Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 20 of 310
Found at i:5207056 original size:73 final size:73
Alignment explanation
Indices: 5206907--5207056 Score: 169
Period size: 73 Copynumber: 2.1 Consensus size: 73
5206897 CATTATGTGA
* * * *
5206907 CTCGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTCGAAAAATAAAAACTGAAAATACCT
1 CTCGAGACTCAACTCACCTCTCGCAATATGAGTTGATTTTCGAAAAACAAAAACTGAAAAGACCT
***
5206972 CAATGTGT
66 CAATACCT
* * * *
5206980 CTCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAGAAA-TTAAAAGA-CT
1 CTCGAGACTCAACTCACCTCTCGCAATATGAGTTGATTTTCGAAAAACAAAAACTGAAAAGACCT
5207043 CAACTCACCT
66 CAA-T-ACCT
5207053 CTCG
1 CTCG
5207057 CAATATGAGT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
71 5 0.08
72 7 0.11
73 52 0.81
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (73 bp):
CTCGAGACTCAACTCACCTCTCGCAATATGAGTTGATTTTCGAAAAACAAAAACTGAAAAGACCT
CAATACCT
Found at i:5207458 original size:14 final size:14
Alignment explanation
Indices: 5207436--5207465 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5207426 ATTTTTTTGC
*
5207436 AAAATATAAATTGA
1 AAAACATAAATTGA
5207450 AAAACATAAATTGA
1 AAAACATAAATTGA
5207464 AA
1 AA
5207466 TTACCTCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAACATAAATTGA
Found at i:5207547 original size:14 final size:14
Alignment explanation
Indices: 5207525--5207554 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5207515 ATTTTTTTGC
*
5207525 AAAATATAAATTGA
1 AAAACATAAATTGA
5207539 AAAACATAAATTGA
1 AAAACATAAATTGA
5207553 AA
1 AA
5207555 TTACCTCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAACATAAATTGA
Found at i:5207636 original size:14 final size:14
Alignment explanation
Indices: 5207614--5207643 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5207604 ATTTTTTTGC
*
5207614 AAAATATAAATTGA
1 AAAACATAAATTGA
5207628 AAAACATAAATTGA
1 AAAACATAAATTGA
5207642 AA
1 AA
5207644 TTACCTCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAACATAAATTGA
Found at i:5207699 original size:89 final size:89
Alignment explanation
Indices: 5207183--5207690 Score: 744
Period size: 89 Copynumber: 5.8 Consensus size: 89
5207173 ATTGACTTTT
* * *
5207183 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
* *
5207248 GTTGA--TTTTTGAAAAATATAAT
66 GTTGATTTTTTTGCAAAATATAAA
* * * * * * *
5207270 TTGGAAAAAAAACATAAATTGAAAATACCTCAACTTTTCCTGAGGCTCAACTCACCTTTTGTAAT
1 TT-G---AAAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
* * * *
5207335 ATGAGTTGA----TTT-AAAAACAGACA
62 ATGAGTTGATTTTTTTGCAAAATATAAA
* * * *
5207358 TT-AAGAATAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
5207422 GTTGATTTTTTTGCAAAATATAAA
66 GTTGATTTTTTTGCAAAATATAAA
5207446 TTGAAAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
5207511 GTTGATTTTTTTGCAAAATATAAA
66 GTTGATTTTTTTGCAAAATATAAA
5207535 TTGAAAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
5207600 GTTGATTTTTTTGCAAAATATAAA
66 GTTGATTTTTTTGCAAAATATAAA
5207624 TTGAAAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
5207689 GT
66 GT
5207691 CGTCTTTTTG
Statistics
Matches: 380, Mismatches: 31, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
83 58 0.15
87 5 0.01
88 19 0.05
89 241 0.63
91 57 0.15
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (89 bp):
TTGAAAAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTTTGCAAAATATAAA
Found at i:5218644 original size:47 final size:45
Alignment explanation
Indices: 5218525--5218704 Score: 170
Period size: 46 Copynumber: 3.9 Consensus size: 45
5218515 TGTAACCCGC
* * * ** **
5218525 CCATAAGCGAACTCGGACTCAACTCAACAAGCTCGGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG-CCGCAT
*
5218571 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC--G---CAT
* *
5218621 -C-TTAG-GAACTCGGACTCAACTCAACGAGTCCGGACAT-CCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCGCAT
5218664 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC
5218705 CAAACATCCT
Statistics
Matches: 111, Mismatches: 12, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
43 3 0.03
44 3 0.03
45 5 0.05
46 61 0.55
47 28 0.25
48 5 0.05
49 3 0.03
50 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCGCAT
Found at i:5218692 original size:93 final size:93
Alignment explanation
Indices: 5218533--5218704 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
5218523 GCCCATAAGC
* * ** *
5218533 GAACTCGGACTCAACTCAACAAGCTCGGGCGTTTGCATCCATGAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTCGGACATCCGCATCCATAAGTGAACTCGGACTCAACTCAA
5218598 CGAGTTCGGATGCCTAGTTACATCTTAG
66 CGAGTTCGGATGCCTAGTTACATCTTAG
*
5218626 GAACTCGGACTCAACTCAACGAG-TCCGGACATCCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACAAGCT-CGGACATCCGCATCCATAAGTGAACTCGGACTCAACTCA
5218690 ACGAGTTCGGATGCC
65 ACGAGTTCGGATGCC
5218705 CAAACATCCT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTCGGACATCCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTTAG
Found at i:5229245 original size:16 final size:17
Alignment explanation
Indices: 5229221--5229253 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5229211 AATAGAAATA
5229221 TTGTAAAAATA-AAGTT
1 TTGTAAAAATATAAGTT
*
5229237 TTGTTAAAATATAAGTT
1 TTGTAAAAATATAAGTT
5229254 CTTTATACAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (17 bp):
TTGTAAAAATATAAGTT
Found at i:5239679 original size:14 final size:15
Alignment explanation
Indices: 5239662--5239691 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5239652 TAAAGAGGTT
5239662 GTTTT-ATTGTTTTA
1 GTTTTAATTGTTTTA
5239676 GTTTTAATTGTTTTA
1 GTTTTAATTGTTTTA
5239691 G
1 G
5239692 CCAAAGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (15 bp):
GTTTTAATTGTTTTA
Found at i:5249303 original size:47 final size:47
Alignment explanation
Indices: 5249229--5249326 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 47
5249219 CGTAAGTTTT
* *
5249229 TTTTAATGATGTTACATTCTGAAATCAAAACACGTGATAAAATAAAA
1 TTTTAATGATCTTACATTCTGAAATCAAAACACATGATAAAATAAAA
* * * *
5249276 TTTTAATGATCTTACATT-TTAGGATCAAAACACATGATGAAATAATA
1 TTTTAATGATCTTACATTCTGA-AATCAAAACACATGATAAAATAAAA
5249323 TTTT
1 TTTT
5249327 TTTTATTTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
46 2 0.05
47 42 0.95
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (47 bp):
TTTTAATGATCTTACATTCTGAAATCAAAACACATGATAAAATAAAA
Found at i:5252104 original size:66 final size:66
Alignment explanation
Indices: 5252021--5252154 Score: 216
Period size: 66 Copynumber: 2.0 Consensus size: 66
5252011 TATCCTTGGC
* *
5252021 AATTTGGCTTATATTTTATTTCTAGTCAAATTATATCAGAATGAG-CTAGCTAGCTTAAGGGGTA
1 AATTTAGCTTATATTTTATTTCTAGTCAAATCATATCAGAATGAGCCT-GCTAGCTTAAGGGGTA
5252085 AG
65 AG
* *
5252087 AATTTAGCTTATATTTTATTTCTAGTCAAATCATATCAGAATGAGCCTGCTGGTTTAAGGGGTAA
1 AATTTAGCTTATATTTTATTTCTAGTCAAATCATATCAGAATGAGCCTGCTAGCTTAAGGGGTAA
5252152 G
66 G
5252153 AA
1 AA
5252155 GTTTGGTTGC
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 61 0.97
67 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (66 bp):
AATTTAGCTTATATTTTATTTCTAGTCAAATCATATCAGAATGAGCCTGCTAGCTTAAGGGGTAA
G
Found at i:5257164 original size:24 final size:25
Alignment explanation
Indices: 5257136--5257182 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5257126 CGTAAATATT
5257136 CTCTTA-ATTGCCATT-GCATTTTTA
1 CTCTTACATTGCC-TTAGCATTTTTA
*
5257160 CTCTTACTTTGCCTTAGCATTTT
1 CTCTTACATTGCCTTAGCATTTT
5257183 CCAATATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.17, C:0.23, G:0.09, T:0.51
Consensus pattern (25 bp):
CTCTTACATTGCCTTAGCATTTTTA
Found at i:5267972 original size:21 final size:21
Alignment explanation
Indices: 5267946--5267987 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5267936 ATTTTATTCA
* *
5267946 AAACCCAACCTAAATAAAAAT
1 AAACCCAACCCAAACAAAAAT
*
5267967 AAACCCATCCCAAACAAAAAT
1 AAACCCAACCCAAACAAAAAT
5267988 TAATATAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.29, G:0.00, T:0.12
Consensus pattern (21 bp):
AAACCCAACCCAAACAAAAAT
Found at i:5272046 original size:33 final size:35
Alignment explanation
Indices: 5271992--5272056 Score: 82
Period size: 33 Copynumber: 1.9 Consensus size: 35
5271982 TAATCCTTGC
* *
5271992 AATTAAGAATAACATTTAAAA-TGT-AATTAATTG
1 AATTAAGAATAAAATTAAAAATTGTAAATTAATTG
5272025 AATTAA-ATATAAAATTAAAAATTGTAAATTAA
1 AATTAAGA-ATAAAATTAAAAATTGTAAATTAA
5272057 AAAAATAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 17 0.63
34 3 0.11
35 6 0.22
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (35 bp):
AATTAAGAATAAAATTAAAAATTGTAAATTAATTG
Found at i:5272175 original size:17 final size:17
Alignment explanation
Indices: 5272153--5272187 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5272143 TTTCTTAAAC
5272153 TTAACATGGTCTAAATA
1 TTAACATGGTCTAAATA
5272170 TTAACATGGTCTAAATA
1 TTAACATGGTCTAAATA
5272187 T
1 T
5272188 GTGTCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (17 bp):
TTAACATGGTCTAAATA
Found at i:5272758 original size:31 final size:31
Alignment explanation
Indices: 5272657--5272824 Score: 129
Period size: 31 Copynumber: 5.5 Consensus size: 31
5272647 TTAATATAAC
* * * *
5272657 ATTTGGTATCTGAACTTGACATTTTTTTCTTA
1 ATTTGGTACCTAAACTTGACA-CTTTTTCCTA
* * *
5272689 ATTCGGTACCTAAACTT----TTTTTTGGCCCA
1 ATTTGGTACCTAAACTTGACACTTTTT--CCTA
*
5272718 ATTTAGTACCTAAACTTGACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
* *
5272749 ATTTGGTACCTAAACTT-----TTTTGGGCCCA
1 ATTTGGTACCTAAACTTGACACTTTT--TCCTA
5272777 ATTTGGTACCTAAACTTGACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
*
5272808 ATTTGGTATCTAAACTT
1 ATTTGGTACCTAAACTT
5272825 TTTTGGGCGG
Statistics
