AAGAGCACAGGGATTTGGATATATTTTAACCTTTAAACAGG--TTGTTTTTCTTCCTCAACTCCA
* * * *
1590290 TTTCTCAAACCTAATACTTTCATCCAAACCATCCCAAAAAACTAATAAAACTTTGAACTTGAACA
128 TTTCTCAAACCAAATACTTTCATCCAAACCACCCCAAAAAACAAATAAAACTTCGAACTTGAACA
* * *
1590355 GGTGGGTCGACGCTCAAAAAAGCCTTAAAGGGGGCAACTTGGATCACCAAGATTGGGTCATCTAA
193 GGTGGGTCGACCCTCAAAAAAGCCCTAAAGGGGGCAACTTGGATCACCAAGATTGAGTCATCTAA
* * * *
1590420 AAATCTGGTTAAACACTACCACAAAATTTATGAAATAAGAAACAAGATACATGAAT
258 AAATATGGTTAAACACTACCACAAAATTCATGAAACAAGAAACAAGATACATGAAC
* * ** * *
1590476 CCATACAAGTATTAATCACACCAATATCAATCAAGTCCAATCGTTAACATCGTTAAAACGTACAA
1 CCATACAAGTATTAATCACACCAATATCAATCAGGTCTAATTATTAACACCATTAAAACGTACAA
* * * **
1590541 AGAGCACAGGGACTTCGA-ACTATTTTAACCTTTAAACAGGTTGTTTTTGCTTCCTTAACTTTAT
66 AGAGCACAGGGATTTGGATA-TATTTTAACCTTTAAACAGGTTGTTTTT-CTTCCTCAACTCCAT
* * * * * ** *
1590605 TTCTCAGACCAAATACTTTCATCCAAATCACCCCAAAGATCAAAATGAGTCTTCGAGCTTGAACA
129 TTCTCAAACCAAATACTTTCATCCAAACCACCCCAAAAAAC-AAATAAAACTTCGAACTTGAACA
* * * * * **
1590670 GG-GAGTTCGACCCTCGAACAAGCCCT-AAGGGGGCAGCTTGGATCACCATGATTGAGTGGTCTA
193 GGTG-GGTCGACCCTCAAAAAAGCCCTAAAGGGGGCAACTTGGATCACCAAGATTGAGTCATCTA
* * * *
1590733 AAAATATTGTTAAACCCTACCCCAGAATTCATG-AACAA-AAACAAGATACATGAAC
257 AAAATATGGTTAAACACTACCACAAAATTCATGAAACAAGAAACAAGATACATGAAC
* *
1590788 CCATACAAGTATTAATCACACCAATAACAATCAGGTCTAATTATTAACACCATTAAAGCGTACAC
1 CCATACAAGTATTAATCACACCAATATCAATCAGGTCTAATTATTAACACCATTAAAACGTACA-
* * * *
1590853 AA-AGCACAGAGATTTGGATATATTTTAA-CTTCTAAACAGGTTTTTTTTCTTCTTCAACTCAAT
65 AAGAGCACAGGGATTTGGATATATTTTAACCTT-TAAACAGGTTGTTTTTCTTCCTCAACTCCAT
1590916 TTCT
129 TTCT
1590920 TGAGCCTATT
Statistics
Matches: 373, Mismatches: 62, Indels: 21
0.82 0.14 0.05
Matches are distributed among these distances:
311 18 0.05
312 108 0.29
313 15 0.04
314 128 0.34
315 104 0.28
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (313 bp):
CCATACAAGTATTAATCACACCAATATCAATCAGGTCTAATTATTAACACCATTAAAACGTACAA
AGAGCACAGGGATTTGGATATATTTTAACCTTTAAACAGGTTGTTTTTCTTCCTCAACTCCATTT
CTCAAACCAAATACTTTCATCCAAACCACCCCAAAAAACAAATAAAACTTCGAACTTGAACAGGT
GGGTCGACCCTCAAAAAAGCCCTAAAGGGGGCAACTTGGATCACCAAGATTGAGTCATCTAAAAA
TATGGTTAAACACTACCACAAAATTCATGAAACAAGAAACAAGATACATGAAC
Found at i:1594633 original size:23 final size:24
Alignment explanation
Indices: 1594590--1594634 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1594580 TTTTAATAAT
**
1594590 ATTAAATATAAAATATGTATTATA
1 ATTAAATATAAAATAAATATTATA
1594614 ATTAAATA-AAAATAAATATTA
1 ATTAAATATAAAATAAATATTA
1594635 AAGATTAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTAAATATAAAATAAATATTATA
Found at i:1594641 original size:24 final size:24
Alignment explanation
Indices: 1594590--1594642 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1594580 TTTTAATAAT
** *
1594590 ATTAAATATAAAATATGTATTATA
1 ATTAAATATAAAATAAATATTAAA
1594614 ATTAAATA-AAAATAAATATTAAA
1 ATTAAATATAAAATAAATATTAAA
1594637 GATTAA
1 -ATTAA
1594643 GTTTTTATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
ATTAAATATAAAATAAATATTAAA
Found at i:1594990 original size:136 final size:135
Alignment explanation
Indices: 1594645--1594991 Score: 561
Period size: 134 Copynumber: 2.6 Consensus size: 135
1594635 AAGATTAAGT
*
1594645 TTTTATCTTATAGTGGGATCATGTAATAGTTTGATGGTCAAAGGTGTTCATTGCCCCAGGTGTGG
1 TTTTATCTTATAGTGGGATCATGTAATAGTTTGATGGTCAAAGGTATTCATTGCCCCAGGTGTGG
* * * *
1594710 CCTGAGTTCGAGTTGCGCTAGTCGAGTTTGTTGTTTGGGCTTTGCCCTGTTATTGCAATTCACCA
66 CCTGAGTTCGAGTCGCGCTAGTCGAGTTTGTTATTCGGGCTTTGCCCTATTATTGCAATTCACCA
1594775 AAAAA
131 AAAAA
* *
1594780 -ATTATCTTATAGTGGGATTATGTAATAGTTTGATGGTCAAAGGTATTCATTGCCCCAGGTGTGG
1 TTTTATCTTATAGTGGGATCATGTAATAGTTTGATGGTCAAAGGTATTCATTGCCCCAGGTGTGG
* *
1594844 CCTGGGTTCGAGTCGCGCTAGTCGAGTTTGTTATTCGGGCTTTGTCCTATTATTGCAATTCACCA
66 CCTGAGTTCGAGTCGCGCTAGTCGAGTTTGTTATTCGGGCTTTGCCCTATTATTGCAATTCACCA
1594909 AAAAA
131 AAAAA
* *
1594914 GTTTTATCTTATAGTGGGATCATGTAATAGTTTGAGGGTCAAATGTATTCATTGCCCCAGGTGTG
1 -TTTTATCTTATAGTGGGATCATGTAATAGTTTGATGGTCAAAGGTATTCATTGCCCCAGGTGTG
* *
1594979 GCTTGAATTCGAG
65 GCCTGAGTTCGAG
1594992 CTTTGCGTTA
Statistics
Matches: 194, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
134 125 0.64
136 69 0.36
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.37
Consensus pattern (135 bp):
TTTTATCTTATAGTGGGATCATGTAATAGTTTGATGGTCAAAGGTATTCATTGCCCCAGGTGTGG
CCTGAGTTCGAGTCGCGCTAGTCGAGTTTGTTATTCGGGCTTTGCCCTATTATTGCAATTCACCA
AAAAA
Found at i:1595420 original size:21 final size:21
Alignment explanation
Indices: 1595379--1595415 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1595369 AGAAGGATAA
1595379 CATCATCTTTATTTGTTTTTT
1 CATCATCTTTATTTGTTTTTT
1595400 CATC-TCTTT-TTT-TTTT
1 CATCATCTTTATTTGTTTT
1595416 CTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.25
19 3 0.19
20 5 0.31
21 4 0.25
ACGTcount: A:0.11, C:0.16, G:0.03, T:0.70
Consensus pattern (21 bp):
CATCATCTTTATTTGTTTTTT
Found at i:1599025 original size:15 final size:14
Alignment explanation
Indices: 1598997--1599029 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1598987 ATTATTTTAC
