Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_pilon, whole genome shotgun sequence
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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 37
Found at i:4307512 original size:21 final size:21
Alignment explanation
Indices: 4307486--4307530 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4307476 GATTTCTGGG
* *
4307486 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4307507 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4307528 CAA
1 CAA
4307531 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4309254 original size:13 final size:13
Alignment explanation
Indices: 4309236--4309276 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
4309226 TCTACGGGCA
4309236 CTACGGTGCAATT
1 CTACGGTGCAATT
4309249 CTACGG-GC-A--
1 CTACGGTGCAATT
4309258 CTACGGTGCAATT
1 CTACGGTGCAATT
4309271 CTACGG
1 CTACGG
4309277 GCACTTCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 2 0.08
11 2 0.08
12 2 0.08
13 12 0.50
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:4309297 original size:22 final size:22
Alignment explanation
Indices: 4309224--4309289 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
4309214 TATGGACATC
4309224 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
4309246 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
4309268 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
4309290 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (22 bp):
ATTCTACGGGCACTACGGTGCA
Found at i:4312394 original size:21 final size:21
Alignment explanation
Indices: 4312368--4312412 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4312358 GATTTCTGGG
* *
4312368 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4312389 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4312410 CAA
1 CAA
4312413 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4314136 original size:13 final size:13
Alignment explanation
Indices: 4314118--4314158 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
4314108 TCTACGGGCA
4314118 CTACGGTGCAATT
1 CTACGGTGCAATT
4314131 CTACGG-GC-A--
1 CTACGGTGCAATT
4314140 CTACGGTGCAATT
1 CTACGGTGCAATT
4314153 CTACGG
1 CTACGG
4314159 GCACTTCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 2 0.08
11 2 0.08
12 2 0.08
13 12 0.50
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:4314179 original size:22 final size:22
Alignment explanation
Indices: 4314106--4314171 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
4314096 TATGGACATC
4314106 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
4314128 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
4314150 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
4314172 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (22 bp):
ATTCTACGGGCACTACGGTGCA
Found at i:4315309 original size:37 final size:38
Alignment explanation
Indices: 4315223--4315302 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 38
4315213 AAAATTAAAA
* * *
4315223 TCAA-TATATTATTTTTTCTAAGTTGCTTGCAAGCTTT
1 TCAAGTATAGTATTTTTTCTAAGTTGCTCGCAACCTTT
* *
4315260 TCAAGTATAGTATTTTTTC-GAGTTGCTCGCGACCTTT
1 TCAAGTATAGTATTTTTTCTAAGTTGCTCGCAACCTTT
4315297 TCAAGT
1 TCAAGT
4315303 TGAGTATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 24 0.65
38 13 0.35
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (38 bp):
TCAAGTATAGTATTTTTTCTAAGTTGCTCGCAACCTTT
Found at i:4325535 original size:2 final size:2
Alignment explanation
Indices: 4325528--4325559 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4325518 ATAAATAGAA
4325528 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4325560 GGGAACCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4325629 original size:4 final size:4
Alignment explanation
Indices: 4325620--4325647 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4325610 ATCGACTGAA
4325620 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
4325648 GCATTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:4326393 original size:16 final size:16
Alignment explanation
Indices: 4326372--4326402 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4326362 TAATATTGAA
4326372 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
4326388 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
4326403 AAAAATTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:4335189 original size:37 final size:37
Alignment explanation
Indices: 4335089--4335191 Score: 118
Period size: 36 Copynumber: 2.8 Consensus size: 37
4335079 ATTTTCGTTT
* *
4335089 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTTAAACTCCTAAAAATAGGATAAAATTC
* * * *
4335126 TGCTAGGA-TTAAACTACTAAAAATAGGATAGAGTTC
1 TACTAGGATTTAAACTCCTAAAAATAGGATAAAATTC
* * *
4335162 TACTAAGATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTTAAACTCCTAAAAATAGGAT
4335192 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
36 29 0.54
37 25 0.46
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.30
Consensus pattern (37 bp):
TACTAGGATTTAAACTCCTAAAAATAGGATAAAATTC
Found at i:4335588 original size:18 final size:17
Alignment explanation
Indices: 4335549--4335591 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
4335539 ATTATATGGA
4335549 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
4335565 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
4335583 TATTATTAT
1 TATTATTAT
4335592 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:4336099 original size:2 final size:2
Alignment explanation
Indices: 4336092--4336145 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
4336082 TAATACTTTG
4336092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4336134 AT AT AT TT AT AT
1 AT AT AT AT AT AT
4336146 TTTTTTCTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4340640 original size:183 final size:183
Alignment explanation
Indices: 4340332--4340861 Score: 954
Period size: 183 Copynumber: 2.9 Consensus size: 183
4340322 ATTAAATCCG
*
4340332 TAAAGCTGAGCTATTCCACTAAGGTAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
4340397 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGTAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
4340462 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTAAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTAAGTGATTTGTCCCTC
4340515 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
4340580 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
4340645 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTAAGTGATTTGTCCCTC
*
4340698 TAAAGCTGAGCTATTCTACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
4340763 ATAGATTACATTCAAA-TCATTACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
4340827 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACC
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACC
4340862 ATTCAGTTAA
Statistics
Matches: 335, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
182 1 0.00
183 334 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTAAGTGATTTGTCCCTC
Found at i:4342041 original size:36 final size:35
Alignment explanation
Indices: 4342001--4342114 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 35
4341991 CACTCAAATT
4342001 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACATA-TTTGTCTCACTTGAGAC
* * * ** *
4342037 TGTTTTTCTCGAAAGA-ATATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACATATTTGTCTCACTTGAGAC
* *
4342073 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-ATATTTGTCTCACTTGAGAC
*
4342109 CGTTTT
1 TGTTTT
4342115 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 48 0.81
37 6 0.10
38 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (35 bp):
TGTTTTTCTTAAAACATATTTGTCTCACTTGAGAC
Found at i:4342077 original size:72 final size:74
Alignment explanation
Indices: 4341985--4342160 Score: 207
Period size: 72 Copynumber: 2.4 Consensus size: 74
4341975 ATGCAGATGA
* * * *
4341985 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
*
4342047 GAAAGAA-TAT
64 GAAAGAAGCAT
*
4342057 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
4342122 AAGAAGGCAT
66 AAGAA-GCAT
** *
4342132 TTCATTTCACTCAAGGCTGTTTTTTTTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
4342161 GAAGATTTTA
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 50 0.56
73 11 0.12
75 4 0.04
76 23 0.26
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (74 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGCAT
Found at i:4342219 original size:39 final size:39
Alignment explanation
Indices: 4342176--4342318 Score: 99
Period size: 39 Copynumber: 3.4 Consensus size: 39
4342166 TTTTATCTTG
*
4342176 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
** * *
4342215 CTTGAGACAGTTTCTTTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGACAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-C