Matches: 108, Mismatches: 15, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
26 4 0.04
27 6 0.06
28 20 0.19
29 17 0.16
31 38 0.35
32 14 0.13
33 9 0.08
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTA
Found at i:5272787 original size:28 final size:27
Alignment explanation
Indices: 5272688--5272852 Score: 109
Period size: 28 Copynumber: 5.7 Consensus size: 27
5272678 TTTTTTTCTT
*
5272688 AATTCGGTACCTAAACTTTTTTTTGGCCC
1 AATTTGGTACCTAAAC--TTTTTTGGCCC
* * *
5272717 AATTTAGTACCTAAACTTGACACTTTT-TCCT
1 AATTTGGTACCTAAACTT-----TTTTGGCCC
5272748 AATTTGGTACCTAAACTTTTTTGGGCCC
1 AATTTGGTACCTAAACTTTTTT-GGCCC
* *
5272776 AATTTGGTACCTAAACTTGACACTTTT-TCCT
1 AATTTGGTACCTAAACTT-----TTTTGGCCC
* **
5272807 AATTTGGTATCTAAACTTTTTTGGGCGG
1 AATTTGGTACCTAAACTTTTTT-GGCCC
5272835 AATTTGGTACCTAAACTT
1 AATTTGGTACCTAAACTT
5272853 GACCTTTTTT
Statistics
Matches: 108, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
26 8 0.07
27 2 0.02
28 38 0.35
29 14 0.13
31 38 0.35
32 4 0.04
33 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (27 bp):
AATTTGGTACCTAAACTTTTTTGGCCC
Found at i:5272793 original size:59 final size:59
Alignment explanation
Indices: 5272657--5272887 Score: 311
Period size: 59 Copynumber: 3.9 Consensus size: 59
5272647 TTAATATAAC
* * * * * *
5272657 ATTTGGTATCTGAACTTGACATTTTTTTCTTAATTCGGTACCTAAACTTTTTTTTGGCCCA
1 ATTTGGTACCTAAACTTGACA-CTTTTTCCTAATTTGGTACCTAAAC-TTTTTTGGGCCCA
*
5272718 ATTTAGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGCCCA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGCCCA
* **
5272777 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTATCTAAACTTTTTTGGGCGGA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGCCCA
* * *
5272836 ATTTGGTACCTAAACTTGAC-CTTTTTTCCTAATTTGATATCTAAGCTTTTTT
1 ATTTGGTACCTAAACTTGACAC-TTTTTCCTAATTTGGTACCTAAACTTTTTT
5272888 TTAGGTTCAA
Statistics
Matches: 156, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
58 1 0.01
59 115 0.74
60 22 0.14
61 18 0.12
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (59 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGCCCA
Found at i:5276466 original size:62 final size:62
Alignment explanation
Indices: 5276369--5276492 Score: 230
Period size: 62 Copynumber: 2.0 Consensus size: 62
5276359 AGGTTGAATT
5276369 ATTGTTAACATAAGCTAAATCAAGCTACCGGGATTTCAAAAACATAAAAATCATTAAAAACG
1 ATTGTTAACATAAGCTAAATCAAGCTACCGGGATTTCAAAAACATAAAAATCATTAAAAACG
* *
5276431 ATTGTTAACATAAGCTAAATCGAGCTACCGGGATTTCAAAAACATAAAAATTATTAAAAACG
1 ATTGTTAACATAAGCTAAATCAAGCTACCGGGATTTCAAAAACATAAAAATCATTAAAAACG
5276493 GGGCTTGAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (62 bp):
ATTGTTAACATAAGCTAAATCAAGCTACCGGGATTTCAAAAACATAAAAATCATTAAAAACG
Found at i:5277289 original size:49 final size:49
Alignment explanation
Indices: 5277217--5277314 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
5277207 GACTAGTCTG
5277217 ATGGAGCTATCGTTTGGGGAATTCGATCTAATGTTGCGGATGGATTGGC
1 ATGGAGCTATCGTTTGGGGAATTCGATCTAATGTTGCGGATGGATTGGC
*
5277266 ATGGAGCTATCGTTTGGGGAATTCGATCTAATGTTGGGGATGGATTGGC
1 ATGGAGCTATCGTTTGGGGAATTCGATCTAATGTTGCGGATGGATTGGC
5277315 TCGTGGAGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.20, C:0.11, G:0.36, T:0.33
Consensus pattern (49 bp):
ATGGAGCTATCGTTTGGGGAATTCGATCTAATGTTGCGGATGGATTGGC
Found at i:5278460 original size:51 final size:50
Alignment explanation
Indices: 5278382--5278479 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 50
5278372 TCTTTAATTG
* *
5278382 CAGATATTCTAACTAAGTTGTTGCGTAAGAATGCACCTTTTTTTCTGGTTA
1 CAGATATTCTAACTAAGTTGTTCCGTAAGAATGCA-CATTTTTTCTGGTTA
5278433 CAGATATTCTAACTAAGTTGTTCCGTAAGAATGCACATTTTTTCTGG
1 CAGATATTCTAACTAAGTTGTTCCGTAAGAATGCACATTTTTTCTGG
5278480 ACTGATGAGG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 11 0.24
51 34 0.76
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (50 bp):
CAGATATTCTAACTAAGTTGTTCCGTAAGAATGCACATTTTTTCTGGTTA
Found at i:5278983 original size:41 final size:41
Alignment explanation
Indices: 5278938--5279020 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
5278928 TATTAATGTC
5278938 AAGAGATTAATCGAAGATATTGAACAGATCAGTGGGAGAAA
1 AAGAGATTAATCGAAGATATTGAACAGATCAGTGGGAGAAA
5278979 AAGAGATTAATCGAAGATATTGAACAGATCAGTGGGAGAAA
1 AAGAGATTAATCGAAGATATTGAACAGATCAGTGGGAGAAA
5279020 A
1 A
5279021 GCAACTGGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.47, C:0.07, G:0.27, T:0.19
Consensus pattern (41 bp):
AAGAGATTAATCGAAGATATTGAACAGATCAGTGGGAGAAA
Found at i:5282015 original size:33 final size:35
Alignment explanation
Indices: 5281961--5282025 Score: 82
Period size: 33 Copynumber: 1.9 Consensus size: 35
5281951 TAATCCTTGC
* *
5281961 AATTAAGAATAACATTTAAAA-TGT-AATTAATTG
1 AATTAAGAATAAAATTAAAAATTGTAAATTAATTG
5281994 AATTAA-ATATAAAATTAAAAATTGTAAATTAA
1 AATTAAGA-ATAAAATTAAAAATTGTAAATTAA
5282026 AAAAATAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 17 0.63
34 3 0.11
35 6 0.22
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (35 bp):
AATTAAGAATAAAATTAAAAATTGTAAATTAATTG
Found at i:5282710 original size:31 final size:31
Alignment explanation
Indices: 5282669--5282776 Score: 118
Period size: 31 Copynumber: 3.6 Consensus size: 31
5282659 TTTTTGGCCC
* *
5282669 AATTTAGTACCTAAACTTGACACTTTTTTCT
1 AATTTGGTACCTAAACTTGACACTTTTTCCT
* *
5282700 AATTTGGTACCTAAACTT-----TTTTGGGCCC
1 AATTTGGTACCTAAACTTGACACTTTT--TCCT
5282728 AATTTGGTACCTAAACTTGACACTTTTTCCT
1 AATTTGGTACCTAAACTTGACACTTTTTCCT
*
5282759 AATTTGGTATCTAAACTT
1 AATTTGGTACCTAAACTT
5282777 TTTTGGGCGG
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
26 4 0.06
28 19 0.30
31 36 0.57
33 4 0.06
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (31 bp):
AATTTGGTACCTAAACTTGACACTTTTTCCT
Found at i:5282739 original size:28 final size:28
Alignment explanation
Indices: 5282700--5282804 Score: 106
Period size: 28 Copynumber: 3.6 Consensus size: 28
5282690 ACTTTTTTCT
5282700 AATTTGGTACCTAAACTTTTTTGGGCCC
1 AATTTGGTACCTAAACTTTTTTGGGCCC
* *
5282728 AATTTGGTACCTAAACTTGACACTTTT--TCCT
1 AATTTGGTACCTAAACTT-----TTTTGGGCCC
* **
5282759 AATTTGGTATCTAAACTTTTTTGGGCGG
1 AATTTGGTACCTAAACTTTTTTGGGCCC
5282787 AATTTGGTACCTAAACTT
1 AATTTGGTACCTAAACTT
5282805 GACCTTTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
26 4 0.06
28 36 0.57
31 19 0.30
33 4 0.06
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (28 bp):
AATTTGGTACCTAAACTTTTTTGGGCCC
Found at i:5282744 original size:59 final size:59
Alignment explanation
Indices: 5282621--5282839 Score: 314
Period size: 59 Copynumber: 3.7 Consensus size: 59
5282611 TTGGTATCAG
* * *
5282621 AACTTGACATTTTTTTCTTAATTTGGTACCTAAACATTTTTTTGGCCCAATTTAGTACCTA
1 AACTTGACACTTTTTTC-TAATTTGGTACCTAAAC-TTTTTTGGGCCCAATTTGGTACCTA
5282682 AACTTGACACTTTTTTCTAATTTGGTACCTAAACTTTTTTGGGCCCAATTTGGTACCTA
1 AACTTGACACTTTTTTCTAATTTGGTACCTAAACTTTTTTGGGCCCAATTTGGTACCTA
* * **
5282741 AACTTGACACTTTTTCCTAATTTGGTATCTAAACTTTTTTGGGCGGAATTTGGTACCTA
1 AACTTGACACTTTTTTCTAATTTGGTACCTAAACTTTTTTGGGCCCAATTTGGTACCTA
* * *
5282800 AACTTGAC-CTTTTTTCCTAATTTGATATCTAAGCTTTTTT
1 AACTTGACACTTTTTT-CTAATTTGGTACCTAAACTTTTTT
5282840 TTAGGTTCAA
Statistics
Matches: 147, Mismatches: 10, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
58 6 0.04
59 108 0.73
60 17 0.12
61 16 0.11
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (59 bp):
AACTTGACACTTTTTTCTAATTTGGTACCTAAACTTTTTTGGGCCCAATTTGGTACCTA
Found at i:5291262 original size:33 final size:35
Alignment explanation
Indices: 5291208--5291272 Score: 82
Period size: 33 Copynumber: 1.9 Consensus size: 35
5291198 TAATCCTTGC
* *
5291208 AATTAAGAATAACATTTAAAA-TGT-AATTAATTG
1 AATTAAGAATAAAATTAAAAATTGTAAATTAATTG
5291241 AATTAA-ATATAAAATTAAAAATTGTAAATTAA
1 AATTAAGA-ATAAAATTAAAAATTGTAAATTAA
5291273 AAAAATAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 17 0.63
34 3 0.11
35 6 0.22
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (35 bp):
AATTAAGAATAAAATTAAAAATTGTAAATTAATTG
Found at i:5291391 original size:17 final size:17
Alignment explanation
Indices: 5291369--5291403 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5291359 TTTCTTAAAC
5291369 TTAACATGGTCTAAATA
1 TTAACATGGTCTAAATA
5291386 TTAACATGGTCTAAATA
1 TTAACATGGTCTAAATA
5291403 T
1 T
5291404 GTGTCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (17 bp):
TTAACATGGTCTAAATA
Found at i:5291975 original size:31 final size:31
Alignment explanation
Indices: 5291934--5292041 Score: 127
Period size: 31 Copynumber: 3.6 Consensus size: 31
5291924 TTTTTGGCCC
*
5291934 AATTTAGTACCTAAACTTGACACTTTTTCCT
1 AATTTGGTACCTAAACTTGACACTTTTTCCT
* *
5291965 AATTTGGTACCTAAACTT-----TTTTGGGCCC
1 AATTTGGTACCTAAACTTGACACTTTT--TCCT
5291993 AATTTGGTACCTAAACTTGACACTTTTTCCT
1 AATTTGGTACCTAAACTTGACACTTTTTCCT
*
5292024 AATTTGGTATCTAAACTT
1 AATTTGGTACCTAAACTT
5292042 TTTTGGGCAG
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
26 4 0.06
28 20 0.31
31 36 0.56
33 4 0.06
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (31 bp):
AATTTGGTACCTAAACTTGACACTTTTTCCT
Found at i:5292004 original size:28 final size:27
Alignment explanation
Indices: 5291905--5292069 Score: 109
Period size: 28 Copynumber: 5.7 Consensus size: 27
5291895 TTTTTTTCTT
*
5291905 AATTGGGTACCTAAACTTTTTTTTGGCCC
1 AATTTGGTACCTAAAC--TTTTTTGGCCC
* * *
5291934 AATTTAGTACCTAAACTTGACACTTTT-TCCT
1 AATTTGGTACCTAAACTT-----TTTTGGCCC
5291965 AATTTGGTACCTAAACTTTTTTGGGCCC
1 AATTTGGTACCTAAACTTTTTT-GGCCC
* *
5291993 AATTTGGTACCTAAACTTGACACTTTT-TCCT
1 AATTTGGTACCTAAACTT-----TTTTGGCCC
* **
5292024 AATTTGGTATCTAAACTTTTTTGGGCAG
1 AATTTGGTACCTAAACTTTTTT-GGCCC