1598997 TATA-TATAATATA
1 TATACTATAATATA
1599010 TATACTATACATATA
1 TATACTATA-ATATA
1599025 TATAC
1 TATAC
1599030 CGACATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 4 0.22
15 10 0.56
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (14 bp):
TATACTATAATATA
Found at i:1601874 original size:3 final size:3
Alignment explanation
Indices: 1601866--1601891 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1601856 CAATTGAAGT
1601866 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
1601892 GTAGCAGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:1607512 original size:139 final size:139
Alignment explanation
Indices: 1607262--1607519 Score: 428
Period size: 139 Copynumber: 1.9 Consensus size: 139
1607252 CTTGCTTATC
*
1607262 ATATTCTAAAGAAAGCCAATTTTAGTTTAAGATATTAAATTAATTCCAATTTATCAATATCATCA
1 ATATTCTAAAGAAAGCCAATTTTAGTTTAAGATATTAAATAAATTCCAATTTATCAATATCATCA
1607327 TTAGATCCTAATTACATCAAAACAAAAACAACCCAAACTTTAAATCTCTAAAAAAATTTTAAAAA
66 TTAGATCCTAATTACATCAAAACAAAAACAACCCAAACTTTAAATCTCTAAAAAAATTTTAAAAA
1607392 GTCATCATT
131 GTCATCATT
* * * *
1607401 ATATTCTAAAGTAAGCTAATTTTAGTTTAAGATATTGAATAAATTCCGATTTATCAATATCATCA
1 ATATTCTAAAGAAAGCCAATTTTAGTTTAAGATATTAAATAAATTCCAATTTATCAATATCATCA
** *
1607466 TTAGATCCTAATTACATTTTAAA-AAAAACCACCCAAACTTTAAATCTCTAAAAA
66 TTAGATCCTAATTACA-TCAAAACAAAAACAACCCAAACTTTAAATCTCTAAAAA
1607520 CATCCATGGG
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
139 106 0.96
140 4 0.04
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (139 bp):
ATATTCTAAAGAAAGCCAATTTTAGTTTAAGATATTAAATAAATTCCAATTTATCAATATCATCA
TTAGATCCTAATTACATCAAAACAAAAACAACCCAAACTTTAAATCTCTAAAAAAATTTTAAAAA
GTCATCATT
Found at i:1608091 original size:20 final size:21
Alignment explanation
Indices: 1608049--1608091 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
1608039 GTTTAATAAA
*
1608049 AAATATTTGAAAGTAAAAGAG
1 AAATATTTGAAAGCAAAAGAG
* *
1608070 AAATTTTTG-AAGCAAAATAG
1 AAATATTTGAAAGCAAAAGAG
1608090 AA
1 AA
1608092 GAAGAAGACG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.26
Consensus pattern (21 bp):
AAATATTTGAAAGCAAAAGAG
Found at i:1615543 original size:9 final size:9
Alignment explanation
Indices: 1615524--1615561 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1615514 CTAGCTTGAA
1615524 TTTTAGATTT
1 TTTTA-ATTT
1615534 TTTT-ATTT
1 TTTTAATTT
*
1615542 TTTTAATAT
1 TTTTAATTT
1615551 TTTTAATTT
1 TTTTAATTT
1615560 TT
1 TT
1615562 AGATACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 8 0.32
9 13 0.52
10 4 0.16
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTTAATTT
Found at i:1616013 original size:31 final size:31
Alignment explanation
Indices: 1615972--1616040 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1615962 ATTTAAGAGA
* *
1615972 GAGTGCCCAAAATATAAATCATCTAAAACGT
1 GAGTGACCAAAATAGAAATCATCTAAAACGT
*
1616003 GAGTGACCAAAATAGAAATGATCTAAAACGT
1 GAGTGACCAAAATAGAAATCATCTAAAACGT
*
1616034 TAGTGAC
1 GAGTGAC
1616041 TAAATTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (31 bp):
GAGTGACCAAAATAGAAATCATCTAAAACGT
Found at i:1617987 original size:3 final size:3
Alignment explanation
Indices: 1617979--1618015 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1617969 TTCTAACCAA
1617979 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1618016 CATATAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1620807 original size:10 final size:11
Alignment explanation
Indices: 1620781--1620820 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
1620771 TCTATTTCTG
1620781 ATTTATATTTAT
1 ATTTAT-TTTAT
1620793 ATTTATTTTAT
1 ATTTATTTTAT
1620804 -TTTATTTTAT
1 ATTTATTTTAT
*
1620814 AATTATT
1 ATTTATT
1620821 CGGACATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.38
11 10 0.38
12 6 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTATTTTAT
Found at i:1621288 original size:24 final size:22
Alignment explanation
Indices: 1621261--1621307 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 22
1621251 ATAAAAAGCA
1621261 AAAATTTTATAAAATA-AAAATATT
1 AAAA-TTTA-AAAATACAAAA-ATT
1621285 AAAATTTAAAAATACAAAAATT
1 AAAATTTAAAAATACAAAAATT
1621307 A
1 A
1621308 TAAAGTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 10 0.45
23 8 0.36
24 4 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAATTTAAAAATACAAAAATT
Found at i:1621304 original size:16 final size:17
Alignment explanation
Indices: 1621225--1621311 Score: 52
Period size: 17 Copynumber: 4.7 Consensus size: 17
1621215 GTTTCCTTTA
1621225 AAAAATTATTAAAAATATC
1 AAAAATTA-TAAAAATA-C
* *
1621244 TAAAATTATAAAAA-GC
1 AAAAATTATAAAAATAC
*
1621260 AAAAATTTTATAAAATA-
1 AAAAATTATA-AAAATAC
1621277 AAAATATTAAAATTTAAAAATAC
1 AAAA-ATT---A--TAAAAATAC
1621300 AAAAATTATAAA
1 AAAAATTATAAA
1621312 GTTGTTGGAG
Statistics
Matches: 53, Mismatches: 6, Indels: 20
0.67 0.08 0.25
Matches are distributed among these distances:
16 9 0.17
17 12 0.23
18 9 0.17
19 8 0.15
22 9 0.17
23 6 0.11
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (17 bp):