* *
4342267 C-TGAGATAGTTTCCCTCGAAACAAAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
4342305 CTTGAGACAGTTTC
1 CTTGAGACAGTTTC
4342319 TTTTGAAACA
Statistics
Matches: 78, Mismatches: 12, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
38 2 0.03
39 36 0.46
40 5 0.06
41 2 0.03
48 1 0.01
49 2 0.03
50 5 0.06
51 23 0.29
52 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:4342412 original size:105 final size:104
Alignment explanation
Indices: 4342231--4342549 Score: 491
Period size: 105 Copynumber: 3.1 Consensus size: 104
4342221 ACAGTTTCTT
* * *
4342231 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAAAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
*
4342296 TTTGTCTCCCTTGAGACAGTTTCTTTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* *
4342335 TTGAAAACATTTCCCTTGAAATGATTTTTTTTATCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
*
4342400 TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACA
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
4342440 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
** *
4342502 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
4342541 TTGAAAACA
1 TTGAAAACA
4342550 ATTTAACGAA
Statistics
Matches: 198, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
101 47 0.24
103 1 0.01
104 52 0.26
105 98 0.49
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:4342496 original size:36 final size:36
Alignment explanation
Indices: 4342449--4342524 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
4342439 ATTGAAAACA
* * *
4342449 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
4342485 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
4342521 TTTC
1 TTTC
4342525 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:4342905 original size:105 final size:104
Alignment explanation
Indices: 4342724--4343248 Score: 761
Period size: 105 Copynumber: 5.0 Consensus size: 104
4342714 ATATCGTGAC
* * * *
4342724 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
4342789 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 A-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
4342829 ACTTCAGACAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
4342894 ATCTCATAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
4342934 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
4342999 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * ** * *
4343039 ACTCCAGACAACGCAATTTCAACTCCACGACGAAGGGACCATTGCTTGTCAA-AAAAAATT--C-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
4343100 ATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
4343139 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
* * *
4343204 AGTTCAAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATTC-AGAGCCAATTTCAACTTCACAACGAAGGATATTGG
4343245 ACTC
1 ACTC
4343249 GGAACAATGC
Statistics
Matches: 379, Mismatches: 34, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
100 78 0.21
101 2 0.01
102 7 0.02
104 8 0.02
105 249 0.66
106 35 0.09
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (104 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:4343844 original size:37 final size:37
Alignment explanation
Indices: 4343791--4343895 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
4343781 CATTTTCGTC
4343791 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
4343828 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
4343865 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
4343896 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:4344279 original size:18 final size:17
Alignment explanation
Indices: 4344236--4344282 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
4344226 TATTAATCCC
4344236 TTTA-TATT-TTATTCA
1 TTTATTATTATTATTCA
*
4344251 TTTATTTTTATTATTCA
1 TTTATTATTATTATTCA
4344268 TGTTATTATTATTAT
1 T-TTATTATTATTAT
4344283 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 3 0.11
17 8 0.30
18 12 0.44
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTATTATTATTATTCA
Found at i:4344530 original size:57 final size:57
Alignment explanation
Indices: 4344452--4344590 Score: 128
Period size: 58 Copynumber: 2.4 Consensus size: 57
4344442 CTTTTAATAG
* *
4344452 TTTATTTATATACCTATTATTA-AA-TATATATATTCTTA-ATTATTTTTTGATTATTTC
1 TTTATTTATATACATATTATTATAACTATATA-ACT-TTATATTATTTTTT-ATTATTTC
* *
4344509 TTTATTTATGTA-ATATATATTATAACTTTATAACTTTATATTATTTTTTATTATTTTC
1 TTTATTTATATACATAT-TATTATAACTATATAACTTTATATTATTTTTTATTA-TTTC
*
4344567 ATTT-TTT-TATTCATTATTATTATA
1 -TTTATTTATATACA-TATTATTATA
4344591 TTATTATTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
56 3 0.04
57 25 0.37
58 29 0.43
59 11 0.16
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (57 bp):
TTTATTTATATACATATTATTATAACTATATAACTTTATATTATTTTTTATTATTTC
Found at i:4344597 original size:21 final size:20
Alignment explanation
Indices: 4344543--4344598 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
4344533 ACTTTATAAC
* *
4344543 TTTATATTATTTTTTATTAT
1 TTTATATTATTATTCATTAT
* *
4344563 TTTCATTTTTTTATTCATTAT
1 TTT-ATATTATTATTCATTAT
4344584 TATTATATTATTATT
1 T-TTATATTATTATT
4344599 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 3 0.11
21 23 0.82
22 2 0.07
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATATTATTATTCATTAT
Found at i:4344793 original size:2 final size:2
Alignment explanation
Indices: 4344786--4344822 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4344776 TATTAATACT
*
4344786 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4344823 TTTTTTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:4348953 original size:6 final size:6
Alignment explanation
Indices: 4348942--4349014 Score: 137
Period size: 6 Copynumber: 12.2 Consensus size: 6
4348932 GACACGTATT
*
4348942 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
4348990 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
4349015 GCCGAGCCGA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.01
Consensus pattern (6 bp):
ACCACG
Found at i:4349022 original size:5 final size:5
Alignment explanation
Indices: 4349012--4349050 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
4349002 ACCACGACCA
* * *
4349012 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
4349051 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:4354925 original size:6 final size:6
Alignment explanation
Indices: 4354914--4354998 Score: 161
Period size: 6 Copynumber: 14.2 Consensus size: 6
4354904 GACACGTATT
4354914 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
4354962 ACCTCG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
4354999 GCCGAGCCGA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.01
Consensus pattern (6 bp):
ACCACG
Found at i:4355006 original size:5 final size:5
Alignment explanation
Indices: 4354996--4355039 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
4354986 ACCACGACCA
* *
4354996 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
4355040 ACGGACGGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.25, C:0.34, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGC
Found at i:4357027 original size:23 final size:21
Alignment explanation
Indices: 4357000--4357042 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4356990 ATATAAAAAA
4357000 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
4357021 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
4357042 T
1 T
4357043 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:4357094 original size:18 final size:18
Alignment explanation
Indices: 4357071--4357105 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4357061 CCGGTTCTTC
4357071 CGACCGGTCGAACCAGTT
1 CGACCGGTCGAACCAGTT
*
4357089 CGACCGGTTGAACCAGT
1 CGACCGGTCGAACCAGT
4357106 GAACCAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.31, G:0.29, T:0.17
Consensus pattern (18 bp):
CGACCGGTCGAACCAGTT
Found at i:4357247 original size:19 final size:19
Alignment explanation
Indices: 4357223--4357268 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
4357213 TTTCCCAATA
*
4357223 TATCACTGGTGATCGGTAT
1 TATCACCGGTGATCGGTAT
*
4357242 TATCACCGGTGATCTGTAT
1 TATCACCGGTGATCGGTAT
*
4357261 TATTACCG
1 TATCACCG
4357269 ATCTAACACC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (19 bp):
TATCACCGGTGATCGGTAT
Found at i:4357377 original size:48 final size:48
Alignment explanation
Indices: 4357325--4357469 Score: 143
Period size: 48 Copynumber: 2.9 Consensus size: 48
4357315 GAAAAGCGCA
* * * * *
4357325 CCCCCTGCACCGCGTTATATGCTGATTTGGCGCCACGTGGGTATAGCG
1 CCCCCTGCACCACGATATACGCTGATCTGGCGCCACGTGGGTATAACG
* *
4357373 CCCCCTGCCCCACGATATACGGTGATCTGGCGCCACGTGGGTATAACG
1 CCCCCTGCACCACGATATACGCTGATCTGGCGCCACGTGGGTATAACG
4357421 CGCCCTCTGTC-CCGA-GATATACAG-TGATCTGGCGCCACGTAGGGGTATA
