Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 5 of 172
Found at i:1395446 original size:25 final size:24
Alignment explanation
Indices: 1395362--1395480 Score: 89
Period size: 25 Copynumber: 4.8 Consensus size: 24
1395352 CCCATTGCAG
*
1395362 CTCGTGAGAGCTTACCAATTCTT-AA
1 CTCGT-AGAGCTTACCGATT-TTCAA
* *
1395387 CTCGTAGGAGCTTACCGA-TTGCAG
1 CTCGTA-GAGCTTACCGATTTTCAA
1395411 CTCGTGAGAGCTTACCGATTTTCAA
1 CTCGT-AGAGCTTACCGATTTTCAA
* ** * *
1395436 TTCGTATGAGCTTACTAATTTACAG
1 CTCGTA-GAGCTTACCGATTTTCAA
*
1395461 CTCGTAAGAGCATACCGATT
1 CTCGT-AGAGCTTACCGATT
1395481 CATGGCTTAT
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
23 1 0.01
24 20 0.27
25 52 0.70
26 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (24 bp):
CTCGTAGAGCTTACCGATTTTCAA
Found at i:1403092 original size:49 final size:49
Alignment explanation
Indices: 1403017--1403149 Score: 151
Period size: 49 Copynumber: 2.7 Consensus size: 49
1403007 GTCATTGGGA
* * *
1403017 TTACCGATTGCAACTCATGAGAGCTTACCAATTTTCAGA-TAGTATGAGC
1 TTACCGATTGCAGCTCGTGAGAGCTTACCAATTCTCA-ACTAGTATGAGC
* ** *
1403066 TTACCGATTGCAGCTCGTGAGGGCTTACTGATTCTCAACTCGTATGAGC
1 TTACCGATTGCAGCTCGTGAGAGCTTACCAATTCTCAACTAGTATGAGC
* * *
1403115 TTACCGATTTACAGCTTGTGAGAGCATACCAATTC
1 TTACCGA-TTGCAGCTCGTGAGAGCTTACCAATTC
1403150 ATGTCTCGTT
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
48 1 0.01
49 47 0.68
50 21 0.30
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (49 bp):
TTACCGATTGCAGCTCGTGAGAGCTTACCAATTCTCAACTAGTATGAGC
Found at i:1403139 original size:25 final size:24
Alignment explanation
Indices: 1403017--1403144 Score: 89
Period size: 25 Copynumber: 5.2 Consensus size: 24
1403007 GTCATTGGGA
* * *
1403017 TTACCGATTGCAACTCATGAGAGC
1 TTACCGATTTCAGCTCGTGAGAGC
* * *
1403041 TTACCAATTTTCAGATAGT-ATGAGC
1 TTACCGA-TTTCAGCTCGTGA-GAGC
* *
1403066 TTACCGATTGCAGCTCGTGAGGGC
1 TTACCGATTTCAGCTCGTGAGAGC
* *
1403090 TTACTGATTCTCAACTCGT-ATGAGC
1 TTACCGATT-TCAGCTCGTGA-GAGC
*
1403115 TTACCGATTTACAGCTTGTGAGAGC
1 TTACCGATTT-CAGCTCGTGAGAGC
*
1403140 ATACC
1 TTACC
1403145 AATTCATGTC
Statistics
Matches: 78, Mismatches: 19, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
24 28 0.36
25 49 0.63
26 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (24 bp):
TTACCGATTTCAGCTCGTGAGAGC
Found at i:1414117 original size:22 final size:22
Alignment explanation
Indices: 1414092--1414148 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
1414082 TGCAGGGCTC
*
1414092 ACACGCTCGTGTGGACCAAGGG
1 ACACGCCCGTGTGGACCAAGGG
**
1414114 ACACGCCCGTGT-GACCCTGGG
1 ACACGCCCGTGTGGACCAAGGG
*
1414135 ACATGCCCGTGTGG
1 ACACGCCCGTGTGG
1414149 GAGGCCGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.18, C:0.32, G:0.35, T:0.16
Consensus pattern (22 bp):
ACACGCCCGTGTGGACCAAGGG
Found at i:1415963 original size:23 final size:23
Alignment explanation
Indices: 1415920--1415963 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1415910 CCAAAGCCCC
*
1415920 ATTAAAAATTTTTCAGCACTTGT
1 ATTAAAAATTTTTCAGAACTTGT
*
1415943 ATTAATAAA-TTTTCTGAACTT
1 ATTAA-AAATTTTTCAGAACTT
1415964 TTCATCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (23 bp):
ATTAAAAATTTTTCAGAACTTGT
Found at i:1415984 original size:20 final size:21
Alignment explanation
Indices: 1415949--1415988 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1415939 TTGTATTAAT
*
1415949 AAATTTTCTGAACTTTTCATC
1 AAATTTTATGAACTTTTCATC
1415970 AAATTTTAT-AACTTTTCAT
1 AAATTTTATGAACTTTTCAT
1415989 TTTAGTCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.50
Consensus pattern (21 bp):
AAATTTTATGAACTTTTCATC
Found at i:1425530 original size:184 final size:184
Alignment explanation
Indices: 1425221--1425588 Score: 736
Period size: 184 Copynumber: 2.0 Consensus size: 184
1425211 GCACTTGCTT
1425221 GTCATGTTGTGAACAATGACCATAATATCATTCATGCTTACAAATTCACCATTTTCCCATTCATA
1 GTCATGTTGTGAACAATGACCATAATATCATTCATGCTTACAAATTCACCATTTTCCCATTCATA
1425286 GCATAATAAGGCAAAACTTAAATACCAAATAAGCTTTTAAGAATTTACATAACATATATCACATA
66 GCATAATAAGGCAAAACTTAAATACCAAATAAGCTTTTAAGAATTTACATAACATATATCACATA
1425351 TTTCATATGTCACTTGTCATGTAGAATCATTTTCTTGCATTTCATGTAATATTC
131 TTTCATATGTCACTTGTCATGTAGAATCATTTTCTTGCATTTCATGTAATATTC
1425405 GTCATGTTGTGAACAATGACCATAATATCATTCATGCTTACAAATTCACCATTTTCCCATTCATA
1 GTCATGTTGTGAACAATGACCATAATATCATTCATGCTTACAAATTCACCATTTTCCCATTCATA
1425470 GCATAATAAGGCAAAACTTAAATACCAAATAAGCTTTTAAGAATTTACATAACATATATCACATA
66 GCATAATAAGGCAAAACTTAAATACCAAATAAGCTTTTAAGAATTTACATAACATATATCACATA
1425535 TTTCATATGTCACTTGTCATGTAGAATCATTTTCTTGCATTTCATGTAATATTC
131 TTTCATATGTCACTTGTCATGTAGAATCATTTTCTTGCATTTCATGTAATATTC
1425589 TTCCACATCA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 184 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (184 bp):
GTCATGTTGTGAACAATGACCATAATATCATTCATGCTTACAAATTCACCATTTTCCCATTCATA
GCATAATAAGGCAAAACTTAAATACCAAATAAGCTTTTAAGAATTTACATAACATATATCACATA
TTTCATATGTCACTTGTCATGTAGAATCATTTTCTTGCATTTCATGTAATATTC
Found at i:1427326 original size:17 final size:17
Alignment explanation
Indices: 1427304--1427336 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1427294 TTTTTATCAT
*
1427304 TTATCATTTATCGGGCA
1 TTATCATTGATCGGGCA
1427321 TTATCATTGATCGGGC
1 TTATCATTGATCGGGC
1427337 TTTGTCAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (17 bp):
TTATCATTGATCGGGCA
Found at i:1428143 original size:15 final size:17
Alignment explanation
Indices: 1428117--1428150 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1428107 TATTTAATTA
1428117 TTTATCATCTTTT-AAT
1 TTTATCATCTTTTCAAT
1428133 TTTATCA-CTTTTCAAT
1 TTTATCATCTTTTCAAT
1428149 TT
1 TT
1428151 AGTCCTTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATCATCTTTTCAAT
Found at i:1428565 original size:14 final size:14
Alignment explanation
Indices: 1428546--1428574 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1428536 CATCTATGGT
1428546 CTTATACCATATAC
1 CTTATACCATATAC
1428560 CTTATACCATATAC
1 CTTATACCATATAC
1428574 C
1 C
1428575 ATGCTACCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (14 bp):
CTTATACCATATAC
Found at i:1432608 original size:22 final size:22
Alignment explanation
Indices: 1432583--1432625 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1432573 CACTAAGTGA
*
1432583 ACAGAACGGCTCAACGCCATAG
1 ACAGAACGGCTAAACGCCATAG
*
1432605 ACAGAACGGCTAAAGGCCATA
1 ACAGAACGGCTAAACGCCATA
1432626 AATATCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.28, G:0.23, T:0.09
Consensus pattern (22 bp):
ACAGAACGGCTAAACGCCATAG
Found at i:1432919 original size:27 final size:27
Alignment explanation
Indices: 1432871--1432923 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1432861 CATTCTAACA
*
1432871 TACAGGGGTATTAAGGTCATTTTACAC
1 TACAAGGGTATTAAGGTCATTTTACAC
** *
1432898 TACAAGGGTATTTCGGTGATTTTACA
1 TACAAGGGTATTAAGGTCATTTTACA
1432924 AACCGGGGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (27 bp):
TACAAGGGTATTAAGGTCATTTTACAC
Found at i:1434623 original size:28 final size:28
Alignment explanation
Indices: 1434583--1434661 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
1434573 GCAATCAAAT
* * *
1434583 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
1434611 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
1434639 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
1434662 CGAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:1436703 original size:57 final size:56
Alignment explanation
Indices: 1436634--1436878 Score: 321
Period size: 57 Copynumber: 4.3 Consensus size: 56
1436624 AAGTGAACAT
* *
1436634 AGGCACTGTGTGTGTGAGTTCCGTAACCGAGCACTGTGTGTGCAAGATCGATTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTATGTGCAAGATCG-TTGTTG
* * *
1436691 AGGCACTGTGTGTGCGATTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTATGTGCAAGATC-GTTGTTG
* * *
1436748 AGGCACTGTGTGTGCAAGTTCCGTAACCAAGCACTGTATGTGCAAGATATGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTATGTGCAAGAT-CGTTGTTG
* * * ** *
1436805 AGGCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTATGTGCGAGTTTCGTAATCG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTATGTGCAAG-ATCGTTGTTG