AAAAATTATAAAAATAC
Found at i:1621591 original size:15 final size:16
Alignment explanation
Indices: 1621571--1621609 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1621561 AAGTTTTTAA
1621571 TATTTTTAATTATTT-
1 TATTTTTAATTATTTC
1621586 TATTTTT-ATTATTTC
1 TATTTTTAATTATTTC
*
1621601 TTTTTTTAA
1 TATTTTTAA
1621610 ATATCAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 13 0.62
16 1 0.05
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTAATTATTTC
Found at i:1621912 original size:13 final size:13
Alignment explanation
Indices: 1621868--1621912 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
1621858 AACCTTCCAA
*
1621868 AATTTATACCTAT
1 AATTTTTACCTAT
1621881 AA-TTTTACCTAT
1 AATTTTTACCTAT
1621893 AATTTTTACCTAT
1 AATTTTTACCTAT
1621906 AATTTTT
1 AATTTTT
1621913 TGGTATAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTTTTACCTAT
Found at i:1622125 original size:18 final size:18
Alignment explanation
Indices: 1622074--1622125 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1622064 GTCCACATAT
*
1622074 AATTCATACAAATTTTAAA
1 AATTCA-ACAAAATTTAAA
* *
1622093 AATTTTAA-AATATTTAAA
1 AA-TTCAACAAAATTTAAA
1622111 AATTCAACAAAATTT
1 AATTCAACAAAATTT
1622126 TTAAAAAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
17 4 0.15
18 16 0.62
19 3 0.12
20 3 0.12
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTCAACAAAATTTAAA
Found at i:1628727 original size:61 final size:61
Alignment explanation
Indices: 1628632--1628761 Score: 145
Period size: 61 Copynumber: 2.1 Consensus size: 61
1628622 TTGGTCTAAT
** * * * * *
1628632 AATAAATTTAGCTTTTAATGTTTGCATATTTTATCAAATTGATACTAAA-TATAAAAAATCC
1 AATAAATTTAGCCCTCAATGTTTACAAAATTTATCAAATTAAT-CTAAATTATAAAAAATCC
** * *
1628693 AATAAATTTAGCCCTCAATGTTTACAAAATTTATCATTTTAATTTAAATTATAAAAAATTC
1 AATAAATTTAGCCCTCAATGTTTACAAAATTTATCAAATTAATCTAAATTATAAAAAATCC
1628754 AATAAATT
1 AATAAATT
1628762 GAACCCTTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 4 0.07
61 53 0.93
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.41
Consensus pattern (61 bp):
AATAAATTTAGCCCTCAATGTTTACAAAATTTATCAAATTAATCTAAATTATAAAAAATCC
Found at i:1632393 original size:4 final size:4
Alignment explanation
Indices: 1632384--1632410 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1632374 TGCAATTTGG
1632384 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1632411 GGAATCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1642101 original size:16 final size:16
Alignment explanation
Indices: 1642080--1642114 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1642070 GTGAACTTTA
1642080 TTTAAATATATTTAAG
1 TTTAAATATATTTAAG
*
1642096 TTTAAATATATTTTAG
1 TTTAAATATATTTAAG
1642112 TTT
1 TTT
1642115 CGATTTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTAAATATATTTAAG
Found at i:1643383 original size:17 final size:17
Alignment explanation
Indices: 1643361--1643394 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1643351 GACTAACCCC
*
1643361 TATACATCACTTAGGTA
1 TATACATCACCTAGGTA
*
1643378 TATACATTACCTAGGTA
1 TATACATCACCTAGGTA
1643395 CATGCCACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (17 bp):
TATACATCACCTAGGTA
Found at i:1645384 original size:40 final size:40
Alignment explanation
Indices: 1645339--1645430 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
1645329 TTTTTCTTTC
1645339 TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
1 TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
*
1645379 TTTCTTTCTTTCTCCCTTCTCTGTTTTGTTTTGCTCTCTG
1 TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
1645419 TTTCTTTTCTTT
1 TTTC-TTTCTTT
1645431 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 43 0.86
41 7 0.14
ACGTcount: A:0.00, C:0.27, G:0.09, T:0.64
Consensus pattern (40 bp):
TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
Found at i:1646234 original size:20 final size:20
Alignment explanation
Indices: 1646211--1646256 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
1646201 ATATGAAATC
1646211 TAAAAATACA-AAAAAAATAT
1 TAAAAAT-CATAAAAAAATAT
*
1646231 T-AAAATCATTAAAAAATTAT
1 TAAAAATCA-TAAAAAAATAT
1646251 TAAAAA
1 TAAAAA
1646257 AATTTTAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 2 0.09
19 5 0.23
20 11 0.50
21 4 0.18
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAAATCATAAAAAAATAT
Found at i:1646639 original size:16 final size:16
Alignment explanation
Indices: 1646618--1646650 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1646608 TCACCCTTGG
1646618 GGGATGCCAAAAATTT
1 GGGATGCCAAAAATTT
1646634 GGGATGCCAAAAATTT
1 GGGATGCCAAAAATTT
1646650 G
1 G
1646651 TACGCTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.24
Consensus pattern (16 bp):
GGGATGCCAAAAATTT
Found at i:1647363 original size:11 final size:11
Alignment explanation
Indices: 1647347--1647372 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1647337 CATGGATTGC
1647347 AAAAAACAAAA
1 AAAAAACAAAA
1647358 AAAAAACAAAA
1 AAAAAACAAAA
1647369 AAAA
1 AAAA