1 C-CCC-CTG-CACC-ACGATATAC-GCTGATCTGGCGCCACGT--GGGTATA
4357470 GCGCGGATCA
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
48 42 0.51
49 3 0.04
50 28 0.34
51 3 0.04
52 7 0.08
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (48 bp):
CCCCCTGCACCACGATATACGCTGATCTGGCGCCACGTGGGTATAACG
Found at i:4357448 original size:50 final size:50
Alignment explanation
Indices: 4357347--4357474 Score: 163
Period size: 50 Copynumber: 2.6 Consensus size: 50
4357337 CGTTATATGC
* *
4357347 TGATTTGGCGCCACGTGGGTAT-A-GCGCCCCCTGCCCCACGATATACGG
1 TGATCTGGCGCCACGTGGGTATAACGCGCCCCCTGCCCCACGATATACAG
* *
4357395 TGATCTGGCGCCACGTGGGTATAACGCGCCCTCTGTCCCGA-GATATACAG
1 TGATCTGGCGCCACGTGGGTATAACGCGCCCCCTG-CCCCACGATATACAG
*
4357445 TGATCTGGCGCCACGTAGGGGTATAGCGCG
1 TGATCTGGCGCCACGT--GGGTATAACGCG
4357475 GATCAGGGGT
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
48 21 0.30
49 1 0.01
50 33 0.47
51 4 0.06
52 11 0.16
ACGTcount: A:0.18, C:0.30, G:0.31, T:0.21
Consensus pattern (50 bp):
TGATCTGGCGCCACGTGGGTATAACGCGCCCCCTGCCCCACGATATACAG
Found at i:4361138 original size:35 final size:34
Alignment explanation
Indices: 4361053--4361139 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
4361043 ATTTGATATT
*
4361053 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
4361087 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
4361125 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
4361140 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:4361370 original size:21 final size:21
Alignment explanation
Indices: 4361346--4361388 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4361336 TTCTGACTCC
4361346 TCGTTGTCATCATCATCATCG
1 TCGTTGTCATCATCATCATCG
* *
4361367 TCGTTGTCGTCATCGTCATCG
1 TCGTTGTCATCATCATCATCG
4361388 T
1 T
4361389 TCTGAGGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGTTGTCATCATCATCATCG
Found at i:4361751 original size:18 final size:18
Alignment explanation
Indices: 4361725--4361764 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
4361715 AAAGGTGATG
*
4361725 GCGGTATCATATATGGCT
1 GCGGCATCATATATGGCT
*
4361743 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGCT
4361761 GCGG
1 GCGG
4361765 TGGCTGCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:4363469 original size:111 final size:111
Alignment explanation
Indices: 4363275--4363488 Score: 358
Period size: 111 Copynumber: 1.9 Consensus size: 111
4363265 ATTACAAAAA
* * *
4363275 TTAATTCTTAATCTAATAACCATGCATTAAATGAATCAACTAATTATTATTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
4363340 AATTAAAACGTTAAAATGTTAATGTATCAGCAAAGTGTCGATATAT
66 AATTAAAACGTTAAAATGTTAACGTATCAGCAAAGTGTCGATATAT
*
4363386 TTAATTCTTAATCTAATAATCATGCA-TATAATAAATCAACTAAATATTACTAATAATTTAAATT
1 TTAATTCTTAATCTAATAACCATGCATTA-AATAAATCAACTAAATATTACTAATAATTTAAATT
*
4363450 AAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
65 AAATTAAAACGTTAAAATGTTAACGTATCAGCAAAGTGT
4363489 AGAGATATAT
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
110 2 0.02
111 94 0.98
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTAACGTATCAGCAAAGTGTCGATATAT
Found at i:4366001 original size:3 final size:3
Alignment explanation
Indices: 4365987--4366033 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
4365977 GTCTTTTTAT
*
4365987 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4366034 TAATTTTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:4368147 original size:15 final size:16
Alignment explanation
Indices: 4368124--4368157 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4368114 TAGAAATTAT
4368124 TTTTATTGTTATTCTA
1 TTTTATTGTTATTCTA
*
4368140 TTTT-TTGTTATTTTA
1 TTTTATTGTTATTCTA
4368155 TTT
1 TTT
4368158 GATGTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTATTGTTATTCTA
Found at i:4379412 original size:23 final size:23
Alignment explanation
Indices: 4379386--4379431 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
4379376 AAAATATGAT
4379386 GGAAAATGAAAAAAAAAGAAAAA
1 GGAAAATGAAAAAAAAAGAAAAA
4379409 GGAAAATGAAAAAAAAAGAAAAA
1 GGAAAATGAAAAAAAAAGAAAAA
4379432 ATAAATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (23 bp):
GGAAAATGAAAAAAAAAGAAAAA
Found at i:4381381 original size:21 final size:21
Alignment explanation
Indices: 4381355--4381399 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4381345 GATTTCTGGG
* *
4381355 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4381376 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4381397 CAA
1 CAA
4381400 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4382239 original size:31 final size:31
Alignment explanation
Indices: 4382201--4382325 Score: 191
Period size: 31 Copynumber: 4.0 Consensus size: 31
4382191 AGAGTCGAGG
4382201 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4382232 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4382263 GTTTACCTATG-TCTTTCGGGACATATGGACT
1 GTTTACCTATGTTC-TTCGGGACATATGGACT
* * *
4382294 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
4382325 G
1 G
4382326 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
30 2 0.02
31 83 0.94
32 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4385408 original size:15 final size:16
Alignment explanation
Indices: 4385383--4385416 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4385373 AGAAATTATT
4385383 TTTTATTGTTATTCTA
1 TTTTATTGTTATTCTA
*
4385399 TTTT-TTGTTATTTTA
1 TTTTATTGTTATTCTA
4385414 TTT
1 TTT
4385417 GATGTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTATTGTTATTCTA
Found at i:4387229 original size:20 final size:20
Alignment explanation
Indices: 4387173--4387232 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
4387163 TATAGAAGTT
*
4387173 ATAATA-TTTATATAATTGG
1 ATAATATTTTATATAATTTG
* *
4387192 ACAATATTTTTACATAATTTG
1 ATAATA-TTTTATATAATTTG
*
4387213 ATAATATTTTATGTAATTTG
1 ATAATATTTTATATAATTTG
4387233 TCTTTAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 5 0.15
20 12 0.36
21 16 0.48
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.50
Consensus pattern (20 bp):
ATAATATTTTATATAATTTG
Found at i:4390477 original size:20 final size:21
Alignment explanation
Indices: 4390448--4390488 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4390438 CTTAAATTAG
*
4390448 TAATTGTTT-ATGATTTAAAT
1 TAATTGTTTAATAATTTAAAT
*
4390468 TAATTTTTTAATAATTTAAAT
1 TAATTGTTTAATAATTTAAAT
4390489 ATCAATCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
TAATTGTTTAATAATTTAAAT
Found at i:4390565 original size:76 final size:76
Alignment explanation
Indices: 4390482--4390631 Score: 291
Period size: 76 Copynumber: 2.0 Consensus size: 76
4390472 TTTTTAATAA
4390482 TTTAAATATCAATCTTTATTTTTAAATATAATTAATTAAAGCAAACTAACTTCCATTAATTTAAT
1 TTTAAATATCAATCTTTATTTTTAAATATAATTAATTAAAGCAAACTAACTTCCATTAATTTAAT
4390547 CAGTATTTTGT
66 CAGTATTTTGT
*
4390558 TTTAAATATCAATCTTTATTTTTAAATATAATTAATTAAATCAAACTAACTTCCATTAATTTAAT
1 TTTAAATATCAATCTTTATTTTTAAATATAATTAATTAAAGCAAACTAACTTCCATTAATTTAAT
4390623 CAGTATTTT
66 CAGTATTTT
4390632 ATTTAGCCGA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.47
Consensus pattern (76 bp):
TTTAAATATCAATCTTTATTTTTAAATATAATTAATTAAAGCAAACTAACTTCCATTAATTTAAT
CAGTATTTTGT
Found at i:4391112 original size:21 final size:21
Alignment explanation
Indices: 4391088--4391156 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
4391078 TTTCAAATCT
* *
4391088 GCAACATAGAATTTAGAATTC
1 GCAACACAAAATTTAGAATTC
*
4391109 GCAACACAAAATTTATAATTC
1 GCAACACAAAATTTAGAATTC
* * *
4391130 GCAACACATAAGTCA-AATTC
1 GCAACACAAAATTTAGAATTC
4391150 GCAACAC
1 GCAACAC
4391157 GAATTTCTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 12 0.29
21 30 0.71
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.23
Consensus pattern (21 bp):
GCAACACAAAATTTAGAATTC
Found at i:4391170 original size:20 final size:20
Alignment explanation
Indices: 4391145--4391213 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
4391135 ACATAAGTCA
4391145 AATTCGCAACACGAATTTCTT
1 AATTCGCAACACGAATTT-TT
* *
4391166 -TTTCGCAACTC-AATTTTT
1 AATTCGCAACACGAATTTTT
4391184 GAATTCGCAACACGAA-TTTT
1 -AATTCGCAACACGAATTTTT
4391204 AATTTCGCAA
1 AA-TTCGCAA
4391214 AAGAGCTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
18 2 0.05
19 7 0.17
20 29 0.73
21 2 0.05
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (20 bp):
AATTCGCAACACGAATTTTT
Found at i:4391346 original size:22 final size:22
Alignment explanation
Indices: 4391321--4391370 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
4391311 TCTCTCACTC
* *
4391321 TCTCTGGCGATATCCGTCTCCA
1 TCTCCGGCGATATCCGTCCCCA
*
4391343 TCTCCGGCGATATTCGTCCCCA
1 TCTCCGGCGATATCCGTCCCCA
*
4391365 TATCCG
1 TCTCCG
4391371 ACAACCCCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.14, C:0.38, G:0.18, T:0.30
Consensus pattern (22 bp):
TCTCCGGCGATATCCGTCCCCA