1436862 A-GCACTGTGTGTGCGAG
1 AGGCACTGTGTGTGCGAG
1436879 ATCGGTTGTT
Statistics
Matches: 167, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
56 16 0.10
57 149 0.89
58 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (56 bp):
AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTATGTGCAAGATCGTTGTTG
Found at i:1436858 original size:85 final size:85
Alignment explanation
Indices: 1436721--1436935 Score: 277
Period size: 85 Copynumber: 2.5 Consensus size: 85
1436711 CCGTAACCGA
* * ** *
1436721 GCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTGTGTGTGCAAGTTCCGTAACCAAGCACTGTA
1 GCACTGTGTGTGCGAGTTCCGTAATCGA-GCACTGTGTGTGCAAGTTCCGTAACCAAGCACTGTA
*
1436786 TGTGCAAGATATGTTGTTGAG
65 TGTGCAAGATAGGTTGTTGAG
* * * * * *
1436807 GCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTATGTGCGAGTTTCGTAATCGAGCACTGTGT
1 GCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTGTGTGCAAGTTCCGTAACCAAGCACTGTAT
* *
1436872 GTGCGAGATCGGTTGTTGAG
66 GTGCAAGATAGGTTGTTGAG
* *
1436892 GCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAG
1 GCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTGTGTGCAAG
1436936 ATCGGTTGTT
Statistics
Matches: 111, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 88 0.79
86 23 0.21
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (85 bp):
GCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTGTGTGCAAGTTCCGTAACCAAGCACTGTAT
GTGCAAGATAGGTTGTTGAG
Found at i:1436872 original size:142 final size:143
Alignment explanation
Indices: 1436693--1436962 Score: 445
Period size: 142 Copynumber: 1.9 Consensus size: 143
1436683 GATTGTTGAG
*
1436693 GCACTGTGTGTGCGATTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTGTG
1 GCACTGTATGTGCGATTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTGTG
*
1436758 TGTGCAAGTTCCGTAACCAAGCACTGTATGTGCAAGATATGTTGTTGAGGCACT-GTGTGTGCGA
66 TGTGCAAGTTCCGTAACCAAGCACTGTATGTGCAAGATAGGTTGTTGAGGCACTAGTGTGTGCGA
1436822 GTTCCGTAATCGA
131 GTTCCGTAATCGA
*
1436835 GCACTGTATGTGCGAGTTT-CGTAATCGAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTGT
1 GCACTGTATGTGCGA-TTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTGT
* * * *
1436899 GTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTGGGGCACTAAGTGTGTG
65 GTGTGCAAGTTCCGTAACCAAGCACTGTATGTGCAAGATAGGTTGTTGAGGCACT-AGTGTGTG
1436963 AAATGAGATC
Statistics
Matches: 118, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
142 108 0.92
143 3 0.03
144 7 0.06
ACGTcount: A:0.19, C:0.18, G:0.33, T:0.30
Consensus pattern (143 bp):
GCACTGTATGTGCGATTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTGTG
TGTGCAAGTTCCGTAACCAAGCACTGTATGTGCAAGATAGGTTGTTGAGGCACTAGTGTGTGCGA
GTTCCGTAATCGA
Found at i:1436896 original size:57 final size:57
Alignment explanation
Indices: 1436807--1436953 Score: 188
Period size: 57 Copynumber: 2.6 Consensus size: 57
1436797 TGTTGTTGAG
* * ** * * * *
1436807 GCACTGTGTGTGCGAGTTCCGTAATCGA-GCACTGTATGTGCGAGTTTCGTAATCGA
1 GCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTGTATGTGCGAGTTCCGTAACCAA
*
1436863 GCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTGTGTGTGCGAGTTCCGTAACCAA
1 GCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTGTATGTGCGAGTTCCGTAACCAA
* *
1436920 GCACTGTGTGTGCAAGATCGGTTGTTGGGGCACT
1 GCACTGTGTGTGCGAGATCGGTTGTTGAGGCACT
1436954 AAGTGTGTGA
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
56 23 0.29
57 56 0.71
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.29
Consensus pattern (57 bp):
GCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTGTATGTGCGAGTTCCGTAACCAA
Found at i:1441942 original size:28 final size:28
Alignment explanation
Indices: 1441902--1441980 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
1441892 GCAATCAAAT
* * *
1441902 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
1441930 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
1441958 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
1441981 CGAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:1449739 original size:17 final size:16
Alignment explanation
Indices: 1449731--1449775 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
1449721 TTCATTTAAT
1449731 TATAATATTAATATAA
1 TATAATATTAATATAA
*
1449747 TATAATAATAATATAA
1 TATAATATTAATATAA
1449763 TATAATA-TAATAT
1 TATAATATTAATAT
1449776 TATTTTCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 6 0.21
16 22 0.79
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAATATTAATATAA
Found at i:1449749 original size:5 final size:5
Alignment explanation
Indices: 1449731--1449775 Score: 72
Period size: 5 Copynumber: 8.6 Consensus size: 5
1449721 TTCATTTAAT
1449731 TATAA TATTAA TATAA TATAA TAATAA TATAA TATAA TATAA TAT
1 TATAA TA-TAA TATAA TATAA T-ATAA TATAA TATAA TATAA TAT
1449776 TATTTTCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 28 0.74
6 10 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:1450732 original size:15 final size:15
Alignment explanation
Indices: 1450708--1450737 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1450698 CCATGTAACT
1450708 TAAACCATTAACATA
1 TAAACCATTAACATA
*
1450723 TAAACTATTAACATA
1 TAAACCATTAACATA
1450738 ACAAACTTTA
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:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAACCATTAACATA
Found at i:1450829 original size:86 final size:86
Alignment explanation
Indices: 1450711--1450968 Score: 491
Period size: 86 Copynumber: 3.0 Consensus size: 86
1450701 TGTAACTTAA
1450711 ACCATTAACATATAAACTATTAACATAACAAACTTTATATACCAATATCTTGATCTATACTCAAC
1 ACCATTAACATATAAACTATTAACATAACAAACTTTATATACCAATATCTTGATCTATACTCAAC
1450776 CTTTTTTTATTAAAATTAGGT
66 CTTTTTTTATTAAAATTAGGT
1450797 ACCATTAACATATAAACTATTAACATAACAAACTTTATATACCAATATCTTGATCTATACTCAAC
1 ACCATTAACATATAAACTATTAACATAACAAACTTTATATACCAATATCTTGATCTATACTCAAC
1450862 CTTTTTTTATTAAAATTAGGT
66 CTTTTTTTATTAAAATTAGGT
*
1450883 ACCATTAACATATAAACTATTAACATAACAAACTTTATATACCAATATCTTAATCTATACTCAAC
1 ACCATTAACATATAAACTATTAACATAACAAACTTTATATACCAATATCTTGATCTATACTCAAC
*
1450948 C-TTTTTGATTAAAATTAGGT
66 CTTTTTTTATTAAAATTAGGT
1450968 A
1 A
1450969 TGTTCATCTA
Statistics
Matches: 170, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 19 0.11
86 151 0.89
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (86 bp):
ACCATTAACATATAAACTATTAACATAACAAACTTTATATACCAATATCTTGATCTATACTCAAC
CTTTTTTTATTAAAATTAGGT
Found at i:1460408 original size:51 final size:49
Alignment explanation
Indices: 1460229--1460416 Score: 234
Period size: 49 Copynumber: 3.8 Consensus size: 49
1460219 TAGTCAAAGC
* * * **
1460229 TATCTGGTACGCATAGTAGCCTGCA-TATAGTACTACACATGCAACCAAT
1 TATCCGGTACACATAGTAGCCTGCACT-TAGTACTACACACGTGACCAAT
* *
1460278 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* *
1460327 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAAT
* * *
1460378 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACA
1460417 TGCGACCTCA
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
49 85 0.68
50 2 0.02
51 38 0.30
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (49 bp):
TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:1468535 original size:25 final size:24
Alignment explanation
Indices: 1468494--1468576 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 24
1468484 CCTTGCAATA
* *
1468494 CACCTCACAATCTCACCTCGTTGTAC
1 CACCTCACAA-CACACCTC-TAGTAC
* *
1468520 CACCTCGCAACACACCTCACAGTAC
1 CACCTCACAACACACCTC-TAGTAC
*
1468545 CACCTCACAACACACCTCTCGCTAC
1 CACCTCACAACACACCTCTAG-TAC
1468570 CACCTCA
1 CACCTCA
1468577 TGATCTCTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
24 1 0.02
25 38 0.79
26 9 0.19
ACGTcount: A:0.28, C:0.48, G:0.06, T:0.18
Consensus pattern (24 bp):
CACCTCACAACACACCTCTAGTAC
Found at i:1469083 original size:29 final size:31
Alignment explanation
Indices: 1469035--1469098 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
1469025 TTTATAGTTA
*
1469035 TTTAATTAGATAATTATTATT-TATTTAATAT