1647373 GAGAGTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:1649691 original size:31 final size:28
Alignment explanation
Indices: 1649635--1649693 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 28
1649625 CAACCTTATT
* *
1649635 ACTTAAATAAAATTTAAATAGTTTAATA
1 ACTTAAATAAAATTTAAACAATTTAATA
1649663 ACTTAAATAAAAACTTTTAAACAATTTAATA
1 ACTTAAAT-AAAA--TTTAAACAATTTAATA
1649694 TTGTACACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.31
29 4 0.15
31 14 0.54
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (28 bp):
ACTTAAATAAAATTTAAACAATTTAATA
Found at i:1653226 original size:24 final size:24
Alignment explanation
Indices: 1653197--1653245 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1653187 CTTTGCTCAT
1653197 ATAAGAAAAACAACCAAATCAGCA
1 ATAAGAAAAACAACCAAATCAGCA
1653221 ATAAGAAAAACAACCAAATCAGCA
1 ATAAGAAAAACAACCAAATCAGCA
1653245 A
1 A
1653246 GTTAAGGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.63, C:0.20, G:0.08, T:0.08
Consensus pattern (24 bp):
ATAAGAAAAACAACCAAATCAGCA
Found at i:1653958 original size:2 final size:2
Alignment explanation
Indices: 1653953--1653980 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1653943 TATATATATA
1653953 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1653981 ATTAAACTTA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1655660 original size:9 final size:9
Alignment explanation
Indices: 1655642--1655699 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
1655632 TTTGGTTAAA
*
1655642 AATTACCCG
1 AATTAACCG
1655651 AATTAACCG
1 AATTAACCG
*
1655660 AATTACCCG
1 AATTAACCG
*
1655669 AATTAACTG
1 AATTAACCG
*
1655678 AATTACCCG
1 AATTAACCG
1655687 AATTAACCG
1 AATTAACCG
1655696 AATT
1 AATT
1655700 GAATCACTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:1655665 original size:18 final size:18
Alignment explanation
Indices: 1655642--1655699 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
1655632 TTTGGTTAAA
1655642 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
*
1655660 AATTACCCGAATTAACTG
1 AATTACCCGAATTAACCG
1655678 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
1655696 AATT
1 AATT
1655700 GAATCACTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:1655750 original size:6 final size:6
Alignment explanation
Indices: 1655739--1655767 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1655729 ACTTTTAGAC
1655739 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1655768 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:1655791 original size:20 final size:20
Alignment explanation
Indices: 1655723--1655780 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
1655713 ATTAAATTAT
* *
1655723 TTTTAGACTTTTAGACTTTAG
1 TTTTAGAATTTTAG-TTTTAG
1655744 TTTTAG--TTTTAGTTTTAG
1 TTTTAGAATTTTAGTTTTAG
*
1655762 TTTTAGAATTTTATTTTTA
1 TTTTAGAATTTTAGTTTTA
1655781 TTTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 11 0.33
19 6 0.18
20 10 0.30
21 6 0.18
ACGTcount: A:0.22, C:0.03, G:0.12, T:0.62
Consensus pattern (20 bp):
TTTTAGAATTTTAGTTTTAG
Found at i:1656931 original size:27 final size:26
Alignment explanation
Indices: 1656871--1656941 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 26
1656861 CTCGGCCCAT
* *
1656871 TTTTAAAAT-AAACATTAAAAAATTA
1 TTTTAAAATAAAAAATAAAAAAATTA
1656896 TTTTAAAAATAAAAAAATAAAAAAATTA
1 TTTT-AAAAT-AAAAAATAAAAAAATTA
1656924 TTTTAAAATTAAAAAATA
1 TTTTAAAA-TAAAAAATA
1656942 TATATTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 4 0.10
26 5 0.12
27 12 0.30
28 19 0.47
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (26 bp):
TTTTAAAATAAAAAATAAAAAAATTA
Found at i:1661843 original size:15 final size:16
Alignment explanation
Indices: 1661813--1661851 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1661803 TGGTAAAAAT
1661813 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
1661830 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
1661845 ATAATTT
1 ATAATTT
1661852 TTAAAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:1665119 original size:90 final size:90
Alignment explanation
Indices: 1664942--1665131 Score: 247
Period size: 90 Copynumber: 2.1 Consensus size: 90
1664932 TTGATCAAAC
* **
1664942 TGAAGAAGAAGAAGAAAAAGGGTTGTTCGAAGTGAAAGAAGTGATAACATCGGAAGCCGAGTCCG
1 TGAAGAAGAAGAAGAAAAAGGGTCGTTCGAAGTGAAAGAAGTGATAACATCGGAAGCCGACCCCG
* *
1665007 GGGAGGAAGAACAAACACGTGAAGT
66 GGGAAGAAGAACAAACACGTGAAAT
* *
1665032 TGAAGAAGAAGAAGAAAAAGGGTCGTTCGAAGTGAAAGACGTGATAACATC-GAAGGTCGACCCC
1 TGAAGAAGAAGAAGAAAAAGGGTCGTTCGAAGTGAAAGAAGTGATAACATCGGAA-GCCGACCCC
** * * *
1665096 TTGGAAGAGGAACGAACATGTGAAAT
65 GGGGAAGAAGAACAAACACGTGAAAT
*
1665122 TAAAGAAGAA
1 TGAAGAAGAA
1665132 AAAGGGTTGA
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
89 3 0.03
90 83 0.97
ACGTcount: A:0.43, C:0.12, G:0.31, T:0.14
Consensus pattern (90 bp):
TGAAGAAGAAGAAGAAAAAGGGTCGTTCGAAGTGAAAGAAGTGATAACATCGGAAGCCGACCCCG
GGGAAGAAGAACAAACACGTGAAAT
Found at i:1665178 original size:14 final size:14
Alignment explanation
