Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 137 of 186
Found at i:45203056 original size:21 final size:21
Alignment explanation
Indices: 45203031--45203071 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
45203021 AAAAAATATC
*
45203031 TTTTAAAAAAAT-TATTTTTA
1 TTTTTAAAAAATATATTTTTA
*
45203051 TTTTTAAGAAATATATTTTTA
1 TTTTTAAAAAATATATTTTTA
45203072 CTAAATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTTAAAAAATATATTTTTA
Found at i:45209389 original size:12 final size:12
Alignment explanation
Indices: 45209366--45209400 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
45209356 AGCTCATGTG
*
45209366 GCTAGCCCGTGT
1 GCTAGGCCGTGT
*
45209378 GTTAGGCCGTGT
1 GCTAGGCCGTGT
45209390 GCTAGGCCGTG
1 GCTAGGCCGTG
45209401 CCAAACCTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.26, G:0.40, T:0.26
Consensus pattern (12 bp):
GCTAGGCCGTGT
Found at i:45210552 original size:39 final size:40
Alignment explanation
Indices: 45210451--45210555 Score: 158
Period size: 40 Copynumber: 2.6 Consensus size: 40
45210441 CGAATTCTTT
* *
45210451 CACACTAAGTGTCATACATAGCTGAAGCTATCTCGAATCG
1 CACACTAAGTGCCATACATAGCCGAAGCTATCTCGAATCG
* *
45210491 CACACTAAGTGCCACACATAGCCGAAGCTATCTTGAATCG
1 CACACTAAGTGCCATACATAGCCGAAGCTATCTCGAATCG
*
45210531 CACACT-AGTGCCGTACATAGCCGAA
1 CACACTAAGTGCCATACATAGCCGAA
45210556 TGTTGTCAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 17 0.29
40 42 0.71
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (40 bp):
CACACTAAGTGCCATACATAGCCGAAGCTATCTCGAATCG
Found at i:45212058 original size:34 final size:34
Alignment explanation
Indices: 45212015--45212087 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
45212005 AGTGGCAGTC
*
45212015 CAGTATCAGT-TAGGGCCATAGCCCATTACAGCAA
1 CAGTATCAGTGT-GGGCCATAACCCATTACAGCAA
* *
45212049 CAGTATCAGTGTGGGCCTTAACCCATTACAGTAA
1 CAGTATCAGTGTGGGCCATAACCCATTACAGCAA
45212083 CAGTA
1 CAGTA
45212088 ACAGAAATGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 34 0.97
35 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (34 bp):
CAGTATCAGTGTGGGCCATAACCCATTACAGCAA
Found at i:45214768 original size:52 final size:52
Alignment explanation
Indices: 45214707--45214810 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
45214697 GCAAGGTGGC
* *
45214707 GCCACTTAGGGGACAAGGAAGTGGCGCCATAGATGAAGCAAGGGGTCCAAGG
1 GCCACTTAGGGGACAAGGAAGTGACGCCATAGAGGAAGCAAGGGGTCCAAGG
45214759 GCCACTTAGGGGACAAGGAAGTGACGCCATAGAGGAAGCAAGGGGTCCAAGG
1 GCCACTTAGGGGACAAGGAAGTGACGCCATAGAGGAAGCAAGGGGTCCAAGG
45214811 TTCAAGTCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.32, C:0.19, G:0.38, T:0.11
Consensus pattern (52 bp):
GCCACTTAGGGGACAAGGAAGTGACGCCATAGAGGAAGCAAGGGGTCCAAGG
Found at i:45216075 original size:27 final size:26
Alignment explanation
Indices: 45216031--45216081 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
45216021 CTCACTACAA
*
45216031 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
45216058 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
45216082 AGTAGCCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:45223968 original size:18 final size:17
Alignment explanation
Indices: 45223929--45223968 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
45223919 AGGCCAGATT
*
45223929 TGGGCTTGTGGGCCACA
1 TGGGCGTGTGGGCCACA
*
45223946 CGGGCGTGTGGGCCCACA
1 TGGGCGTGTGGG-CCACA
45223964 TGGGC
1 TGGGC
45223969 CTGTATTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.10, C:0.28, G:0.45, T:0.17
Consensus pattern (17 bp):
TGGGCGTGTGGGCCACA
Found at i:45227248 original size:18 final size:18
Alignment explanation
Indices: 45227225--45227260 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
45227215 TTCGATGTAA
45227225 GGCACATGGCCGTGTCCT
1 GGCACATGGCCGTGTCCT
*
45227243 GGCACATGGCTGTGTCCT
1 GGCACATGGCCGTGTCCT
45227261 AGCCCATGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.31, G:0.33, T:0.25
Consensus pattern (18 bp):
GGCACATGGCCGTGTCCT
Found at i:45227268 original size:18 final size:18
Alignment explanation
Indices: 45227226--45227268 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
45227216 TCGATGTAAG
*
45227226 GCACATGGCCGTGTCCTG
1 GCACATGGCCGTGTCCTA
*
45227244 GCACATGGCTGTGTCCTA
1 GCACATGGCCGTGTCCTA
*
45227262 GCCCATG
1 GCACATG
45227269 TCCTTACCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.33, G:0.30, T:0.23
Consensus pattern (18 bp):
GCACATGGCCGTGTCCTA
Found at i:45228007 original size:24 final size:23
Alignment explanation
Indices: 45227968--45228017 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
45227958 CGAGCACTAA
45227968 TAAAACAGAGAAAGAAAACCTAG
1 TAAAACAGAGAAAGAAAACCTAG
* *
45227991 TAAAACTGAGTAAAGAAAATCTAG
1 TAAAACAGAG-AAAGAAAACCTAG
45228015 TAA
1 TAA
45228018 GCATTTAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.58, C:0.10, G:0.16, T:0.16
Consensus pattern (23 bp):
TAAAACAGAGAAAGAAAACCTAG
Found at i:45230254 original size:13 final size:13
Alignment explanation
Indices: 45230238--45230263 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45230228 TTATTTACCG
45230238 AAATTATTATAAT
1 AAATTATTATAAT
45230251 AAATTATTATAAT
1 AAATTATTATAAT
45230264 TATGATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTATTATAAT
Found at i:45237708 original size:50 final size:50
Alignment explanation
Indices: 45237594--45237882 Score: 285
Period size: 50 Copynumber: 5.7 Consensus size: 50
45237584 GTGAGAACAC
* * * *
45237594 GTGTAGTACTATGTGCAGGCTACTATGTATTTAAGACAG-TT-TTAGGTCACGT
1 GTGTAGTACTAAGTGCAGGCTACTATG--TGT-A-CCAGATTGTTAGGTCACAT
* *
45237646 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATTGTTAGGTCGCAT
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTCACAT
* * * * * * *
45237696 GTGTCGTACTAAGTGCAGGCTACTATGCGTACCCGATAGCTTCGATCACGT
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTG-TTAGGTCACAT
* * * *
45237747 GTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGGTTAGGTCACAT
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTCACAT
* * * * **
45237797 GTGTAGTACTAAGTGCAGGCTTCTACGTGTACCAGATTATTTGGTCGTAT
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTCACAT
* * *
45237847 GTGTAGTACTAAGTGCAGGATACTATCTGTATCAGA
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
45237883 GAGCTTCGGT
Statistics
Matches: 197, Mismatches: 37, Indels: 8
0.81 0.15 0.03
Matches are distributed among these distances:
48 2 0.01
49 3 0.02
50 127 0.64
51 39 0.20
52 26 0.13
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (50 bp):
GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTAGGTCACAT
Found at i:45237829 original size:101 final size:101
Alignment explanation
Indices: 45237640--45237829 Score: 290
Period size: 101 Copynumber: 1.9 Consensus size: 101
45237630 CAGTTTTAGG
* * * * *
45237640 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATTGTTAGGTCGCATGTGTCGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCACATGTGTAGTAC
*
45237705 TAAGTGCAGGCTACTATGCGTACCCGATAGCTTCGA
66 TAAGTGCAGGCTACTACGCGTACCCGATAGCTTCGA
* *
45237741 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGGTTAGGTCACATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCACATGTGTAGTAC
* *
45237806 TAAGTGCAGGCTTCTACGTGTACC
66 TAAGTGCAGGCTACTACGCGTACC
45237830 AGATTATTTG
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 79 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGTTAGGTCACATGTGTAGTAC
TAAGTGCAGGCTACTACGCGTACCCGATAGCTTCGA
Found at i:45241940 original size:56 final size:56
Alignment explanation
Indices: 45241809--45241944 Score: 211
Period size: 56 Copynumber: 2.4 Consensus size: 56
45241799 TCCCAGACAA
* *
45241809 GGTCTTACTCGCACACATAAATCAGAATCACATATCGATGCCAACATATTAAACGT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACATATTAAACGT
* **
45241865 GGTCTTACTCGGACACATATATCGGAATCACATATCGATGCCAATGTATTAAACGT
1 GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACATATTAAACGT
45241921 GGTCTTAC-CTGCACACATATATCG
1 GGTCTTACTC-GCACACATATATCG
45241945 ATGCCATGGT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
55 1 0.01
56 72 0.99
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACATATTAAACGT
Found at i:45250445 original size:44 final size:44
Alignment explanation
Indices: 45250395--45250553 Score: 173
Period size: 43 Copynumber: 3.7 Consensus size: 44
45250385 TATGTGTTAT
*
45250395 CGTGTAAGACCATGCCTGGGACATTGGCATCGAT-TTGTGATTTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATT-TGATTTA
*
45250439 CGTGTAAGAGCATGTCTGGGACATTGGCATCG-TATTTGATTT-
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATTTGATTTA
* ** * * * *
45250481 TGTGTAAGACCCGGTATAGGATAGTGGCATCGATATTTGA-TTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGATATTTGATTTA
* * *
45250524 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCATGTCTGGGACATTGGCAT
45250554 TGTATGAGCT
Statistics
Matches: 93, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
42 26 0.28
43 35 0.38
44 32 0.34
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.31
Consensus pattern (44 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCGATATTTGATTTA
Found at i:45254252 original size:30 final size:30
Alignment explanation
Indices: 45254218--45254278 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
45254208 TCCTTAACTC
45254218 AAACTTTTACAAAATTACAATTTTGCCCCT
1 AAACTTTTACAAAATTACAATTTTGCCCCT
* * * * *
45254248 AAACTTTTTCATATTTATATTTTTGCCCCT
1 AAACTTTTACAAAATTACAATTTTGCCCCT
45254278 A
1 A
45254279 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.44
Consensus pattern (30 bp):
AAACTTTTACAAAATTACAATTTTGCCCCT
Found at i:45260127 original size:44 final size:44
Alignment explanation
Indices: 45260077--45260191 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