1 TTTAATAAGATAATTATTATTAT-TTTAATAT
*
1469066 TTTAATAAGAT-ATT-TTATTATTTTATTAT
1 TTTAATAAGATAATTATTATTATTTTAATAT
1469095 TTTA
1 TTTA
1469099 TTTAGTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTAATAAGATAATTATTATTATTTTAATAT
Found at i:1469087 original size:8 final size:8
Alignment explanation
Indices: 1469076--1469100 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1469066 TTTAATAAGA
1469076 TATTTTAT
1 TATTTTAT
1469084 TATTTTAT
1 TATTTTAT
1469092 TATTTTAT
1 TATTTTAT
1469100 T
1 T
1469101 TAGTCTATAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:1473834 original size:21 final size:22
Alignment explanation
Indices: 1473801--1473841 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1473791 TTCATTTATG
*
1473801 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
1473822 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
1473842 CAATACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:1474290 original size:28 final size:28
Alignment explanation
Indices: 1474257--1474319 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
1474247 TCGACATTTT
1474257 GCACACTAAGTGTCATTCTAAATATCTC
1 GCACACTAAGTGTCATTCTAAATATCTC
* *
1474285 GCACACTAAGTGTCATTCTCAATATTTC
1 GCACACTAAGTGTCATTCTAAATATCTC
*
1474313 GTACACT
1 GCACACT
1474320 GAGTCCCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.33
Consensus pattern (28 bp):
GCACACTAAGTGTCATTCTAAATATCTC
Found at i:1480480 original size:25 final size:25
Alignment explanation
Indices: 1480438--1480507 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
1480428 GAGGAAGTGC
*
1480438 AAAAGGGCTTTGCCCCAGTTTA-CG
1 AAAAGGGCTTTGCCCCAGTTTATCA
1480462 AAAAGGGCTTTTGCCCCAGTTTATCA
1 AAAAGGGC-TTTGCCCCAGTTTATCA
1480488 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
1480508 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
24 8 0.19
25 26 0.60
26 9 0.21
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:1480520 original size:24 final size:24
Alignment explanation
Indices: 1480437--1480520 Score: 109
Period size: 25 Copynumber: 3.4 Consensus size: 24
1480427 GGAGGAAGTG
1480437 CAAAAGGGCTTTGCCCCAGTTTA-
1 CAAAAGGGCTTTGCCCCAGTTTAT
1480460 CGAAAAGGGCTTTTGCCCCAGTTTAT
1 C-AAAAGGGC-TTTGCCCCAGTTTAT
1480486 CAAAAAGGGCTTTGCCCCAG-TTAT
1 C-AAAAGGGCTTTGCCCCAGTTTAT
*
1480510 TAAAAGAGGCT
1 CAAAAG-GGCT
1480521 AGGCCTCCAG
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
23 6 0.11
24 16 0.29
25 24 0.44
26 9 0.16
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
CAAAAGGGCTTTGCCCCAGTTTAT
Found at i:1480531 original size:50 final size:50
Alignment explanation
Indices: 1480438--1480532 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
1480428 GAGGAAGTGC
**
1480438 AAAAGGGCTTTGCCCCAGTTTACGAAAAGGGCTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACGAAAAGGGCTTAGGCCCCAGTTTATCA
**
1480488 AAAAGGGCTTTGCCCCAG-TTATTAAAAGAGGC-TAGGCCTCCAGTT
1 AAAAGGGCTTTGCCCCAGTTTACGAAAAG-GGCTTAGGCC-CCAGTT
1480533 ATATGACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
49 12 0.31
50 27 0.69
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (50 bp):
AAAAGGGCTTTGCCCCAGTTTACGAAAAGGGCTTAGGCCCCAGTTTATCA
Found at i:1480765 original size:31 final size:31
Alignment explanation
Indices: 1480727--1480810 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
1480717 TTGTTACAGT
*
1480727 AAAGGCTTTGACCCAGTGATATGAATAATGA
1 AAAGGCTTTGGCCCAGTGATATGAATAATGA
* * *
1480758 AAAGGCTTCGGCCCAGTGATATGAGTAATGT
1 AAAGGCTTTGGCCCAGTGATATGAATAATGA
1480789 AAAGGCTTTGGCCCAGT-ATATG
1 AAAGGCTTTGGCCCAGTGATATG
1480811 CTGAGATTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 5 0.10
31 43 0.90
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (31 bp):
AAAGGCTTTGGCCCAGTGATATGAATAATGA
Found at i:1485352 original size:14 final size:14
Alignment explanation
Indices: 1485333--1485362 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1485323 CACACTATCA
1485333 CAGGTTAAATGTGG
1 CAGGTTAAATGTGG
1485347 CAGGTTAAATGTGG
1 CAGGTTAAATGTGG
1485361 CA
1 CA
1485363 TGTATAGCTA
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:0.30, C:0.10, G:0.33, T:0.27
Consensus pattern (14 bp):
CAGGTTAAATGTGG
Found at i:1487046 original size:21 final size:22
Alignment explanation
Indices: 1487013--1487053 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1487003 TTCATTTATG
*
1487013 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
1487034 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
1487054 CAACACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:1487235 original size:39 final size:39
Alignment explanation
Indices: 1487192--1487306 Score: 108
Period size: 41 Copynumber: 2.9 Consensus size: 39
1487182 TATAATAATT
1487192 CACCGGCATAAAGCCTGCTAGGCCTAAGCCTG-TATCT-CA
1 CACCGGCA-AAAGCCTGCTAGGCCTAAGCCTGAT-TCTACA
* * * * * *
1487231 CACCGGCACAAGGCCTGCTAGACTCAAAGTCTGATTTTATA
1 CACCGGCA-AAAGCCTGCTAGGC-CTAAGCCTGATTCTACA
*
1487272 CACCGGCAATAAGCCTGCTAGGCATAAGCCTGATT
1 CACCGGCAA-AAGCCTGCTAGGCCTAAGCCTGATT
1487307 TAATTCTGAT
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
39 20 0.33
40 19 0.32
41 21 0.35
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (39 bp):
CACCGGCAAAAGCCTGCTAGGCCTAAGCCTGATTCTACA
Found at i:1487542 original size:28 final size:28
Alignment explanation
Indices: 1487476--1487548 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
1487466 ATCATTTGAC
1487476 ATTTCGCACACTAAGTGTCATTCTAAAT
1 ATTTCGCACACTAAGTGTCATTCTAAAT
* * *
1487504 ATCTCACACACTAAGTGTCATTCTCAAT
1 ATTTCGCACACTAAGTGTCATTCTAAAT
* *
1487532 ATTTCGTACACTGAGTG
1 ATTTCGCACACTAAGTG
1487549 CCATATTTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34
Consensus pattern (28 bp):
ATTTCGCACACTAAGTGTCATTCTAAAT
Found at i:1489713 original size:624 final size:623
Alignment explanation
Indices: 1488526--1489774 Score: 2372
Period size: 624 Copynumber: 2.0 Consensus size: 623
1488516 TTTTTTTGAC
1488526 CAATTTACGATATTAACCTTTATACACTTTATTTATTACACCAAATGCCAAGCCATCATATCCCA
1 CAATTTACGATATTAACCTTTATACACTTTATTTATTACACCAAATGCCAAGCCATCATATCCCA
*
1488591 CTATCTCTTTAATGGGCTAATTACCAAATAAAGACTTCCACTTTAAATTTCTATAGCTCTTTAAT
66 CTATCTCTTTAATGGGCTAATTACCAAATAAAGACTTCCACTTTAAATTTCTATAGCTATTTAAT
*
1488656 ACCTTTAGCTTATAGAACACAACTTTTGTACTTTACGCGATTTAGTCCTTTTTGCTTAATTAACT
131 ACCTTTAGCTTATAGAACACAACTTTTGTACTTTACACGATTTAGTCCTTTTTGCTTAATTAACT
*
1488721 ATCAAACGATAAAATTTTTCAACGAAACTTTAATACCATCTTATTGCCACAACGTAAATATTTAT
196 ATCAAACGATAAAAGTTTTCAACGAAACTTTAATACCATCTTATTGCCACAACGTAAATATTTAT
1488786 AAAAATATTTACGACTCAGTTTATAGAAACAAGGTCCCGATACCTCATTTTCTAAACCCACTTGA
261 AAAAATATTTACGACTCAGTTTATAGAAACAAGGTCCCGATACCTCATTTTCTAAACCCACTTGA
*
1488851 CCTTAGGGTCATACCACTTGAACTTAATAAATCGCTTATAAAACAAAAATCACAATATCAAAAAC
326 CCTTAGGGTCATACCACTTGAACTTAATAAATCGCTTATAAAACAAAAATCACAATATCAAAAAA
**
1488916 ATTTTTAAAATCACAATTAACTCGTAAATATTAAATATAATATTTACAAACCTACTCGTCGGATT
391 AAATTTAAAATCACAATTAACTCGTAAATATTAAATATAATATTTACAAACCTACTCGTCGGATT
*
1488981 TGGTGGCCCCGAAACCACTGTTCCGATTAACCCTAAAAACGGGTTGTTACATCATCAAGTATTTA
456 TGGTGGCCCCGAAACCACTGTTCCGATTAACCCTAAAAACGGGCTGTTACATCATCAAGTATTTA
1489046 TTTGATTTGATAAAGTAGAAATTATTTTCCATCAATCCATTACAAATTAAACAATAATTTCTGTG
521 TTTGATTTGATAAAGTAGAAATTATTTTCCATCAATCCATTACAAATTAAACAATAATTTCTGTG
1489111 AATAACAATCCCTTTACTGAATGTCACAGAATAATAAA
586 AATAACAATCCCTTTACTGAATGTCACAGAATAATAAA
1489149 CAATTTACGATATTAACCTTTATACACTTTATTTATTACACCAAATGCCAAGCCATCATATCCCA
1 CAATTTACGATATTAACCTTTATACACTTTATTTATTACACCAAATGCCAAGCCATCATATCCCA
*
1489214 CTATCTCTTTAATGGGCTAATTGCCAAATAAAGACTTCCACTTTAAATTTCTATAGCTATTTAAT
66 CTATCTCTTTAATGGGCTAATTACCAAATAAAGACTTCCACTTTAAATTTCTATAGCTATTTAAT
1489279 ACCTTTAGCTTATAGAACACAACTTTTGTACTTTACACGATTTAGTCCTTTTTGCTTAATTAACT
131 ACCTTTAGCTTATAGAACACAACTTTTGTACTTTACACGATTTAGTCCTTTTTGCTTAATTAACT
1489344 ATCAAAACGATAAAAGTTTTCAACGAAACTTTAATACCATCTTATTGCCACAACGTAAATATTTA
196 ATC-AAACGATAAAAGTTTTCAACGAAACTTTAATACCATCTTATTGCCACAACGTAAATATTTA
1489409 TAAAAATATTTACGACTCAGTTTATAGAAACAAGGTCCCGATACCTCATTTTCTAAACCCACTTG