5292052 AATTTGGTACCTAAACTT
1 AATTTGGTACCTAAACTT
5292070 GACCTTTTTT
Statistics
Matches: 108, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
26 8 0.07
27 2 0.02
28 38 0.35
29 14 0.13
31 38 0.35
32 4 0.04
33 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.41
Consensus pattern (27 bp):
AATTTGGTACCTAAACTTTTTTGGCCC
Found at i:5292010 original size:59 final size:59
Alignment explanation
Indices: 5291873--5292105 Score: 297
Period size: 59 Copynumber: 3.9 Consensus size: 59
5291863 TTAATATAAC
* * * * * *
5291873 ATTTGGTATCTGAACTTGACATTTTTTTTCTTAATTGGGTACCTAAACTTTTTTTTGGCCCA
1 ATTTGGTACCTAAACTTGACA--CTTTTTCCTAATTTGGTACCTAAAC-TTTTTTGGGCCCA
*
5291935 ATTTAGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGCCCA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGCCCA
* **
5291994 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTATCTAAACTTTTTTGGGCAGA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGCCCA
* * *
5292053 ATTTGGTACCTAAACTTGAC-CTTTTTTTCCTAATTTGATATCTAAGCTTTTTT
1 ATTTGGTACCTAAACTTGACAC--TTTTTCCTAATTTGGTACCTAAACTTTTTT
5292106 TTAGGTTCAA
Statistics
Matches: 156, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
58 1 0.01
59 87 0.56
60 50 0.32
62 18 0.12
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (59 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGCCCA
Found at i:5292086 original size:119 final size:120
Alignment explanation
Indices: 5291873--5292105 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
5291863 TTAATATAAC
* * * * * *
5291873 ATTTGGTATCTGAACTTGACATTTTTTTTCTTAATTGGGTACCTAAACTTTTTTTTGGCCCAATT
1 ATTTGGTACCTAAACTTGACA-TCTTTTTCCTAATTGGGTACCTAAACTTTTTTTGGGCACAATT
*
5291938 TAGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTGGGCCCA
65 TAGTACCTAAACTTGACACTTTTTCCTAATTTGATACCTAAACTTTTTTGGGCCCA
* * *
5291994 ATTTGGTACCTAAACTTGACA-CTTTTTCCTAATTTGGTATCTAAAC-TTTTTTGGGCAGAATTT
1 ATTTGGTACCTAAACTTGACATCTTTTTCCTAATTGGGTACCTAAACTTTTTTTGGGCACAATTT
* * *
5292057 GGTACCTAAACTTGAC-CTTTTTTTCCTAATTTGATATCTAAGCTTTTTT
66 AGTACCTAAACTTGACAC--TTTTTCCTAATTTGATACCTAAACTTTTTT
5292106 TTAGGTTCAA
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
117 1 0.01
118 29 0.30
119 48 0.49
121 19 0.20
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (120 bp):
ATTTGGTACCTAAACTTGACATCTTTTTCCTAATTGGGTACCTAAACTTTTTTTGGGCACAATTT
AGTACCTAAACTTGACACTTTTTCCTAATTTGATACCTAAACTTTTTTGGGCCCA
Found at i:5295578 original size:13 final size:13
Alignment explanation
Indices: 5295562--5295586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5295552 TGCAAACATT
5295562 AAAGAAAGAAAAG
1 AAAGAAAGAAAAG
5295575 AAAGAAAGAAAA
1 AAAGAAAGAAAA
5295587 TGAGAAGAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAAG
Found at i:5296763 original size:43 final size:45
Alignment explanation
Indices: 5296696--5296783 Score: 108
Period size: 43 Copynumber: 2.0 Consensus size: 45
5296686 TATGTGATTG
* * * * * *
5296696 ATATTGAAATGGCAAATATTAG-AAATAAATATGAAATGA-GAAA
1 ATATTAAAATGGAAAAGATGAGAAAAGAAATATCAAATGATGAAA
5296739 ATATTAAAATGGAAAAGATGAGAAAAGAAATATCAAATGATGAAA
1 ATATTAAAATGGAAAAGATGAGAAAAGAAATATCAAATGATGAAA
5296784 TGAGATGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
43 18 0.49
44 15 0.41
45 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.17, T:0.23
Consensus pattern (45 bp):
ATATTAAAATGGAAAAGATGAGAAAAGAAATATCAAATGATGAAA
Found at i:5298315 original size:49 final size:49
Alignment explanation
Indices: 5298254--5298347 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
5298244 TAAAAAGGGG
*
5298254 ATAAATAATGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAATGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCAATGT
*
5298303 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCA
1 ATAAATAATGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCA
5298348 TTGCATAGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.43, C:0.07, G:0.26, T:0.24
Consensus pattern (49 bp):
ATAAATAATGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCAATGT
Found at i:5300002 original size:46 final size:46
Alignment explanation
Indices: 5299935--5300148 Score: 274
Period size: 46 Copynumber: 4.6 Consensus size: 46
5299925 NNNNNNNNNN
* ** *
5299935 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGT
* * *
5299981 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-TCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCATCCATAAGT
*
5300028 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGT
*
5300074 GAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGT
5300120 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
5300149 TGCTCAACCA
Statistics
Matches: 146, Mismatches: 13, Indels: 18
0.82 0.07 0.10
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 2 0.01
45 2 0.01
46 99 0.68
47 29 0.20
48 2 0.01
49 1 0.01
50 3 0.02
51 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGT
Found at i:5306207 original size:22 final size:25
Alignment explanation
Indices: 5306182--5306228 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
5306172 ATTCATAATT
5306182 ATTATTT-T-ATT-TAAATTAAAAA
1 ATTATTTATAATTCTAAATTAAAAA
5306204 ATTATTTAATAATTCTAAATTAAAA
1 ATTATTT-ATAATTCTAAATTAAAA
5306229 TATATGAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 7 0.33
24 1 0.05
25 3 0.14
26 10 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATTTATAATTCTAAATTAAAAA
Found at i:5306490 original size:26 final size:25
Alignment explanation
Indices: 5306447--5306506 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
5306437 TGTAACTAAT
* *
5306447 TGAATTAAATATAGAATAAAAAGTTG
1 TGAATTAAAAAAAGAATAAAAA-TTG
* *
5306473 TGAATTAAAAAAATAATAAAAATTT
1 TGAATTAAAAAAAGAATAAAAATTG
5306498 TG-ATTAAAA
1 TGAATTAAAA
5306507 GATATTCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 7 0.23
25 4 0.13
26 19 0.63
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (25 bp):
TGAATTAAAAAAAGAATAAAAATTG
Found at i:5307021 original size:18 final size:18
Alignment explanation
Indices: 5306981--5307035 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
5306971 AAATTTCAAA
*
5306981 AAAAATTCAAAATAATTTTT
1 AAAAATT-AAAAT-ATTTAT
5307001 AAAAATTAAAATATTTAT
1 AAAAATTAAAATATTTAT
*
5307019 -AAAATTCAAA-ATTTAT
1 AAAAATTAAAATATTTAT
5307035 A
1 A
5307036 TTTTTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 6 0.19
17 9 0.28
18 5 0.16
19 5 0.16
20 7 0.22
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATTAAAATATTTAT
Found at i:5307526 original size:31 final size:30
Alignment explanation
Indices: 5307488--5307590 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
5307478 TTAATATAAT
*
5307488 ATTTGGTATCTAAACTTGATACTTTTTCCTA
1 ATTTGGTACCTAAACTTGATA-TTTTTCCTA
* * *
5307519 ATTTGGTACCCAAACTT--T-TTTTGCCCCA
1 ATTTGGTACCTAAACTTGATATTTT-TCCTA
* *
5307547 ATTTGGTACCTAAACTTGACATTTTTTCCTT
1 ATTTGGTACCTAAACTTGATA-TTTTTCCTA
5307578 ATTTGGTACCTAA
1 ATTTGGTACCTAA
5307591 GTTTTTTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
27 4 0.07
28 19 0.33
29 1 0.02
31 30 0.52
32 4 0.07
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (30 bp):
ATTTGGTACCTAAACTTGATATTTTTCCTA
Found at i:5311694 original size:4 final size:4
Alignment explanation
Indices: 5311685--5311715 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
5311675 ATTTGGCAAT
5311685 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
5311716 TCTCTTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:5313209 original size:17 final size:18
Alignment explanation
Indices: 5313184--5313224 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
5313174 TTAAAAGCTT
5313184 AAATCCATTAAAATTTAA
1 AAATCCATTAAAATTTAA
*
5313202 AAAT-CATTAATATTT-A
1 AAATCCATTAAAATTTAA
5313218 AAATCCA
1 AAATCCA
5313225 AATTGATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 12 0.57
18 4 0.19
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATCCATTAAAATTTAA
Found at i:5319754 original size:10 final size:10
Alignment explanation
Indices: 5319735--5319808 Score: 55
Period size: 10 Copynumber: 7.4 Consensus size: 10
5319725 ATATTTAAAT
*
5319735 TTATAAAAAA
1 TTATAGAAAA
5319745 TTATAGAAAA
1 TTATAGAAAA
**
5319755 TTTATTTAAAA
1 -TTATAGAAAA
*
5319766 TTATATAAGAA
1 TTATAGAA-AA
5319777 -TATAGAAAA
1 TTATAGAAAA
*
5319786 TTATTGCAAAA
1 TTATAG-AAAA
5319797 -TATA-AAAA
1 TTATAGAAAA
5319805 TTAT
1 TTAT
5319809 TAACATTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
8 4 0.08
9 5 0.10
10 29 0.56
11 14 0.27
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.36
Consensus pattern (10 bp):
TTATAGAAAA
Found at i:5319755 original size:21 final size:21
Alignment explanation
Indices: 5319731--5319770 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5319721 AAGAATATTT
5319731 AAATTTATAAAAAATTATAGA
1 AAATTTATAAAAAATTATAGA
**
5319752 AAATTTATTTAAAATTATA
1 AAATTTATAAAAAATTATA
5319771 TAAGAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
AAATTTATAAAAAATTATAGA
Found at i:5319764 original size:31 final size:31
Alignment explanation
Indices: 5319726--5319787 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
5319716 TCTAAAAGAA
*
5319726 TATTTAAATTTATA-AAAAATTATAGAAAATT
1 TATTTAAAATTATATAAAAA-TATAGAAAATT
*
5319757 TATTTAAAATTATATAAGAATATAGAAAATT
1 TATTTAAAATTATATAAAAATATAGAAAATT
5319788 ATTGCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (31 bp):
TATTTAAAATTATATAAAAATATAGAAAATT
Found at i:5319929 original size:20 final size:20
Alignment explanation
Indices: 5319874--5319930 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
5319864 AATTTTTACA
* *
5319874 TAAAAATTATTCAAA-TGAT