Found at i:4391775 original size:33 final size:34
Alignment explanation
Indices: 4391733--4391807 Score: 118
Period size: 34 Copynumber: 2.2 Consensus size: 34
4391723 CTTGAAACAT
*
4391733 AAATTCGCAACAC-GAAATC-ACAACTCGAAAATG
1 AAATTCGCAACACAAAAATCGA-AACTCGAAAATG
4391766 AAATTCGCAACACAAAAATCGAAACTCGAAAATG
1 AAATTCGCAACACAAAAATCGAAACTCGAAAATG
4391800 AAATTCGC
1 AAATTCGC
4391808 GTTGCGAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 13 0.33
34 25 0.64
35 1 0.03
ACGTcount: A:0.49, C:0.23, G:0.12, T:0.16
Consensus pattern (34 bp):
AAATTCGCAACACAAAAATCGAAACTCGAAAATG
Found at i:4392079 original size:20 final size:20
Alignment explanation
Indices: 4392051--4392098 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
4392041 CCCAAAACAT
4392051 TTGTGTTGCGAAAATAAAAG
1 TTGTGTTGCGAAAATAAAAG
* *
4392071 TTGTTTTGCGAAATTAAAA-
1 TTGTGTTGCGAAAATAAAAG
4392090 TTCGTGTTG
1 TT-GTGTTG
4392099 TGAATTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGTGTTGCGAAAATAAAAG
Found at i:4392143 original size:20 final size:20
Alignment explanation
Indices: 4392120--4392182 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
4392110 ATCAAATTGT
4392120 GAAAAAGAAATTCGTGTTGC
1 GAAAAAGAAATTCGTGTTGC
* *
4392140 GAAAAAAAAAATC-TAGTTGC
1 GAAAAAGAAATTCGT-GTTGC
*
4392160 AAAAAAGAAATTCGTGTTGC
1 GAAAAAGAAATTCGTGTTGC
4392180 GAA
1 GAA
4392183 TTCGAAAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.22
Consensus pattern (20 bp):
GAAAAAGAAATTCGTGTTGC
Found at i:4392189 original size:20 final size:20
Alignment explanation
Indices: 4392166--4392350 Score: 76
Period size: 22 Copynumber: 9.1 Consensus size: 20
4392156 TTGCAAAAAA
4392166 GAAATTCGTGTTGCGAATTC
1 GAAATTCGTGTTGCGAATTC
* *
4392186 GAAAATCGAGTTGCGAAATT-
1 GAAATTCGTGTTGCG-AATTC
*
4392206 GTCAAATTCGAGTTGCGAAATT-
1 G--AAATTCGTGTTGCG-AATTC
* *
4392228 GTCAAATTCGAGTTGCGAATTT
1 G--AAATTCGTGTTGCGAATTC
* * *
4392250 G-ACTTATGTGTTGCAAATTC
1 GAAATT-CGTGTTGCGAATTC
* * * *
4392270 CAAATTATGTGTCGCGAATTTG
1 GAAATT-CGTGTTGCGAA-TTC
* * *
4392292 GAAACT-ATATTGCGAAATT-
1 GAAATTCGTGTTGCG-AATTC
* *
4392311 GGAGTTCGTGTTGCGAATTC
1 GAAATTCGTGTTGCGAATTC
*
4392331 GAAA-TCGAGTTGCGAATTC
1 GAAATTCGTGTTGCGAATTC
4392350 G
1 G
4392351 TTGGTTATTT
Statistics
Matches: 129, Mismatches: 26, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
19 25 0.19
20 39 0.30
21 23 0.18
22 42 0.33
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (20 bp):
GAAATTCGTGTTGCGAATTC
Found at i:4392198 original size:40 final size:40
Alignment explanation
Indices: 4392087--4392199 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
4392077 TGCGAAATTA
* * **
4392087 AAATTCGTGTTGTGAATTCGAAAATCAAATTGTGAAAAAG
1 AAATTCGTGTTGCGAATTCGAAAATCAAGTTGCAAAAAAG
**** *
4392127 AAATTCGTGTTGCGAAAAAAAAAATCTAGTTGCAAAAAAG
1 AAATTCGTGTTGCGAATTCGAAAATCAAGTTGCAAAAAAG
*
4392167 AAATTCGTGTTGCGAATTCGAAAATCGAGTTGC
1 AAATTCGTGTTGCGAATTCGAAAATCAAGTTGC
4392200 GAAATTGTCA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (40 bp):
AAATTCGTGTTGCGAATTCGAAAATCAAGTTGCAAAAAAG
Found at i:4392219 original size:22 final size:22
Alignment explanation
Indices: 4392167--4392246 Score: 112
Period size: 22 Copynumber: 3.7 Consensus size: 22
4392157 TGCAAAAAAG
*
4392167 AAATTCGTGTTGCG-AA-T-TC
1 AAATTCGAGTTGCGAAATTGTC
*
4392186 GAAAATCGAGTTGCGAAATTGTC
1 -AAATTCGAGTTGCGAAATTGTC
4392209 AAATTCGAGTTGCGAAATTGTC
1 AAATTCGAGTTGCGAAATTGTC
4392231 AAATTCGAGTTGCGAA
1 AAATTCGAGTTGCGAA
4392247 TTTGACTTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
20 12 0.22
21 2 0.04
22 38 0.70
23 2 0.04
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30
Consensus pattern (22 bp):
AAATTCGAGTTGCGAAATTGTC
Found at i:4396507 original size:16 final size:18
Alignment explanation
Indices: 4396486--4396536 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 18
4396476 TTAATAGATT
4396486 TTAAAT-TTTTATAA-AA
1 TTAAATATTTTATAATAA
*
4396502 TTAAATATTTTGTAATAA
1 TTAAATATTTTATAATAA
**
4396520 TTATTTTATTTTATAAT
1 TTA-AATATTTTATAAT
4396537 TTATATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 6 0.21
17 7 0.25
18 5 0.18
19 10 0.36
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTAAATATTTTATAATAA
Found at i:4409684 original size:85 final size:85
Alignment explanation
Indices: 4409541--4409717 Score: 284
Period size: 85 Copynumber: 2.1 Consensus size: 85
4409531 AATGGATACC
* * * *
4409541 AAACATTGCATGAACTCAGCCAAGGATCGAGTTTCTGGAAAAGAGTTCGAGTCTTCATCGGCAAA
1 AAACATTGCATGAACTCAGCCAAGGATCGAGCTTCCGGAAAAAAGTTCGAGTCTTCATCAGCAAA
4409606 TGGCATGGCT-ACAAGGTGCT
66 TGGCATGGCTGA-AAGGTGCT
* *
4409626 AAACATTGCATGATCTCAGCCAAGGATTGAGCTTCCGGAAAAAAGTTCGAGTCTTCATCAGCAAA
1 AAACATTGCATGAACTCAGCCAAGGATCGAGCTTCCGGAAAAAAGTTCGAGTCTTCATCAGCAAA
4409691 TGGCATGGCTGAAAGGTGCT
66 TGGCATGGCTGAAAGGTGCT
4409711 AAACATT
1 AAACATT
4409718 ATCGCATCAA
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
85 84 0.99
86 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (85 bp):
AAACATTGCATGAACTCAGCCAAGGATCGAGCTTCCGGAAAAAAGTTCGAGTCTTCATCAGCAAA
TGGCATGGCTGAAAGGTGCT
Found at i:4413192 original size:23 final size:23
Alignment explanation
Indices: 4413166--4413221 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
4413156 CAGTGCTGAC
*
4413166 TGATTCAGCAAAACAGTCTTGAA
1 TGATTCAGCAAAACAATCTTGAA
* *
4413189 TGATTTAGCAAAACAATGTTGAA
1 TGATTCAGCAAAACAATCTTGAA
4413212 TGATTCAGCA
1 TGATTCAGCA
4413222 CATAAGTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (23 bp):
TGATTCAGCAAAACAATCTTGAA
Found at i:4414727 original size:22 final size:22
Alignment explanation
Indices: 4414700--4414762 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
4414690 TCAAACAATC
4414700 GAAAACGTGCC-AAAAGGAAAA
1 GAAAACGTGCCAAAAAGGAAAA
* *
4414721 GAGAAACGTACCATAAAAGGAAAG
1 GA-AAACGTGCCA-AAAAGGAAAA
*
4414745 GAAAACGTGTCATAAAAG
1 GAAAACGTGCCA-AAAAG
4414763 CAATTGTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.06
22 8 0.23
23 14 0.40
24 11 0.31
ACGTcount: A:0.54, C:0.13, G:0.24, T:0.10
Consensus pattern (22 bp):
GAAAACGTGCCAAAAAGGAAAA
Found at i:4414740 original size:24 final size:23
Alignment explanation
Indices: 4414711--4414762 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
4414701 AAAACGTGCC
4414711 AAAAGGAAAAGAGAAACGTACCAT
1 AAAAGGAAAAGA-AAACGTACCAT
* **
4414735 AAAAGGAAAGGAAAACGTGTCAT
1 AAAAGGAAAAGAAAACGTACCAT
4414758 AAAAG
1 AAAAG
4414763 CAATTGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.58, C:0.10, G:0.23, T:0.10
Consensus pattern (23 bp):
AAAAGGAAAAGAAAACGTACCAT
Found at i:4417909 original size:16 final size:16
Alignment explanation
Indices: 4417888--4417921 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4417878 TTACTATTCA
*
4417888 CGTGAACAGTGAATTT
1 CGTGAACAGTGAAATT
*
4417904 CGTGAATAGTGAAATT
1 CGTGAACAGTGAAATT
4417920 CG
1 CG
4417922 GTCGGCGATA
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:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (16 bp):
CGTGAACAGTGAAATT
Found at i:4423213 original size:16 final size:16
Alignment explanation
Indices: 4423180--4423209 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4423170 CGTTTGCATC
4423180 ATTTAGGATCCTATAT
1 ATTTAGGATCCTATAT
4423196 ATTTAGGAT-CTATA
1 ATTTAGGATCCTATA
4423210 ATATATGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (16 bp):
ATTTAGGATCCTATAT
Found at i:4426813 original size:128 final size:128
Alignment explanation
Indices: 4426597--4426874 Score: 511
Period size: 128 Copynumber: 2.2 Consensus size: 128
4426587 GAAAGCGCAT
* *
4426597 CCCCGGGAATGCACCTTCATGTCCCCTGAGAAATAATAGGTACTGATATATCTAGTGTCCCCGAG
1 CCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTACTGATATATCTAGTGTCCCCGAG
* *
4426662 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGCCC
66 GGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACGAAATAATAGAAGGCGCCC
4426725 CCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTACTGATATATCTAGTGTCCCCGAG
1 CCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTACTGATATATCTAGTGTCCCCGAG
*
4426790 GGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACGAAATAATAGAAGGCGCGC
66 GGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACGAAATAATAGAAGGCGCCC
4426853 CCCCGGGAACGCGCCTTCATGT
1 CCCCGGGAACGCGCCTTCATGT
4426875 GAATAGTACT
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 145 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (128 bp):
CCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTACTGATATATCTAGTGTCCCCGAG
GGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACGAAATAATAGAAGGCGCCC
Found at i:4426965 original size:8 final size:8
Alignment explanation
Indices: 4426952--4426992 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
4426942 TCACAATCTT
4426952 TCAAATTC
1 TCAAATTC
4426960 TCAAATTC
1 TCAAATTC
* *
4426968 CCAAACTC
1 TCAAATTC