260 TAAAAATATTTACGACTCAGTTTATAGAAACAAGGTCCCGATACCTCATTTTCTAAACCCACTTG
* *
1489474 ACCTTAGGGTCATACCACTTGAACTTAATAAATTGCTTATAAAATAAAAATCACAATATCAAAAA
325 ACCTTAGGGTCATACCACTTGAACTTAATAAATCGCTTATAAAACAAAAATCACAATATCAAAAA
*
1489539 AAAATTTAAGATCACAATTAACTCGTAAATATTAAATATAATATTTACAAACCTACTCGTCGGAT
390 AAAATTTAAAATCACAATTAACTCGTAAATATTAAATATAATATTTACAAACCTACTCGTCGGAT
1489604 TTGGTGGCCCCGAAACCACTGTTCCGATTAACCCTAAAAACGGGCTGTTACATCATCAAGTATTT
455 TTGGTGGCCCCGAAACCACTGTTCCGATTAACCCTAAAAACGGGCTGTTACATCATCAAGTATTT
* *
1489669 ATTTGATTTGATAAAGTAGAAATTATTTTCCATCAATCCATTACAAATTAAAGAATGATTTCTGT
520 ATTTGATTTGATAAAGTAGAAATTATTTTCCATCAATCCATTACAAATTAAACAATAATTTCTGT
1489734 GAATAACAATCCCTTTACTGAATGTCACAGAATAATAAA
585 GAATAACAATCCCTTTACTGAATGTCACAGAATAATAAA
1489773 CA
1 CA
1489775 TGCTACAGAA
Statistics
Matches: 612, Mismatches: 13, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
623 195 0.32
624 417 0.68
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (623 bp):
CAATTTACGATATTAACCTTTATACACTTTATTTATTACACCAAATGCCAAGCCATCATATCCCA
CTATCTCTTTAATGGGCTAATTACCAAATAAAGACTTCCACTTTAAATTTCTATAGCTATTTAAT
ACCTTTAGCTTATAGAACACAACTTTTGTACTTTACACGATTTAGTCCTTTTTGCTTAATTAACT
ATCAAACGATAAAAGTTTTCAACGAAACTTTAATACCATCTTATTGCCACAACGTAAATATTTAT
AAAAATATTTACGACTCAGTTTATAGAAACAAGGTCCCGATACCTCATTTTCTAAACCCACTTGA
CCTTAGGGTCATACCACTTGAACTTAATAAATCGCTTATAAAACAAAAATCACAATATCAAAAAA
AAATTTAAAATCACAATTAACTCGTAAATATTAAATATAATATTTACAAACCTACTCGTCGGATT
TGGTGGCCCCGAAACCACTGTTCCGATTAACCCTAAAAACGGGCTGTTACATCATCAAGTATTTA
TTTGATTTGATAAAGTAGAAATTATTTTCCATCAATCCATTACAAATTAAACAATAATTTCTGTG
AATAACAATCCCTTTACTGAATGTCACAGAATAATAAA
Found at i:1498721 original size:228 final size:228
Alignment explanation
Indices: 1498317--1498771 Score: 766
Period size: 228 Copynumber: 2.0 Consensus size: 228
1498307 CCGCTCGGTT
* * *
1498317 GGGATCGGGATCCATTACTATAAATAAACATATTTTCAATTGTCAGAAATCACCACACTATCAAA
1 GGGATCGGGATCCATTACTATAAATAAACACATTTGCAAATGTCAGAAATCACCACACTATCAAA
* * *
1498382 TAATCACATAATGGCATGTATAGCTAGACCCAAACGTATTACGGTAGTGCTAGAATCGACTAAAC
66 TAATCACATAATGGCATGTATAGCTAGACCCAAACGAAGTACGGTAGTCCTAGAATCGACTAAAC
* * *
1498447 CGTAGCTCTGATACCAATAAAATTGTAACGCCCCGTACCAGAGACCGTTTCCGGAGTCGAACACG
131 CGTAGCTCTGATACCAATAAAATTGTAACACCCCATACCAGAGACCGTTGCCGGAGTCGAACACG
* *
1498512 AGGTGCTAACAGACTTAATTCATTTATTTTCAC
196 AGGTGCTAACAGACATAATACATTTATTTTCAC
*
1498545 GGGATCGGGATCCATTACTATAAATACACACATTTGCAAATGTCAGAAATCACCACACTATCAAA
1 GGGATCGGGATCCATTACTATAAATAAACACATTTGCAAATGTCAGAAATCACCACACTATCAAA
1498610 TAATCACATAATGGCATGTATAGCTAGACCCAAACGAAGTACGGTAGTCCTAGAATCGACTAAAC
66 TAATCACATAATGGCATGTATAGCTAGACCCAAACGAAGTACGGTAGTCCTAGAATCGACTAAAC
* ** *
1498675 CGTGGCTCTGATACCAATTTAATTGTAACACCCCATACCCGAGACCGTTGCCGGAGTCGAACACG
131 CGTAGCTCTGATACCAATAAAATTGTAACACCCCATACCAGAGACCGTTGCCGGAGTCGAACACG
1498740 AGGTGCTAACAGACATAATACATTTATTTTCA
196 AGGTGCTAACAGACATAATACATTTATTTTCA
1498772 TAGTCCATTT
Statistics
Matches: 211, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
228 211 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (228 bp):
GGGATCGGGATCCATTACTATAAATAAACACATTTGCAAATGTCAGAAATCACCACACTATCAAA
TAATCACATAATGGCATGTATAGCTAGACCCAAACGAAGTACGGTAGTCCTAGAATCGACTAAAC
CGTAGCTCTGATACCAATAAAATTGTAACACCCCATACCAGAGACCGTTGCCGGAGTCGAACACG
AGGTGCTAACAGACATAATACATTTATTTTCAC
Found at i:1500127 original size:40 final size:40
Alignment explanation
Indices: 1500081--1500269 Score: 240
Period size: 40 Copynumber: 4.7 Consensus size: 40
1500071 GCTACTCACT
*
1500081 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
1500121 CCAATGCCTTTGGGACTTAGCCCGGATT-TGGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* * *
1500161 CAAATGCCTTCGAGACTTAGCCCGG-AATTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* *
1500201 CAAATGCCTTCGGGACTTAGCCCGGATT-TGGTAAGTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
*
1500241 CAAATGCCTTCAGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1500270 CATCCGAATA
Statistics
Matches: 127, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 2 0.02
40 123 0.97
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:1500196 original size:80 final size:80
Alignment explanation
Indices: 1500081--1500265 Score: 275
Period size: 80 Copynumber: 2.3 Consensus size: 80
1500071 GCTACTCACT
* * * * * *
1500081 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACCAATGCCTTTGGGACTTAGCCCGG
1 CAAATGCCTTCGAGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGG
1500146 ATTTGGTAACTCGCA
66 ATTTGGTAACTCGCA
1500161 CAAATGCCTTCGAGACTTAGCCCGGA-ATTAGTAACTCACACAAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGAGACTTAGCCCGGATA-TAGTAACTCACACAAATGCCTTCGGGACTTAGCCCG
*
1500225 GATTTGGTAAGTCGCA
65 GATTTGGTAACTCGCA
1500241 CAAATGCCTTC-AGGACTTAGCCCGG
1 CAAATGCCTTCGA-GACTTAGCCCGG
1500266 TTATCATCCG
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
79 2 0.02
80 94 0.98
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (80 bp):
CAAATGCCTTCGAGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGG
ATTTGGTAACTCGCA
Found at i:1502861 original size:61 final size:61
Alignment explanation
Indices: 1502796--1502931 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 61
1502786 CAGAGCTATT
* *
1502796 TGGGCCTTAGCCCATAACAATATTAATCTAGGCCATAGCCC-CTTACAGTATC-AGAGTATAC
1 TGGGCCTTAGCCCATAACAATATTAATCTAGGCCATAGCCCTATTACAAT-TCGAGA-TATAC
* * * *
1502857 TGGGCC-TAGCCCATATCAGTATTAATCTAGGCCGTAGCCCTATTACAATTCGAGATATAT
1 TGGGCCTTAGCCCATAACAATATTAATCTAGGCCATAGCCCTATTACAATTCGAGATATAC
1502917 TGGGCCTT-GCCCATA
1 TGGGCCTTAGCCCATA
1502932 TTAACACAGT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
60 50 0.76
61 16 0.24
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (61 bp):
TGGGCCTTAGCCCATAACAATATTAATCTAGGCCATAGCCCTATTACAATTCGAGATATAC
Found at i:1502950 original size:20 final size:19
Alignment explanation
Indices: 1502925--1502968 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1502915 ATTGGGCCTT
1502925 GCCCATATT-AACACAGTTGG
1 GCCCAT-TTCAACACAGTT-G
*
1502945 GCCCATTTCAATACAGTTG
1 GCCCATTTCAACACAGTTG
1502964 GCCCA
1 GCCCA
1502969 CAACAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (19 bp):
GCCCATTTCAACACAGTTG
Found at i:1504899 original size:15 final size:15
Alignment explanation
Indices: 1504862--1504890 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1504852 ATTTCCTATC
1504862 TAATAATAATAATTA
1 TAATAATAATAATTA
1504877 TAATAATAATAATT
1 TAATAATAATAATT
1504891 TTATAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:1513725 original size:40 final size:40
Alignment explanation
Indices: 1513644--1513733 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 40
1513634 ATTTGAATAC
* * *
1513644 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
** *
1513684 ATCCGGGCTAAGACCCGAAGGCAATTGAGCTTGTGGTTAT
1 ATCCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
1513724 ATCC-GGCTAA
1 ATCCGGGCTAA
1513734 ATTCCAAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 6 0.14
40 38 0.86
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
Found at i:1513818 original size:40 final size:40
Alignment explanation
Indices: 1513773--1513884 Score: 179
Period size: 40 Copynumber: 2.8 Consensus size: 40
1513763 GCATTTTGTG
*
1513773 AGTTGATATATACGGGCTAAGACCCGAAGGCATTTGTGCA
1 AGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
*
1513813 AGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCG
1 AGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* * *
1513853 AGTTGCTATACCCGGGTTAAGACCCGAAGGCA
1 AGTTGATATATCCGGGCTAAGACCCGAAGGCA
1513885 ATTGAGCTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (40 bp):
AGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
Found at i:1513903 original size:80 final size:78
Alignment explanation
Indices: 1513763--1513911 Score: 181
Period size: 80 Copynumber: 1.9 Consensus size: 78
1513753 TTGAATGTGA
* * * * *
1513763 GCATTTTGTGAGTTGATATATACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGG
1 GCATTTTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATATATCC-G