1 TAAAAATTATTAAAATTTAT
*
5319893 AAAAAATTA-TAAGAATTTAT
1 TAAAAATTATTAA-AATTTAT
5319913 TAAAAATTATTAAAATTT
1 TAAAAATTATTAAAATTT
5319931 TAGTTGGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 2 0.06
19 10 0.32
20 16 0.52
21 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (20 bp):
TAAAAATTATTAAAATTTAT
Found at i:5320079 original size:29 final size:27
Alignment explanation
Indices: 5320015--5320086 Score: 67
Period size: 29 Copynumber: 2.6 Consensus size: 27
5320005 GTAGTGTTTT
*
5320015 TAATTTTTTTAATAATTTTCTACATTTC
1 TAATTTTTTT-ATAATTTTATACATTTC
*
5320043 T-ATATTTTTATAATGTTTTAATAC-TTTC
1 TAATTTTTTTATAA--TTTT-ATACATTTC
*
5320071 TAATTTTTTTAAAATT
1 TAATTTTTTTATAATT
5320087 AATAACTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
26 4 0.11
27 9 0.25
28 10 0.28
29 13 0.36
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.61
Consensus pattern (27 bp):
TAATTTTTTTATAATTTTATACATTTC
Found at i:5323937 original size:46 final size:46
Alignment explanation
Indices: 5323885--5324057 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
5323875 TTGGGCATCT
*
5323885 GAGCTCGTTGAGTCGAGTCCGAGTTCACTTATGGATGTGAATGTCC
1 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCC
* *
5323931 GAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACTAGGCATCC
1 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA-T--G--TCC
* * *
5323978 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCC
* *
5324024 GAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5324058 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 6 0.06
45 3 0.03
46 59 0.55
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (46 bp):
GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCC
Found at i:5324037 original size:93 final size:93
Alignment explanation
Indices: 5323878--5324050 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
5323868 AGGATATTTG
* * * * *
5323878 GGCATCTGAGCTCGTTGAGTCGAGTCCGAGTTCACTTATGGATGTGAATGTCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTCGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG
5323943 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
5323971 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG
1 GGCATCCGAGCTCGTTGAGTCGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG
5324036 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
5324051 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTCGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:5329306 original size:21 final size:21
Alignment explanation
Indices: 5329264--5329307 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
5329254 CTTAATTCAT
* *
5329264 TTCATACTAAAACATTCCCAA
1 TTCATACTAAAACATACACAA
* *
5329285 TTCATATTTAAACATACACAA
1 TTCATACTAAAACATACACAA
5329306 TT
1 TT
5329308 GTCCATAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (21 bp):
TTCATACTAAAACATACACAA
Found at i:5333370 original size:84 final size:85
Alignment explanation
Indices: 5333269--5333472 Score: 259
Period size: 86 Copynumber: 2.4 Consensus size: 85
5333259 CGAAGAATAA
* * ** * *
5333269 TGACACATATAGTGCATCTTCAAATATACCGAAGCATTTACACTGG-CATACAGTGCATCATC-A
1 TGACACACATAGTGCATCATCGGATATACCGAAGCATTTACACTGGACACACAATGCATCATCGA
*
5333332 GATAAACCAAAAAAAATGTAT
66 -ATAAACCAAAAAAAATGTAC
* *
5333353 TGACACACATAGTGCATCATCGGATATACCGAAACATTTATACTGGCACACACAATGCATCATCG
1 TGACACACATAGTGCATCATCGGATATACCGAAGCATTTACACTGG-ACACACAATGCATCATCG
** *
5333418 AATAAACTGAAAGAAATGTAC
65 AATAAACCAAAAAAAATGTAC
*
5333439 TGGCACACATAGTGCATCATCGGATATACCGAAG
1 TGACACACATAGTGCATCATCGGATATACCGAAG
5333473 TATAACTTGT
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
84 40 0.39
86 62 0.60
87 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.23
Consensus pattern (85 bp):
TGACACACATAGTGCATCATCGGATATACCGAAGCATTTACACTGGACACACAATGCATCATCGA
ATAAACCAAAAAAAATGTAC
Found at i:5333403 original size:43 final size:43
Alignment explanation
Indices: 5333222--5333471 Score: 170
Period size: 43 Copynumber: 6.0 Consensus size: 43
5333212 AAACTAAAGG
* * * * *
5333222 AAATATGCTGGCACACATAGTGCATAATCAGATAAATCG-AA-
1 AAATATACTGGCACACATAGTGCATCATCGGATATACCGAAAC
* * * * ** *
5333263 GAATA-A-TGACACATATAGTGCATCTTCAAATATACCGAAGC
1 AAATATACTGGCACACATAGTGCATCATCGGATATACCGAAAC
** * * * * * *
5333304 ATTTACACTGGCATAC--AGTGCATCATCAGATAAACCAAAAA
1 AAATATACTGGCACACATAGTGCATCATCGGATATACCGAAAC
* * *
5333345 AAATGTATTGACACACATAGTGCATCATCGGATATACCGAAAC
1 AAATATACTGGCACACATAGTGCATCATCGGATATACCGAAAC
** * * * * * *
5333388 ATTTATACTGGCACACACAATGCATCATCGAATAAACTGAAAG
1 AAATATACTGGCACACATAGTGCATCATCGGATATACCGAAAC
*
5333431 AAATGTACTGGCACACATAGTGCATCATCGGATATACCGAA
1 AAATATACTGGCACACATAGTGCATCATCGGATATACCGAA
5333472 GTATAACTTG
Statistics
Matches: 151, Mismatches: 52, Indels: 10
0.71 0.24 0.05
Matches are distributed among these distances:
39 24 0.16
40 1 0.01
41 34 0.23
42 1 0.01
43 91 0.60
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (43 bp):
AAATATACTGGCACACATAGTGCATCATCGGATATACCGAAAC
Found at i:5347462 original size:15 final size:15
Alignment explanation
Indices: 5347444--5347499 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
5347434 TGAAGTCGAA
5347444 GATGATGAAGATTAT
1 GATGATGAAGATTAT
** *
5347459 GATGATGGTGATGAT
1 GATGATGAAGATTAT
5347474 GTAT-ATGAAG-TTGAT
1 G-ATGATGAAGATT-AT
5347489 GATGATGAAGA
1 GATGATGAAGA
5347500 GCTGGAGGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
14 3 0.10
15 26 0.84
16 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (15 bp):
GATGATGAAGATTAT
Found at i:5348002 original size:166 final size:160
Alignment explanation
Indices: 5347728--5348053 Score: 580
Period size: 166 Copynumber: 2.0 Consensus size: 160
5347718 TCTTGGAAGG
*
5347728 TTTGTATGTTTATGAAATTTCATGACTATTTTTAGTGTTAAATGAAGAAATTATATTTTTGATAT
1 TTTGTATGTTTATGAAATTTCATGACTATTTTTAGTATTAAATGAAGAAATTATATTTTTGATAT
5347793 GAACAATGGAAATCATCTACAAACCTCAAGACCCACACTTGCTATGACAACACTTTCAATGCCAA
66 GAACAATGGAAATCATCTACAAACCTCAAGACCCACACTTGCTATGACAACACTTTCAATG-C--
5347858 GTTAAAATTACTGATAGAAAACACTTCAGCTGACCC
128 --T-AAATTACTGATAGAAAACACTTCAGCTGACCC
5347894 TTTGTATGTTTATGAAATTTCATGACTATTTTTAGTATTAAATGAAGAAATTATATTTTTGATAT
1 TTTGTATGTTTATGAAATTTCATGACTATTTTTAGTATTAAATGAAGAAATTATATTTTTGATAT
5347959 GAACAATGGAAATCATCTACAAACCTCAAGACCCACACTTGCTATGACAACACTTTCAATGCTAA
66 GAACAATGGAAATCATCTACAAACCTCAAGACCCACACTTGCTATGACAACACTTTCAATGCTAA
*
5348024 CTTACTGATAGAAAACACTTCAGCTGACCC
131 ATTACTGATAGAAAACACTTCAGCTGACCC
5348054 AACCATTGAT
Statistics
Matches: 158, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
160 31 0.20
161 1 0.01
165 1 0.01
166 125 0.79
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (160 bp):
TTTGTATGTTTATGAAATTTCATGACTATTTTTAGTATTAAATGAAGAAATTATATTTTTGATAT
GAACAATGGAAATCATCTACAAACCTCAAGACCCACACTTGCTATGACAACACTTTCAATGCTAA
ATTACTGATAGAAAACACTTCAGCTGACCC
Found at i:5350409 original size:23 final size:25
Alignment explanation
Indices: 5350364--5350411 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
5350354 TGTTAAATTA
*
5350364 AAATACATTACAATATTATTTTTTT
1 AAATACATTACAATATTAATTTTTT
*
5350389 AAATACATTGC-A-ATTAATTTTTT
1 AAATACATTACAATATTAATTTTTT
5350412 TAAAATTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 1 0.05
25 10 0.48
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (25 bp):
AAATACATTACAATATTAATTTTTT
Found at i:5350417 original size:25 final size:26
Alignment explanation
Indices: 5350361--5350417 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
5350351 ATTTGTTAAA
*
5350361 TTAAAATACATTACAATATTATTTTT
1 TTAAAATACATTACAATATAATTTTT
*
5350387 TT-AAATACATTGCAAT-TAATTTTT
1 TTAAAATACATTACAATATAATTTTT
5350411 TTAAAAT
1 TTAAAAT
5350418 TTCAAAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 9 0.32
25 17 0.61
26 2 0.07
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (26 bp):
TTAAAATACATTACAATATAATTTTT
Found at i:5350892 original size:119 final size:121
Alignment explanation
Indices: 5350701--5350917 Score: 332
Period size: 119 Copynumber: 1.8 Consensus size: 121
5350691 TCTTTCATCT
* * *
5350701 TCTTCTTCTTTTTAACATGAGAACATAATGAGTAAAGTTTAATTCTAACCCCTCTAATTTTTTAA
1 TCTTCTTCTTTTTAACATGAGAACATAATGAGTAAAGTTTAACTCCAACCCCTCTAATTCTTTAA
5350766 GATTATAAGAATGGTGAAATTTCAATTTGATCCATGGACACTTGTCGATTGTTTTA
66 GATTATAAGAATGGTGAAATTTCAATTTGATCCATGGACACTTGTCGATTGTTTTA
* * *
5350822 TCTT-TTCTTTTTTACATGAGAACAT-ATGGGTAAA-TTTCAACTCCAATCCCTCTAATTCTTTA
1 TCTTCTTCTTTTTAACATGAGAACATAATGAGTAAAGTTT-AACTCCAACCCCTCTAATTCTTTA
* *
5350884 CGATTATAAGAATGGTTAAATTTCAATTTGATCC
65 AGATTATAAGAATGGTGAAATTTCAATTTGATCC
5350918 TCATATTTCA
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
118 3 0.03
119 60 0.69
120 20 0.23
121 4 0.05
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (121 bp):
TCTTCTTCTTTTTAACATGAGAACATAATGAGTAAAGTTTAACTCCAACCCCTCTAATTCTTTAA
GATTATAAGAATGGTGAAATTTCAATTTGATCCATGGACACTTGTCGATTGTTTTA
Found at i:5355361 original size:32 final size:32
Alignment explanation
Indices: 5355325--5355385 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
5355315 GCTCCTGGCA
5355325 TTTGCAATCGGATTCCATGTTTTTGTTACTTT
1 TTTGCAATCGGATTCCATGTTTTTGTTACTTT
5355357 TTTGCAATCGGATTCCATGTTTTTGTTAC
1 TTTGCAATCGGATTCCATGTTTTTGTTAC
5355386 CTTTCTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (32 bp):
TTTGCAATCGGATTCCATGTTTTTGTTACTTT
Found at i:5365893 original size:20 final size:20
Alignment explanation
Indices: 5365846--5365884 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5365836 CTAAGTCAAT
* *
5365846 GGAATGGAAAGTAAGTAAAA
1 GGAATGGTAAGTAAATAAAA