Indices: 1665161--1665189 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1665151 AAGAAACGAA
1665161 AACATGGAAGGTCG
1 AACATGGAAGGTCG
1665175 AACATGGAAGGTCG
1 AACATGGAAGGTCG
1665189 A
1 A
1665190 TTGTTGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.34, T:0.14
Consensus pattern (14 bp):
AACATGGAAGGTCG
Found at i:1666946 original size:66 final size:66
Alignment explanation
Indices: 1666840--1666972 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1666830 GGATTAAATG
* *
1666840 GTTCCTAGGTAACTCATGGCAGAGGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGCGACT
1 GTTCCTAGGTAACTCATGGCAGACGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGCAACT
1666905 T
66 T
1666906 GTTCCTAGGTAACTCATGGCAGACGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGCAACT
1 GTTCCTAGGTAACTCATGGCAGACGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGCAACT
1666971 T
66 T
1666972 G
1 G
1666973 AACTATAAAC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (66 bp):
GTTCCTAGGTAACTCATGGCAGACGGATAAACTGGAGATATGCAGGTAATCCAACAAAAGCAACT
T
Found at i:1670785 original size:26 final size:27
Alignment explanation
Indices: 1670725--1670785 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
1670715 CCGAATATAA
*
1670725 TAAATATATTTTTTAATTTTTTTAATT
1 TAAAAATATTTTTTAATTTTTTTAATT
* * *
1670752 TTAGAATACTTTTTT-A-TTTTTTATTT
1 TAAAAATA-TTTTTTAATTTTTTTAATT
1670778 TAAAAATA
1 TAAAAATA
1670786 AATATTTGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
26 15 0.56
27 6 0.22
28 6 0.22
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
TAAAAATATTTTTTAATTTTTTTAATT
Found at i:1671659 original size:12 final size:12
Alignment explanation
Indices: 1671644--1671668 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1671634 ATATTTTGGA
1671644 TAATAAAATATT
1 TAATAAAATATT
1671656 TAATAAAATATT
1 TAATAAAATATT
1671668 T
1 T
1671669 CATGCTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATAAAATATT
Found at i:1674130 original size:26 final size:26
Alignment explanation
Indices: 1674090--1674141 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1674080 TAAGGATACC
*
1674090 TTAATTATAGTTTCTTATTCTACAAG
1 TTAATTATAGATTCTTATTCTACAAG
*
1674116 TTAATTTTAGATTCTTATTCTACAAG
1 TTAATTATAGATTCTTATTCTACAAG
1674142 ACTAAAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.50
Consensus pattern (26 bp):
TTAATTATAGATTCTTATTCTACAAG
Found at i:1691261 original size:26 final size:26
Alignment explanation
Indices: 1691225--1691278 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1691215 TTGTCAATGA
1691225 CAATGAGTAAAACATTCCTCCTTTTT
1 CAATGAGTAAAACATTCCTCCTTTTT
1691251 CAATGAGTAAAACATTCCTCCTTTTT
1 CAATGAGTAAAACATTCCTCCTTTTT
1691277 CA
1 CA
1691279 GTCGCACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.37
Consensus pattern (26 bp):
CAATGAGTAAAACATTCCTCCTTTTT
Found at i:1693965 original size:26 final size:28
Alignment explanation
Indices: 1693900--1693965 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
1693890 GTACTTTTCG
1693900 TAAATTT-AAAAAGTAATCCCTATATTT
1 TAAATTTCAAAAAGTAATCCCTATATTT
* *
1693927 T-TATTTACAAAAAAGTAATCTCT-T-TTT
1 TAAATTT-C-AAAAAGTAATCCCTATATTT
1693954 TAAATTTCAAAA
1 TAAATTTCAAAA
1693966 TTCAGGTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
26 8 0.25
27 6 0.19
28 5 0.16
29 13 0.41
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (28 bp):
TAAATTTCAAAAAGTAATCCCTATATTT
Found at i:1694234 original size:23 final size:21
Alignment explanation
Indices: 1694184--1694234 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
1694174 CTAAAAATGA
*
1694184 TAAAAATTTAATTTAATCATT
1 TAAAAATTTAATTTAAACATT
1694205 TAAAAATTATAATTATAAAC-TAT
1 TAAAAATT-TAATT-TAAACAT-T
1694228 TAAAAAT
1 TAAAAAT
1694235 GTGAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.31
22 6 0.23
23 12 0.46
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAATTTAATTTAAACATT
Found at i:1694417 original size:29 final size:30
Alignment explanation
Indices: 1694360--1694425 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
1694350 GGTCAAATTT
*
1694360 AAATTTTAAAATCTAAAAAATAGAGAGACTA
1 AAATTTTAAAATATAAAAAATAGAGAGAC-A
*
1694391 AAATTTTAAAA-ATAAAAATATA-A-AGACG
1 AAATTTTAAAATATAAAAA-ATAGAGAGACA
1694419 AAATTTT
1 AAATTTT
1694426 GAATTTACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 7 0.22
29 4 0.12
30 7 0.22
31 14 0.44
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.29
Consensus pattern (30 bp):
AAATTTTAAAATATAAAAAATAGAGAGACA
Found at i:1703595 original size:23 final size:23
Alignment explanation
Indices: 1703566--1703620 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1703556 ATGCAGAATT
1703566 TAAAAATAATGTAA-TA-AAAAAA
1 TAAAAATAAT-TAAGTATAAAAAA
*
1703588 TCATAAATAATTAAGTATAAAAAA
1 T-AAAAATAATTAAGTATAAAAAA
1703612 TAAAAATAA
1 TAAAAATAA
1703621 AAAGTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 4 0.14
23 17 0.61
24 7 0.25
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (23 bp):
TAAAAATAATTAAGTATAAAAAA
Found at i:1728320 original size:50 final size:50