4426976 T-AAATTC
1 TCAAATTC
4426983 TCAAATTC
1 TCAAATTC
4426991 TC
1 TC
4426993 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:4434043 original size:105 final size:105
Alignment explanation
Indices: 4433859--4435165 Score: 2159
Period size: 105 Copynumber: 12.4 Consensus size: 105
4433849 CAATGCAAGC
* * * *
4433859 TGCGTTGTTTTGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
*
4433924 TTGTTGAGAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * *
4433964 TACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
4434029 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
*
4434069 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAGATGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
4434134 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * *
4434174 TGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTAAAATTGAGAGATGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
4434239 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* *
4434279 TACGTTGTCTGGAGTCCAATATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
* *
4434344 TTATGGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* *
4434384 TGTGTTGTCTGGAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
4434449 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * *
4434489 TACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
*
4434554 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* *
4434594 TGTGTTGTCTGGAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
4434659 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * *
4434699 TACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
4434764 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
*
4434804 TGCGTTGTCTGGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAAATT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAA-T
* *
4434868 GTTTATTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACT
64 GTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* *
4434910 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTG
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TG
*
4434975 TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
65 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * * *
4435016 TGCATTGTCTAGAGT-CAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
*
4435080 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * * * *
4435120 TGCGTTGTCTAGAGCGACCCGATATCCTCCGTTGTGAATTTGAAAT
1 TGCGTTGTCT-G-GAG-TCCAATATCCTTCGTTGTGAAGTTGAAAT
4435166 CGTGGATATT
Statistics
Matches: 1127, Mismatches: 68, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
104 53 0.05
105 894 0.79
106 157 0.14
107 1 0.00
108 22 0.02
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
Found at i:4439056 original size:27 final size:27
Alignment explanation
Indices: 4439001--4439060 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
4438991 TTAAAAGAAT
* *
4439001 TAAAAAAATAACATAATATATATATAA
1 TAAAAAAATAACAAAATATATATAAAA
4439028 TAAAAAAATAAACAGAAATA-ATA-AAAA
1 TAAAAAAAT-AACA-AAATATATATAAAA
4439055 TAAAAA
1 TAAAAA
4439061 TAATCAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 18 0.62
28 7 0.24
29 4 0.14
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (27 bp):
TAAAAAAATAACAAAATATATATAAAA
Found at i:4439080 original size:25 final size:24
Alignment explanation
Indices: 4439052--4439098 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
4439042 GAAATAATAA
* *
4439052 AAATAAAAATAATCAGTAAAAAATG
1 AAATAAAAAGAAT-AATAAAAAATG
*
4439077 AAATTAAAAGAATAATAAAAAA
1 AAATAAAAAGAATAATAAAAAA
4439099 GATCTAAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.19
Consensus pattern (24 bp):
AAATAAAAAGAATAATAAAAAATG
Found at i:4445466 original size:17 final size:17
Alignment explanation
Indices: 4445444--4445477 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4445434 ACTGGCCAAT
4445444 TCAGCTGTGAAAGTTGG
1 TCAGCTGTGAAAGTTGG
4445461 TCAGCTGTGAAAGTTGG
1 TCAGCTGTGAAAGTTGG
4445478 AAACTTGATA
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:0.24, C:0.12, G:0.35, T:0.29
Consensus pattern (17 bp):
TCAGCTGTGAAAGTTGG
Found at i:4452852 original size:23 final size:23
Alignment explanation
Indices: 4452802--4452852 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
4452792 CCTCCACAAT
* * *
4452802 GAATGGTGGAGATTACTTATATC
1 GAATGGTGGAAATTAATTATATA
* *
4452825 CAATGGTGGAAATTAATTATCTA
1 GAATGGTGGAAATTAATTATATA
4452848 GAATG
1 GAATG
4452853 CTCCACACAC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (23 bp):
GAATGGTGGAAATTAATTATATA
Found at i:4457634 original size:20 final size:20
Alignment explanation
Indices: 4457611--4457652 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4457601 CATATTCTTC
*
4457611 CATACTCTTCCATAAGATTT
1 CATACTATTCCATAAGATTT
*
4457631 CATACTATTCCATAAGGTTT
1 CATACTATTCCATAAGATTT
4457651 CA
1 CA
4457653 CACATCTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (20 bp):
CATACTATTCCATAAGATTT
Found at i:4459785 original size:5 final size:5
Alignment explanation
Indices: 4459775--4459799 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4459765 TTGTTTGGAG
4459775 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
4459800 ACTCTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:4464448 original size:23 final size:23
Alignment explanation
Indices: 4464418--4464521 Score: 127
Period size: 23 Copynumber: 4.5 Consensus size: 23
4464408 AATTTTATAT
*
4464418 GGCACTACGGTGCAACTCTACGC
1 GGCACTTCGGTGCAACTCTACGC
*
4464441 GGCACTACGGTGCAACTCTACGC
1 GGCACTTCGGTGCAACTCTACGC
* * * *
4464464 GACACTTCGGTGCAATTCTATGT
1 GGCACTTCGGTGCAACTCTACGC
* * *
4464487 GGCACTTCGGTGCAATTCTATGT
1 GGCACTTCGGTGCAACTCTACGC
4464510 GGCACTTCGGTG
1 GGCACTTCGGTG
4464522 TATTTATACG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.26
Consensus pattern (23 bp):
GGCACTTCGGTGCAACTCTACGC
Found at i:4465228 original size:32 final size:32
Alignment explanation
Indices: 4465192--4465262 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
4465182 TATTTTATGT
4465192 AATTATTCATTTGTGTTTAGTAAAAGTTTTAA
1 AATTATTCATTTGTGTTTAGTAAAAGTTTTAA
4465224 AATTATTCATTTGTGTTTAGTAAAAGTTTTAA
1 AATTATTCATTTGTGTTTAGTAAAAGTTTTAA
*
4465256 AAGTATT
1 AATTATT
4465263 AACTATTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (32 bp):
AATTATTCATTTGTGTTTAGTAAAAGTTTTAA
Found at i:4466247 original size:94 final size:94
Alignment explanation
Indices: 4466086--4466274 Score: 351
Period size: 94 Copynumber: 2.0 Consensus size: 94
4466076 AACACGTGTC
*
4466086 ACTTAACGGTGAAAATTAACAGTCTGTCACGGTGTGACCATTCTAAGTTACGGAATGTAACGTTA
1 ACTTAACGGTGAAAATTAACAGTCTGTCACGGCGTGACCATTCTAAGTTACGGAATGTAACGTTA
*
4466151 GGCACCAAACTAAAACGAAAAAAAACCTT
66 GGCACCAAACTAAAACAAAAAAAAACCTT
4466180 ACTTAACGGTGAAAATTAACAGTCTGTCACGGCGTGACCATTCTAAGTTACGGAATGTAACGTTA
1 ACTTAACGGTGAAAATTAACAGTCTGTCACGGCGTGACCATTCTAAGTTACGGAATGTAACGTTA
*
4466245 GGCACCAAACTAAAATAAAAAAAAACCTT
66 GGCACCAAACTAAAACAAAAAAAAACCTT
4466274 A
1 A
4466275 GGCCCTGAAC
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (94 bp):
ACTTAACGGTGAAAATTAACAGTCTGTCACGGCGTGACCATTCTAAGTTACGGAATGTAACGTTA
GGCACCAAACTAAAACAAAAAAAAACCTT
Found at i:4479873 original size:20 final size:18
Alignment explanation
Indices: 4479826--4479877 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
4479816 CATCCGTATG
*
4479826 ATGCACCGATGCATGAAT
1 ATGCACCGATGCATGAAC
* *
4479844 ATGCATCGATGCATAAGACC
1 ATGCACCGATGCAT--GAAC
4479864 ATGCACCGATGCAT
1 ATGCACCGATGCAT
4479878 CCGTCGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (18 bp):
ATGCACCGATGCATGAAC
Found at i:4480265 original size:16 final size:16
Alignment explanation
Indices: 4480246--4480278 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4480236 ATAATTTTTC
4480246 AAAATTAAAATTTCGA
1 AAAATTAAAATTTCGA
4480262 AAAATTAAAATTTCGA
1 AAAATTAAAATTTCGA
4480278 A
1 A
4480279 TTAAAAAAAA
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:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (16 bp):
AAAATTAAAATTTCGA
Found at i:4481443 original size:21 final size:21
Alignment explanation
Indices: 4481401--4481444 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4481391 ACCCCGGGAG
*
4481401 CTAGTTCTTCATGAGCTGCTC
1 CTAGTTCTTCATGAGCTCCTC
*
4481422 CTAGTTCTTC-TCGTGCTCCTC
1 CTAGTTCTTCAT-GAGCTCCTC
4481443 CT
1 CT
4481445 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.09, C:0.34, G:0.16, T:0.41
Consensus pattern (21 bp):
CTAGTTCTTCATGAGCTCCTC
Found at i:4485112 original size:40 final size:40
Alignment explanation
Indices: 4485044--4485570 Score: 287
Period size: 41 Copynumber: 12.9 Consensus size: 40
4485034 CGTTTATTCA
* * *
4485044 AAAAACGCCACTAAAGTATGAGTATTTGGCAGCGTTTGTAT
1 AAAAACG-CACTAAAGTACGAGTATTTAGCGGCGTTTGTAT
* * *