5365866 GGAATGGTAAGTAAATAAA
1 GGAATGGTAAGTAAATAAA
5365885 CGGAGTGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.28, T:0.18
Consensus pattern (20 bp):
GGAATGGTAAGTAAATAAAA
Found at i:5370113 original size:12 final size:12
Alignment explanation
Indices: 5370096--5370125 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5370086 TCAAGGTGTT
5370096 ACACGGCCTAGC
1 ACACGGCCTAGC
*
5370108 ACACGGCCTGGC
1 ACACGGCCTAGC
5370120 ACACGG
1 ACACGG
5370126 GCGTGTGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:5378082 original size:70 final size:70
Alignment explanation
Indices: 5377943--5378103 Score: 171
Period size: 70 Copynumber: 2.3 Consensus size: 70
5377933 ACCTATATAG
* * * * * * *
5377943 CCAAATACACAAGGTTCATTATATTATCTCATATGGCCGAATATATAAGTTCAAATTATCATCAC
1 CCAAATATACAA-GTTCAATAAAATATCTCATATGGCCGAATATACAAATTCAAATTAACATCAC
5378008 ATGTAA
65 ATGTAA
* * * * * *
5378014 CCTAATGTTCAAGTTCAATAAAATATCTCATATGGCTGAATATACAAATTC-AATATAACCTCAT
1 CCAAATATACAAGTTCAATAAAATATCTCATATGGCCGAATATACAAATTCAAAT-TAACATCAC
5378078 ATGTAA
65 ATGTAA
*
5378084 TCAAATATACAAGTTCAATA
1 CCAAATATACAAGTTCAATA
5378104 TAACTTCACA
Statistics
Matches: 72, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
69 3 0.04
70 61 0.85
71 8 0.11
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (70 bp):
CCAAATATACAAGTTCAATAAAATATCTCATATGGCCGAATATACAAATTCAAATTAACATCACA
TGTAA
Found at i:5387112 original size:46 final size:46
Alignment explanation
Indices: 5386986--5387146 Score: 161
Period size: 46 Copynumber: 3.5 Consensus size: 46
5386976 GTGCCGATTT
* *
5386986 CATGTCCCAGACATGGTCTTACAC-TG-ACACATCTCGTAGCCGATG
1 CATGTCCCAGACATGGTCTTACACTTGCACTCGTCTCG-AGCCGATG
* * *
5387031 CATGTCCTAGACAT-GTCTTACACTGGCA-TAGGTCTCGAGGCCGATG
1 CATGTCCCAGACATGGTCTTACACTTGCACT-CGTCTCGA-GCCGATG
* * *
5387077 CATGTCCTAGACAT-GTCTTACACTTGCACTCGTCTCAATGCTGATG
1 CATGTCCCAGACATGGTCTTACACTTGCACTCGTCTCGA-GCCGATG
*
5387123 TCATGTCCCAGGCATGGTCTTACA
1 -CATGTCCCAGACATGGTCTTACA
5387147 TTGGTTCTCA
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
44 9 0.09
45 15 0.15
46 52 0.54
47 13 0.13
48 8 0.08
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGGTCTTACACTTGCACTCGTCTCGAGCCGATG
Found at i:5392863 original size:64 final size:64
Alignment explanation
Indices: 5392747--5392883 Score: 184
Period size: 64 Copynumber: 2.1 Consensus size: 64
5392737 GCACAGGGTT
* *
5392747 CACACAGGCCACGGACACGAGCGTGTGCCCAGGCCATGTAACTAACTAATTCACAACTTAGAGA
1 CACACGGGCCACGGACACGAGCGTGTGCCCAGGCCATGTAACTAACTAATTCACAACTTAAAGA
* * * * * * * *
5392811 CACATGGGCCAGGGACACGGGCGTGTGTCGAGGCCGTGTAACTCACTGATTCACAACTTAAAGA
1 CACACGGGCCACGGACACGAGCGTGTGCCCAGGCCATGTAACTAACTAATTCACAACTTAAAGA
5392875 CACACGGGC
1 CACACGGGC
5392884 AGGTACGTGG
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.16
Consensus pattern (64 bp):
CACACGGGCCACGGACACGAGCGTGTGCCCAGGCCATGTAACTAACTAATTCACAACTTAAAGA
Found at i:5395120 original size:22 final size:20
Alignment explanation
Indices: 5395082--5395122 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
5395072 GAATGGATAA
*
5395082 TATATTTTTAATTACAATTT
1 TATATTTTTAATCACAATTT
5395102 TATATTATTTAATACACAATT
1 TATATT-TTTAAT-CACAATT
5395123 AGTGAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 6 0.33
22 6 0.33
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTTTTAATCACAATTT
Found at i:5395921 original size:18 final size:18
Alignment explanation
Indices: 5395898--5395934 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5395888 GAAATAAAAA
5395898 AAAATTGTAACTTTCATG
1 AAAATTGTAACTTTCATG
* *
5395916 AAAATTGTGATTTTCATG
1 AAAATTGTAACTTTCATG
5395934 A
1 A
5395935 TATGATTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (18 bp):
AAAATTGTAACTTTCATG
Found at i:5402613 original size:16 final size:17
Alignment explanation
Indices: 5402574--5402613 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
5402564 AGTAAAAATG
5402574 TAATTTTATCATTTTAA
1 TAATTTTATCATTTTAA
*
5402591 TAA-TTTAT-ATTTTTA
1 TAATTTTATCATTTTAA
5402606 TAATTTTA
1 TAATTTTA
5402614 AAAGGATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 9 0.43
16 9 0.43
17 3 0.14
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATTTTATCATTTTAA
Found at i:5403066 original size:6 final size:6
Alignment explanation
Indices: 5403055--5403087 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
5403045 CTCATTCTTT
*
5403055 AATAGC AATAGC AATAGC AATAGC AATAAC AAT
1 AATAGC AATAGC AATAGC AATAGC AATAGC AAT
5403088 GACAGCTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.18
Consensus pattern (6 bp):
AATAGC
Found at i:5403462 original size:6 final size:6
Alignment explanation
Indices: 5403453--5403487 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5403443 TGAATGTGTA
* *
5403453 TGTGAC TGTGAC TGTGAC TGTGAT TGTGAT TGTGA
1 TGTGAC TGTGAC TGTGAC TGTGAC TGTGAC TGTGA
5403488 GTACATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (6 bp):
TGTGAC
Found at i:5404213 original size:8 final size:8
Alignment explanation
Indices: 5404200--5404224 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5404190 AATTATTTTT
5404200 AAAATTTA
1 AAAATTTA
5404208 AAAATTTA
1 AAAATTTA
5404216 AAAATTTA
1 AAAATTTA
5404224 A
1 A
5404225 TGTCTTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAATTTA
Found at i:5404785 original size:23 final size:23
Alignment explanation
Indices: 5404748--5404797 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5404738 AGTTGATATG
* *
5404748 ATTTTTATAATTTTTAATATTTT
1 ATTTTTATAATTTTTAAGAATTT
5404771 ATTTTT-TAATTTTTTAAGAATTT
1 ATTTTTATAA-TTTTTAAGAATTT
5404794 ATTT
1 ATTT
5404798 GCTTTGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
ATTTTTATAATTTTTAAGAATTT
Found at i:5408654 original size:11 final size:11
Alignment explanation
Indices: 5408638--5408662 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5408628 TTCAGCTAAT
5408638 GAAAATGAAGA
1 GAAAATGAAGA
5408649 GAAAATGAAGA
1 GAAAATGAAGA
5408660 GAA
1 GAA
5408663 TTCTAGATAT
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:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (11 bp):
GAAAATGAAGA
Found at i:5410520 original size:3 final size:3
Alignment explanation
Indices: 5410512--5410536 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5410502 TCATAGTTTG
5410512 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
5410537 GTAATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5411868 original size:16 final size:16
Alignment explanation
Indices: 5411849--5411880 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5411839 GGTTAAATTC
5411849 AACTCATTTTAAAAAG
1 AACTCATTTTAAAAAG
5411865 AACTCATTTTAAAAAG
1 AACTCATTTTAAAAAG
5411881 GTTAAAAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (16 bp):
AACTCATTTTAAAAAG
Found at i:5412308 original size:18 final size:19
Alignment explanation
Indices: 5412285--5412327 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
5412275 TTACCACTAT
5412285 ATTTTAA-CTTT-GTATTGA
1 ATTTTAAGCTTTAG-ATTGA
5412303 ATTTTAAGGCTTTAGATTGA
1 ATTTTAA-GCTTTAGATTGA
5412323 ATTTT
1 ATTTT
5412328 TTTCACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.32
20 14 0.64
21 1 0.05
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (19 bp):
ATTTTAAGCTTTAGATTGA
Found at i:5412589 original size:24 final size:24
Alignment explanation
Indices: 5412543--5412589 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5412533 ATAGAAATTT
*
5412543 TAATTTTAAATATTTCAAGTTTAC
1 TAATTTTAAATATTTCAAATTTAC
*
5412567 TAATTTTTAATATTT-ATAATTTA
1 TAATTTTAAATATTTCA-AATTTA
5412590 AGTCATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (24 bp):
TAATTTTAAATATTTCAAATTTAC
Found at i:5412716 original size:30 final size:29
Alignment explanation
Indices: 5412678--5412735 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
5412668 ATTGAAGGGT
5412678 AAAATTTAATCAAAAATTAAAG-TTAGTGA
1 AAAATTTAAT-AAAAATTAAAGTTTAGTGA
*
5412707 AAAACTTTAATAAAATTTAAAGTTTAGTG
1 AAAA-TTTAATAAAAATTAAAGTTTAGTG
5412736 GTAAAATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.34
Consensus pattern (29 bp):
AAAATTTAATAAAAATTAAAGTTTAGTGA
Found at i:5412721 original size:29 final size:30
Alignment explanation
Indices: 5412678--5412749 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
5412668 ATTGAAGGGT
5412678 AAAATTTAATCAAAAATTAAAG-TTAGTGA
1 AAAATTTAATCAAAAATTAAAGTTTAGTGA
* *
5412707 AAAACTTTAAT-AAAATTTAAAGTTTAGTGGT
1 AAAA-TTTAATCAAAAATTAAAGTTTAGT-GA
*
5412738 AAAATTCAATCA
1 AAAATTTAATCA
5412750 TACGTAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 14 0.39
30 16 0.44
31 6 0.17
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (30 bp):
AAAATTTAATCAAAAATTAAAGTTTAGTGA
Found at i:5416782 original size:21 final size:19
Alignment explanation
Indices: 5416758--5416803 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
5416748 ATTCCAAATA
*
5416758 TTCCATAAAGTTCATACTGAC
1 TTCCA-AAA-TTCATACTAAC
5416779 TTCC-AAATTCATACTAAC
1 TTCCAAAATTCATACTAAC
5416797 TTCCAAA
1 TTCCAAA
5416804 TGTCATAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 14 0.61
19 5 0.22
21 4 0.17
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (19 bp):
TTCCAAAATTCATACTAAC
Found at i:5416791 original size:18 final size:18
Alignment explanation
Indices: 5416768--5416810 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
5416758 TTCCATAAAG
*
5416768 TTCATACTGACTTCCAAA
1 TTCATACTAACTTCCAAA
5416786 TTCATACTAACTTCCAAA
1 TTCATACTAACTTCCAAA
5416804 TGTCATA
1 T-TCATA
5416811 ACTCAGTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.35
Consensus pattern (18 bp):