1513828 GCTAAGACCCGAAG
65 GCTAAGACCCGAAG
* * * ** *
1513842 GCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGAGCTTGTGGTTATATCCG
1 GCATTT-TGCGAGTTGATATACACGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATATATCCG
1513907 GCTAA
65 GCTAA
1513912 ATTCCAAAGA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
79 12 0.21
80 46 0.79
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (78 bp):
GCATTTTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATATATCCGG
CTAAGACCCGAAG
Found at i:1514450 original size:200 final size:200
Alignment explanation
Indices: 1514107--1514506 Score: 773
Period size: 200 Copynumber: 2.0 Consensus size: 200
1514097 TGTATATGTT
1514107 GATGAAGTGTGAAGTAAGTATGATTATGAGAATGTGAATTAATAAAGTGATTCATTTAGCTATGT
1 GATGAAGTGTGAAGTAAGTATGATTATGAGAATGTGAATTAATAAAGTGATTCATTTAGCTATGT
1514172 GAATGTAATACTTTAGTCAAAGCCGATTTCATTACTTGAAACTTACTAAGCTTTAAAATGCTTAC
66 GAATGTAATACTTTAGTCAAAGCCGATTTCATTACTTGAAACTTACTAAGCTTTAAAATGCTTAC
*
1514237 CCCGTTGCTTTGGCTCTCTGTTTTATAGATATTGTTCGTTAGCTATCGGATTTGGGATCATCGAA
131 CCCGTTGCTTTGGCTCTCTGTTTTATAGATATTGTTCGTTAGCTATCGGATTCGGGATCATCGAA
1514302 GTCGA
196 GTCGA
1514307 GATGAAGTGTGAAGTAAGTATGATTATGAGAATGTGAATTAATAAAGTGATTCATTTAGCTATGT
1 GATGAAGTGTGAAGTAAGTATGATTATGAGAATGTGAATTAATAAAGTGATTCATTTAGCTATGT
*
1514372 GGATGTAATACTTTAGTCAAAGCCGATTTCATTACTTGAAACTTACTAAGCTTTAAAATGCTTAC
66 GAATGTAATACTTTAGTCAAAGCCGATTTCATTACTTGAAACTTACTAAGCTTTAAAATGCTTAC
*
1514437 CCCGTTGCTTTGGCTCTCTGTTTTATAGATATTGTTCGTTAGCTATCGGATTCGGGATCATCGAG
131 CCCGTTGCTTTGGCTCTCTGTTTTATAGATATTGTTCGTTAGCTATCGGATTCGGGATCATCGAA
1514502 GTCGA
196 GTCGA
1514507 AGTCATCCAC
Statistics
Matches: 197, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 197 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (200 bp):
GATGAAGTGTGAAGTAAGTATGATTATGAGAATGTGAATTAATAAAGTGATTCATTTAGCTATGT
GAATGTAATACTTTAGTCAAAGCCGATTTCATTACTTGAAACTTACTAAGCTTTAAAATGCTTAC
CCCGTTGCTTTGGCTCTCTGTTTTATAGATATTGTTCGTTAGCTATCGGATTCGGGATCATCGAA
GTCGA
Found at i:1520881 original size:39 final size:39
Alignment explanation
Indices: 1520827--1520905 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
1520817 TTAAGTCAAA
*
1520827 TAGCTAATTTCATATTAGCCCATTTGAAAACTTGGAATT
1 TAGCTAATTCCATATTAGCCCATTTGAAAACTTGGAATT
*
1520866 TAGCTAGTTCCATATTAGCCCATTTGAAAACTTGGAATT
1 TAGCTAATTCCATATTAGCCCATTTGAAAACTTGGAATT
1520905 T
1 T
1520906 TAGATGTTGG
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:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (39 bp):
TAGCTAATTCCATATTAGCCCATTTGAAAACTTGGAATT
Found at i:1522601 original size:40 final size:40
Alignment explanation
Indices: 1522538--1522770 Score: 342
Period size: 40 Copynumber: 5.8 Consensus size: 40
1522528 ATTTGAATTT
*
1522538 TATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATA
*
1522578 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATA
1522618 TATCCGGGCTAAGACCCGCAA-GCATTTGTGCGAGTTGATATA
1 TATCCGGGCTAAGACCCG-AAGGCATTTGTGCGAGTTG--ATA
* *
1522660 TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATA
* *
1522700 TATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATA
** * *
1522740 TGCCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1522771 TTGTGGTAAT
Statistics
Matches: 175, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
40 137 0.78
41 3 0.02
42 35 0.20
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATA
Found at i:1522696 original size:82 final size:80
Alignment explanation
Indices: 1522538--1522770 Score: 351
Period size: 82 Copynumber: 2.9 Consensus size: 80
1522528 ATTTGAATTT
* * *
1522538 TATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGCAGGCAT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAA
*
1522603 TTGTGCGAGTTGATA
66 TTGTGCAAGTTGATA
1522618 TATCCGGGCTAAGACCCGCAA-GCATTTGTGCGAGTTGATATATATCCGGGCTAAGACCCGAAGG
1 TATCCGGGCTAAGACCCG-AAGGCATTTGTGCGAGTTG--ATATATCCGGGCTAAGACCCGAAGG
1522682 CAATTGTGCAAGTTGATA
63 CAATTGTGCAAGTTGATA
* * ** *
1522700 TATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATGCCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAA
1522765 TTGTGC
66 TTGTGC
1522771 TTGTGGTAAT
Statistics
Matches: 140, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
80 63 0.45
81 4 0.03
82 73 0.52
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTTGATA
Found at i:1522755 original size:122 final size:122
Alignment explanation
Indices: 1522538--1522770 Score: 360
Period size: 122 Copynumber: 1.9 Consensus size: 122
1522528 ATTTGAATTT
* * * *
1522538 TATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGCAGGCAT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAT
* * *
1522603 TTGTGCGAGTTGATATATCCGGGCTAAGACCCGCAA-GCATTTGTGCGAGTTGATATA
66 TCGTGCGAGTTGATATACCCGGGCTAAGACCCG-AAGGCAATTGTGCGAGTTGATATA
1522660 TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAT
* * *
1522725 TCGTGCGAGTTGCTATGCCCGGGTTAAGACCCGAAGGCAATTGTGC
66 TCGTGCGAGTTGATATACCCGGGCTAAGACCCGAAGGCAATTGTGC
1522771 TTGTGGTAAT
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
121 2 0.02
122 98 0.98
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (122 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAT
TCGTGCGAGTTGATATACCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATATA
Found at i:1539066 original size:22 final size:22
Alignment explanation
Indices: 1539008--1539069 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
1538998 AATCTTTCAA
* *
1539008 GGTGGTGTAAGGGTAGTGGTAT
1 GGTGGTGCAAGGGTGGTGGTAT
*
1539030 GGTGGTGCTAGGGTGGTGGTAT
1 GGTGGTGCAAGGGTGGTGGTAT
* *
1539052 GGTGGTTCAATGGTGGTG
1 GGTGGTGCAAGGGTGGTG
1539070 ATTTAATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.13, C:0.03, G:0.52, T:0.32
Consensus pattern (22 bp):
GGTGGTGCAAGGGTGGTGGTAT
Found at i:1542059 original size:47 final size:47
Alignment explanation
Indices: 1542005--1542198 Score: 271
Period size: 47 Copynumber: 4.1 Consensus size: 47
1541995 TTAGGATTTT
** * *
1542005 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
1542052 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGACCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
1542099 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGTCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
1542146 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1542193 ATGTGA
1 ATGTGA
1542199 AATATGTATG
Statistics
Matches: 130, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 130 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:1542330 original size:97 final size:97
Alignment explanation
Indices: 1542169--1543030 Score: 1667
Period size: 97 Copynumber: 8.9 Consensus size: 97
1542159 GAACATGCAT
*
1542169 ATATGTGGTAAAGCCGAATGG-CTAATGTG-AA-ATATGTATGAGATATGTATATGTGGTAAAGC
1 ATATGTGGTAAAGCCGAATGGTC-AATGTGAAATATATATATGAGATATGTATATGTGGTAAAGC
1542231 CGAATGGCTAATGTGAAAATGTATGAGATATGC
65 CGAATGGCTAATGTGAAAATGTATGAGATATGC
1542264 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1542329 GAATGGCTAATGTGAAAATGTATGAGATATGC
66 GAATGGCTAATGTGAAAATGTATGAGATATGC
1542361 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1542426 GAATGGCTAATGTGAAAATGTATGAGATATGC
66 GAATGGCTAATGTGAAAATGTATGAGATATGC
1542458 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1542523 GAATGGCTAATGTGAAAATGTATGAGATATGC
66 GAATGGCTAATGTGAAAATGTATGAGATATGC
1542555 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1542620 GAATGGCTAATGTGAAAATGTATGAGATATGC
66 GAATGGCTAATGTGAAAATGTATGAGATATGC
1542652 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1542717 GAATGGCTAATGTGAAAATGTATGAGATATGC
66 GAATGGCTAATGTGAAAATGTATGAGATATGC
1542749 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1542814 GAATGGCTAATGTGAAAATGTATGAGATATGC
66 GAATGGCTAATGTGAAAATGTATGAGATATGC
1542846 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1542911 GAATGGCTAATGTGAAAATGTATGAGATATGC
66 GAATGGCTAATGTGAAAATGTATGAGATATGC
1542943 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