45260067 TATGTGTTAT
* *
45260077 CATGTAAGACCACGTCTGGGACATTGGCATTGATTTGTGAATTA
1 CATGTAAGACCACGTCTGGGACATTGGCATCGATTTGGGAATTA
* * * * *
45260121 CGTGTAAGATCACATCTAGGACATTGGCATCGATTTGGGATTTA
1 CATGTAAGACCACGTCTGGGACATTGGCATCGATTTGGGAATTA
* *
45260165 CATGTGAGACCATGTCTGGGACATTGG
1 CATGTAAGACCACGTCTGGGACATTGG
45260192 TGATAAACCG
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (44 bp):
CATGTAAGACCACGTCTGGGACATTGGCATCGATTTGGGAATTA
Found at i:45261633 original size:43 final size:42
Alignment explanation
Indices: 45261566--45261660 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 42
45261556 ACGTATCAAT
* * * * *
45261566 TGGCATCGTATTTGATTTCGTGTAAGACCATGTCTGGGACAG
1 TGGCATTGTATTTGATTACCTGTAAGACCACGTCTGAGACAG
*
45261608 TGGCATTGATATTTGATTACCTGTAAGACCACGTCTGAGACAT
1 TGGCATTG-TATTTGATTACCTGTAAGACCACGTCTGAGACAG
45261651 TGGCATTGTA
1 TGGCATTGTA
45261661 CGAGCTTATG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 9 0.20
43 37 0.80
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (42 bp):
TGGCATTGTATTTGATTACCTGTAAGACCACGTCTGAGACAG
Found at i:45278122 original size:56 final size:54
Alignment explanation
Indices: 45278026--45278182 Score: 163
Period size: 56 Copynumber: 2.8 Consensus size: 54
45278016 TTTGATGACA
* * * * *
45278026 TGATACATGCTAGGTTCGGGAGCTTGTGTTGCCCCGTTGAGAGGCAT-GTAATTATG
1 TGATACAAGCTAGGTCCGGGAGCTTATGTAGCCCTGTTGAGAGGCATGGT-A--ATG
* * *
45278082 TGGTACACGTTAGGTCCGGGAGCTTATGTAGCCCTGTTGAGAGGCATGGTAATG
1 TGATACAAGCTAGGTCCGGGAGCTTATGTAGCCCTGTTGAGAGGCATGGTAATG
* * *
45278136 TGATGCAAGCTAGGTCTGGGTGCTCATATGTAGCCCTGTTGAGAGGC
1 TGATACAAGCTAGGTCCGGGAGCT--TATGTAGCCCTGTTGAGAGGC
45278183 GTGCTATGTC
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
54 21 0.25
56 62 0.73
57 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (54 bp):
TGATACAAGCTAGGTCCGGGAGCTTATGTAGCCCTGTTGAGAGGCATGGTAATG
Found at i:45285458 original size:46 final size:46
Alignment explanation
Indices: 45285408--45285583 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
45285398 TGGTTGAGCA
45285408 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
45285454 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
45285499 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
45285547 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
45285584 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:45285564 original size:93 final size:93
Alignment explanation
Indices: 45285405--45285575 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
45285395 GGATGGTTGA
* *
45285405 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
45285470 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
45285498 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
45285563 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
45285576 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:45287023 original size:87 final size:85
Alignment explanation
Indices: 45286879--45287051 Score: 301
Period size: 87 Copynumber: 2.0 Consensus size: 85
45286869 GGCGTGGGGG
*
45286879 CGTTACATTTAGTGTTATCAAACAGGTTTAGTCATTCTCGGACTAACCTAGCATGTGTAAAAGTT
1 CGTTACATTTAGTGGTATCAAACAGGTTTAGTCATTCTCGGACTAACCTAGCATGTGTAAAAGTT
45286944 TAGCTATACATGCCACTGAT
66 TAGCTATACATGCCACTGAT
* *
45286964 CGTTACATTTAGTGGTATCAGAGCAGGTTTAGTCGGTTCTCGGACTAACCTAGCATGTGTAAAAG
1 CGTTACATTTAGTGGTATCA-AACAGGTTTAGTC-ATTCTCGGACTAACCTAGCATGTGTAAAAG
45287029 TTTAGCTATACATGCCACTGAT
64 TTTAGCTATACATGCCACTGAT
45287051 C
1 C
45287052 TGTGATAGTG
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
85 19 0.23
86 12 0.14
87 52 0.63
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (85 bp):
CGTTACATTTAGTGGTATCAAACAGGTTTAGTCATTCTCGGACTAACCTAGCATGTGTAAAAGTT
TAGCTATACATGCCACTGAT
Found at i:45296010 original size:24 final size:24
Alignment explanation
Indices: 45295980--45296025 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
45295970 ATGTATCGGC
* *
45295980 AAAAGCTGAAATGCCAAAAAGCCA
1 AAAAGCTAAAATACCAAAAAGCCA
*
45296004 AAAAGCTAAAATACCGAAAAGC
1 AAAAGCTAAAATACCAAAAAGC
45296026 TGAAAGTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.20, G:0.15, T:0.09
Consensus pattern (24 bp):
AAAAGCTAAAATACCAAAAAGCCA
Found at i:45296322 original size:28 final size:28
Alignment explanation
Indices: 45296241--45296326 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 28
45296231 GTGAGCATGA
* * **
45296241 ATATGAATGTGACTGTGCCTAACAGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
*
45296269 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGA-TTGGGCCTAATGGGCC
*
45296298 ATATGAATGTGATTGGGCTTAATGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
45296326 A
1 A
45296327 GATATAGGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 27 0.54
29 23 0.46
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:45307385 original size:46 final size:46
Alignment explanation
Indices: 45307332--45307504 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
45307322 TGATTGAGCA
*
45307332 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACG
* * * *
45307378 TCCGAACTCGTTGAGTTGAGTCCGAGTT--CGT-GAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAA--A--CG
* * * *
45307425 TCCGAACTCGTTGAGTCGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACG
* * *
45307471 CCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
45307505 GGGGCGAGTT
Statistics
Matches: 102, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
43 7 0.07
44 2 0.02
45 1 0.01
46 58 0.57
47 27 0.26
48 1 0.01
49 1 0.01
50 5 0.05
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACG
Found at i:45307488 original size:93 final size:93
Alignment explanation
Indices: 45307329--45307499 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
45307319 GGATGATTGA
* * *
45307329 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTCGAGTCCGAGTTCACTTATAGATGCAAACGCCCGAACTCGTTGAGT
*
45307394 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCAAGTTCGTGAGATGTAACTAG
* * * *
45307422 GCATCCGAACTCGTTGAGTCGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTCGAGTCCGAGTTCACTTATAGATGCAAACGCCCGAACTCGTTGAGT
45307487 TGAGTCCAAGTTC
66 TGAGTCCAAGTTC
45307500 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTCGAGTCCGAGTTCACTTATAGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCAAGTTCGTGAGATGTAACTAG
Found at i:45311448 original size:20 final size:20
Alignment explanation
Indices: 45311423--45311476 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
45311413 TTTCATGGGC
**
45311423 TTGGGCCGTTATGGGCCACG
1 TTGGGCCGAAATGGGCCACG
*
45311443 TTGGGCCGAAATGGGCCATG
1 TTGGGCCGAAATGGGCCACG
45311463 -TGGGCCG-AATGGGC
1 TTGGGCCGAAATGGGC
45311477 TCATGGGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 7 0.23
19 7 0.23
20 17 0.55
ACGTcount: A:0.15, C:0.22, G:0.43, T:0.20
Consensus pattern (20 bp):
TTGGGCCGAAATGGGCCACG
Found at i:45311751 original size:27 final size:27
Alignment explanation
Indices: 45311716--45311839 Score: 187
Period size: 27 Copynumber: 4.6 Consensus size: 27
45311706 CCCAAAAATA
*
45311716 GGTAAAATGACTGTAATGCCCTTGTAG
1 GGTAAAATGACCGTAATGCCCTTGTAG
*
45311743 GGTAAAATGACCGTAATACCCTTGTAG
1 GGTAAAATGACCGTAATGCCCTTGTAG
*
45311770 GGTAAAATGAACGTAATGCCC-TGTAG
1 GGTAAAATGACCGTAATGCCCTTGTAG
* *
45311796 GGTAAAATGACCGTAGTGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCTTGTAG
*
45311823 GGTAAAATGACCATAAT
1 GGTAAAATGACCGTAAT
45311840 ATCCCTATAC
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
26 24 0.27
27 64 0.73
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (27 bp):
GGTAAAATGACCGTAATGCCCTTGTAG
Found at i:45311810 original size:53 final size:53
Alignment explanation
Indices: 45311716--45311860 Score: 184
Period size: 53 Copynumber: 2.7 Consensus size: 53
45311706 CCCAAAAATA
*
45311716 GGTAAAATG-ACTGTAATGCCCTTGTAGGGTAAAATGACCGTAATACCCTTGTAG
1 GGTAAAATGAAC-GTAATGCCC-TGTAGGGTAAAATGACCGTAATACCCCTGTAG
* *
45311770 GGTAAAATGAACGTAATGCCCTGTAGGGTAAAATGACCGTAGTGCCCCTGTAG
1 GGTAAAATGAACGTAATGCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAG
* * * * *
45311823 GGTAAAATGACCATAATATCCCTATACGGTAAAATGAC
1 GGTAAAATGAACGTAAT-GCCCTGTAGGGTAAAATGAC
45311861 GATTATGACC
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
53 44 0.54
54 35 0.43
55 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (53 bp):
GGTAAAATGAACGTAATGCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAG
Found at i:45311845 original size:27 final size:26
Alignment explanation
Indices: 45311716--45311860 Score: 182
Period size: 27 Copynumber: 5.4 Consensus size: 26
45311706 CCCAAAAATA
*
45311716 GGTAAAATGACTGTAATGCCCTTGTAG
1 GGTAAAATGACCGTAATGCCC-TGTAG
*
45311743 GGTAAAATGACCGTAATACCCTTGTAG
1 GGTAAAATGACCGTAATGCCC-TGTAG
*
45311770 GGTAAAATGAACGTAATGCCCTGTAG
1 GGTAAAATGACCGTAATGCCCTGTAG
*
45311796 GGTAAAATGACCGTAGTGCCCCTGTAG
1 GGTAAAATGACCGTAATG-CCCTGTAG
* * * *
45311823 GGTAAAATGACCATAATATCCCTATAC
1 GGTAAAATGACCGTAAT-GCCCTGTAG
45311850 GGTAAAATGAC
1 GGTAAAATGAC
45311861 GATTATGACC
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
26 21 0.20
27 84 0.80
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (26 bp):
GGTAAAATGACCGTAATGCCCTGTAG
Found at i:45315925 original size:23 final size:23
Alignment explanation
Indices: 45315906--45315958 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
45315896 TTCAAAAAAT
*
45315906 AAATAAAACA-AAACTAAAAACAA
1 AAATAAAA-ATAAAATAAAAACAA
*
45315929 AAATAAAAATAAAATAAAAATAA
1 AAATAAAAATAAAATAAAAACAA
45315952 AAATAAA
1 AAATAAA
45315959 TGGACTCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (23 bp):
AAATAAAAATAAAATAAAAACAA
Found at i:45315942 original size:17 final size:17