TTCATACTAACTTCCAAA
Found at i:5418605 original size:43 final size:43
Alignment explanation
Indices: 5418557--5418740 Score: 199
Period size: 43 Copynumber: 4.3 Consensus size: 43
5418547 TTTTAGAAAT
* * *
5418557 AAACGCCGCTATAGATCAGGATCTTTAGCGGCGCTTTTCTAAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCTAAC
* *** * *
5418600 AAACGCCGCTATAGCTTGGGATCTTTAGCGGCGCTTTTCTAAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCTAAC
* * *
5418643 AAACGCCACTATAGCTCAAGACCTTTAGCGACGCTTTTAC-CAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTT-CTAAC
* ** *
5418686 AAACGCCACTATAGATCAAAGACCTTTAGCGACGCTTTGATTAC
1 AAACGCCGCTATAGATC-AAGACCTTTAGCGACGCTTTTCTAAC
5418730 AAACGCCGCTA
1 AAACGCCGCTA
5418741 AAAACACCAT
Statistics
Matches: 123, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
43 90 0.73
44 33 0.27
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCTAAC
Found at i:5418833 original size:16 final size:16
Alignment explanation
Indices: 5418812--5418845 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5418802 AAATATTAAA
*
5418812 TATTAAAATAAAACAT
1 TATTAAAATAAAAAAT
*
5418828 TATTAATATAAAAAAT
1 TATTAAAATAAAAAAT
5418844 TA
1 TA
5418846 ATTAGTATTA
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:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATAAAAAAT
Found at i:5419099 original size:15 final size:15
Alignment explanation
Indices: 5419079--5419108 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5419069 TGGATCATCT
5419079 TCATCTTCATCTTCA
1 TCATCTTCATCTTCA
*
5419094 TCATCTTCTTCTTCA
1 TCATCTTCATCTTCA
5419109 CTTTCAACTC
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:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (15 bp):
TCATCTTCATCTTCA
Found at i:5420292 original size:14 final size:14
Alignment explanation
Indices: 5420273--5420302 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5420263 CAGATTAGGT
5420273 GTGGGAAAAGGTTA
1 GTGGGAAAAGGTTA
5420287 GTGGGAAAAGGTTA
1 GTGGGAAAAGGTTA
5420301 GT
1 GT
5420303 TGCTTTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.23
Consensus pattern (14 bp):
GTGGGAAAAGGTTA
Found at i:5423471 original size:47 final size:46
Alignment explanation
Indices: 5423417--5423517 Score: 157
Period size: 47 Copynumber: 2.2 Consensus size: 46
5423407 ATACATAGGT
* * *
5423417 TTTTTTAAGTTATATTTATAAAAATTAGATAAATTTAAAAATTTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATT-AAAAGTTTAG
5423464 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAGTTTAG
1 TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAGTTTAG
5423510 TGTTTTTA
1 T-TTTTTA
5423518 TTTCATTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
46 10 0.20
47 40 0.80
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (46 bp):
TTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAGTTTAG
Found at i:5424037 original size:14 final size:15
Alignment explanation
Indices: 5424014--5424051 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5424004 GTCCCTTAAT
5424014 TAAA-CCATAATACC
1 TAAATCCATAATACC
*
5424028 T-AATCCATAATCCC
1 TAAATCCATAATACC
5424042 TAAATCCATA
1 TAAATCCATA
5424052 TATGTAGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATACC
Found at i:5424311 original size:22 final size:21
Alignment explanation
Indices: 5424286--5424328 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
5424276 TAGCTAACAT
5424286 CTAACTCCTAAACCCCTAACCC
1 CTAACTCCTAAACCCC-AACCC
* * *
5424308 CTAAGTCTTAAATCCCAACCC
1 CTAACTCCTAAACCCCAACCC
5424329 TTAATTAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (21 bp):
CTAACTCCTAAACCCCAACCC
Found at i:5424358 original size:17 final size:17
Alignment explanation
Indices: 5424332--5424375 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
5424322 CCAACCCTTA
*
5424332 ATTAAACCATAATCCCT
1 ATTAATCCATAATCCCT
5424349 ATTAATCCATAATCCCT
1 ATTAATCCATAATCCCT
5424366 A--AATCCATAA
1 ATTAATCCATAA
5424376 ATACTCCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 9 0.35
17 17 0.65
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTAATCCATAATCCCT
Found at i:5424396 original size:323 final size:312
Alignment explanation
Indices: 5423843--5424433 Score: 708
Period size: 323 Copynumber: 1.8 Consensus size: 312
5423833 TAAATTATAC
* * *
5423843 ATCTTTTACAATTACATAATAACATATTTAAAATATAAATAAAAATCTAAACCCAAAACCCTAAC
1 ATCTTTTACAACTACATAATAACATATTTAAAATATAAATAAAAACCAAAACCCAAAACCCTAAC
* * *
5423908 CCGACCCCTAAAACTCTAAACCCTAAATCCCTAACTCTTAACCACTAACGTCTAACCCCTAAACT
66 CCGACCCATAAAACTCTAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCCTAAACC
*
5423973 CTTAACCCCTAAACCTTAAATCTCGACCAACGTCCCTTAATTAAACCATAATACCTAATCCATAA
131 CCTAACCCCTAAACCTTAAA-CTC-ACCAAC--CCCTTAATTAAACCATAATACCTAATCCATAA
* * * ** * *
5424038 TCCCTAAATCCATATATGTAGTAGTCCCTAAACCTTTAAATATGAACCCCTAAACCGGCCTTAAA
192 TCCCTAAATCCATATATATACTACTAACTAAACCTTAAAATATGAACCCCTAAACCGACCTTAAA
5424103 TATTAAATTTATCATATACTCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
257 TATTAAATTTATCATATACTCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
*
5424159 ATCTTTTACAACTACATAATAACATATTTTAAATATAATAATAATCTAAACCCAAAACCCAAAAC
1 ATCTTTTACAACTACATAATAACATATTTAAAATAT-A-AATAA---AAA-CCAAAACCCAAAAC
* * *
5424224 CCTAACCTGACCCATGAAAC-CTTAAGCCCCTAAATCCCTAACTCTTAACCCTTAGCTAACATCT
60 CCTAACCCGACCCATAAAACTC-TAA-ACCCTAAATCCCTAACTCTTAA-CC--A-CTAACATCT
* ** *
5424288 AACTCCTAAACCCCTAACCCCTAAGTCTTAAA-TC-CCAA-CCCTTAATTAAACCATAATCCCTA
119 AACCCCTAAACCCCTAACCCCTAAACCTTAAACTCACCAACCCCTTAATTAAACCATAATACC--
* * * *
5424350 TTAATCCATAATCCCTAAATCCATA-A-ATACTCCCTAACTAAAACCTTAAAATATGATCTCTTA
182 -TAATCCATAATCCCTAAATCCATATATATACT-ACTAACT-AAACCTTAAAATATGAACCCCTA
*
5424413 AACCGACCTTAAATCTTAAAT
244 AACCGACCTTAAATATTAAAT
5424434 AAAATTATAT
Statistics
Matches: 231, Mismatches: 27, Indels: 27
0.81 0.09 0.09
Matches are distributed among these distances:
316 34 0.15
317 1 0.00
318 5 0.02
320 21 0.09
321 7 0.03
322 36 0.16
323 87 0.38
324 2 0.01
325 2 0.01
326 1 0.00
327 35 0.15
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.28
Consensus pattern (312 bp):
ATCTTTTACAACTACATAATAACATATTTAAAATATAAATAAAAACCAAAACCCAAAACCCTAAC
CCGACCCATAAAACTCTAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCCTAAACC
CCTAACCCCTAAACCTTAAACTCACCAACCCCTTAATTAAACCATAATACCTAATCCATAATCCC
TAAATCCATATATATACTACTAACTAAACCTTAAAATATGAACCCCTAAACCGACCTTAAATATT
AAATTTATCATATACTCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
Found at i:5424853 original size:73 final size:73
Alignment explanation
Indices: 5424729--5424887 Score: 237
Period size: 73 Copynumber: 2.2 Consensus size: 73
5424719 TAAATCAATT
* * *
5424729 AAACACCGCTAAATCCCCGAAAGCGCAAAAAAAGGTGTAGTTTTGGCTTAGGTTTTTTGCGGCGC
1 AAACGCCGCTAAATCCCCGAAAGCGCAAAAAAAGGCGTAGTTTTGGATTAGGTTTTTTGCGGCGC
*
5424794 TTTCTAAA
66 TTTCCAAA
* * * *
5424802 AAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGATTAGGTTTTTTGCGGCGC
1 AAACGCCGCTAAATCCCCGAAAGCGCAAAAAAAGGCGTAGTTTTGGATTAGGTTTTTTGCGGCGC
*
5424867 TTTCCCAA
66 TTTCCAAA
5424875 AAACGCCGCTAAA
1 AAACGCCGCTAAA
5424888 GCCCTGAGCA
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (73 bp):
AAACGCCGCTAAATCCCCGAAAGCGCAAAAAAAGGCGTAGTTTTGGATTAGGTTTTTTGCGGCGC
TTTCCAAA
Found at i:5425266 original size:113 final size:113
Alignment explanation
Indices: 5424787--5425340 Score: 910
Period size: 113 Copynumber: 4.9 Consensus size: 113
5424777 TAGGTTTTTT
* * * *
5424787 GCGGCGCTTTCTAAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGATTA
1 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCAC-AAAGCTCACAAAACTGCGTCGTTTTGGATTA
*
5424852 GGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTA
65 GGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * **
5424901 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAAACTGCGTCGTTTTACATT
1 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCAC-AAAGCTCAC-AAAACTGCGTCGTTTTGGATT
* *
5424966 AGGTTTTTTGCGGCGCTATCTCAAAAACGCCGCTAAAGCCGTGAGCATTA
64 AGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
*
5425016 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCACAAAGCTCACAAAACTGCATCGTTTTGGATTAG
1 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCACAAAGCTCACAAAACTGCGTCGTTTTGGATTAG
5425081 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
66 G-TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* *
5425130 GCGGCGCTTCCTTAAAAATGCCGCTAAATCCACAAAGCTCACAAAACTGCGTCGTTTTGGATTAT
1 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCACAAAGCTCACAAAACTGCGTCGTTTTGGATTAG
5425195 GTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
66 GTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* *
5425243 GCGGCACTTCCTTAAAAACGCCGCTAAATCCACAAAGCTCACAAAACTGCGTTGTTTTGGATTAG
1 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCACAAAGCTCACAAAACTGCGTCGTTTTGGATTAG
* *
5425308 GTTTTTTGCGGCGCTTTTTAAAAAACGCCGCTA
66 GTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTA
5425341 TTGCTTATTG
Statistics
Matches: 415, Mismatches: 23, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
113 160 0.39
114 159 0.38
115 96 0.23
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (113 bp):
GCGGCGCTTCCTTAAAAACGCCGCTAAATCCACAAAGCTCACAAAACTGCGTCGTTTTGGATTAG
GTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:5425274 original size:227 final size:228
Alignment explanation
Indices: 5424800--5425340 Score: 906
Period size: 227 Copynumber: 2.4 Consensus size: 228
5424790 GCGCTTTCTA
* *
5424800 AAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGATTAGGTTTTTTGCGGC
1 AAAAACGCCGCTAAATCCAC-AAAGCTCACAAAACTGCGTCGTTTTGGATTAGGTTTTTTGCGGC