4485085 AAAAACGCACTAAAGTACGAGTTTTTGGCGGTGTTTGTAT
1 AAAAACGCACTAAAGTACGAGTATTTAGCGGCGTTTGTAT
* * * * *
4485125 AGAAACAC-CTCTAAAGTACGAATCTTTGGCGGCGTTTGTGCT
1 A-AAA-ACGCACTAAAGTACGAGTATTTAGCGGCGTTTGT-AT
* * * *
4485167 TAAAACGGCACTAAAGTA-TAGTATTTAGCGGCGTTTATAC
1 AAAAAC-GCACTAAAGTACGAGTATTTAGCGGCGTTTGTAT
* * * * * *
4485207 AAAAACACCGCTAAAGTACAAGCATTTAGCAGCGTTTGTGCT
1 AAAAAC-GCACTAAAGTACGAGTATTTAGCGGCGTTTGT-AT
* * * *
4485249 TAAAGCGCCACTAAAGTAC-AGTATTTAGCGGCGTTTATAC
1 AAAAACG-CACTAAAGTACGAGTATTTAGCGGCGTTTGTAT
* * * * *
4485289 AAAAATGCCACTAATGTACGAGCACTTT-GCGGCATTTGTGCT
1 AAAAACG-CACTAAAGTACGAGTA-TTTAGCGGCGTTTGT-AT
* * * * *
4485331 TAAAACGCCACTAAAGTAC-AATATTTAGCGGCGGTTATAC
1 AAAAACG-CACTAAAGTACGAGTATTTAGCGGCGTTTGTAT
* * * * *
4485371 AAAAACGCCACTAAAGAACGAGCACTTAGTGGCGTTTGTGCT
1 AAAAACG-CACTAAAGTACGAGTATTTAGCGGCGTTTGT-AT
* * * *
4485413 TAAAACGCCACTAAAGTAC-AATATTTAGCGGCGTTTATGCT
1 AAAAACG-CACTAAAGTACGAGTATTTAGCGGCGTTTGT-AT
** * * * *
4485454 TGAAATGCTACTAAAGTAC-ATTATTTAGCGGCGTTTATAC
1 AAAAACGC-ACTAAAGTACGAGTATTTAGCGGCGTTTGTAT
* * * * *
4485494 AAAAATGCCACTAAAGTAC-ATTATTTAACTGCGTTTATAT
1 AAAAACG-CACTAAAGTACGAGTATTTAGCGGCGTTTGTAT
* * * * *
4485534 AAAAGCGCCACTAAAGAACAAGTATTTACCGACGTTT
1 AAAAACG-CACTAAAGTACGAGTATTTAGCGGCGTTT
4485571 TTTCAAAAAA
Statistics
Matches: 379, Mismatches: 90, Indels: 34
0.75 0.18 0.07
Matches are distributed among these distances:
40 131 0.35
41 186 0.49
42 62 0.16
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (40 bp):
AAAAACGCACTAAAGTACGAGTATTTAGCGGCGTTTGTAT
Found at i:4485223 original size:82 final size:81
Alignment explanation
Indices: 4485032--4485549 Score: 460
Period size: 82 Copynumber: 6.3 Consensus size: 81
4485022 GATAAATTGT
* * * * * *
4485032 GGCGTTTATTCAAAAAACGCCACTAAAGTATGAGTA-TTTGGCAGCGTTTGT-ATAAAAACG-CA
1 GGCGTTTATAC-AAAAACGCCACTAAAGTACGA--ACTTTAGCGGCGTTTGTGCTTAAAACGCCA
* *
4485094 CTAAAGTACGAGTTTTTGGC
63 CTAAAGTAC-AGTATTTAGC
* * * * * * * *
4485114 GGTGTTTGTATAGAAACACCTCTAAAGTACGAATCTTTGGCGGCGTTTGTGCTTAAAACGGCACT
1 GGCGTTTATACAAAAACGCCACTAAAGTACGAA-CTTTAGCGGCGTTTGTGCTTAAAACGCCACT
*
4485179 AAAGTATAGTATTTAGC
65 AAAGTACAGTATTTAGC
* * * *
4485196 GGCGTTTATACAAAAACACCGCTAAAGTAC-AAGCATTTAGCAGCGTTTGTGCTTAAAGCGCCAC
1 GGCGTTTATACAAAAACGCCACTAAAGTACGAA-C-TTTAGCGGCGTTTGTGCTTAAAACGCCAC
4485260 TAAAGTACAGTATTTAGC
64 TAAAGTACAGTATTTAGC
* * *
4485278 GGCGTTTATACAAAAATGCCACTAATGTACGAGCACTTT-GCGGCATTTGTGCTTAAAACGCCAC
1 GGCGTTTATACAAAAACGCCACTAAAGTACGA--ACTTTAGCGGCGTTTGTGCTTAAAACGCCAC
*
4485342 TAAAGTACAATATTTAGC
64 TAAAGTACAGTATTTAGC
* * *
4485360 GGCGGTTATACAAAAACGCCACTAAAGAACGAGCAC-TTAGTGGCGTTTGTGCTTAAAACGCCAC
1 GGCGTTTATACAAAAACGCCACTAAAGTACGA--ACTTTAGCGGCGTTTGTGCTTAAAACGCCAC
*
4485424 TAAAGTACAATATTTAGC
64 TAAAGTACAGTATTTAGC
* ** * * * * * *
4485442 GGCGTTTATGCTTGAAATGCTACTAAAGTAC-ATTA-TTTAGCGGCGTTTATAC-AAAAATGCCA
1 GGCGTTTATAC-AAAAACGCCACTAAAGTACGA--ACTTTAGCGGCGTTTGTGCTTAAAACGCCA
* *
4485504 CTAAAGTACATTATTTAAC
63 CTAAAGTACAGTATTTAGC
* * *
4485523 TGCGTTTATATAAAAGCGCCACTAAAG
1 GGCGTTTATACAAAAACGCCACTAAAG
4485550 AACAAGTATT
Statistics
Matches: 362, Mismatches: 63, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
79 1 0.00
80 11 0.03
81 69 0.19
82 251 0.69
83 28 0.08
84 1 0.00
85 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (81 bp):
GGCGTTTATACAAAAACGCCACTAAAGTACGAACTTTAGCGGCGTTTGTGCTTAAAACGCCACTA
AAGTACAGTATTTAGC
Found at i:4486882 original size:18 final size:18
Alignment explanation
Indices: 4486859--4486908 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
4486849 AAAATCAATC
4486859 TTTGATTTTGAAAACTGT
1 TTTGATTTTGAAAACTGT
4486877 TTTGATTTTGAAAACTGT
1 TTTGATTTTGAAAACTGT
4486895 TTTGATTTTGAAAA
1 TTTGATTTTGAAAA
4486909 ATAAGCGCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.50
Consensus pattern (18 bp):
TTTGATTTTGAAAACTGT
Found at i:4493010 original size:2 final size:2
Alignment explanation
Indices: 4493005--4493040 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4492995 GTGTTGTGTG
4493005 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
4493041 GAACATAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4493850 original size:63 final size:62
Alignment explanation
Indices: 4493771--4493889 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 62
4493761 GAGGGTTTAC
* * *
4493771 CTATGTTCTACGGAACATATGGACAGAATTACCTATG-TCTTTCGGGACATATGGACAATATAT
1 CTATGTTCTAAGGAACATATGGAAAG-ATTACCTAGGTTC-TTCGGGACATATGGACAATATAT
* *
4493834 CTATGTTCTAAGGAACATATGGAAAGTTTACCTAGGTTCTTCGGGACCTATGGACA
1 CTATGTTCTAAGGAACATATGGAAAGATTACCTAGGTTCTTCGGGACATATGGACA
4493890 GTTGTCGAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
62 24 0.48
63 26 0.52
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (62 bp):
CTATGTTCTAAGGAACATATGGAAAGATTACCTAGGTTCTTCGGGACATATGGACAATATAT
Found at i:4493852 original size:31 final size:32
Alignment explanation
Indices: 4493767--4493890 Score: 112
Period size: 31 Copynumber: 3.9 Consensus size: 32
4493757 AGTTGAGGGT
4493767 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGAACATATGGACAGAA
* *
4493799 TTACCTATG-TCTTTCGGGACATATGGAC--AA
1 TTACCTATGTTC-TACGGAACATATGGACAGAA
* * * *
4493829 TATATCTATGTTCTAAGGAACATATGGAAAG-T
1 T-TACCTATGTTCTACGGAACATATGGACAGAA
* * * *
4493861 TTACCTAGGTTCTTCGGGACCTATGGACAG
1 TTACCTATGTTCTACGGAACATATGGACAG
4493891 TTGTCGAGGT
Statistics
Matches: 72, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
30 3 0.04
31 43 0.60
32 26 0.36
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (32 bp):
TTACCTATGTTCTACGGAACATATGGACAGAA
Found at i:4493888 original size:62 final size:63
Alignment explanation
Indices: 4493771--4493889 Score: 170
Period size: 62 Copynumber: 1.9 Consensus size: 63
4493761 GAGGGTTTAC
* * *
4493771 CTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGACAATATAT
1 CTATGTTCTAAGGAACATATGGAAAGAATTACCTAGGTCTTTCGGGACATATGGACAATATAT
* *
4493834 CTATGTTCTAAGGAACATATGGAAAG-TTTACCTAGGT-TCTTCGGGACCTATGGACA
1 CTATGTTCTAAGGAACATATGGAAAGAATTACCTAGGTCT-TTCGGGACATATGGACA
4493890 GTTGTCGAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
61 1 0.02
62 25 0.50
63 24 0.48
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (63 bp):
CTATGTTCTAAGGAACATATGGAAAGAATTACCTAGGTCTTTCGGGACATATGGACAATATAT
Found at i:4494647 original size:18 final size:19
Alignment explanation
Indices: 4494609--4494655 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
4494599 ACGAAAGTTA
4494609 CTGTAGCAGAGTATCGGTAC
1 CTGTAGCAGAGTA-CGGTAC
4494629 CTGTAGCAGAGTA-GGTAC
1 CTGTAGCAGAGTACGGTAC
4494647 CTGTAGCAG
1 CTGTAGCAG
4494656 GGGTATCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 14 0.52
20 13 0.48
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (19 bp):
CTGTAGCAGAGTACGGTAC
Found at i:4502213 original size:7 final size:8
Alignment explanation
Indices: 4502197--4502224 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
4502187 GAAAAGGTTG
4502197 AAAAGAAA
1 AAAAGAAA
4502205 AAAAGAAA
1 AAAAGAAA
4502213 AAAAGAAA
1 AAAAGAAA
4502221 AAAA
1 AAAA
4502225 ACTCGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:4503162 original size:31 final size:31
Alignment explanation
Indices: 4503122--4503217 Score: 149
Period size: 31 Copynumber: 3.1 Consensus size: 31
4503112 ATGGATCAGA
*
4503122 TTAGCCCTTTTATTATATGGATCGGTTCAAT
1 TTAGTCCTTTTATTATATGGATCGGTTCAAT
*
4503153 TTAGTCCTTTTATTTTATGGATCGGTTCAAT
1 TTAGTCCTTTTATTATATGGATCGGTTCAAT
*
4503184 TTAGTCCTTTTATTATATGGAAT-GATTCAAT
1 TTAGTCCTTTTATTATATGG-ATCGGTTCAAT
4503215 TTA
1 TTA
4503218 TTTTCATCTG
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 58 0.97
32 2 0.03
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (31 bp):
TTAGTCCTTTTATTATATGGATCGGTTCAAT
Found at i:4509736 original size:26 final size:26
Alignment explanation
Indices: 4509707--4509759 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
4509697 GTGGGTTAAT
*
4509707 AGACGTGTGTTAGAATTGAAGATGCA
1 AGACGTATGTTAGAATTGAAGATGCA
*
4509733 AGACTTATGTTAGAATTGAAGATGCA
1 AGACGTATGTTAGAATTGAAGATGCA
4509759 A
1 A
4509760 TGTATGTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (26 bp):
AGACGTATGTTAGAATTGAAGATGCA
Found at i:4511126 original size:13 final size:13
Alignment explanation
Indices: 4511110--4511152 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
4511100 GCATGAATAA
4511110 TATGCAATAACAT
1 TATGCAATAACAT
* *
4511123 TATGCAGTAACAA
1 TATGCAATAACAT
*
4511136 TATGTAATAACAT
1 TATGCAATAACAT
4511149 TATG
1 TATG
4511153 ATGAAGAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (13 bp):
TATGCAATAACAT
Found at i:4513097 original size:45 final size:45
Alignment explanation
Indices: 4513042--4513151 Score: 175
Period size: 45 Copynumber: 2.4 Consensus size: 45
4513032 CACCTCATCA
* *
4513042 GGTTCTGGTTCATCAATTTCAGGTTCATTAATTTTTGGCTCAACT