Alignment explanation
Indices: 45315922--45315958 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
45315912 AACAAAACTA
45315922 AAAACAAAAATAAAAAT
1 AAAACAAAAATAAAAAT
*
45315939 AAAATAAAAATAAAAAT
1 AAAACAAAAATAAAAAT
45315956 AAA
1 AAA
45315959 TGGACTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAACAAAAATAAAAAT
Found at i:45315948 original size:6 final size:6
Alignment explanation
Indices: 45315900--45315958 Score: 66
Period size: 6 Copynumber: 9.5 Consensus size: 6
45315890 AAAGTCTTCA
* *
45315900 AAAAAT AAATAAA ACAAAACT AAAAAC AAAAAT AAAAAT -AAAAT AAAAAT
1 AAAAAT AAA-AAT A-AAAA-T AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
45315950 AAAAAT AAA
1 AAAAAT AAA
45315959 TGGACTCAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 5 0.11
6 28 0.62
7 9 0.20
8 3 0.07
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:45318807 original size:15 final size:15
Alignment explanation
Indices: 45318783--45318812 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45318773 CTAATGTATT
45318783 TTTTGAGGTTTCGGC
1 TTTTGAGGTTTCGGC
*
45318798 TTTTGTGGTTTCGGC
1 TTTTGAGGTTTCGGC
45318813 ACAAGTTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.13, G:0.33, T:0.50
Consensus pattern (15 bp):
TTTTGAGGTTTCGGC
Found at i:45319852 original size:20 final size:20
Alignment explanation
Indices: 45319806--45319844 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
45319796 CATGAAAAAC
45319806 ATCGTGGATACGATGCAGTA
1 ATCGTGGATACGATGCAGTA
45319826 ATCGTGGATACGATGCAGT
1 ATCGTGGATACGATGCAGT
45319845 TCTGGTGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (20 bp):
ATCGTGGATACGATGCAGTA
Found at i:45327264 original size:26 final size:27
Alignment explanation
Indices: 45327183--45327267 Score: 84
Period size: 30 Copynumber: 3.0 Consensus size: 27
45327173 TCAAACACAT
*
45327183 AATAATAAATAAATAAAGAATTAATAAA
1 AATAA-AAATAAATAAAGAATAAATAAA
*
45327211 AGATAAATAA-AAATAAAGAGAATGAAATAGA
1 A-ATAAA-AATAAAT-AA-AGAAT-AAATAAA
45327242 AATAAAAATAAATAAAGAA-AAATAAA
1 AATAAAAATAAATAAAGAATAAATAAA
45327268 GAAAAGCAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
26 6 0.12
28 10 0.21
29 12 0.25
30 14 0.29
31 6 0.12
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (27 bp):
AATAAAAATAAATAAAGAATAAATAAA
Found at i:45337589 original size:21 final size:21
Alignment explanation
Indices: 45337546--45337598 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
45337536 TGGGCAACAG
**
45337546 CATGGGCGTGTCCTATGGTCA
1 CATGGGCGTGTCCTATGACCA
45337567 CATGGGCGTGTCTCT-TGACCA
1 CATGGGCGTGTC-CTATGACCA
*
45337588 CACGGGCGTGT
1 CATGGGCGTGT
45337599 GTGCCCTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (21 bp):
CATGGGCGTGTCCTATGACCA
Found at i:45339834 original size:14 final size:15
Alignment explanation
Indices: 45339804--45339836 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
45339794 TGCCCCAAAT
45339804 TTGGGCCTAGAAGTA
1 TTGGGCCTAGAAGTA
*
45339819 TTGGGCCTTG-AGTA
1 TTGGGCCTAGAAGTA
45339833 TTGG
1 TTGG
45339837 TCTGTAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.18, C:0.12, G:0.36, T:0.33
Consensus pattern (15 bp):
TTGGGCCTAGAAGTA
Found at i:45341618 original size:28 final size:28
Alignment explanation
Indices: 45341565--45341630 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
45341555 GCATCTGATA
* * * *
45341565 CTGATTCT-ATATTGGGTTTAATCCCAC
1 CTGATTCTGTTATTGGGCTAAAGCCCAC
45341592 CTGATTCTGTTATTGGGCTAAAGCCCAC
1 CTGATTCTGTTATTGGGCTAAAGCCCAC
* *
45341620 ATGATACTGTT
1 CTGATTCTGTT
45341631 TCTGCGATGG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 8 0.25
28 24 0.75
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (28 bp):
CTGATTCTGTTATTGGGCTAAAGCCCAC
Found at i:45343225 original size:28 final size:28
Alignment explanation
Indices: 45343176--45343238 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
45343166 TCTAATACTA
*
45343176 ATTCTG-TATTGGACTTAAGCCCACCTG
1 ATTCTGTTATTGGACTTAAGCCCACATG
*
45343203 ATTCTGTTATTGGGC-TAAGGCCCACATG
1 ATTCTGTTATTGGACTTAA-GCCCACATG
*
45343231 ATACTGTT
1 ATTCTGTT
45343239 TCTGCGATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 9 0.29
28 22 0.71
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (28 bp):
ATTCTGTTATTGGACTTAAGCCCACATG
Found at i:45344284 original size:28 final size:28
Alignment explanation
Indices: 45344244--45344306 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
45344234 TCTGATACTT
*
45344244 ATTCTG-TATTGGGCTTAA-GCCCACCTG
1 ATTCTGTTATTGGGC-TAAGGCCCACATG
45344271 ATTCTGTTATTGGGCTAAGGCCCACATG
1 ATTCTGTTATTGGGCTAAGGCCCACATG
*
45344299 ATACTGTT
1 ATTCTGTT
45344307 TTTGTGATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (28 bp):
ATTCTGTTATTGGGCTAAGGCCCACATG
Found at i:45348929 original size:23 final size:21
Alignment explanation
Indices: 45348903--45348955 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
45348893 TAGCTCATTG
*
45348903 GAGCTTACCGATTCAATTCAAAA
1 GAGCTTACCG-TTCAACTC-AAA
* *
45348926 GAGCTTACTGTTCAACTCATA
1 GAGCTTACCGTTCAACTCAAA
45348947 GAGCTTACC
1 GAGCTTACC
45348956 ATTTTCAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 10 0.38
22 7 0.27
23 9 0.35
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (21 bp):
GAGCTTACCGTTCAACTCAAA
Found at i:45364144 original size:44 final size:43
Alignment explanation
Indices: 45364068--45364231 Score: 152
Period size: 43 Copynumber: 3.8 Consensus size: 43
45364058 ACATAGGATC
* * * *
45364068 CGATATGTATTTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATCTGTTTTCGTGTAAGACCATGTCTGGGACATTGGCAT
* *
45364111 CGACT-TCTGTTTTACGTGTAAGACCATGTCTGGGACATCGACAT
1 CGA-TATCTGTTTT-CGTGTAAGACCATGTCTGGGACATTGGCAT
* * * *
45364155 CG-TATCTGATTTCGTGTAAGACCTTGTCTGGGATAATGGCAT
1 CGATATCTGTTTTCGTGTAAGACCATGTCTGGGACATTGGCAT
* * * * * *
45364197 TGATGTTTGATTACATGTAAGACCATGTCTGGGAC
1 CGATATCTGTTTTCGTGTAAGACCATGTCTGGGAC
45364232 GCTTGCATTG
Statistics
Matches: 98, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
42 27 0.28
43 42 0.43
44 29 0.30
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (43 bp):
CGATATCTGTTTTCGTGTAAGACCATGTCTGGGACATTGGCAT
Found at i:45365669 original size:27 final size:27
Alignment explanation
Indices: 45365572--45365670 Score: 76
Period size: 27 Copynumber: 3.7 Consensus size: 27
45365562 TTAGTTTACC
* *
45365572 AAATTACTGAAATACCCTCAACTTGTA
1 AAATTACTGAAATACCCTCAATTTATA
* * * *
45365599 AAATTACTGAAGTACTAC-CGATTTACA
1 AAATTACTGAAATAC-CCTCAATTTATA
* * **
45365626 GAATTACCG-TTTCACCCTCAATTTATA
1 AAATTACTGAAAT-ACCCTCAATTTATA
45365653 AAATTACTGAAATACCCT
1 AAATTACTGAAATACCCT
45365671 TGTAGGTAGA
Statistics
Matches: 51, Mismatches: 17, Indels: 8
0.67 0.22 0.11
Matches are distributed among these distances:
26 2 0.04
27 47 0.92
28 2 0.04
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCAATTTATA
Found at i:45365686 original size:26 final size:26
Alignment explanation
Indices: 45365654--45365767 Score: 129
Period size: 27 Copynumber: 4.3 Consensus size: 26
45365644 CAATTTATAA
* *
45365654 AATTACTGAAATACCCTTGTAGGTAG
1 AATTACCGAAATACCCTTATAGGTAG
* *
45365680 AGTTACTGAAATACCCTTATAAGGTAG
1 AATTACCGAAATACCCTTAT-AGGTAG
* *
45365707 AAATACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCTTATA-GGTAG
* *
45365734 AATTACCGAGATACCCTTATAGGATAA
1 AATTACCGAAATACCCTTATAGG-TAG
45365761 AATTACC
1 AATTACC
45365768 ATTTTGCCCC
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
26 21 0.28
27 54 0.72
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (26 bp):
AATTACCGAAATACCCTTATAGGTAG
Found at i:45366207 original size:22 final size:22
Alignment explanation
Indices: 45366155--45366219 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
45366145 GCCAATTATT
* *
45366155 CTGATTATGGTTTTGCGCCAAC
1 CTGATTATGGTTCTGTGCCAAC
* *
45366177 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGTTCTGTGCCAAC
*
45366199 CTGATTATGGTTGTGTGCCAA
1 CTGATTATGGTTCTGTGCCAA
45366220 ACGTATTTGC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
CTGATTATGGTTCTGTGCCAAC
Found at i:45366408 original size:27 final size:26
Alignment explanation
Indices: 45366378--45366485 Score: 117
Period size: 27 Copynumber: 4.0 Consensus size: 26
45366368 ATTCTGTTAA
* *
45366378 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTG-TTCTG
45366405 GTGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTATGCCAC-AATATCTGTTCTG
* *
45366432 GTGGCTCTGCCACAATATCTATATCTG
1 GTGGCTATGCCACAATATCTGT-TCTG
* * * *
45366459 ATGACTCTGTCACAATATCTGTTCTG
1 GTGGCTATGCCACAATATCTGTTCTG
45366485 G
1 G
45366486 CAGCCATGCT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
26 12 0.17
27 51 0.73
28 7 0.10
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.37
Consensus pattern (26 bp):
GTGGCTATGCCACAATATCTGTTCTG
Found at i:45366436 original size:54 final size:53
Alignment explanation
Indices: 45366378--45366485 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 53
45366368 ATTCTGTTAA
* * * * * *
45366378 GTGGCTTTGCCACATTATCTGTTTCTGGTGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTCTGCCACAATATCTATATCTGATGACTATGCCAC-AATATCTGTTCTG
* *
45366432 GTGGCTCTGCCACAATATCTATATCTGATGACTCTGTCACAATATCTGTTCTG
1 GTGGCTCTGCCACAATATCTATATCTGATGACTATGCCACAATATCTGTTCTG
45366485 G
1 G
45366486 CAGCCATGCT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
53 14 0.30
54 32 0.70
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.37
Consensus pattern (53 bp):
GTGGCTCTGCCACAATATCTATATCTGATGACTATGCCACAATATCTGTTCTG
Found at i:45366611 original size:6 final size:6
Alignment explanation
Indices: 45366602--45366714 Score: 54
Period size: 6 Copynumber: 18.3 Consensus size: 6
45366592 TTGCATTCAC