Alignment explanation
Indices: 1728205--1728379 Score: 242
Period size: 50 Copynumber: 3.5 Consensus size: 50
1728195 GATAATAACA
* ** * *
1728205 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
1728256 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
1728306 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
1728356 TGCCCATGCCATGTCCCAGACATG
1 TGCCAATGCCATGTCCCAGACATG
1728380 NNNNNNNNNN
Statistics
Matches: 109, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 76 0.70
51 33 0.30
ACGTcount: A:0.19, C:0.31, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:1728836 original size:29 final size:31
Alignment explanation
Indices: 1728786--1728843 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1728776 CCTCGACTCT
* *
1728786 AACTTTTTCAAAATTATGA-TTTTGCCCCTA
1 AACTTTTACAAAATTATCATTTTTGCCCCTA
*
1728816 AACTTTTACATAATTA-CATTTTTGCCCC
1 AACTTTTACAAAATTATCATTTTTGCCCC
1728844 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.43
Consensus pattern (31 bp):
AACTTTTACAAAATTATCATTTTTGCCCCTA
Found at i:1735689 original size:13 final size:13
Alignment explanation
Indices: 1735668--1735699 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1735658 GCTTGGATCA
*
1735668 TCATCAAATAAAT
1 TCATAAAATAAAT
1735681 TCATAAAATAAAT
1 TCATAAAATAAAT
1735694 TCATAA
1 TCATAA
1735700 TTGCTGGAAA
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:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1735946 original size:29 final size:30
Alignment explanation
Indices: 1735909--1735968 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1735899 GCCCTCGACT
*
1735909 CTAACTTTTT-CAAAATTACGA-TTTTGCCC
1 CTAAATTTTTACAAAATTAC-ATTTTTGCCC
*
1735938 CTAAATTTTTACATAATTACATTTTTGCCC
1 CTAAATTTTTACAAAATTACATTTTTGCCC
1735968 C
1 C
1735969 AAGGCTCGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.43
Consensus pattern (30 bp):
CTAAATTTTTACAAAATTACATTTTTGCCC
Found at i:1740756 original size:18 final size:19
Alignment explanation
Indices: 1740733--1740771 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1740723 CTCATCATCG
1740733 AATTTAATAAA-AATATTT
1 AATTTAATAAATAATATTT
*
1740751 AATTTAATAAATAATTTTT
1 AATTTAATAAATAATATTT
1740770 AA
1 AA
1740772 AAAGTAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTTAATAAATAATATTT
Found at i:1750157 original size:27 final size:24
Alignment explanation
Indices: 1750118--1750168 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
1750108 TTTATTAATA
1750118 TGGTATATAAAAAATATATAATAAATT
1 TGGTATAT-AAAAAT-TATAA-AAATT
1750145 TGGTAT-TATAAAATTATAAAAATT
1 TGGTATATA-AAAATTATAAAAATT
1750169 ATAATTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 5 0.22
25 6 0.26
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (24 bp):
TGGTATATAAAAATTATAAAAATT
Found at i:1751239 original size:2 final size:2
Alignment explanation
Indices: 1751232--1751268 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1751222 GATGCTATCT
* *
1751232 TA TA TA TA TA CA TA TA TA TA TA TA TA CA 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
1751269 TGATAATTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1751253 original size:16 final size:16
Alignment explanation
Indices: 1751232--1751268 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1751222 GATGCTATCT
1751232 TATATATATACATATA
1 TATATATATACATATA
1751248 TATATATATACATATA
1 TATATATATACATATA
1751264 TATAT
1 TATAT
1751269 TGATAATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
TATATATATACATATA
Found at i:1752728 original size:19 final size:18
Alignment explanation
Indices: 1752700--1752753 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
1752690 ATATATTTTT
*
1752700 ATTATCAAATAATTTCTAA
1 ATTATAAAATAATTT-TAA
*
1752719 ATTATAAAATAATTATTGA
1 ATTATAAAATAATT-TTAA
*
1752738 ATTATTAAATAATTTT
1 ATTATAAAATAATTTT
1752754 TATTTAAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.06
19 28 0.90
20 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (18 bp):
ATTATAAAATAATTTTAA
Found at i:1757731 original size:30 final size:30
Alignment explanation
Indices: 1757697--1757755 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1757687 TACTATTTTG
1757697 TATGAATCATAAAAGTAAGTTTATTTGTTT
1 TATGAATCATAAAAGTAAGTTTATTTGTTT
* *
1757727 TATGAGTCATAAAAGTAAGTTTGTTTGTT
1 TATGAATCATAAAAGTAAGTTTATTTGTT
1757756 ATGTAAAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (30 bp):
TATGAATCATAAAAGTAAGTTTATTTGTTT
Found at i:1762888 original size:12 final size:12
Alignment explanation
Indices: 1762865--1762896 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1762855 ATGTTCTTAA
1762865 AAAATT-AT-AT
1 AAAATTAATAAT
1762875 AAAATTAATAAT
1 AAAATTAATAAT
1762887 AAAATTAATA
1 AAAATTAATA
1762897 CGAGCGAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.30
11 2 0.10
12 12 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAAATTAATAAT
Found at i:1777367 original size:15 final size:15
Alignment explanation
Indices: 1777346--1777381 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1777336 ATTTTGAGAA