1 GGTTCTGGTTCATTAATTTCAGGTTCATTAATTTCTGGCTCAACT
* *
4513087 GGTTTTGGTTCATTAATTTCAGGTTCATTAATTTCTGGCTCAGCT
1 GGTTCTGGTTCATTAATTTCAGGTTCATTAATTTCTGGCTCAACT
*
4513132 TGTTCTGGTTCATTAATTTC
1 GGTTCTGGTTCATTAATTTC
4513152 TGGCTCGGCT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.47
Consensus pattern (45 bp):
GGTTCTGGTTCATTAATTTCAGGTTCATTAATTTCTGGCTCAACT
Found at i:4513136 original size:24 final size:27
Alignment explanation
Indices: 4513108--4513175 Score: 70
Period size: 30 Copynumber: 2.5 Consensus size: 27
4513098 ATTAATTTCA
*
4513108 GGTTCATTAATTTCTGGCTCAGCTTGTTCT
1 GGTTCATTAATTTCTGGCTCAGC---TTCG
*
4513138 GGTTCATTAATTTCTGGCTCGGC-T--
1 GGTTCATTAATTTCTGGCTCAGCTTCG
4513162 GGTTCATTAATTTC
1 GGTTCATTAATTTC
4513176 GGGTTCAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
24 14 0.38
26 1 0.03
30 22 0.59
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.46
Consensus pattern (27 bp):
GGTTCATTAATTTCTGGCTCAGCTTCG
Found at i:4513144 original size:30 final size:30
Alignment explanation
Indices: 4513108--4513166 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
4513098 ATTAATTTCA
*
4513108 GGTTCATTAATTTCTGGCTCAGCTTGTTCT
1 GGTTCATTAATTTCTGGCTCAGCTGGTTCT
*
4513138 GGTTCATTAATTTCTGGCTCGGCTGGTTC
1 GGTTCATTAATTTCTGGCTCAGCTGGTTC
4513167 ATTAATTTCG
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:0.12, C:0.20, G:0.24, T:0.44
Consensus pattern (30 bp):
GGTTCATTAATTTCTGGCTCAGCTGGTTCT
Found at i:4513152 original size:15 final size:15
Alignment explanation
Indices: 4513044--4513154 Score: 84
Period size: 15 Copynumber: 7.4 Consensus size: 15
4513034 CCTCATCAGG
*
4513044 TTCTGGTTCATCAAT
1 TTCTGGTTCATTAAT
*
4513059 TTCAGGTTCATTAAT
1 TTCTGGTTCATTAAT
* * * **
4513074 TTTTGGCTCAACTGGT
1 TTCTGGTTC-ATTAAT
4513090 TT-TGGTTCATTAAT
1 TTCTGGTTCATTAAT
*
4513104 TTCAGGTTCATTAAT
1 TTCTGGTTCATTAAT
* *
4513119 TTCTGGCTCAGCTT--G
1 TTCTGGTTCA--TTAAT
4513134 TTCTGGTTCATTAAT
1 TTCTGGTTCATTAAT
4513149 TTCTGG
1 TTCTGG
4513155 CTCGGCTGGT
Statistics
Matches: 72, Mismatches: 18, Indels: 12
0.71 0.18 0.12
Matches are distributed among these distances:
13 2 0.03
14 5 0.07
15 58 0.81
16 5 0.07
17 2 0.03
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (15 bp):
TTCTGGTTCATTAAT
Found at i:4513206 original size:69 final size:69
Alignment explanation
Indices: 4513092--4513220 Score: 168
Period size: 69 Copynumber: 1.9 Consensus size: 69
4513082 CAACTGGTTT
* ** * * * *
4513092 TGGTTCATTAATTTCAGGTTCATTAATTTCTGGCTCAGCTTGTTCTGGTTCATTAATTTCTGGCT
1 TGGTTCATTAATTTCAGGTTCAGTAATTTCTAACTCAACTGGTTCTGCTTCATCAATTTCTGGCT
4513157 CGGC
66 CGGC
* * *
4513161 TGGTTCATTAATTTCGGGTTCAGTAATTTCTAATTGAACTGGTTCTGCTTCATCAATTTC
1 TGGTTCATTAATTTCAGGTTCAGTAATTTCTAACTCAACTGGTTCTGCTTCATCAATTTC
4513221 AGGTTCATTA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
69 50 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.45
Consensus pattern (69 bp):
TGGTTCATTAATTTCAGGTTCAGTAATTTCTAACTCAACTGGTTCTGCTTCATCAATTTCTGGCT
CGGC
Found at i:4514431 original size:24 final size:24
Alignment explanation
Indices: 4514396--4514462 Score: 125
Period size: 24 Copynumber: 2.8 Consensus size: 24
4514386 ACAGGGAGGT
4514396 TGAAGGCGAATGGGTTTTCTGCGA
1 TGAAGGCGAATGGGTTTTCTGCGA
*
4514420 TGAAGGCTAATGGGTTTTCTGCGA
1 TGAAGGCGAATGGGTTTTCTGCGA
4514444 TGAAGGCGAATGGGTTTTC
1 TGAAGGCGAATGGGTTTTC
4514463 AGACGAAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.21, C:0.12, G:0.36, T:0.31
Consensus pattern (24 bp):
TGAAGGCGAATGGGTTTTCTGCGA
Found at i:4514550 original size:64 final size:63
Alignment explanation
Indices: 4514476--4514664 Score: 306
Period size: 64 Copynumber: 3.0 Consensus size: 63
4514466 CGAAATCTTT
* *
4514476 CGAAATCTCTCTAAAGTGCGAAGGATTTTTAGATGAGGAGGTTGAAGGCGAATGAGTTTTCAGA
1 CGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGAGGTTGAAGGCGAATG-GTTTTCAGA
* *
4514540 CGAAATCTCTCTAAAGTGCGAATGATTTTCAGACGATGAGGTTGAAGGCGAATGGATTTTCAGA
1 CGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGAGGTTGAAGGCGAATGG-TTTTCAGA
*
4514604 CGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGAGGTTGAAGGCAAATGGGTTTTC
1 CGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGAGGTTGAAGGCGAAT-GGTTTTC
4514665 TGCGATGAAG
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
63 1 0.01
64 113 0.97
65 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.28
Consensus pattern (63 bp):
CGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGAGGTTGAAGGCGAATGGTTTTCAGA
Found at i:4514572 original size:33 final size:33
Alignment explanation
Indices: 4514523--4514639 Score: 134
Period size: 33 Copynumber: 3.6 Consensus size: 33
4514513 GAGGTTGAAG
4514523 GCGAATGAGTTTTCAGACGAAATCTCTCTAAAGT
1 GCGAATGA-TTTTCAGACGAAATCTCTCTAAAGT
*** *
4514557 GCGAATGATTTTCAGACG--ATGAGGT-TGAAG-
1 GCGAATGATTTTCAGACGAAAT-CTCTCTAAAGT
4514587 GCGAATGGATTTTCAGACGAAATCTCTCTAAAGT
1 GCGAAT-GATTTTCAGACGAAATCTCTCTAAAGT
*
4514621 GCGAAGGATTTTCAGACGA
1 GCGAATGATTTTCAGACGA
4514640 GGAGGTTGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
30 6 0.09
31 18 0.26
32 2 0.03
33 29 0.43
34 13 0.19
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (33 bp):
GCGAATGATTTTCAGACGAAATCTCTCTAAAGT
Found at i:4514593 original size:30 final size:30
Alignment explanation
Indices: 4514493--4514606 Score: 95
Period size: 31 Copynumber: 3.6 Consensus size: 30
4514483 TCTCTAAAGT
* * * *
4514493 GCGAAGGATTTTTAGATGAGGAGGTTGAAG
1 GCGAATGATTTTCAGACGATGAGGTTGAAG
*** *
4514523 GCGAATGAGTTTTCAGACGAAAT-CTCTCTAAAG
1 GCGAATGA-TTTTCAGACG--ATGAGGT-TGAAG
4514556 TGCGAATGATTTTCAGACGATGAGGTTGAAG
1 -GCGAATGATTTTCAGACGATGAGGTTGAAG
4514587 GCGAATGGATTTTCAGACGA
1 GCGAAT-GATTTTCAGACGA
4514607 AATCTCTCTA
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
30 13 0.20
31 27 0.42
32 2 0.03
33 15 0.23
34 8 0.12
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.27
Consensus pattern (30 bp):
GCGAATGATTTTCAGACGATGAGGTTGAAG
Found at i:4514601 original size:31 final size:31
Alignment explanation
Indices: 4514557--4514672 Score: 96
Period size: 31 Copynumber: 3.7 Consensus size: 31
4514547 TCTCTAAAGT
4514557 GCGAAT-GATTTTCAGACGATGAGGTTGAAG
1 GCGAATGGATTTTCAGACGATGAGGTTGAAG
*** *
4514587 GCGAATGGATTTTCAGACGAAAT-CTCTCTAAAG
1 GCGAATGGATTTTCAGACG--ATGAGGT-TGAAG
*
4514620 TGCGAA-GGATTTTCAGACGAGGAGGTTGAAG
1 -GCGAATGGATTTTCAGACGATGAGGTTGAAG
* * *
4514651 GCAAATGGGTTTTCTG-CGATGA
1 GCGAATGGATTTTCAGACGATGA
4514673 AGGCGAATGT
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
30 15 0.23
31 25 0.38
32 2 0.03
33 19 0.29
34 5 0.08
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (31 bp):
GCGAATGGATTTTCAGACGATGAGGTTGAAG
Found at i:4518051 original size:3 final size:3
Alignment explanation
Indices: 4518043--4518075 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
4518033 TTGAATCCAA
4518043 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4518076 GAATTTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4519105 original size:17 final size:16
Alignment explanation
Indices: 4519083--4519135 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
4519073 ATTAAAATAA
4519083 TATTAAAAATGCTTAAT
1 TATTAAAAAT-CTTAAT
4519100 TATT-AAAA---TAA-
1 TATTAAAAATCTTAAT
4519111 TATTAAAAATTCTTAAT
1 TATTAAAAA-TCTTAAT
4519128 TATTAAAA
1 TATTAAAA
4519136 TAACACTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
11 4 0.13
12 7 0.23
16 7 0.23
17 12 0.40
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (16 bp):
TATTAAAAATCTTAAT
Found at i:4519106 original size:28 final size:28
Alignment explanation
Indices: 4519071--4519138 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
4519061 TAATATTTAT
4519071 TTATTAAAATAATATTAAAAATGCTTAA
1 TTATTAAAATAATATTAAAAATGCTTAA
*
4519099 TTATTAAAATAATATTAAAAATTCTTAA
1 TTATTAAAATAATATTAAAAATGCTTAA
4519127 TTATTAAAATAA
1 TTATTAAAATAA
4519139 CACTCGTAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (28 bp):
TTATTAAAATAATATTAAAAATGCTTAA
Found at i:4533049 original size:24 final size:24
Alignment explanation
Indices: 4533031--4533077 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
4533021 CTTATTAATG
4533031 AGTAGATAAACGAGATTATAAACT
1 AGTAGATAAACGAGATTATAAACT
*
4533055 AGTAGATAAACGAGTTTATAAAC
1 AGTAGATAAACGAGATTATAAAC
4533078 AAGCAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.26
Consensus pattern (24 bp):
AGTAGATAAACGAGATTATAAACT
Found at i:4533087 original size:24 final size:24
Alignment explanation
Indices: 4533036--4533094 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
4533026 TAATGAGTAG
* * *
4533036 ATAAACGAGATTATAAACTAGTAG
1 ATAAACGAGATTATAAACAAGCAA
*
4533060 ATAAACGAGTTTATAAACAAGCAA
1 ATAAACGAGATTATAAACAAGCAA
*
4533084 ATAAATGAGAT
1 ATAAACGAGAT
4533095 CCTTTATGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.24
Consensus pattern (24 bp):
ATAAACGAGATTATAAACAAGCAA