* * * * *
45366602 ATTCTG ATTCTG ATTCT- ATTACCTG ATACCG ATTCTA ATTCTG -TCACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG
* * * *
45366652 ATTTTG ATTCTG ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTC ATTTTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
45366701 ATTCT- AGTTCTG AT
1 ATTCTG A-TTCTG AT
45366715 AATGTTTCTT
Statistics
Matches: 78, Mismatches: 18, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
5 6 0.08
6 60 0.77
7 8 0.10
8 4 0.05
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.47
Consensus pattern (6 bp):
ATTCTG
Found at i:45366635 original size:25 final size:25
Alignment explanation
Indices: 45366602--45366693 Score: 121
Period size: 25 Copynumber: 3.7 Consensus size: 25
45366592 TTGCATTCAC
* *
45366602 ATTCTGATTCTGATTCTATTACCTG
1 ATTCTGATTCTGATTCTGTCACCTG
* * * *
45366627 ATACCGATTCTAATTCTGTCACCTA
1 ATTCTGATTCTGATTCTGTCACCTG
*
45366652 ATTTTGATTCTGATTCTGTCACCTG
1 ATTCTGATTCTGATTCTGTCACCTG
45366677 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
45366694 CATTTTGATT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.46
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTGTCACCTG
Found at i:45373910 original size:40 final size:40
Alignment explanation
Indices: 45373855--45374078 Score: 306
Period size: 40 Copynumber: 5.5 Consensus size: 40
45373845 TATTCGGATG
45373855 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
45373895 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
45373938 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
45373978 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
45374018 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
45374058 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
45374079 ATACTTGGGT
Statistics
Matches: 165, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
39 13 0.08
40 114 0.69
41 1 0.01
43 37 0.22
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:45373998 original size:83 final size:80
Alignment explanation
Indices: 45373859--45374078 Score: 302
Period size: 83 Copynumber: 2.7 Consensus size: 80
45373849 CGGATGATAT
* **
45373859 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
45373924 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
*
45373942 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
45374007 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* * *
45374022 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
45374079 ATACTTGGGT
Statistics
Matches: 127, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
79 16 0.13
80 45 0.35
81 2 0.02
83 64 0.50
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:45378165 original size:287 final size:287
Alignment explanation
Indices: 45377660--45378221 Score: 1090
Period size: 287 Copynumber: 2.0 Consensus size: 287
45377650 CATATGAGTT
*
45377660 GTATGTTAAGAGATATTTAGGCTTTCGTGAAACAGGGTCAGAACGGTTTCTGGATTCCCTGTTCC
1 GTATGTTAAGAGATATTTAGGCTTTCGTGAAACAGGGCCAGAACGGTTTCTGGATTCCCTGTTCC
45377725 GACTTTGGAAATTCATTATAAATTAACCAGAGATAATTAGGAGTCATGCCATATATGTATAGATT
66 GACTTTGGAAATTCATTATAAATTAACCAGAGATAATTAGGAGTCATGCCATATATGTATAGATT
45377790 TCTCTCTGAGTCTAGTTTCTATAGAAACAAACGGTATCAGTATTGAAGCTCTGTGAAGGGAGATA
131 TCTCTCTGAGTCTAGTTTCTATAGAAACAAACGGTATCAGTATTGAAGCTCTGTGAAGGGAGATA
45377855 TCCAAATCGTAATGCATGAAGGTCAGTGTAGTCGCACCCTGTAACAGGGGAGAATTTAACTAATA
196 TCCAAATCGTAATGCATGAAGGTCAGTGTAGTCGCACCCTGTAACAGGGGAGAATTTAACTAATA
45377920 AACTGTACTAATTGGATCATATGGACA
261 AACTGTACTAATTGGATCATATGGACA
*
45377947 GTATGTTAAGAGATATTTAGG-TTCTCGTGAGACAGGGCCAGAACGGTTTCTGGATTCCCTGTTC
1 GTATGTTAAGAGATATTTAGGCTT-TCGTGAAACAGGGCCAGAACGGTTTCTGGATTCCCTGTTC
45378011 CGACTTTGGAAATTCATTATAAATTAACCAGAGATAATTAGGAGTCATGCCATATATGTATAGAT
65 CGACTTTGGAAATTCATTATAAATTAACCAGAGATAATTAGGAGTCATGCCATATATGTATAGAT
45378076 TTCTCTCTGAGTCTAGTTTCTATAGAAACAAACGGTATCAGTATTGAAGCTCTGTGAAGGGAGAT
130 TTCTCTCTGAGTCTAGTTTCTATAGAAACAAACGGTATCAGTATTGAAGCTCTGTGAAGGGAGAT
45378141 ATCCAAATCGTAATGCATGAAGGTCAGTGTAGTCGCACCCTGTAACAGGGGAGAATTTAACTAAT
195 ATCCAAATCGTAATGCATGAAGGTCAGTGTAGTCGCACCCTGTAACAGGGGAGAATTTAACTAAT
45378206 AAACTGTACTAATTGG
260 AAACTGTACTAATTGG
45378222 CCCAACCAAA
Statistics
Matches: 272, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
286 2 0.01
287 270 0.99
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (287 bp):
GTATGTTAAGAGATATTTAGGCTTTCGTGAAACAGGGCCAGAACGGTTTCTGGATTCCCTGTTCC
GACTTTGGAAATTCATTATAAATTAACCAGAGATAATTAGGAGTCATGCCATATATGTATAGATT
TCTCTCTGAGTCTAGTTTCTATAGAAACAAACGGTATCAGTATTGAAGCTCTGTGAAGGGAGATA
TCCAAATCGTAATGCATGAAGGTCAGTGTAGTCGCACCCTGTAACAGGGGAGAATTTAACTAATA
AACTGTACTAATTGGATCATATGGACA
Found at i:45384940 original size:229 final size:229
Alignment explanation
Indices: 45384539--45384983 Score: 784
Period size: 229 Copynumber: 1.9 Consensus size: 229
45384529 CATATGAGTT
*
45384539 GTATGTTAAGAGATATTTAGGCTTTCGTGAAACAGGGTCAGAACGGTTTCTGGATTCCCTGTTCC
1 GTATGTTAAGAGATATTTAGGCTTTCGTGAAACAGGGCCAGAACGGTTTCTGGATTCCCTGTTCC
* *
45384604 GACTTTGGAAATTCATTATAAATTAACCAGAGATAATTAGGAGTCATGCCATATATGTATAGATT
66 AACTTTGGAAATTCATTAGAAATTAACCAGAGATAATTAGGAGTCATGCCATATATGTATAGATT
* *
45384669 TCTCTCTGAGTCTAGTTTCTATAGAAACAAACGGTATCAGTATTGAAGCTCTGTGAAGGGAGATA
131 CCTCTCTGAGTCTAGTTTCTATAGAAACAAACGGCATCAGTATTGAAGCTCTGTGAAGGGAGATA
45384734 TCCAAATCGTAATGCATGAAGAATTATATGGACA
196 TCCAAATCGTAATGCATGAAGAATTATATGGACA
* * *
45384768 GTATGTTAAGAGATA-TTCGGGTTCTCGTGAGACAGGGCCAGAACGGTTTCTGGATTCCCTGTTC
1 GTATGTTAAGAGATATTTAGGCTT-TCGTGAAACAGGGCCAGAACGGTTTCTGGATTCCCTGTTC
*
45384832 CAACTTTGGAAATTCATTAGAAATTAACCAGAGATAATTAGGAGTCATTCCATATATGTATAGAT
65 CAACTTTGGAAATTCATTAGAAATTAACCAGAGATAATTAGGAGTCATGCCATATATGTATAGAT
*
45384897 TCCTCTCTGAGTCTAGTTTCTATAGAAACAAACGGCATCAGTATTGAAGCTCTGTGCAGGGAGAT
130 TCCTCTCTGAGTCTAGTTTCTATAGAAACAAACGGCATCAGTATTGAAGCTCTGTGAAGGGAGAT
45384962 ATCCAAATCGTAATGCATGAAG
195 ATCCAAATCGTAATGCATGAAG
45384984 GTCAGTGTAG
Statistics
Matches: 205, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
228 6 0.03
229 199 0.97
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (229 bp):
GTATGTTAAGAGATATTTAGGCTTTCGTGAAACAGGGCCAGAACGGTTTCTGGATTCCCTGTTCC
AACTTTGGAAATTCATTAGAAATTAACCAGAGATAATTAGGAGTCATGCCATATATGTATAGATT
CCTCTCTGAGTCTAGTTTCTATAGAAACAAACGGCATCAGTATTGAAGCTCTGTGAAGGGAGATA
TCCAAATCGTAATGCATGAAGAATTATATGGACA
Found at i:45385101 original size:39 final size:39
Alignment explanation
Indices: 45385047--45385125 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
45385037 AATTGGCCCA
*
45385047 ACCAAAAATTCTAGAAAAAAATATATAGATGGGCATATG
1 ACCAAAAATTCTAGAAAAAAATATATAGATGGGAATATG
*
45385086 ACCAAAAATTCTAGAAAAAAATATGTAGATGGGAATATG
1 ACCAAAAATTCTAGAAAAAAATATATAGATGGGAATATG
45385125 A
1 A
45385126 GTCTAGTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.52, C:0.09, G:0.16, T:0.23
Consensus pattern (39 bp):
ACCAAAAATTCTAGAAAAAAATATATAGATGGGAATATG
Found at i:45389935 original size:37 final size:37
Alignment explanation
Indices: 45389885--45389963 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
45389875 TTATTACGAA
* *
45389885 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
45389922 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
45389959 GTCTT
1 GTCTT
45389964 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:45390160 original size:47 final size:47
Alignment explanation
Indices: 45390082--45390304 Score: 304
Period size: 47 Copynumber: 4.7 Consensus size: 47
45390072 CCCTTCGGGA
* * * * * * *
45390082 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45390129 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45390176 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45390223 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
45390270 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
45390305 AGAATCCTAA
Statistics
Matches: 157, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
46 1 0.01
47 156 0.99
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:45393944 original size:42 final size:46
Alignment explanation
Indices: 45393847--45394032 Score: 158
Period size: 42 Copynumber: 4.2 Consensus size: 46
45393837 AGTCTCACGT
* * * * * *
45393847 CAATGTCATGTCCCAAACATGGTCTTATACGAAATCACGTATCAATG
1 CAATGTCATATCCCAGATATGGTCTTACACGAAATCTCATATC-ATG
* *
45393894 C--TG-C--ATCCCAGACACGGTCTTACACGAAATCTCATA-C-TG
1 CAATGTCATATCCCAGATATGGTCTTACACGAAATCTCATATCATG
*
45393933 -AA-GTCATATCCCAGATATGGTCTTACACGTAATCTCATATCGATG
1 CAATGTCATATCCCAGATATGGTCTTACACGAAATCTCATATC-ATG
*
45393978 CTAATGTCATATCCCAGATATGGTCTTACAC-AGGATCTCATATCGATG
1 C-AATGTCATATCCCAGATATGGTCTTACACGA-AATCTCATATC-ATG
*
45394026 CCATGTC
1 CAATGTC
45394033 TCAGTCATGG
Statistics
Matches: 115, Mismatches: 12, Indels: 24
0.76 0.08 0.16
Matches are distributed among these distances:
39 3 0.03
40 1 0.01
41 1 0.01
42 55 0.48
43 1 0.01
44 1 0.01
45 4 0.03
47 8 0.07
48 41 0.36
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (46 bp):
CAATGTCATATCCCAGATATGGTCTTACACGAAATCTCATATCATG
Found at i:45393991 original size:48 final size:45
Alignment explanation
Indices: 45393898--45394026 Score: 158
Period size: 48 Copynumber: 2.8 Consensus size: 45
45393888 TCAATGCTGC
* *
45393898 ATCCCAGACACGGTCTTACACGAAATCTCATA-C--TG-AAGTCAT
1 ATCCCAGATATGGTCTTACACG-AATCTCATATCGATGCAAGTCAT
45393940 ATCCCAGATATGGTCTTACACGTAATCTCATATCGATGCTAATGTCAT
1 ATCCCAGATATGGTCTTACACG-AATCTCATATCGATGC-AA-GTCAT
*
45393988 ATCCCAGATATGGTCTTACACAGGATCTCATATCGATGC
1 ATCCCAGATATGGTCTTACAC-GAATCTCATATCGATGC
45394027 CATGTCTCAG
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
42 29 0.38
43 1 0.01
45 2 0.03
47 2 0.03
48 41 0.54
49 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (45 bp):