1777346 AAAAATAAATATTGT
1 AAAAATAAATATTGT
* *
1777361 TAAAATAAATGTTGT
1 AAAAATAAATATTGT
1777376 AAAAAT
1 AAAAAT
1777382 CTTGATTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (15 bp):
AAAAATAAATATTGT
Found at i:1779416 original size:34 final size:34
Alignment explanation
Indices: 1779374--1779455 Score: 155
Period size: 34 Copynumber: 2.4 Consensus size: 34
1779364 GTTGATTGAA
1779374 AATTTTGATATATAAATGTGATTTCTCGTTCACT
1 AATTTTGATATATAAATGTGATTTCTCGTTCACT
1779408 AATTTTGATATATAAATGTGATTTCTCGTTCACT
1 AATTTTGATATATAAATGTGATTTCTCGTTCACT
*
1779442 AATTTTGACATATA
1 AATTTTGATATATA
1779456 TTATTCTGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (34 bp):
AATTTTGATATATAAATGTGATTTCTCGTTCACT
Found at i:1781744 original size:27 final size:27
Alignment explanation
Indices: 1781714--1781771 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
1781704 ATTATAAAAA
1781714 ATTAA-AATATTA-AAAATATTATTTTTT
1 ATTAATAAT-TTACAAAATATT-TTTTTT
*
1781741 ATTAATAATTTATCACAATATTTTTTTT
1 ATTAATAATTTA-CAAAATATTTTTTTT
1781769 ATT
1 ATT
1781772 CCATTCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 8 0.30
28 12 0.44
29 7 0.26
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTAATAATTTACAAAATATTTTTTTT
Found at i:1782083 original size:29 final size:30
Alignment explanation
Indices: 1782034--1782100 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
1782024 TCAAAATTTA
*
1782034 TTTAAAATTAAAAAAGTATTTTAAAAA-TAT
1 TTTAAAATTAAAAAAG-AATTTAAAAAGTAT
*
1782064 TTTAAAATTAAAAAA-AATTTAAAAAGTGT
1 TTTAAAATTAAAAAAGAATTTAAAAAGTAT
1782093 TTTAAAAT
1 TTTAAAAT
1782101 ATTTTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 9 0.26
29 10 0.29
30 15 0.44
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (30 bp):
TTTAAAATTAAAAAAGAATTTAAAAAGTAT
Found at i:1782100 original size:39 final size:39
Alignment explanation
Indices: 1782037--1782164 Score: 179
Period size: 40 Copynumber: 3.3 Consensus size: 39
1782027 AAATTTATTT
*
1782037 AAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
1 AAAATTTAAAAAGTATTTT-AAAATATTTTAAAATTAAAA
*
1782077 AAAATTTAAAAAGTGTTTTAAAATATTTTAAAATTAAAA
1 AAAATTTAAAAAGTATTTTAAAATATTTTAAAATTAAAA
* * *
1782116 ATAATAATAAAAAGTATTTTAAAATATTTTAAAATT--TA
1 AAAAT-TTAAAAAGTATTTTAAAATATTTTAAAATTAAAA
1782154 AAAATTTAAAA
1 AAAATTTAAAA
1782165 TAAATATATT
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
37 5 0.06
38 5 0.06
39 24 0.30
40 45 0.57
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (39 bp):
AAAATTTAAAAAGTATTTTAAAATATTTTAAAATTAAAA
Found at i:1782105 original size:10 final size:10
Alignment explanation
Indices: 1782045--1782150 Score: 51
Period size: 10 Copynumber: 10.5 Consensus size: 10
1782035 TTAAAATTAA
1782045 AAAAGTATTTT
1 AAAA-TATTTT
1782056 AAAAATATTTT
1 -AAAATATTTT
**
1782067 -AAA-ATTAA
1 AAAATATTTT
* *
1782075 AAAAAATTTA
1 AAAATATTTT
*
1782085 AAAAGTGTTTT
1 AAAA-TATTTT
1782096 AAAATATTTT
1 AAAATATTTT
*
1782106 -AAA-A-TTA
1 AAAATATTTT
* *
1782113 AAAATAATAATA
1 AAAAT-AT-TTT
1782125 AAAAGTATTTT
1 AAAA-TATTTT
1782136 AAAATATTTT
1 AAAATATTTT
1782146 AAAAT
1 AAAAT
1782151 TTAAAAATTT
Statistics
Matches: 74, Mismatches: 11, Indels: 20
0.70 0.10 0.19
Matches are distributed among these distances:
7 2 0.03
8 7 0.09
9 9 0.12
10 25 0.34
11 18 0.24
12 12 0.16
13 1 0.01
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (10 bp):
AAAATATTTT
Found at i:1786162 original size:40 final size:39
Alignment explanation
Indices: 1786091--1786169 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 39
1786081 CTACAGCTGA
*
1786091 AATGAACTTGAAATGACTCAAACCGAGAATGATTTGAAT
1 AATGAACTTGAAATGACTCAAACCGAGAATGATTAGAAT
*
1786130 AATGTAACTTGAAATGAC-CTGAACCTGA-AATGATTAGAAT
1 AATG-AACTTGAAATGACTC-AAACC-GAGAATGATTAGAAT
1786170 CCAAAATGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 5 0.14
40 28 0.80
41 2 0.06
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.27
Consensus pattern (39 bp):
AATGAACTTGAAATGACTCAAACCGAGAATGATTAGAAT
Found at i:1790405 original size:105 final size:105
Alignment explanation
Indices: 1790202--1790444 Score: 382
Period size: 105 Copynumber: 2.3 Consensus size: 105
1790192 CCTTCATAAA
* *
1790202 CGGTGATCACAGGATTATTTCTGGCCAATTTATGGAAATGTTAAAATAATTGTCTTTACGCTTGT
1 CGGTGATCACAGTATTATTTCTGGCCAATTTATGGAAATGTTAAAACAATTGTCTTTACGCTTGT
* * *
1790267 TGCTTCGTTGCAAGCAACTCAATCATTTTCACCAATCCAT
66 TGCTTCATTACAAGCAACTCAACCATTTTCACCAATCCAT
* *
1790307 TGGTGATCACAGTATTACTTCTGG-CAATTTATGGAAATGTTAAAACAATTGTCTTTACGCTTGT
1 CGGTGATCACAGTATTATTTCTGGCCAATTTATGGAAATGTTAAAACAATTGTCTTTACGCTTGT
1790371 TGCTTCCATTACAAGCAACTCAACCATTTTCACCAATCCAT
66 TGCTT-CATTACAAGCAACTCAACCATTTTCACCAATCCAT
*
1790412 CGTTGATCACA-TAATTATTTCTGGCCAATTTAT
1 CGGTGATCACAGT-ATTATTTCTGGCCAATTTAT
1790445 CTTAACGCTT
Statistics
Matches: 125, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
104 45 0.36
105 72 0.58
106 8 0.06
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (105 bp):
CGGTGATCACAGTATTATTTCTGGCCAATTTATGGAAATGTTAAAACAATTGTCTTTACGCTTGT