* *
5424865 GCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAT
65 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAAT
*
5424930 CCCCGAAAGCTCACAAAAACTGCGTCGTTTTACATTAGGTTTTTTGCGGCGCTATCTCAAAAACG
130 CCACGAAAGCTCACAAAAACTGCGTCGTTTTACATTAGGTTTTTTGCGGCGCTATCTCAAAAACG
* *
5424995 CCGCTAAAGCCGTGAGCATTAGCGGCGCTTCCTT
195 CCGCTAAAGCCCTGAGCATTAGCGGCACTTCCTT
*
5425029 AAAAACGCCGCTAAATCCACAAAGCTCACAAAACTGCATCGTTTTGGATTAGGTTTTTTTGCGGC
1 AAAAACGCCGCTAAATCCACAAAGCTCACAAAACTGCGTCGTTTTGGATTAGG-TTTTTTGCGGC
*
5425094 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAAATGCCGCTAAAT
65 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAAT
** * *
5425159 CCAC-AAAGCTCAC-AAAACTGCGTCGTTTTGGATTATGTTTTTTGCGGCGCTTTCTCAAAAACG
130 CCACGAAAGCTCACAAAAACTGCGTCGTTTTACATTAGGTTTTTTGCGGCGCTATCTCAAAAACG
5425222 CCGCTAAAGCCCTGAGCATTAGCGGCACTTCCTT
195 CCGCTAAAGCCCTGAGCATTAGCGGCACTTCCTT
*
5425256 AAAAACGCCGCTAAATCCACAAAGCTCACAAAACTGCGTTGTTTTGGATTAGGTTTTTTGCGGCG
1 AAAAACGCCGCTAAATCCACAAAGCTCACAAAACTGCGTCGTTTTGGATTAGGTTTTTTGCGGCG
* *
5425321 CTTTTTAAAAAACGCCGCTA
66 CTTTCTCAAAAACGCCGCTA
5425341 TTGCTTATTG
Statistics
Matches: 294, Mismatches: 17, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
226 30 0.10
227 129 0.44
228 40 0.14
229 95 0.32
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (228 bp):
AAAAACGCCGCTAAATCCACAAAGCTCACAAAACTGCGTCGTTTTGGATTAGGTTTTTTGCGGCG
CTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATC
CACGAAAGCTCACAAAAACTGCGTCGTTTTACATTAGGTTTTTTGCGGCGCTATCTCAAAAACGC
CGCTAAAGCCCTGAGCATTAGCGGCACTTCCTT
Found at i:5429096 original size:21 final size:21
Alignment explanation
Indices: 5429070--5429111 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5429060 ATACCTGTCA
5429070 AAGTTAGTAGAAACTTCATCG
1 AAGTTAGTAGAAACTTCATCG
*
5429091 AAGTTATTAGAAACTTCATCG
1 AAGTTAGTAGAAACTTCATCG
5429112 GATTCAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (21 bp):
AAGTTAGTAGAAACTTCATCG
Found at i:5429316 original size:31 final size:30
Alignment explanation
Indices: 5429281--5429339 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
5429271 TATATATTAA
5429281 TATTTAAAATATAAGTAAAATA-AATTATAAT
1 TATTTAAAATATAA--AAAATATAATTATAAT
**
5429312 TATTTAATTTATAAAAAATATAATTATA
1 TATTTAAAATATAAAAAATATAATTATA
5429340 TATCATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 7 0.28
31 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
TATTTAAAATATAAAAAATATAATTATAAT
Found at i:5440736 original size:33 final size:33
Alignment explanation
Indices: 5440699--5440762 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
5440689 ACAGCACTAA
5440699 GTATCTTTTATCCCTAATATTTATAATAAATAT
1 GTATCTTTTATCCCTAATATTTATAATAAATAT
5440732 GTATCTTTTATCCCTAATATTTATAATAAAT
1 GTATCTTTTATCCCTAATATTTATAATAAAT
5440763 TTATAATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (33 bp):
GTATCTTTTATCCCTAATATTTATAATAAATAT
Found at i:5442640 original size:18 final size:20
Alignment explanation
Indices: 5442614--5442653 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
5442604 AATTTATGTT
5442614 AAATAATT-AAAATAT-TAA
1 AAATAATTAAAAATATATAA
*
5442632 AAATTATTAAAAATATATAA
1 AAATAATTAAAAATATATAA
5442652 AA
1 AA
5442654 TGAACTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAATTAAAAATATATAA
Found at i:5448166 original size:20 final size:20
Alignment explanation
Indices: 5448138--5448200 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
5448128 ACACATCAAT
* *
5448138 TTGTGGATAAGCCACCAGTA
1 TTGTAGATAAGCCACTAGTA
****
5448158 TTGTAGATAAATTGCTAGTA
1 TTGTAGATAAGCCACTAGTA
5448178 TTGTAGATAAGCCACTAGTA
1 TTGTAGATAAGCCACTAGTA
5448198 TTG
1 TTG
5448201 CAAACAAATT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (20 bp):
TTGTAGATAAGCCACTAGTA
Found at i:5448198 original size:40 final size:40
Alignment explanation
Indices: 5448138--5448247 Score: 148
Period size: 40 Copynumber: 2.8 Consensus size: 40
5448128 ACACATCAAT
* * *
5448138 TTGTGGATAAGCCACCAGTATTGTAGATAAATTGCTAGTA
1 TTGTGGATAAGCCACCAGTATTGCAAACAAATTGCTAGTA
* *
5448178 TTGTAGATAAGCCACTAGTATTGCAAACAAATTGCTAGTA
1 TTGTGGATAAGCCACCAGTATTGCAAACAAATTGCTAGTA
* * *
5448218 TTGTGGACAAGCTACCAGTATTGCAGACAA
1 TTGTGGATAAGCCACCAGTATTGCAAACAA
5448248 GCTGCCAGTA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (40 bp):
TTGTGGATAAGCCACCAGTATTGCAAACAAATTGCTAGTA
Found at i:5448227 original size:20 final size:20
Alignment explanation
Indices: 5448154--5448227 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 20
5448144 ATAAGCCACC
*
5448154 AGTATTGTAGATAAATTGCT
1 AGTATTGTAGACAAATTGCT
* ****
5448174 AGTATTGTAGATAAGCCACT
1 AGTATTGTAGACAAATTGCT
* *
5448194 AGTATTGCAAACAAATTGCT
1 AGTATTGTAGACAAATTGCT
*
5448214 AGTATTGTGGACAA
1 AGTATTGTAGACAA
5448228 GCTACCAGTA
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (20 bp):
AGTATTGTAGACAAATTGCT
Found at i:5452372 original size:35 final size:35
Alignment explanation
Indices: 5452333--5452404 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
5452323 AAGAGTGATA
*
5452333 AAATATTTCGTAATATAAACTTTAAGACTATGTAC
1 AAATATCTCGTAATATAAACTTTAAGACTATGTAC
5452368 AAATATCTCGTAATATAAACTTTAAGACTATGTAC
1 AAATATCTCGTAATATAAACTTTAAGACTATGTAC
5452403 AA
1 AA
5452405 GAGAAAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.35
Consensus pattern (35 bp):
AAATATCTCGTAATATAAACTTTAAGACTATGTAC
Found at i:5454100 original size:43 final size:43
Alignment explanation
Indices: 5453963--5454136 Score: 167
Period size: 43 Copynumber: 4.0 Consensus size: 43
5453953 CATAGGATTC
* *
5453963 TGATATGTGATTTCGTGTAAGACCACATCTGGGAC-GTTGGCAT
1 TGATATTTGATTTCGTGTAAGACCACGTCTGGGACAG-TGGCAT
* * * * * * *
5454006 CGAT-TTGAGATTTACGTGTAAAACTATGTCTGGGACATTGACAT
1 TGATATT-TGATTT-CGTGTAAGACCACGTCTGGGACAGTGGCAT
*
5454050 CG-TATTTGATTTCGTGTAAGACC-CTGTCTGGGACAGTGGCAT
1 TGATATTTGATTTCGTGTAAGACCAC-GTCTGGGACAGTGGCAT
** *
5454092 TGATATTTGATTTTATGTAAGACCACGTCTGGGACATTGGCAT
1 TGATATTTGATTTCGTGTAAGACCACGTCTGGGACAGTGGCAT
5454135 TG
1 TG
5454137 TACGAGCTTT
Statistics
Matches: 105, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
42 26 0.25
43 51 0.49
44 28 0.27
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (43 bp):
TGATATTTGATTTCGTGTAAGACCACGTCTGGGACAGTGGCAT
Found at i:5454104 original size:86 final size:85
Alignment explanation
Indices: 5453970--5454130 Score: 195
Period size: 86 Copynumber: 1.9 Consensus size: 85
5453960 TTCTGATATG
* *
5453970 TGATTTCGTGTAAGACCACATCTGGGACGTTGGCATCGATTTGAGA-TTTACGTGTAAAACTATG
1 TGATTTCGTGTAAGACCACATCTGGGACGTTGGCATCGATTTGAGATTTTA--TGTAAAACCACG
5454034 TCTGGGACATTGACATCGTATT
64 TCTGGGACATTGACATCGTATT
* * * *
5454056 TGATTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATTGATATT-TGATTTTATGTAAGACCAC
1 TGATTTCGTGTAAGACCAC-ATCTGGGAC-GTTGGCATCGAT-TTGAGATTTTATGTAAAACCAC
5454118 GTCTGGGACATTG
63 GTCTGGGACATTG
5454131 GCATTGTACG
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
85 22 0.34
86 36 0.55
87 7 0.11
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (85 bp):
TGATTTCGTGTAAGACCACATCTGGGACGTTGGCATCGATTTGAGATTTTATGTAAAACCACGTC
TGGGACATTGACATCGTATT
Found at i:5458002 original size:53 final size:53
Alignment explanation
Indices: 5457904--5458011 Score: 126
Period size: 53 Copynumber: 2.0 Consensus size: 53
5457894 GATAAAATAC
* * ** * * *
5457904 TATAAGGCAAAGATCCCATGTAAGACCATGCCAAGGCATGGAAATGGTGAGTT
1 TATAAGGCAAAGATACCATGTAACACCATGCCAAAACATGAAAATGATAAGTT
* * *
5457957 TATAAGGCAAGGATACCATGTAACACTATGTCAAAACATGAAAATGATAAGTT
1 TATAAGGCAAAGATACCATGTAACACCATGCCAAAACATGAAAATGATAAGTT
5458010 TA
1 TA
5458012 AAAAGGAAAG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (53 bp):
TATAAGGCAAAGATACCATGTAACACCATGCCAAAACATGAAAATGATAAGTT
Found at i:5472466 original size:14 final size:15
Alignment explanation
Indices: 5472447--5472480 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5472437 TTAGTTAGAG
5472447 AAGAAAATT-AAAGA
1 AAGAAAATTGAAAGA
*
5472461 AAGAAAATTGAATGA
1 AAGAAAATTGAAAGA
5472476 AAGAA
1 AAGAA
5472481 TGAGAGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (15 bp):
AAGAAAATTGAAAGA
Found at i:5482386 original size:26 final size:26
Alignment explanation
Indices: 5482357--5482444 Score: 65
Period size: 26 Copynumber: 3.5 Consensus size: 26
5482347 ATCTAAAATT
5482357 TCAATTCATCATATTCCATTTATCAG
1 TCAATTCATCATATTCCATTTATCAG
* * * * ** *
5482383 TCAATTTATTA-AAT--ATCTAAAATT
1 TCAATTCATCATATTCCATTTATCA-G
*
5482407 TCAATTCACCATATTCCATTTATCAG
1 TCAATTCATCATATTCCATTTATCAG
*
5482433 TCAATTTATCAT
1 TCAATTCATCAT
5482445 TTTACAAAAG
Statistics
Matches: 41, Mismatches: 17, Indels: 8
0.62 0.26 0.12
Matches are distributed among these distances:
23 5 0.12
24 8 0.20
25 4 0.10
26 19 0.46
27 5 0.12
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.43
Consensus pattern (26 bp):
TCAATTCATCATATTCCATTTATCAG
Found at i:5482393 original size:50 final size:50
Alignment explanation
Indices: 5482335--5482441 Score: 205
Period size: 50 Copynumber: 2.1 Consensus size: 50
5482325 ATCAAATAAT
*
5482335 AATTTATTAAATATCTAAAATTTCAATTCATCATATTCCATTTATCAGTC
1 AATTTATTAAATATCTAAAATTTCAATTCACCATATTCCATTTATCAGTC
5482385 AATTTATTAAATATCTAAAATTTCAATTCACCATATTCCATTTATCAGTC
1 AATTTATTAAATATCTAAAATTTCAATTCACCATATTCCATTTATCAGTC
5482435 AATTTAT
1 AATTTAT
5482442 CATTTTACAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (50 bp):
AATTTATTAAATATCTAAAATTTCAATTCACCATATTCCATTTATCAGTC
Found at i:5484421 original size:57 final size:57
Alignment explanation
Indices: 5484298--5484439 Score: 162
Period size: 57 Copynumber: 2.5 Consensus size: 57