ATCCCAGATATGGTCTTACACGAATCTCATATCGATGCAAGTCAT
Found at i:45394101 original size:37 final size:37
Alignment explanation
Indices: 45394039--45394162 Score: 189
Period size: 37 Copynumber: 3.4 Consensus size: 37
45394029 TGTCTCAGTC
*
45394039 ATGGTCTTACACGT-ATCACAATGCCATAGCCCAGCT
1 ATGGTCTTACACGTCATCACGATGCCATAGCCCAGCT
*
45394075 ATGGTCTTACATGTCATCACGATGCCATAGCCCAGCT
1 ATGGTCTTACACGTCATCACGATGCCATAGCCCAGCT
* *
45394112 ATGGTCTTACACG-CTATTACGATGCCATAGCCCAGTT
1 ATGGTCTTACACGTC-ATCACGATGCCATAGCCCAGCT
45394149 ATGGTCTTACACGT
1 ATGGTCTTACACGT
45394163 ACTACATGTA
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
36 14 0.17
37 66 0.82
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (37 bp):
ATGGTCTTACACGTCATCACGATGCCATAGCCCAGCT
Found at i:45394409 original size:19 final size:19
Alignment explanation
Indices: 45394381--45394422 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
45394371 ATACTGATTA
45394381 TACA-TTATTCGATAAGTG
1 TACATTTATTCGATAAGTG
45394399 TACATTTATTCGATAAGTG
1 TACATTTATTCGATAAGTG
45394418 TACAT
1 TACAT
45394423 AAACACACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (19 bp):
TACATTTATTCGATAAGTG
Found at i:45398313 original size:20 final size:20
Alignment explanation
Indices: 45398263--45398351 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
45398253 CGGGGCTCCA
* *
45398263 AAGTGCAAACAAGGGCA-CA
1 AAGTGCAAACAGGGGCACCG
45398282 AATGTGCAAACAGGGGCACCG
1 AA-GTGCAAACAGGGGCACCG
* ** * *
45398303 TAGTGTGAACAGAGACACCG
1 AAGTGCAAACAGGGGCACCG
*
45398323 AAGTGCAAACAGGGGCATCG
1 AAGTGCAAACAGGGGCACCG
45398343 AAGTGCAAA
1 AAGTGCAAA
45398352 TCCCGTACAA
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
19 2 0.04
20 51 0.93
21 2 0.04
ACGTcount: A:0.39, C:0.20, G:0.30, T:0.10
Consensus pattern (20 bp):
AAGTGCAAACAGGGGCACCG
Found at i:45399465 original size:4 final size:4
Alignment explanation
Indices: 45399451--45399487 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
45399441 GAATGAATCA
*
45399451 TCTT TCCT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
45399488 TTTATTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:45403731 original size:29 final size:29
Alignment explanation
Indices: 45403698--45403754 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
45403688 TTTACAACTC
45403698 ACATAACTGATAGCTCATACTTGACAGAG
1 ACATAACTGATAGCTCATACTTGACAGAG
45403727 ACATAACTGATAGCTCATACTTGACAGA
1 ACATAACTGATAGCTCATACTTGACAGA
45403755 CTTATTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.25
Consensus pattern (29 bp):
ACATAACTGATAGCTCATACTTGACAGAG
Found at i:45403876 original size:28 final size:29
Alignment explanation
Indices: 45403814--45403886 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
45403804 TCTGACAGAT
* * *
45403814 TTCCACTTATAATATAGTTCCAATGAACG
1 TTCCACATATAAGATAGTCCCAATGAACG
**
45403843 TT-CACATATAAGATAGTCCCAATGGTC-
1 TTCCACATATAAGATAGTCCCAATGAACG
45403870 TTCCACATATAAGATAG
1 TTCCACATATAAGATAG
45403887 CCTTGACGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 2 0.05
28 34 0.89
29 2 0.05
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.32
Consensus pattern (29 bp):
TTCCACATATAAGATAGTCCCAATGAACG
Found at i:45409995 original size:36 final size:36
Alignment explanation
Indices: 45409944--45410012 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
45409934 TGTGTTTTAG
*
45409944 AATTCGAAGGTAGTTGGGAGAAATACCGTTGGTCGA
1 AATTCGAAGGCAGTTGGGAGAAATACCGTTGGTCGA
45409980 AATTCGAAGGCAGTTGGGAGAAATACCGTTGGT
1 AATTCGAAGGCAGTTGGGAGAAATACCGTTGGT
45410013 TGAATTTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (36 bp):
AATTCGAAGGCAGTTGGGAGAAATACCGTTGGTCGA
Found at i:45410449 original size:36 final size:36
Alignment explanation
Indices: 45410402--45410476 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
45410392 TGCCATCAAA
45410402 GTTAGAAAGGATCCACAATGTATTTCATGTGTCGAT
1 GTTAGAAAGGATCCACAATGTATTTCATGTGTCGAT
*
45410438 GTTAGAAAGGATCCACACTGTATTTCATGTGTCGAT
1 GTTAGAAAGGATCCACAATGTATTTCATGTGTCGAT
45410474 GTT
1 GTT
45410477 GCAACGATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (36 bp):
GTTAGAAAGGATCCACAATGTATTTCATGTGTCGAT
Found at i:45415385 original size:45 final size:45
Alignment explanation
Indices: 45415321--45415578 Score: 257
Period size: 45 Copynumber: 5.9 Consensus size: 45
45415311 TAGGATTCTG
* * * *
45415321 ATATGTTTTTTCGTGTAAGACCCCGTCTAGGACGTTGGCATCAAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
*
45415366 ATATGTGTTTTGGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
*
45415411 ATATGTG-TTTCGTGTAAGACCACGTTTGGGACGTTGGCATCGAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* * * * * *
45415455 ATATGTGGTTACGTGTAAGACCATGTCTGGGACATCGACAT---T
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* *
45415497 GTAT-TGATTT-GTGTAAGACC-CTGTCTGGGACAG-TGGCATCG--
1 ATATGTGTTTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT
* * ** *
45415538 ATATGAGATAGCATGTAAGACCACGTCTGGGACGTTGGCAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
45415579 TGTTCATATA
Statistics
Matches: 179, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
40 23 0.13
41 7 0.04
42 8 0.04
43 24 0.13
44 43 0.24
45 74 0.41
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (45 bp):
ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
Found at i:45415483 original size:89 final size:85
Alignment explanation
Indices: 45415329--45415578 Score: 258
Period size: 89 Copynumber: 2.9 Consensus size: 85
45415319 TGATATGTTT
* * * **
45415329 TTTCGTGTAAGACCCCGTCTAGGACGTTGGCATCAATATATGTGTTTTGGTGTAAGACCACGTCT
1 TTTCGTGTAAGA-CCCGTCTGGGACGTTGGCATCGATATATGTGGTTACGTGTAAGACCACGTCT
*
45415394 GGGACGTTGGCATCGATATATGTG
65 GGGACGTTGGCATCG-TAT-TG-A
* *
45415418 TTTCGTGTAAGACCACGTTTGGGACGTTGGCATCGATATATGTGGTTACGTGTAAGACCATGTCT
1 TTTCGTGTAAGACC-CGTCTGGGACGTTGGCATCGATATATGTGGTTACGTGTAAGACCACGTCT
* * * *
45415483 GGGACATCGACATTGTATTGA
65 GGGACGTTGGCATCGTATTGA
* * *
45415504 TTT-GTGTAAGACCCTGTCTGGGACAG-TGGCATCG--ATATG-AGATAGCATGTAAGACCACGT
1 TTTCGTGTAAGACCC-GTCTGGGAC-GTTGGCATCGATATATGTGGTTA-CGTGTAAGACCACGT
45415564 CTGGGACGTTGGCAT
63 CTGGGACGTTGGCAT
45415579 TGTTCATATA
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
82 3 0.02
83 30 0.22
84 1 0.01
85 26 0.19
86 4 0.03
87 2 0.01
88 5 0.04
89 66 0.48
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (85 bp):
TTTCGTGTAAGACCCGTCTGGGACGTTGGCATCGATATATGTGGTTACGTGTAAGACCACGTCTG
GGACGTTGGCATCGTATTGA
Found at i:45424396 original size:10 final size:11
Alignment explanation
Indices: 45424365--45424397 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
45424355 CGGCTCGCCC
45424365 ATATTAATTTT
1 ATATTAATTTT
*
45424376 ATATTATTTTT
1 ATATTAATTTT
45424387 ATA-TAATTTT
1 ATATTAATTTT
45424397 A
1 A
45424398 AAATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:45427236 original size:40 final size:40
Alignment explanation
Indices: 45427152--45427227 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
45427142 TATTCGAATG
*
45427152 ATATCCGGGCTAAGTACCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGTACCGAAGGCATTTATGCGAGTGACT
* *
45427192 ATATCTGGGCTAAG-ACCCGAAGGCATTTGTGCGAGT
1 ATATCCGGGCTAAGTA-CCGAAGGCATTTATGCGAGT
45427228 TCTTATATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 1 0.03
40 31 0.97
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTACCGAAGGCATTTATGCGAGTGACT
Found at i:45429490 original size:22 final size:22
Alignment explanation
Indices: 45429464--45429520 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
45429454 TCTACCATCA
* *
45429464 ATGTCATGACACCAGTCATGTG
1 ATGTCATGACACCAGCCATGGG
*
45429486 ATGTC-TCGACACTAGCCATGGG
1 ATGTCAT-GACACCAGCCATGGG
*
45429508 ATGTCACGACACC
1 ATGTCATGACACC
45429521 CAACCTAGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (22 bp):
ATGTCATGACACCAGCCATGGG
Found at i:45432052 original size:29 final size:29
Alignment explanation
Indices: 45432017--45432090 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
45432007 GTTGTGAGAT
* *
45432017 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
45432046 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
45432075 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
45432091 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:45435363 original size:33 final size:33
Alignment explanation
Indices: 45435321--45435387 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
45435311 TGTTATTGCC
45435321 TTAATTGATCCAGGGTCTACTCATTCCTATGTA
1 TTAATTGATCCAGGGTCTACTCATTCCTATGTA
45435354 TTAATTGATCCAGGGTCTACTCATTCCTATGTA
1 TTAATTGATCCAGGGTCTACTCATTCCTATGTA
45435387 T
1 T
45435388 GCATGAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (33 bp):
TTAATTGATCCAGGGTCTACTCATTCCTATGTA
Found at i:45442921 original size:19 final size:20
Alignment explanation
Indices: 45442886--45442926 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
45442876 TTATTTTTAT
* *
45442886 AAATTTTTAAAACAATATTA
1 AAATTTATAAAACAATACTA
45442906 AAATTTATAAAA-AATACTA
1 AAATTTATAAAACAATACTA
45442925 AA
1 AA
45442927 TAAATTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTTATAAAACAATACTA
Found at i:45448481 original size:19 final size:19
Alignment explanation
Indices: 45448457--45448494 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
45448447 CCCTATTTTC
45448457 CCTTCTCTTGTCTTTCTAT
1 CCTTCTCTTGTCTTTCTAT
45448476 CCTTCTCTTGTCTTTCTAT
1 CCTTCTCTTGTCTTTCTAT
45448495 GCCAAAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.05, C:0.32, G:0.05, T:0.58
Consensus pattern (19 bp):
CCTTCTCTTGTCTTTCTAT
Found at i:45450783 original size:29 final size:29
Alignment explanation