TGCTTCATTACAAGCAACTCAACCATTTTCACCAATCCAT
Found at i:1799016 original size:49 final size:48
Alignment explanation
Indices: 1798912--1799014 Score: 165
Period size: 46 Copynumber: 2.2 Consensus size: 48
1798902 TTCATCCTTG
*
1798912 TATTATTAATGTTATGTGGTGAAAGAACTTAGCAAGTCTCTAGTCTTAT
1 TATTATTAATGTTATGTGGTG-AAGAACCTAGCAAGTCTCTAGTCTTAT
*
1798961 TATTATTGATGTTATGTGGTG-A-AACCTAGCAAGTCTCTAGTCTTAT
1 TATTATTAATGTTATGTGGTGAAGAACCTAGCAAGTCTCTAGTCTTAT
1799007 TATTATTA
1 TATTATTA
1799015 TTAGGATAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
46 30 0.59
47 1 0.02
49 20 0.39
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (48 bp):
TATTATTAATGTTATGTGGTGAAGAACCTAGCAAGTCTCTAGTCTTAT
Found at i:1799075 original size:31 final size:29
Alignment explanation
Indices: 1799040--1799097 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
1799030 ATTTGATATC
1799040 TGTACATTTATAAAATATCCAATGTGGTACT
1 TGTAC-TTTA-AAAATATCCAATGTGGTACT
* **
1799071 TGTACTTTAAAATTATTTAATGTGGTA
1 TGTACTTTAAAAATATCCAATGTGGTA
1799098 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.62
30 4 0.17
31 5 0.21
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (29 bp):
TGTACTTTAAAAATATCCAATGTGGTACT
Found at i:1802464 original size:196 final size:197
Alignment explanation
Indices: 1802130--1802519 Score: 604
Period size: 196 Copynumber: 2.0 Consensus size: 197
1802120 GATTATGATA
* * *
1802130 GTGGTATGCTTTTGGATCACTATCTTCTTTGGTTGAATGCCCTTTATTCTTTTGAGCATATATCT
1 GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCCCTTTATGCTTTTGAGCATATATCT
* * *
1802195 GTATGTCTGTGTATTCTCAATGGTTATAATGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
66 CTATGTCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
* * * *
1802260 TAAATCCAACATTGTCTCC-AAAACAATGAGTGATTAAATTGAATGG-CATGGTAAGAAGATTGG
131 TAAATCCAACATTATCTCCAAAAACAATGAGTGACTAAATGGAATGGTC-TGATAAGAAGATTGG
1802323 GTT
195 GTT
* * * *
1802326 GTGGTATGCTTTTAGATCACTTTCATCTTTGGTTGAATGCTCTTTATGCTTTTGAGCATATGTTT
1 GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCCCTTTATGCTTTTGAGCATATATCT
* *
1802391 CTATGTCAGTGTATTCTCAATTGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATGT
66 CTATGTCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
*
1802456 TAAATCCAACATTATCTCCAAAAACAATGTGTGACTAAATGGAATGGTCTGATAAGAAGATTGG
131 TAAATCCAACATTATCTCCAAAAACAATGAGTGACTAAATGGAATGGTCTGATAAGAAGATTGG
1802520 ATTGCATTCA
Statistics
Matches: 175, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
196 136 0.78
197 38 0.22
198 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (197 bp):
GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCCCTTTATGCTTTTGAGCATATATCT
CTATGTCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
TAAATCCAACATTATCTCCAAAAACAATGAGTGACTAAATGGAATGGTCTGATAAGAAGATTGGG
TT
Found at i:1826739 original size:38 final size:36
Alignment explanation
Indices: 1826669--1826758 Score: 90
Period size: 36 Copynumber: 2.4 Consensus size: 36
1826659 ATTTTTTTGA
* * * *
1826669 AAACACGAATTTTTTTTTAAAATACAATAATTTTAG
1 AAACACGAAATTTTTTTAAAAAAACAAAAATTTTAG
* *
1826705 AAGCACGAAATTTTTTTAAAAAAACAAGAAAATTTTCG
1 AAACACGAAATTTTTTTAAAAAAAC-A-AAAATTTTAG
*
1826743 AAATACGAGAATTTTT
1 AAACACGA-AATTTTT
1826759 GAAAACACGG
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
36 21 0.49
37 1 0.02
38 14 0.33
39 7 0.16
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (36 bp):
AAACACGAAATTTTTTTAAAAAAACAAAAATTTTAG
Found at i:1826776 original size:19 final size:19
Alignment explanation
Indices: 1826752--1826817 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 19
1826742 GAAATACGAG
*
1826752 AATTTTTGAAAACACGGGA
1 AATTTTTGAAAACACTGGA
*
1826771 AATTTTTTGAAAACA-TGAA
1 AA-TTTTTGAAAACACTGGA
1826790 AATTTTTG-AAACACTGG-
1 AATTTTTGAAAACACTGGA
1826807 AA-TTTTGAAAA
1 AATTTTTGAAAA
1826818 TTTATTTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.12
17 10 0.24
18 8 0.20
19 6 0.15
20 12 0.29
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (19 bp):
AATTTTTGAAAACACTGGA
Found at i:1826794 original size:38 final size:37
Alignment explanation
Indices: 1826752--1826920 Score: 110
Period size: 38 Copynumber: 4.7 Consensus size: 37
1826742 GAAATACGAG
1826752 AATTTTTGAAAACACGGGAAATTTTTTGAAAACATGAA
1 AATTTTTGAAAACAC-GGAAATTTTTTGAAAACATGAA
*
1826790 AATTTTTG-AAACACTGG-AA--TTTTG-AAA-AT--T
1 AATTTTTGAAAACAC-GGAAATTTTTTGAAAACATGAA
* * *
1826820 TATTTTTG-AAACA-TGAGAATTTTTT-AAAACACGAA
1 AATTTTTGAAAACACGGA-AATTTTTTGAAAACATGAA
* * *
1826855 ATTTTTTTTAAAAACACGGAAA-TTTTTGAAACACAAGAA
1 A--ATTTTTGAAAACACGGAAATTTTTTGAAA-ACATGAA
* *
1826894 ATTTTTTTGAAAACACGAAAATTTTTT
1 A-ATTTTTGAAAACACGGAAATTTTTT
1826921 AAACACGATT
Statistics
Matches: 103, Mismatches: 13, Indels: 29
0.71 0.09 0.20
Matches are distributed among these distances:
28 1 0.01
30 14 0.14
32 9 0.09
33 4 0.04
34 5 0.05
36 2 0.02
37 18 0.17
38 36 0.35
39 14 0.14
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (37 bp):
AATTTTTGAAAACACGGAAATTTTTTGAAAACATGAA
Done.