5484288 CTCGTTATAG
* * * *
5484298 AAAGGATTTAGCCCGGACGGGTAATCCTGATATAATCTCTCTCTAGCATATGTTACA
1 AAAGGATTTAGCCTGGACTGGTAATCCTAATATAAGCTCTCTCTAGCATATGTTACA
* * * *
5484355 ATTAGGATTTAGCCTAGACTGGTAATCCTAAT-TGAGCTCT-TTTGAGCATATGTTACA
1 A-AAGGATTTAGCCTGGACTGGTAATCCTAATATAAGCTCTCTCT-AGCATATGTTACA
*
5484412 TAAAGGATTTAGCCTGGTCTGGTAATCC
1 -AAAGGATTTAGCCTGGACTGGTAATCC
5484440 CGTAATATGA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
56 2 0.03
57 43 0.61
58 26 0.37
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (57 bp):
AAAGGATTTAGCCTGGACTGGTAATCCTAATATAAGCTCTCTCTAGCATATGTTACA
Found at i:5493067 original size:59 final size:53
Alignment explanation
Indices: 5492963--5493094 Score: 126
Period size: 59 Copynumber: 2.4 Consensus size: 53
5492953 TAGGATCAGA
* * *
5492963 ATTTAGCCTGGACTGGTAATTCAGATCCAATCTCATTTGAGTATATGTCGTCGTAGGGG
1 ATTTAGCCTGGACTGGTAATCCAGA-CCAATCTCATATGAGTATAT-T--ACG--GGGG
5493022 ATTTAGCCTGGACTGGTAATCCCA-A-CAATACTC-TATGAGTTTATATTACGGGGG
1 ATTTAGCCTGGACTGGTAAT-CCAGACCAAT-CTCATATGAG--TATATTACGGGGG
5493076 ATTTAGCCTGGACTGGTAA
1 ATTTAGCCTGGACTGGTAA
5493095 ACCCGCCGAA
Statistics
Matches: 66, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
54 23 0.35
56 2 0.03
57 9 0.14
58 4 0.06
59 26 0.39
60 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (53 bp):
ATTTAGCCTGGACTGGTAATCCAGACCAATCTCATATGAGTATATTACGGGGG
Found at i:5496051 original size:22 final size:21
Alignment explanation
Indices: 5495998--5496051 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
5495988 TGGCCTGTAG
* *
5495998 CACGGGCATGTCCTAGGATCA
1 CACGGGCGTGTCCTAGGACCA
*
5496019 CACGAGG-GTGTCCCTTGGACCA
1 CACG-GGCGTGT-CCTAGGACCA
5496041 CACGGGCGTGT
1 CACGGGCGTGT
5496052 GAGCCTTGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.19, C:0.30, G:0.33, T:0.19
Consensus pattern (21 bp):
CACGGGCGTGTCCTAGGACCA
Found at i:5497129 original size:30 final size:30
Alignment explanation
Indices: 5497093--5497151 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5497083 TATTTTCTTA
5497093 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
* *
5497123 TTAATTTTTTTATTATTTTAGAGGCATTT
1 TTAATTTTGTTATTATTTTAAAGGCATTT
5497152 ACTTGTTAAG
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:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:5503034 original size:30 final size:31
Alignment explanation
Indices: 5502993--5503094 Score: 81
Period size: 30 Copynumber: 3.4 Consensus size: 31
5502983 AAAAAAAATG
5502993 ATAGTT-AGGTGACAAAAAAAGAAAAAGAGCA
1 ATAGTTGA-GTGACAAAAAAAGAAAAAGAGCA
** * **
5503024 ATAGTTG-GTGACCAAATTAA-AAGAATTG--
1 ATAGTTGAGTGA-CAAAAAAAGAAAAAGAGCA
* *
5503052 ATAGTTGAGTGACTAAAAAAG-AAAAGGGCA
1 ATAGTTGAGTGACAAAAAAAGAAAAAGAGCA
5503082 ATAGTTGAGTGAC
1 ATAGTTGAGTGAC
5503095 CGAATTAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
28 16 0.30
29 4 0.07
30 22 0.41
31 12 0.22
ACGTcount: A:0.48, C:0.07, G:0.25, T:0.21
Consensus pattern (31 bp):
ATAGTTGAGTGACAAAAAAAGAAAAAGAGCA
Found at i:5503036 original size:59 final size:57
Alignment explanation
Indices: 5502965--5503130 Score: 233
Period size: 59 Copynumber: 2.8 Consensus size: 57
5502955 CAATTTTAAT
* *
5502965 TAGTTGGGTGACCAAATTAAAAAAAATGATAGTTAGGTGACAAAAAAAGAAAAAGAGCAA
1 TAGTT-GGTGACCAAATTAAAAGAATTGATAGTT-GGTGACAAAAAAAG-AAAAGAGCAA
* *
5503025 TAGTTGGTGACCAAATTAAAAGAATTGATAGTTGAGTGACTAAAAAAGAAAAGGGCAA
1 TAGTTGGTGACCAAATTAAAAGAATTGATAGTTG-GTGACAAAAAAAGAAAAGAGCAA
*
5503083 TAGTTGAGTGACCGAATTAAAAGAATTGATAGTTGGGTGACAAAAAAA
1 TAGTTG-GTGACCAAATTAAAAGAATTGATAGTT-GGTGACAAAAAAA
5503131 AAAGGGGATA
Statistics
Matches: 97, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
58 16 0.16
59 75 0.77
60 6 0.06
ACGTcount: A:0.48, C:0.07, G:0.23, T:0.22
Consensus pattern (57 bp):
TAGTTGGTGACCAAATTAAAAGAATTGATAGTTGGTGACAAAAAAAGAAAAGAGCAA
Found at i:5503115 original size:29 final size:29
Alignment explanation
Indices: 5503024--5503123 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
5503014 AAAAAGAGCA
5503024 ATAGTTG-GTGACCAAATTAAAAGAATTG
1 ATAGTTGAGTGACCAAATTAAAAGAATTG
* * **
5503052 ATAGTTGAGTGACTAAA--AAAGAAAAGGG
1 ATAGTTGAGTGACCAAATTAAA-AGAATTG
*
5503080 CAATAGTTGAGTGACCGAATTAAAAGAATTG
1 --ATAGTTGAGTGACCAAATTAAAAGAATTG
*
5503111 ATAGTTGGGTGAC
1 ATAGTTGAGTGAC
5503124 AAAAAAAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
27 3 0.05
28 11 0.20
29 20 0.36
30 15 0.27
31 4 0.07
32 3 0.05
ACGTcount: A:0.42, C:0.07, G:0.26, T:0.25
Consensus pattern (29 bp):
ATAGTTGAGTGACCAAATTAAAAGAATTG
Found at i:5503133 original size:29 final size:29
Alignment explanation
Indices: 5502965--5503134 Score: 89
Period size: 29 Copynumber: 5.8 Consensus size: 29
5502955 CAATTTTAAT
*
5502965 TAGTTGGGTGACCAAATTAAAAAA-AA-TGA
1 TAGTTGGGTGA-CAAA-AAAAAAAGAAGTGA
* *
5502994 TAGTTAGGTGACAAAAAAAGAAA-AAGAGCAA
1 TAGTTGGGTGACAAAAAAA-AAAGAAGTG--A
* ** *
5503025 TAGTT-GGTGACCAAATTAAAAGAATTGA
1 TAGTTGGGTGACAAAAAAAAAAGAAGTGA
* * **
5503053 TAGTTGAGTGACTAAAAAAGAAAAG-GGCAA
1 TAGTTGGGTGAC-AAAAAA-AAAAGAAGTGA
* ** ** *
5503083 TAGTTGAGTGACCGAATTAAAAGAATTGA
1 TAGTTGGGTGACAAAAAAAAAAGAAGTGA
5503112 TAGTTGGGTGACAAAAAAAAAAG
1 TAGTTGGGTGACAAAAAAAAAAG
5503135 GGGATAATAA
Statistics
Matches: 103, Mismatches: 29, Indels: 18
0.69 0.19 0.12
Matches are distributed among these distances:
27 3 0.03
28 20 0.19
29 40 0.39
30 29 0.28
31 11 0.11
ACGTcount: A:0.49, C:0.06, G:0.24, T:0.21
Consensus pattern (29 bp):
TAGTTGGGTGACAAAAAAAAAAGAAGTGA
Found at i:5510413 original size:20 final size:21
Alignment explanation
Indices: 5510375--5510413 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5510365 CAAAGATATG
* *
5510375 ATGATGAAGCTTTTGTCATCT
1 ATGATGAAGCTCTTCTCATCT
5510396 ATGATG-AGCTCTTCTCAT
1 ATGATGAAGCTCTTCTCAT
5510414 ATGCATGTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (21 bp):
ATGATGAAGCTCTTCTCATCT
Found at i:5514000 original size:13 final size:14
Alignment explanation
Indices: 5513982--5514012 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
5513972 AATGTTTTGA
5513982 AATTTTTTATTT-T
1 AATTTTTTATTTAT
5513995 AATTTTTTATTTAT
1 AATTTTTTATTTAT
5514009 AATT
1 AATT
5514013 CCAACTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
AATTTTTTATTTAT
Found at i:5524045 original size:21 final size:20
Alignment explanation
Indices: 5524007--5524063 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
5523997 ATTAAATTTT
* *
5524007 TATAAAAACATATTAAAATTC
1 TATAAAAA-ATATAAAAATTA
5524028 TATAAAAAATCATAAAAATTA
1 TATAAAAAAT-ATAAAAATTA
5524049 TA-AAAATAATATAAA
1 TATAAAA-AATATAAA
5524064 CTTATAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
TATAAAAAATATAAAAATTA
Found at i:5524052 original size:19 final size:18
Alignment explanation
Indices: 5524006--5524072 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 18
5523996 AATTAAATTT
*
5524006 TTATAAAAACATATTAAAAT
1 TTATAAAAA-ATA-TAAAAA
5524026 TCTATAAAAAATCATAAAAA
1 T-TATAAAAAAT-ATAAAAA
*
5524046 TTAT-AAAAATAATATAAAC
1 TTATAAAAAAT-ATA-AAAA
5524065 TTATAAAA
1 TTATAAAA
5524073 GTTGTTAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 9 0.22
19 10 0.25
20 12 0.30
21 9 0.22
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
TTATAAAAAATATAAAAA
Found at i:5524055 original size:18 final size:19
Alignment explanation
Indices: 5524006--5524072 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
5523996 AATTAAATTT
*
5524006 TTATAAAAA-CATATTAAAA
1 TTATAAAAATAATA-TAAAA
*
5524025 TTCTATAAAA-AATCATAAAAA
1 TTATA-AAAATAAT-AT-AAAA
*
5524046 TTATAAAAATAATATAAAC
1 TTATAAAAATAATATAAAA
5524065 TTATAAAA
1 TTATAAAA
5524073 GTTGTTAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 15 0.38
20 13 0.32
21 12 0.30
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (19 bp):
TTATAAAAATAATATAAAA
Found at i:5524535 original size:20 final size:19
Alignment explanation
Indices: 5524491--5524660 Score: 83
Period size: 19 Copynumber: 9.2 Consensus size: 19
5524481 GTTTGTATTT
*
5524491 TTTTTATATAATTTTTATA
1 TTTTTATATAATTTTAATA
**
5524510 AGTTTATATCAATTTTAATA
1 TTTTTATAT-AATTTTAATA
*
5524530 TTTTTA-ATATTTTTTACA-A
1 TTTTTATATA-ATTTTA-ATA
* *
5524549 TTTTTAT-TAGTTTTTAAGA
1 TTTTTATATA-ATTTTAATA
* *
5524568 ATTTTA-A-ATTTTTAA-A
1 TTTTTATATAATTTTAATA
**
5524584 AATTTATAT-ATTTTAAATAA
1 TTTTTATATAATTTT-AAT-A
*
5524604 GTTTTAT-TAA-TTTAATA
1 TTTTTATATAATTTTAATA
*
5524621 TTTTTATA-ACTTATT-ATA
1 TTTTTATATAATT-TTAATA
*
5524639 TTTTTATATATTTTTAATA
1 TTTTTATATAATTTTAATA
5524658 TTT
1 TTT
5524661 ACAAGTTTTT
Statistics
Matches: 119, Mismatches: 15, Indels: 34
0.71 0.09 0.20
Matches are distributed among these distances:
16 6 0.05
17 20 0.17
18 22 0.18
19 50 0.42
20 21 0.18
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTATATAATTTTAATA
Found at i:5524554 original size:47 final size:45
Alignment explanation
Indices: 5524491--5524646 Score: 127
Period size: 45 Copynumber: 3.4 Consensus size: 45
5524481 GTTTGTATTT
*
5524491 TTTTTATATAATTTTTATAAGTTTATATCAATTTTAATATTTTTAATA
1 TTTTT-TA-AATTTTTATAAGTTT-TATCAATTTTAATATTTTTAAAA
* **
5524539 TTTTTTACAATTTTTATTAGTTTTTAAGAATTTTAA-ATTTTTAAAA
1 TTTTTTA-AATTTTTATAAG-TTTTATCAATTTTAATATTTTTAAAA
* * * * * *
5524585 ATTTATATATTTTAAATAAGTTTTATTAA-TTTAATATTTTTATAA
1 TTTTTTAAATTTT-TATAAGTTTTATCAATTTTAATATTTTTAAAA
* * *
5524630 CTTATTATATTTTTATA
1 TTTTTTAAATTTTTATA
5524647 TATTTTTAAT
Statistics
Matches: 88, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
44 8 0.09
45 31 0.35
46 18 0.20
47 23 0.26
48 8 0.09
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.60
Consensus pattern (45 bp):
TTTTTTAAATTTTTATAAGTTTTATCAATTTTAATATTTTTAAAA
Done.