Indices: 45450730--45450785 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
45450720 TAACATCATT
* * *
45450730 TTATATTTATCTATTACATACATAAATGA
1 TTATATTTATCTAATACAAAAATAAATGA
*
45450759 TTATATTTATCTAATATAAAAATAAAT
1 TTATATTTATCTAATACAAAAATAAAT
45450786 TGATGTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (29 bp):
TTATATTTATCTAATACAAAAATAAATGA
Found at i:45450860 original size:31 final size:30
Alignment explanation
Indices: 45450815--45450909 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 30
45450805 AGTATGTATG
*
45450815 ATTAAATCAAAATTAAAGTTTTAAGTATACA
1 ATTAAA-CCAAATTAAAGTTTTAAGTATACA
* * * *
45450846 TTTAAACCACAATTAAAGTTTCACGTATATA
1 ATTAAACCA-AATTAAAGTTTTAAGTATACA
* * *
45450877 ATTACACCAAATTAAA-ATTTATGTATACA
1 ATTAAACCAAATTAAAGTTTTAAGTATACA
45450906 ATTA
1 ATTA
45450910 CACTTAAATC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
29 13 0.25
30 9 0.17
31 30 0.58
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (30 bp):
ATTAAACCAAATTAAAGTTTTAAGTATACA
Found at i:45458782 original size:25 final size:25
Alignment explanation
Indices: 45458748--45458797 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
45458738 ATATACTATG
45458748 TTCATTTCCTAAGCTACCCCTTTAA
1 TTCATTTCCTAAGCTACCCCTTTAA
45458773 TTCATTTCCTAAGCTACCCCTTTAA
1 TTCATTTCCTAAGCTACCCCTTTAA
45458798 ACCTCTCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.32, G:0.04, T:0.40
Consensus pattern (25 bp):
TTCATTTCCTAAGCTACCCCTTTAA
Found at i:45460382 original size:19 final size:19
Alignment explanation
Indices: 45460358--45460414 Score: 114
Period size: 19 Copynumber: 3.0 Consensus size: 19
45460348 AGGTACACAG
45460358 TAAACATTATAGGTTAGGT
1 TAAACATTATAGGTTAGGT
45460377 TAAACATTATAGGTTAGGT
1 TAAACATTATAGGTTAGGT
45460396 TAAACATTATAGGTTAGGT
1 TAAACATTATAGGTTAGGT
45460415 CTATTTACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (19 bp):
TAAACATTATAGGTTAGGT
Found at i:45469815 original size:38 final size:38
Alignment explanation
Indices: 45469689--45469815 Score: 182
Period size: 38 Copynumber: 3.3 Consensus size: 38
45469679 AACCGTACTA
*
45469689 TTATTCAGGCTTAGTGCCTAGCAGGTTTAGTGCTGGTG
1 TTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCTGGTG
* *
45469727 TTATTTAGGCTTAGTGCCTAGCAGGCTTAGTACTGGTG
1 TTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCTGGTG
* * * *
45469765 TTTTTCAGGCTTAGTGCCTACCAGGCTTAGTGCCGATG
1 TTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCTGGTG
*
45469803 TTATTCAAGCTTA
1 TTATTCAGGCTTA
45469816 TTTCTAGTGT
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 78 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (38 bp):
TTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCTGGTG
Found at i:45471721 original size:75 final size:75
Alignment explanation
Indices: 45471594--45471744 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 75
45471584 CCCCTTTTTA
* * *
45471594 ACACTTATACTTAATGAATATTAAAAACAAAGTAAAACATAATTATGTTCTCATAAATGATTTTT
1 ACACTTATACTTAATGAATATTAAAAACAAAGTAAAACATAATTATGCTCTCATAAATAATCTTT
45471659 GCAAAAACTC
66 GCAAAAACTC
45471669 ACACTTATACTTAATGAATATTAAAAACAAAGTAAAACATAATTATGCTCTCATAAATAATCTTT
1 ACACTTATACTTAATGAATATTAAAAACAAAGTAAAACATAATTATGCTCTCATAAATAATCTTT
45471734 GCAAAAACTC
66 GCAAAAACTC
45471744 A
1 A
45471745 TTGCATGGAA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.32
Consensus pattern (75 bp):
ACACTTATACTTAATGAATATTAAAAACAAAGTAAAACATAATTATGCTCTCATAAATAATCTTT
GCAAAAACTC
Found at i:45480373 original size:22 final size:22
Alignment explanation
Indices: 45480348--45480391 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
45480338 GGTAAGAAAA
*
45480348 TTATTTAATTGAAAAAATTAAT
1 TTATCTAATTGAAAAAATTAAT
**
45480370 TTATCTAATTGAATTAATTAAT
1 TTATCTAATTGAAAAAATTAAT
45480392 AAATAATGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (22 bp):
TTATCTAATTGAAAAAATTAAT
Found at i:45483683 original size:27 final size:26
Alignment explanation
Indices: 45483646--45483757 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
45483636 AGCATGGCTG
*
45483646 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGACAGAGCCA
* *
45483672 CCAGATACAGATCATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGACAGAGCCA
45483700 CCAGAACAGATATATGTGACAGAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCA
* * * *
45483727 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCA
45483754 CCAG
1 CCAG
45483758 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.07
27 52 0.70
28 17 0.23
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAGCCA
Found at i:45483705 original size:54 final size:54
Alignment explanation
Indices: 45483646--45483757 Score: 165
Period size: 54 Copynumber: 2.1 Consensus size: 54
45483636 AGCATGGCTG
*
45483646 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATCA-TCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGAT-ATTCGTGGCAGAGCCA
* *
45483700 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATATTCGTGGCAGAGCCA
45483754 CCAG
1 CCAG
45483758 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
53 1 0.02
54 33 0.62
55 19 0.36
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATATTCGTGGCAGAGCCA
Found at i:45484790 original size:49 final size:49
Alignment explanation
Indices: 45484718--45484813 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
45484708 TAATTTATTT
*
45484718 AGCTTCTAATTCATCTCCCACAATTTATGGTGATTTTCCAAAGTCACAC
1 AGCTTCTAATTCATCTCCCACAATTTATGGTAATTTTCCAAAGTCACAC
45484767 AGCTTCTAATTCATCTCCCACAATTTATGGTAATTTTCCAAAGTCAC
1 AGCTTCTAATTCATCTCCCACAATTTATGGTAATTTTCCAAAGTCAC
45484814 GTTACTGCTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.35
Consensus pattern (49 bp):
AGCTTCTAATTCATCTCCCACAATTTATGGTAATTTTCCAAAGTCACAC
Found at i:45490275 original size:27 final size:26
Alignment explanation
Indices: 45490238--45490349 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
45490228 AGTATGGCTG
* *
45490238 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
45490264 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
45490292 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
45490319 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
45490346 CCAG
1 CCAG
45490350 GACGCTTCCT
Statistics
Matches: 78, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
26 5 0.06
27 56 0.72
28 17 0.22
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:45490297 original size:54 final size:54
Alignment explanation
Indices: 45490238--45490349 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
45490228 AGTATGGCTG
*
45490238 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
45490292 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
45490346 CCAG
1 CCAG
45490350 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:45495098 original size:95 final size:95
Alignment explanation
Indices: 45494874--45495113 Score: 243
Period size: 95 Copynumber: 2.5 Consensus size: 95
45494864 AATTACTTCT
* * * * * *
45494874 AGCCTTTTAAGGCACTTAGCCAAAATTCAAT--ATTTATAAAGTAGATACTCTTAGAGGAAACTA
1 AGCCTATTAAGGCACTTAG-CTAAATTCAATAAAGTTATAAAGTAGACACCCTGAGAGGAAACTA
* * *
45494937 CTCACTAATTCTAATAATAGATATACTGCTA
65 CTCACTAAGTCTAATAATAGATACAATGCTA
* * * * *
45494968 AGCCTATTAGGGCACTTAGCTAAATTCAATGAAGTTATAAAGCAGACACCCTGAGAGGAAATTGC
1 AGCCTATTAAGGCACTTAGCTAAATTCAATAAAGTTATAAAGTAGACACCCTGAGAGGAAACTAC
* *
45495033 TCACTAAGTCTAATACTAGATACAATGTTA
66 TCACTAAGTCTAATAATAGATACAATGCTA
* * *** *
45495063 AGCC-ATTTAAGGCACTTATCTAAGTTTTGTAAAGTTAAAAAGTAGACACCC
1 AGCCTA-TTAAGGCACTTAGCTAAATTCAATAAAGTTATAAAGTAGACACCC
45495114 GAAGTGGGTA
Statistics
Matches: 119, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
93 10 0.08
94 18 0.15
95 91 0.76
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (95 bp):
AGCCTATTAAGGCACTTAGCTAAATTCAATAAAGTTATAAAGTAGACACCCTGAGAGGAAACTAC
TCACTAAGTCTAATAATAGATACAATGCTA
Found at i:45506839 original size:90 final size:91
Alignment explanation
Indices: 45506672--45506840 Score: 205
Period size: 90 Copynumber: 1.9 Consensus size: 91
45506662 TGGCGTTGAT
* * * * * *
45506672 ATGAGATTTGCGTGTAAGACCATGTCTGGGACATGGCATCGATGTGAGGCCCCGTATAAGACCAT
1 ATGAGACTTGCGTATAAGACCATATCTGGGACATGGCATCGATATGAGGACCCATATAAGACCAT
45506737 CTCAGGGACATGGCATCGGTACCGAC
66 CTCAGGGACATGGCATCGGTACCGAC
* * * * * *
45506763 ATGAGACTT-CGTATAAGACCATATCTGGGATATGGCATCGGTATGTGTACCCATGTAATACCAT
1 ATGAGACTTGCGTATAAGACCATATCTGGGACATGGCATCGATATGAGGACCCATATAAGACCAT
* *
45506827 GTCGGGGACATGGC
66 CTCAGGGACATGGC
45506841 TTTGACATTT
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
90 56 0.88
91 8 0.12
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (91 bp):
ATGAGACTTGCGTATAAGACCATATCTGGGACATGGCATCGATATGAGGACCCATATAAGACCAT
CTCAGGGACATGGCATCGGTACCGAC
Found at i:45512023 original size:17 final size:17
Alignment explanation
Indices: 45512001--45512036 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
45511991 ATTCGAATTT
45512001 TACAAGTTCGACAACTC
1 TACAAGTTCGACAACTC
45512018 TACAAGTTCGACAACTC
1 TACAAGTTCGACAACTC
45512035 TA
1 TA
45512037 TGTACTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.25
Consensus pattern (17 bp):
TACAAGTTCGACAACTC
Found at i:45515067 original size:46 final size:46
Alignment explanation
Indices: 45514903--45515075 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
45514893 AACCTGCCCC
* * * * *
45514903 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * * * *
45514949 TAAATGAAATCGGACTCAACTCAACAAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
45514997 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
45515042 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
45515076 TACTCAACCA
Statistics