Found at i:4539173 original size:75 final size:77
Alignment explanation
Indices: 4538965--4539174 Score: 273
Period size: 75 Copynumber: 2.8 Consensus size: 77
4538955 CAAAGCCAAA
* * * * **
4538965 AATTACAGATTGCTCAGAGGGAATCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGA-TCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
4539030 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
* * *
4539043 ATTTCTAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
4539107 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * *
4539118 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCT
4539175 TGTACAACGG
Statistics
Matches: 115, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
74 12 0.10
75 45 0.39
76 14 0.12
77 23 0.20
78 21 0.18
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.21
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:4546982 original size:9 final size:8
Alignment explanation
Indices: 4546960--4547010 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
4546950 TGTTTCAACA
4546960 TTTTGGAT
1 TTTTGGAT
4546968 ATTTTGGAT
1 -TTTTGGAT
4546977 TGTTT-GAT
1 T-TTTGGAT
4546985 TTTGTGGAT
1 TTT-TGGAT
*
4546994 TGTTGGA-
1 TTTTGGAT
4547001 TTTTGGAT
1 TTTTGGAT
4547009 TT
1 TT
4547011 ATGAATAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:4546994 original size:17 final size:17
Alignment explanation
Indices: 4546962--4547005 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
4546952 TTTCAACATT
4546962 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
4546979 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
4546996 TTGGATTTTG
1 TTGGATTTTG
4547006 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:4547748 original size:75 final size:76
Alignment explanation
Indices: 4547579--4547783 Score: 288
Period size: 75 Copynumber: 2.7 Consensus size: 76
4547569 CAAAGCCAAA
* * * **
4547579 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCTAAACAGT
4547644 TTTGGCCCCGAG
65 TTTGGCCCCGAG
*
4547656 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
*
4547721 TT-GCTCCGAG
66 TTGGCCCCGAG
* * * *
4547731 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCC
4547784 TCTTGTACAA
Statistics
Matches: 116, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
74 15 0.13
75 40 0.34
76 36 0.31
77 25 0.22
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TTGGCCCCGAG
Found at i:4555421 original size:35 final size:35
Alignment explanation
Indices: 4555375--4555450 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
4555365 AAAACAGTCC
* *
4555375 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
4555410 TCAATTTCATTCTCAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
4555445 TCAATT
1 TCAATT
4555451 AAATTTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:4556000 original size:130 final size:130
Alignment explanation
Indices: 4555847--4556094 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
4555837 TATTTATATA
* ** *
4555847 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
4555912 TTAGCACATGATCATGACACGTGTCATTGGTGACGCATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
4555977 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGATATATG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
4556042 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
4556095 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:4556060 original size:23 final size:21
Alignment explanation
Indices: 4556021--4556067 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
4556011 AATTAATCAT
4556021 TTAACCAGGATCTGATATATG
1 TTAACCAGGATCTGATATATG
*
4556042 TTAACACATGATCATGATATATG
1 TTAAC-CAGGATC-TGATATATG
4556065 TTA
1 TTA
4556068 TTGGTGACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 6 0.26
23 12 0.52
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (21 bp):
TTAACCAGGATCTGATATATG
Found at i:4556125 original size:130 final size:129
Alignment explanation
Indices: 4555861--4556125 Score: 282
Period size: 130 Copynumber: 2.0 Consensus size: 129
4555851 ATTTGGTCCT
* ** * *
4555861 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* * *** * * **** *
4555926 TGACACGTGTCATTGGTGACGCATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
4555991 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGATATATGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* * * *
4556056 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
4556120 -A
128 CA
4556121 AAATT
1 AAATT
4556126 TGGGTCTTGG
Statistics
Matches: 110, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
130 97 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:4556453 original size:28 final size:27
Alignment explanation
Indices: 4556422--4556484 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
4556412 AGTTGATACA
4556422 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGATTT
** * *
4556450 ATATATTTTTAAACTAAATTTAATATTT
1 ATAT-TTTAAAAAATAAATTTAAGATTT
*
4556478 ATGTTTT
1 ATATTTT
4556485 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGATTT
Found at i:4556587 original size:16 final size:18
Alignment explanation
Indices: 4556566--4556599 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
4556556 ATTTCTTATT
4556566 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
4556582 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
4556600 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:4558228 original size:19 final size:19
Alignment explanation
Indices: 4558184--4558248 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
4558174 ATCAAATCTG
*
4558184 TTTGACCCGAACCAAGTTAAC
1 TTTGACCC-AACC-CGTTAAC
*
4558205 -CTGACCCAACCCGTTGAA-
1 TTTGACCCAACCCGTT-AAC
*
4558223 TTTGACCCGACCCGTTAAC
1 TTTGACCCAACCCGTTAAC
4558242 TTTGACC
1 TTTGACC
4558249 AGAGTTGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 5 0.14
19 26 0.70
20 6 0.16
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.25
Consensus pattern (19 bp):
TTTGACCCAACCCGTTAAC
Found at i:4571354 original size:2 final size:2
Alignment explanation
Indices: 4571347--4571385 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4571337 ATGTTTCATA
4571347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4571386 ACCTAGATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4576386 original size:3 final size:3
Alignment explanation
Indices: 4576373--4576442 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
4576363 GTAATATTTA
* * *
4576373 AAT AAT AAAT AAT ATT ACT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
4576419 AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
4576443 TTAAAATGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:4576387 original size:18 final size:18
Alignment explanation
Indices: 4576364--4576442 Score: 81
Period size: 18 Copynumber: 4.2 Consensus size: 18
4576354 TTGGGCTTTG
4576364 TAATATTTA-AATAATAAA
1 TAATATTTATAATAAT-AA
4576382 TAATATTACTATTAATAATAA
1 TAATATT--TA-TAATAATAA
* *
4576403 TAATAATAATAATAATAA
1 TAATATTTATAATAATAA
4576421 TAATAATTT-TAATAATAA
1 TAAT-ATTTATAATAATAA
4576439 TAAT
1 TAAT
4576443 TTAAAATGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 33 0.63
19 3 0.06
20 2 0.04
21 8 0.15
22 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATATTTATAATAATAA
Found at i:4576724 original size:76 final size:76
Alignment explanation
Indices: 4576598--4577361 Score: 1440
Period size: 76 Copynumber: 10.0 Consensus size: 76
4576588 GGTCTTATGA
*
4576598 ATGACCCTG-AGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
* *
4576662 TAGGGCTTACAG
65 AAGGACTTACAG
4576674 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
4576739 AGGACTTACAG
66 AGGACTTACAG
4576750 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
4576815 AGGACTTACAG
66 AGGACTTACAG
*
4576826 ATGACCCGAAGGCTTTGACAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
4576891 AGGACTTACAG
66 AGGACTTACAG
4576902 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTG
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTG
4576967 AAGGACTTACAG
65 AAGGACTTACAG
*
4576979 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
4577044 AGGACTTACAG
66 AGGACTTACAG
4577055 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
4577120 AGGACTTACAG
66 AGGACTTACAG
*
4577131 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
4577196 AGGACTTACAG
66 AGGACTTACAG
*
4577207 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
4577272 AGGACTTACAG
66 AGGACTTACAG
4577283 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
4577348 AGGACTTACAG
66 AGGACTTACAG
4577359 ATG
1 ATG
4577362 TGAGAAATAG
Statistics
Matches: 677, Mismatches: 9, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
75 1 0.00
76 601 0.89
77 75 0.11
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Done.