1 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
*
1543008 GAATGGCTAGTGTGAAATATGTA
66 GAATGGCTAATGTGAAA-ATGTA
1543031 GGCGATGTGC
Statistics
Matches: 761, Mismatches: 2, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
95 27 0.04
96 3 0.00
97 726 0.95
98 5 0.01
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (97 bp):
ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCC
GAATGGCTAATGTGAAAATGTATGAGATATGC
Found at i:1543285 original size:37 final size:37
Alignment explanation
Indices: 1543177--1543285 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
1543167 GGAAATATAT
*
1543177 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
1543214 TCCCGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
1543251 TTCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
1543286 CGTCTGAGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:1544730 original size:62 final size:62
Alignment explanation
Indices: 1544653--1545482 Score: 1635
Period size: 62 Copynumber: 13.4 Consensus size: 62
1544643 TCAATCTCAG
1544653 CATAT-ACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1544714 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1544776 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1544838 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1544900 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1544962 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1545024 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1545086 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1545148 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1545210 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1545272 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1545334 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
*
1545396 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGGGCCAAAGCTTTTTCATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
*
1545458 CATATCACTAGGCCGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
1545483 TGTAAACGAC
Statistics
Matches: 766, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
61 5 0.01
62 761 0.99
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (62 bp):
CATATCACTGGGCCGAAGCCTTTACATTATTCATGTCACTGAGCCAAAGCTTTTTCATTGTT
Found at i:1545737 original size:25 final size:25
Alignment explanation
Indices: 1545700--1545768 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
1545690 CTCTTTTAAT
1545700 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTTGATA
*
1545725 AAGTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTTGATA
*
1545750 AACTGGCGCAAAGCCCTTT
1 AACTGGGGCAAAGCCCTTT
1545769 GGCACTTTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTTGATA
Found at i:1550283 original size:31 final size:31
Alignment explanation
Indices: 1550220--1550303 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
1550210 TCAATCTCAG
* *
1550220 CATAT-ACTAGGCCGAAGCCTTTCCATTATT
1 CATATCACTTGGCCAAAGCCTTTCCATTATT
* *
1550250 CATGTCACTTGGCCAAAGCCATTT-CATTGTT
1 CATATCACTTGGCCAAAGCC-TTTCCATTATT
* **
1550281 CATATCACTAGGCTGAAGCCTTT
1 CATATCACTTGGCCAAAGCCTTT
1550304 ACTGTAAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
30 7 0.16
31 34 0.77
32 3 0.07
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.33
Consensus pattern (31 bp):
CATATCACTTGGCCAAAGCCTTTCCATTATT
Found at i:1550548 original size:24 final size:25
Alignment explanation
Indices: 1550516--1550567 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1550506 GCCTAGCCTC
*
1550516 TTTTAAT-AACTGGGGCAAAACCCT
1 TTTTAATAAACTAGGGCAAAACCCT
* *
1550540 TTTTGATAAACTAGGGCAAAGCCCT
1 TTTTAATAAACTAGGGCAAAACCCT
1550565 TTT
1 TTT
1550568 GCACTTCCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTAGGGCAAAACCCT
Found at i:1550568 original size:24 final size:23
Alignment explanation
Indices: 1550510--1550568 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
1550500 CTGGAGGCCT
* *
1550510 AGCCTCTTTTAATAACTGGGGCAA
1 AGCC-CTTTTGATAACTAGGGCAA
*
1550534 AACCCTTTTTGATAAACTAGGGCAA
1 AGCCC-TTTTGAT-AACTAGGGCAA
1550559 AGCCCTTTTG
1 AGCCCTTTTG
1550569 CACTTCCTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 14 0.48
25 14 0.48
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (23 bp):
AGCCCTTTTGATAACTAGGGCAA
Found at i:1551867 original size:14 final size:14
Alignment explanation
Indices: 1551848--1551874 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1551838 GTTCGGCTAG
1551848 AGAAGAAGAAAGAA
1 AGAAGAAGAAAGAA
1551862 AGAAGAAGAAAGA
1 AGAAGAAGAAAGA
1551875 GAACAGCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAAGAA
Found at i:1552915 original size:3 final size:3
Alignment explanation
Indices: 1552907--1552937 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1552897 ATTTAATTAC
1552907 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1552938 TTCAGAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1554239 original size:40 final size:40
Alignment explanation
Indices: 1554182--1554267 Score: 165
Period size: 40 Copynumber: 2.2 Consensus size: 40
1554172 TGAAGACAAC
1554182 AAATTT-GGAAAAAAACTCTCTTTAAAATAATAATTTTGG
1 AAATTTCGGAAAAAAACTCTCTTTAAAATAATAATTTTGG
1554221 AAATTTCGGAAAAAAACTCTCTTTAAAATAATAATTTTGG
1 AAATTTCGGAAAAAAACTCTCTTTAAAATAATAATTTTGG
1554261 AAATTTC
1 AAATTTC
1554268 TTTTCCAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 6 0.13
40 40 0.87
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (40 bp):
AAATTTCGGAAAAAAACTCTCTTTAAAATAATAATTTTGG
Found at i:1555109 original size:31 final size:31
Alignment explanation
Indices: 1555066--1555151 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
1555056 TCAATCTCAG
1555066 CATAT-ACTGGGCCGAAGCCTTTACATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* *
1555096 CATGTCACTGGGCCGAAGCCCTTT-CATTGTT
1 CATATCACTGGGCCGAAG-CCTTTACATTATT
*
1555127 CATATCACTGGGCTGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
1555152 TATAAATGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 9 0.18
31 35 0.71
32 5 0.10
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATT
Found at i:1555389 original size:24 final size:25
Alignment explanation
Indices: 1555362--1555413 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1555352 GCCTAGCCTC
*
1555362 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGAGCAAAGCCCT
*
1555386 TTTTGATAAACTGGAGCAAAGCCCT
1 TTTTAATAAACTGGAGCAAAGCCCT
1555411 TTT
1 TTT
1555414 GCACTTCCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTGGAGCAAAGCCCT
Found at i:1555414 original size:24 final size:23
Alignment explanation
Indices: 1555342--1555414 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 23
1555332 GCTTTATCAT
** *
1555342 ATAACTGGAGGCCTAGCCTCTTTTA
1 ATAACTGGA-GCAAAGCC-CTTTTG
*
1555367 ATAACTGGGGCAAAGCCCTTTTTG
1 ATAACTGGAGCAAAGCCC-TTTTG
1555391 ATAAACTGGAGCAAAGCCCTTTTG
1 AT-AACTGGAGCAAAGCCCTTTTG
1555415 CACTTCCTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.02
24 17 0.41
25 23 0.56
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (23 bp):
ATAACTGGAGCAAAGCCCTTTTG
Found at i:1560454 original size:40 final size:40
Alignment explanation
Indices: 1560392--1560716 Score: 476
Period size: 40 Copynumber: 8.2 Consensus size: 40
1560382 AAACCAAGTA
* * *
1560392 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
1560431 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
1560471 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
1560511 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
1560551 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
1560591 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
1560631 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
1560671 CCTTCGGGACTTAGCCC-GAAATTAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
1560711 CCTTCG
1 CCTTCG
1560717 TTATCATCCG
Statistics
Matches: 260, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 16 0.06
40 244 0.94
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:1578096 original size:27 final size:27