Matches: 102, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 57 0.56
47 27 0.26
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:45515072 original size:93 final size:93
Alignment explanation
Indices: 45514908--45515076 Score: 266
Period size: 93 Copynumber: 1.8 Consensus size: 93
45514898 GCCCCTAAGT
* * *
45514908 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAATGAAATCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAAATCGGACTCAACTCAA
45514973 CAAGTTCGGATGCCTAGTTACATCTCAC
66 CAAGTTCGGATGCCTAGTTACATCTCAC
* * * *
45515001 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAAATCGGACTCAACTCAA
*
45515066 CGAGTTCGGAT
66 CAAGTTCGGAT
45515077 ACTCAACCAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 68 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAAATCGGACTCAACTCAA
CAAGTTCGGATGCCTAGTTACATCTCAC
Found at i:45530340 original size:14 final size:14
Alignment explanation
Indices: 45530323--45530363 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
45530313 AAAGTAGTCT
45530323 TAAAAAAATAAAAG
1 TAAAAAAATAAAAG
*
45530337 TAAAAACATAAAA-
1 TAAAAAAATAAAAG
*
45530350 T-AATAAATAAAAG
1 TAAAAAAATAAAAG
45530363 T
1 T
45530364 TTTTAAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 9 0.39
13 2 0.09
14 12 0.52
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (14 bp):
TAAAAAAATAAAAG
Found at i:45545376 original size:29 final size:27
Alignment explanation
Indices: 45545344--45545399 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
45545334 ATGATGAAGA
45545344 AAAAAAAAGGAAAAAGTTCTCATGTTGTT
1 AAAAAAAA-G-AAAAGTTCTCATGTTGTT
45545373 AAAAAAAAGAAAAGTTCTCATGTTGTT
1 AAAAAAAAGAAAAGTTCTCATGTTGTT
45545400 GAACTTGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 18 0.67
28 1 0.04
29 8 0.30
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (27 bp):
AAAAAAAAGAAAAGTTCTCATGTTGTT
Found at i:45546705 original size:40 final size:40
Alignment explanation
Indices: 45546643--45546846 Score: 250
Period size: 40 Copynumber: 5.1 Consensus size: 40
45546633 CGGATGATAA
* * *
45546643 CCGGGCTAAGTCCCGAACGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
45546683 CTGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
45546723 CCGGGCTTAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* ** *
45546763 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAACTACTTTAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * **
45546803 CTGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
45546843 CCGG
1 CCGG
45546847 TTGAAGCCCG
Statistics
Matches: 141, Mismatches: 22, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
40 140 0.99
41 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:45554728 original size:40 final size:40
Alignment explanation
Indices: 45554673--45554876 Score: 286
Period size: 40 Copynumber: 5.1 Consensus size: 40
45554663 CGGATGATAA
* *
45554673 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
45554713 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
45554753 CCGGGCTAAGTCCCGAAGGTATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* **
45554793 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAACTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * **
45554833 CCGGGCTAAGTCGCGAAGGCATTTGAGCGAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
45554873 CCGG
1 CCGG
45554877 TTGAAGCCCG
Statistics
Matches: 149, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
40 148 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:45560948 original size:101 final size:98
Alignment explanation
Indices: 45560766--45561049 Score: 397
Period size: 101 Copynumber: 3.0 Consensus size: 98
45560756 TAACACAGTT
* *
45560766 TGAATTTAACAATGAATTTAGCAATCCTACCTATGCCGAGCCTTGCTTAGAAATAATTTTATTTA
1 TGAATTTAACAATGAATTTAACAATCCTACCTATGCAGAGCCTTGCTTAGAAATAATTTTATTTA
* *
45560831 ACAATTAATTAGGAACAACTCTTGATTTAATAA
66 ACAATTAATCAGGAACAACTCTTGATTTAACAA
*
45560864 TGATTAATTTAACAATGAATTTAACAATCCTACCTATGCGGAGCCTTGCTTAGAAATAATTTTAT
1 TG---AATTTAACAATGAATTTAACAATCCTACCTATGCAGAGCCTTGCTTAGAAATAATTTTAT
*
45560929 TTAACAATTAATCAAGAACAACTCTTGATTTAACAA
63 TTAACAATTAATCAGGAACAACTCTTGATTTAACAA
* *
45560965 TG-A--T-----T-AATTTAACAATCCTACCTATGCAGAGTCTTACTTAGAAATAATTTTATTTA
1 TGAATTTAACAATGAATTTAACAATCCTACCTATGCAGAGCCTTGCTTAGAAATAATTTTATTTA
*
45561021 ACAATTAATCAGGAACAACTCTTAATTTA
66 ACAATTAATCAGGAACAACTCTTGATTTA
45561050 GGCCCAGTTT
Statistics
Matches: 173, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
89 75 0.43
90 1 0.01
95 1 0.01
97 1 0.01
98 2 0.01
101 93 0.54
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (98 bp):
TGAATTTAACAATGAATTTAACAATCCTACCTATGCAGAGCCTTGCTTAGAAATAATTTTATTTA
ACAATTAATCAGGAACAACTCTTGATTTAACAA
Found at i:45560982 original size:89 final size:86
Alignment explanation
Indices: 45560867--45561049 Score: 294
Period size: 89 Copynumber: 2.1 Consensus size: 86
45560857 TTAATAATGA
* *
45560867 TTAATTTAACAATGAATTTAACAATCCTACCTATGCGGAGCCTTGCTTAGAAATAATTTTATTTA
1 TTAATTTAACAATGAATTTAACAATCCTACCTATGCAGAGCCTTACTTAGAAATAATTTTATTTA
45560932 ACAATTAATCAAGAACAACTC
66 ACAATTAATCAAGAACAACTC
* *
45560953 TTGATTTAACAATGATTAATTTAACAATCCTACCTATGCAGAGTCTTACTTAGAAATAATTTTAT
1 TTAATTTAACAATG---AATTTAACAATCCTACCTATGCAGAGCCTTACTTAGAAATAATTTTAT
*
45561018 TTAACAATTAATCAGGAACAACTC
63 TTAACAATTAATCAAGAACAACTC
45561042 TTAATTTA
1 TTAATTTA
45561050 GGCCCAGTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
86 13 0.15
89 75 0.85
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (86 bp):
TTAATTTAACAATGAATTTAACAATCCTACCTATGCAGAGCCTTACTTAGAAATAATTTTATTTA
ACAATTAATCAAGAACAACTC
Found at i:45561303 original size:11 final size:11
Alignment explanation
Indices: 45561287--45561311 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
45561277 CATCCCAAGT
45561287 AAAAAAAAAAG
1 AAAAAAAAAAG
45561298 AAAAAAAAAAG
1 AAAAAAAAAAG
45561309 AAA
1 AAA
45561312 GATAGATCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:45562518 original size:24 final size:24
Alignment explanation
Indices: 45562491--45562538 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
45562481 ACTTATTAAA
45562491 AAATAGAAATATAAATATTTTATT
1 AAATAGAAATATAAATATTTTATT
45562515 AAATAGAAATATAAATATTTTATT
1 AAATAGAAATATAAATATTTTATT
45562539 TTGGCAAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AAATAGAAATATAAATATTTTATT
Found at i:45567897 original size:35 final size:35
Alignment explanation
Indices: 45567851--45567917 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
45567841 TTTTTATATT
45567851 CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
1 CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
* * *
45567886 CTTTAACTGTTTATGTAAGTTGTGATTATCAT
1 CTTTAAATGTTTATGTAAGTTATGATAATCAT
45567918 CTTTTAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.46
Consensus pattern (35 bp):
CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
Found at i:45573446 original size:42 final size:42
Alignment explanation
Indices: 45573399--45573484 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
45573389 TTTGTTAACC
45573399 ATAAGGCCTTGTACCATGGCCTTGAACTCTTCGCAATTTTGG
1 ATAAGGCCTTGTACCATGGCCTTGAACTCTTCGCAATTTTGG
*
45573441 ATAAGGCCTTGTACCATGGCCTTGAACTCTTTGCAATTTTGG
1 ATAAGGCCTTGTACCATGGCCTTGAACTCTTCGCAATTTTGG
45573483 AT
1 AT
45573485 CATATGACCC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (42 bp):
ATAAGGCCTTGTACCATGGCCTTGAACTCTTCGCAATTTTGG
Found at i:45578863 original size:33 final size:33
Alignment explanation
Indices: 45578824--45578893 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
45578814 ACAAACATAC
45578824 AAAGTAATAATTAAATAATGCATGATATACAAA
1 AAAGTAATAATTAAATAATGCATGATATACAAA
*
45578857 AAAGTAATAATTAAATAATGTATGATATACAAA
1 AAAGTAATAATTAAATAATGCATGATATACAAA
45578890 AAAG
1 AAAG
45578894 AGTAATACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.59, C:0.04, G:0.10, T:0.27
Consensus pattern (33 bp):
AAAGTAATAATTAAATAATGCATGATATACAAA
Found at i:45579129 original size:24 final size:24
Alignment explanation
Indices: 45579083--45579130 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
45579073 CTATACAATA
*
45579083 TATAAAACATGATAACAAAATATT
1 TATAAAAAATGATAACAAAATATT
*
45579107 TATAAAAGAATGATAA-AATATATT
1 TATAAAA-AATGATAACAAAATATT
45579131 GGGTTNTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (24 bp):
TATAAAAAATGATAACAAAATATT
Found at i:45579199 original size:30 final size:30
Alignment explanation
Indices: 45579165--45579340 Score: 102
Period size: 30 Copynumber: 5.9 Consensus size: 30
45579155 AAGTAAAAAT
*
45579165 ATAATAATAATATATAAATAATAATGTAAA
1 ATAATAATAATATATAAATAATAATATAAA
* * * *
45579195 ATAATAAT-ATTTCGTGAAA-AGTAATATATA
1 ATAATAATAATAT-AT-AAATAATAATATAAA
45579225 ATAAATAATAATAATATAAATAATATATAATAAA
1 AT-AATAATAAT-ATATAAATAATA-AT-ATAAA
*
45579259 ATAATTATATAATATATAATATAA-AA-ATAAGG
1 ATAA-TA-ATAATATATAA-ATAATAATATAA-A
* * * *
45579291 TTAAAAATAA-A-ACAAATAACAATATAAA
1 ATAATAATAATATATAAATAATAATATAAA
45579319 AT-AT-AT-ATATAT-AATAATAATA
1 ATAATAATAATATATAAATAATAATA
45579341 AATATATAGG
Statistics
Matches: 112, Mismatches: 18, Indels: 36
0.67 0.11 0.22
Matches are distributed among these distances:
25 1 0.01
26 12 0.11
27 6 0.05
28 6 0.05
29 8 0.07
30 23 0.21
31 17 0.15
32 9 0.08
33 6 0.05
34 15 0.13
35 9 0.08
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (30 bp):
ATAATAATAATATATAAATAATAATATAAA
Found at i:45579234 original size:3 final size:3
Alignment explanation
Indices: 45579216--45579288 Score: 55
Period size: 3 Copynumber: 24.0 Consensus size: 3
45579206 TCGTGAAAAG
45579216 TAA TATA TAA TAAA TAA TAA TAA T-A TAAA TAA TATA TAA TAA -AA TAA