Alignment explanation
Indices: 1577906--1578083 Score: 311
Period size: 27 Copynumber: 6.6 Consensus size: 27
1577896 TAAATTGTGC
* *
1577906 AGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
1577933 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
1577961 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
1577988 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
1578015 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
1578042 AGCACTAAGTGTGCGAGTTGACTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
1578069 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
1578084 GACTTAATAT
Statistics
Matches: 146, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
27 120 0.82
28 26 0.18
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:1583290 original size:7 final size:7
Alignment explanation
Indices: 1583280--1583307 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1583270 TTAATAAGAC
1583280 ATAAATA
1 ATAAATA
1583287 ATAAATA
1 ATAAATA
1583294 ATAAATA
1 ATAAATA
1583301 ATAAATA
1 ATAAATA
1583308 GGGCCAAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATAAATA
Found at i:1584992 original size:34 final size:35
Alignment explanation
Indices: 1584921--1585001 Score: 119
Period size: 34 Copynumber: 2.3 Consensus size: 35
1584911 TACTACTAAT
* *
1584921 AAATTTTTTTACATATTTACTTTAAATCGAAAAAA
1 AAATATTTTTAAATATTTACTTTAAATCGAAAAAA
*
1584956 AAATATTTTTAAATATTTACTTT-AATCGAAAGAA
1 AAATATTTTTAAATATTTACTTTAAATCGAAAAAA
*
1584990 AAATATGTTTAA
1 AAATATTTTTAA
1585002 CGCATTTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 21 0.50
35 21 0.50
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (35 bp):
AAATATTTTTAAATATTTACTTTAAATCGAAAAAA
Found at i:1586539 original size:27 final size:27
Alignment explanation
Indices: 1586501--1586557 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1586491 AAGATAGACA
1586501 AAGATGCACTAACTGATTTTTCTGTCT
1 AAGATGCACTAACTGATTTTTCTGTCT
1586528 AAGATGCACTAACTGATTTTTCTGTCT
1 AAGATGCACTAACTGATTTTTCTGTCT
1586555 AAG
1 AAG
1586558 TACTCAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.39
Consensus pattern (27 bp):
AAGATGCACTAACTGATTTTTCTGTCT
Found at i:1596384 original size:15 final size:15
Alignment explanation
Indices: 1596360--1596389 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1596350 TTTATATCTT
1596360 TATAAATTTTTTAAA
1 TATAAATTTTTTAAA
*
1596375 TATAATTTTTTTAAA
1 TATAAATTTTTTAAA
1596390 GGGTTAAATT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATAAATTTTTTAAA
Found at i:1599085 original size:18 final size:18
Alignment explanation
Indices: 1599062--1599098 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1599052 TGGAAAAAAC
1599062 TATTTTTATACCTAGATG
1 TATTTTTATACCTAGATG
1599080 TATTTTTATACCTAGATG
1 TATTTTTATACCTAGATG
1599098 T
1 T
1599099 TCTAAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (18 bp):
TATTTTTATACCTAGATG
Found at i:1601499 original size:19 final size:19
Alignment explanation
Indices: 1601475--1601523 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
1601465 TTATAACTTA
1601475 TAAATAAATAAAATTA-TAC
1 TAAATAAATAAAATTAGT-C
* *
1601494 TAAATATATAATATTAGTC
1 TAAATAAATAAAATTAGTC
1601513 TAATATAAATA
1 TAA-ATAAATA
1601524 TTAAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAATAAATAAAATTAGTC
Found at i:1602433 original size:26 final size:26
Alignment explanation
Indices: 1602391--1602441 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1602381 AAGCACTGAA
* *
1602391 AAACAAAGTTATTCCAATTT-TTTTG
1 AAACAAAATTATCCCAATTTGTTTTG
1602416 AAACGAAAATTATCCCAATTTGTTTT
1 AAAC-AAAATTATCCCAATTTGTTTT
1602442 TAAAATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 14 0.64
27 4 0.18
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (26 bp):
AAACAAAATTATCCCAATTTGTTTTG
Found at i:1603768 original size:21 final size:20
Alignment explanation
Indices: 1603742--1603790 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
1603732 ATATAAATAA
**
1603742 ATTATTTATATTAAATTTTTT
1 ATTATTTAT-TTAAAAATTTT
1603763 ATTA-TTATTTAAAAATTTT
1 ATTATTTATTTAAAAATTTT
1603782 ATATATTTA
1 AT-TATTTA
1603791 GTAGTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 11 0.46
20 6 0.25
21 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTATTTATTTAAAAATTTT
Found at i:1604285 original size:32 final size:30
Alignment explanation
Indices: 1604226--1604289 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
1604216 CTTTTTTAAA
*
1604226 ATTAAAAAAATCATAATTATCTTAAAAATT
1 ATTAAAAAAATCATAATCATCTTAAAAATT
1604256 ATTAAAAAAATCA-AATCATTCATTAAAAAATT
1 ATTAAAAAAATCATAATCA-TC-TT-AAAAATT
1604288 AT
1 AT
1604290 AAATTTCAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.13
30 15 0.50
31 2 0.07
32 9 0.30
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (30 bp):
ATTAAAAAAATCATAATCATCTTAAAAATT
Found at i:1605187 original size:24 final size:24
Alignment explanation
Indices: 1605159--1605240 Score: 62
Period size: 24 Copynumber: 3.3 Consensus size: 24
1605149 TTCTCTTCAC
1605159 AATAAAAATAATTGAATCTTGCAA
1 AATAAAAATAATTGAATCTTGCAA
*
1605183 AAT-AAAATATTCTGAAATCTTATG-AA
1 AATAAAAATAAT-TG-AATC-T-TGCAA
* *
1605209 CAA-AAACAAAAATTGAGTCTTGCAA
1 -AATAAA-AATAATTGAATCTTGCAA
1605234 AATAAAA
1 AATAAAA
1605241 TATTTCAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 18
0.67 0.06 0.27
Matches are distributed among these distances:
23 7 0.16
24 10 0.22
25 10 0.22
26 6 0.13
27 8 0.18
28 4 0.09
ACGTcount: A:0.55, C:0.10, G:0.09, T:0.27
Consensus pattern (24 bp):
AATAAAAATAATTGAATCTTGCAA
Found at i:1609048 original size:15 final size:15
Alignment explanation
Indices: 1609028--1609061 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1609018 GAGTTCCATA
*
1609028 AGAAATATATCAGCC
1 AGAAATATATCAACC
*
1609043 AGAAATTTATCAACC
1 AGAAATATATCAACC
1609058 AGAA
1 AGAA
1609062 CCACAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.21
Consensus pattern (15 bp):
AGAAATATATCAACC
Found at i:1611422 original size:79 final size:81
Alignment explanation
Indices: 1611286--1611470 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
1611276 TTGAATGATG
* *
1611286 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
1611350 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
1611365 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
1611427 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
1611445 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1611471 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:1611484 original size:40 final size:40
Alignment explanation
Indices: 1611287--1611470 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
1611277 TGAATGATGT
* * * *
1611287 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
1611327 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
1611367 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
1611405 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
1611446 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
1611471 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:1611492 original size:79 final size:79
Alignment explanation
Indices: 1611339--1611503 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
1611329 GGACTAAGAT
* * **
1611339 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
1611404 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
1611418 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
1611481 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
1611497 CCGAAGG
1 CCGAAGG
1611504 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:1614849 original size:44 final size:44
Alignment explanation
Indices: 1614773--1614856 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
1614763 ATTATCACCC
* ** *
1614773 GGGAAAGGCTAATGTTGGGCAATTTAGAAATTCCTGTAATTCCT
1 GGGAAAAGCTAATGTTGGGCAAACTAGAAATTCCCGTAATTCCT
* * *
1614817 GGGAAAAGCTAATGTTGTGCAAACTCGTAATTCCCGTAAT
1 GGGAAAAGCTAATGTTGGGCAAACTAGAAATTCCCGTAAT
1614857 AATCCATTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (44 bp):