1 TAA TA-A TAA T-AA TAA TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA
* *
45579263 TTA T-A TAA TATA TAA T-A TAA AAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA
45579289 GGTTAAAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
2 8 0.14
3 36 0.62
4 14 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:45579267 original size:16 final size:15
Alignment explanation
Indices: 45579211--45579281 Score: 85
Period size: 15 Copynumber: 4.7 Consensus size: 15
45579201 ATATTTCGTG
45579211 AAAAGTAATATATAAT
1 AAAA-TAATATATAAT
45579227 -AAATAATA-ATAAT
1 AAAATAATATATAAT
45579240 ATAAATAATATATAAT
1 A-AAATAATATATAAT
45579256 AAAATAATTATATAAT
1 AAAATAA-TATATAAT
*
45579272 -ATATAATATA
1 AAAATAATATA
45579282 AAAATAAGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
13 5 0.10
14 9 0.18
15 22 0.44
16 14 0.28
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (15 bp):
AAAATAATATATAAT
Found at i:45579280 original size:7 final size:7
Alignment explanation
Indices: 45579216--45579281 Score: 71
Period size: 7 Copynumber: 9.0 Consensus size: 7
45579206 TCGTGAAAAG
45579216 TAATATA
1 TAATATA
*
45579223 TAATAAA
1 TAATATA
45579230 TAATA-A
1 TAATATA
45579236 TAATATAAA
1 TAATAT--A
45579245 TAATATA
1 TAATATA
*
45579252 TAATAAAA
1 TAAT-ATA
45579260 TAATTATA
1 TAA-TATA
45579268 TAATATA
1 TAATATA
45579275 TAATATA
1 TAATATA
45579282 AAAATAAGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
6 6 0.12
7 27 0.53
8 10 0.20
9 8 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
TAATATA
Found at i:45579282 original size:25 final size:25
Alignment explanation
Indices: 45579216--45579348 Score: 86
Period size: 25 Copynumber: 5.4 Consensus size: 25
45579206 TCGTGAAAAG
45579216 TAATATATAATA-AATAATAATAATA
1 TAATATATAATATAA-AATAATAATA
*
45579241 TAA-ATAATATATAATAAAATAATTATA
1 TAATAT-ATA-AT-ATAAAATAATAATA
45579268 TAATATATAATAT-AAA-AATAAGGT-
1 TAATATATAATATAAAATAATAA--TA
* *
45579292 TAA-AAATAA-A-ACAAATAACAATA
1 TAATATATAATATA-AAATAATAATA
* *
45579315 TAAAATATATATATATAATAATAATA
1 TAATATATA-ATATAAAATAATAATA
45579341 -AATATATA
1 TAATATATA
45579349 GGGGTTGATT
Statistics
Matches: 85, Mismatches: 8, Indels: 30
0.69 0.07 0.24
Matches are distributed among these distances:
22 2 0.02
23 15 0.18
24 16 0.19
25 17 0.20
26 14 0.16
27 17 0.20
28 4 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
TAATATATAATATAAAATAATAATA
Found at i:45584775 original size:19 final size:19
Alignment explanation
Indices: 45584751--45584841 Score: 134
Period size: 19 Copynumber: 4.9 Consensus size: 19
45584741 AATCATATCT
*
45584751 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
45584770 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
45584788 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
* *
45584805 TCTAAGATTCCATATCACA
1 TCTAAGATTGCATATCATA
45584824 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
45584842 TGAAGATTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
17 15 0.23
18 16 0.25
19 33 0.52
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:45584809 original size:35 final size:37
Alignment explanation
Indices: 45584751--45584841 Score: 132
Period size: 35 Copynumber: 2.5 Consensus size: 37
45584741 AATCATATCT
* *
45584751 TCTAAGATTGTATATCATATCTAAGATTGCA-ATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTCCATATCACA
45584788 TCTAAGATTG-TATCATATCTAAGATTCCATATCACA
1 TCTAAGATTGATATCATATCTAAGATTCCATATCACA
45584824 TCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCAT
45584842 TGAAGATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
35 18 0.37
36 15 0.31
37 10 0.20
38 6 0.12
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (37 bp):
TCTAAGATTGATATCATATCTAAGATTCCATATCACA
Found at i:45597302 original size:19 final size:19
Alignment explanation
Indices: 45597278--45597368 Score: 125
Period size: 19 Copynumber: 4.9 Consensus size: 19
45597268 TATCATATCT
*
45597278 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
45597297 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
45597315 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
* * *
45597332 TCAAAGATTCCATATCACA
1 TCTAAGATTGCATATCATA
45597351 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
45597369 TGAAGATTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
17 14 0.23
18 16 0.26
19 32 0.52
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:45597339 original size:35 final size:37
Alignment explanation
Indices: 45597278--45597368 Score: 123
Period size: 35 Copynumber: 2.5 Consensus size: 37
45597268 TATCATATCT
* * *
45597278 TCTAAGATTGTATATCATATCTAAGATTGCA-ATCATA
1 TCTAAGATTG-ATATCATATCAAAGATTCCATATCACA
45597315 TCTAAGATTG-TATCATATCAAAGATTCCATATCACA
1 TCTAAGATTGATATCATATCAAAGATTCCATATCACA
45597351 TCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCAT
45597369 TGAAGATTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
35 17 0.35
36 15 0.31
37 10 0.21
38 6 0.12
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (37 bp):
TCTAAGATTGATATCATATCAAAGATTCCATATCACA
Found at i:45599210 original size:27 final size:26
Alignment explanation
Indices: 45599179--45599342 Score: 195
Period size: 27 Copynumber: 6.0 Consensus size: 26
45599169 AGCATGGCTG
* *
45599179 CCAGATACAGATAATGTGACAGAGTCA
1 CCAGAT-CAGATAATGTGGCAGAGCCA
*
45599206 CCAGATACAGATAATTGTGGTAGAGCCA
1 CCAGAT-CAGATAA-TGTGGCAGAGCCA
*
45599234 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGATCAGATA-ATGTGGCAGAGCCA
*
45599261 CCAGATCAGATAATCGTGGCATAGCCA
1 CCAGATCAGATAAT-GTGGCAGAGCCA
45599288 CCAGGAT-AGATATATGTGGCAGAGCCA
1 CCA-GATCAGATA-ATGTGGCAGAGCCA
*
45599315 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGATCAGATAA-TGTGGCAGAGCCA
45599342 C
1 C
45599343 TAGGACGCTT
Statistics
Matches: 121, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.05
27 94 0.78
28 21 0.17
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (26 bp):
CCAGATCAGATAATGTGGCAGAGCCA
Found at i:45599243 original size:54 final size:54
Alignment explanation
Indices: 45599179--45599342 Score: 240
Period size: 54 Copynumber: 3.0 Consensus size: 54
45599169 AGCATGGCTG
* * * *
45599179 CCAGATACAGATA-ATGTGACAGAGTCACCAGATACAGATAATTGTGGTAGAGCCA
1 CCAGA-ACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
*
45599234 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
* *
45599288 CCAGGATAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
45599342 C
1 C
45599343 TAGGACGCTT
Statistics
Matches: 100, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
54 77 0.77
55 23 0.23
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (54 bp):
CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
Found at i:45607296 original size:27 final size:27
Alignment explanation
Indices: 45607265--45607431 Score: 216
Period size: 27 Copynumber: 6.1 Consensus size: 27
45607255 AGCATGGCTG
* *
45607265 CCAGATACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
45607292 CCAGATACAGATAATTGTGGCAGAGCCA
1 CCAGATACAGATAA-TGTGGCAGAGCCA
*
45607320 CCAGA-ATAGATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
*
45607347 CCAGAT-CAGATAATCGTGGCATAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
45607374 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
*
45607401 CCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGATACAGATAA-TGTGGCAGAGCCA
45607428 CCAG
1 CCAG
45607432 GACGCTTCCT
Statistics
Matches: 125, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
26 3 0.02
27 103 0.82
28 19 0.15
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:45607331 original size:54 final size:54
Alignment explanation
Indices: 45607265--45607431 Score: 264
Period size: 54 Copynumber: 3.1 Consensus size: 54
45607255 AGCATGGCTG
* * *
45607265 CCAGATACAGATA-ATGTGACAGAGTCACCAGATACAGATAATTGTGGCAGAGCCA
1 CCAGA-ACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
* *
45607320 CCAGAATAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
45607374 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
45607428 CCAG
1 CCAG
45607432 GACGCTTCCT
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
54 81 0.78
55 23 0.22
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
Found at i:45609398 original size:46 final size:47
Alignment explanation
Indices: 45609292--45609407 Score: 144
Period size: 50 Copynumber: 2.4 Consensus size: 47
45609282 TGTCTTCGAC
** * *
45609292 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
45609342 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
45609388 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
45609408 TTTGTCCTGT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
46 29 0.49
50 30 0.51
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:45613192 original size:42 final size:43
Alignment explanation
Indices: 45613093--45613283 Score: 156
Period size: 42 Copynumber: 4.5 Consensus size: 43
45613083 CAATGCTAAC
* * * *
45613093 ATCCCAGACATTGTCTTACATGTAATCATATATCGATGTC-AT
1 ATCCCAGACATGGTCTTACATGAAATCAAATATCGATGCCAAT
* * *
45613135 -TGCCCATACAGGGTCTTACATGAAATTAAATAT-GATGCCAAT
1 AT-CCCAGACATGGTCTTACATGAAATCAAATATCGATGCCAAT
* * * * *
45613177 ATCCCAAACATGGTCTTATACGTAAATCTCAA-ATCGATGCCAAC
1 ATCCCAGACATGGTCTTACATG-AAATC-AAATATCGATGCCAAT
* * * * *
45613221 GTCCCAGACGTGGTCTTACATGAAATCATATATCGTTGCCACT
1 ATCCCAGACATGGTCTTACATGAAATCAAATATCGATGCCAAT
* *
45613264 GTCCCAGACAGGGTCTTACA
1 ATCCCAGACATGGTCTTACA
45613284 CGATATCTCA
Statistics
Matches: 116, Mismatches: 26, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
41 6 0.05
42 44 0.38
43 39 0.34
44 27 0.23
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (43 bp):
ATCCCAGACATGGTCTTACATGAAATCAAATATCGATGCCAAT
Done.