GGGAAAAGCTAATGTTGGGCAAACTAGAAATTCCCGTAATTCCT
Found at i:1634196 original size:47 final size:47
Alignment explanation
Indices: 1634132--1634290 Score: 175
Period size: 47 Copynumber: 3.4 Consensus size: 47
1634122 CAAATGTCCA
*
1634132 AGCTTGTTGAGTTGAGTCCAAGGTTGTGAGATGTAACTAGGCATCCG
1 AGCTCGTTGAGTTGAGTCCAAGGTTGTGAGATGTAACTAGGCATCCG
* * * * * *
1634179 AGCTCGTTGAGTTGAGTCCGA-GTTCACTTATGGATGCAA--ATG--TCCA
1 AGCTCGTTGAGTTGAGTCCAAGGTT--GTGA--GATGTAACTAGGCATCCG
*
1634225 AGCTTGTTGAGTTGAGTCCAAGGTTGTGAGATGTAACTAGGCATCCG
1 AGCTCGTTGAGTTGAGTCCAAGGTTGTGAGATGTAACTAGGCATCCG
1634272 AGCTCGTTGAGTTGAGTCC
1 AGCTCGTTGAGTTGAGTCC
1634291 GAGTTTGCTT
Statistics
Matches: 88, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
43 6 0.07
45 4 0.05
46 25 0.28
47 43 0.49
48 4 0.05
50 6 0.07
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (47 bp):
AGCTCGTTGAGTTGAGTCCAAGGTTGTGAGATGTAACTAGGCATCCG
Found at i:1634237 original size:93 final size:93
Alignment explanation
Indices: 1634078--1634304 Score: 436
Period size: 93 Copynumber: 2.4 Consensus size: 93
1634068 AGGATATTTT
1634078 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAGCTTGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAGCTTGTTGAG
1634143 TTGAGTCCAAGGTTGTGAGATGTAACTA
66 TTGAGTCCAAGGTTGTGAGATGTAACTA
1634171 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAGCTTGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAGCTTGTTGAG
1634236 TTGAGTCCAAGGTTGTGAGATGTAACTA
66 TTGAGTCCAAGGTTGTGAGATGTAACTA
**
1634264 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTTGCTTATGG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1634305 GCGGGTTACA
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 132 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAGCTTGTTGAG
TTGAGTCCAAGGTTGTGAGATGTAACTA
Found at i:1634243 original size:46 final size:46
Alignment explanation
Indices: 1634086--1634243 Score: 171
Period size: 46 Copynumber: 3.4 Consensus size: 46
1634076 TTGGCATCCG
1634086 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCA
1 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCA
* * * * * * *
1634132 AGCTTGTTGAGTTGAGTCCAAG----GTTGTGAGATGTAACTAGGCATCCG
1 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAA--ATG--TCCA
1634179 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCA
1 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCA
*
1634225 AGCTTGTTGAGTTGAGTCC
1 AGCTCGTTGAGTTGAGTCC
1634244 AAGGTTGTGA
Statistics
Matches: 88, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
42 4 0.05
43 6 0.07
45 2 0.02
46 41 0.47
47 23 0.26
48 2 0.02
50 6 0.07
51 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (46 bp):
AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCA
Found at i:1640316 original size:38 final size:38
Alignment explanation
Indices: 1640216--1640379 Score: 229
Period size: 38 Copynumber: 4.2 Consensus size: 38
1640206 TCGAAATATG
*
1640216 ATATCTGGGTTAAATCCCGCAGGCTTCGTGCTGGTATT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATT
* *
1640254 ATATCTGGGTTGTTAAATCCCGCAGGCTTCGTGCTGGTAAT
1 ATATC-CGG--GTTAAATCCCGCAGGCTTCGTGCTGGTATT
*
1640295 ATATCCGGGTTAAATCTCGCAGGCTTCGTGCTGGTATT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATT
* * *
1640333 ATATCCAGGTTAAATCCCGCAGGCCTAGTGCTGGTATT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATT
*
1640371 ATATTCGGG
1 ATATCCGGG
1640380 CCTTTAAGCC
Statistics
Matches: 112, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
38 74 0.66
39 2 0.02
40 2 0.02
41 34 0.30
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (38 bp):
ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATT
Found at i:1640469 original size:45 final size:45
Alignment explanation
Indices: 1640373--1640500 Score: 140
Period size: 46 Copynumber: 2.9 Consensus size: 45
1640363 CTGGTATTAT
* * * * *
1640373 ATTCGGGCCTTT-AAGCCTAACAGACTATTATGCCGGTGAGACATT
1 ATTCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCGGTGA-ACATG
1640418 ATTCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCGGTGAA-ATG
1 ATTCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCGGTGAACATG
* *
1640462 ATATCGGGCC--TCGAGCCTAGCAGGCGA-AATGCTGGTGAA
1 AT-TCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCGGTGAA
1640501 TGAATAAAAG
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
42 11 0.15
43 16 0.22
44 4 0.05
45 20 0.27
46 23 0.31
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (45 bp):
ATTCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCGGTGAACATG
Found at i:1643873 original size:43 final size:42
Alignment explanation
Indices: 1643776--1643880 Score: 122
Period size: 43 Copynumber: 2.5 Consensus size: 42
1643766 CTCATCCATA
* *
1643776 ATGAACTCGAACCTCTCAACAAGTTCAAGTGCCACATAAATC
1 ATGAACTCGGACCACTCAACAAGTTCAAGTGCCACATAAATC
* * * * *
1643818 ACGAACTTGGACCACTCAACAAGTTC-GGATTCTCACATATATC
1 ATGAACTCGGACCACTCAACAAGTTCAAG-TGC-CACATAAATC
1643861 ATGAACTCGGACCACTCAAC
1 ATGAACTCGGACCACTCAAC
1643881 GAGCTCGAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.02
42 24 0.46
43 27 0.52
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (42 bp):
ATGAACTCGGACCACTCAACAAGTTCAAGTGCCACATAAATC
Found at i:1654006 original size:79 final size:82
Alignment explanation
Indices: 1653895--1654078 Score: 231
Period size: 79 Copynumber: 2.3 Consensus size: 82
1653885 GCTACTCGTT
* *
1653895 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
*
1653958 GGAT-TTAGTAAC-TCGCA
65 GGATATT-GTAACTTAGCA
* **
1653975 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
*
1654038 GATATTGTCACTTAGCA
66 GATATTGTAACTTAGCA
1654055 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1654079 CATCATTCAA
Statistics
Matches: 92, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
78 12 0.13
79 58 0.63
80 22 0.24
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATTGTAACTTAGCA
Found at i:1654012 original size:39 final size:40
Alignment explanation
Indices: 1653895--1654078 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
1653885 GCTACTCGTT
* *
1653895 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
1653935 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
1653975 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
1654014 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
1654055 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1654079 CATCATTCAA
Statistics
Matches: 128, Mismatches: 10, Indels: 13
0.85 0.07 0.09
Matches are distributed among these distances:
38 2 0.02
39 49 0.38
40 67 0.52
41 10 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:1662434 original size:79 final size:82
Alignment explanation
Indices: 1662323--1662507 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
1662313 GCTACTCGTT
* * *
1662323 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
1662386 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
1662403 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
1662466 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
1662483 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1662508 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:1662507 original size:40 final size:40
Alignment explanation
Indices: 1662304--1662507 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
1662294 CGGAATTTAA
** *
1662304 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
1662344 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
1662384 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1662423 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
1662463 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
1662503 CCGGA
1 CCGGA
1662508 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:1668624 original size:26 final size:26
Alignment explanation
Indices: 1668595--1668644 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1668585 AATCATGCAT
*
1668595 CACATA-AGGGCAAAACAGTCATTTGC
1 CACATAGA-GGCAAAACAATCATTTGC
*
1668621 CACATAGAGGCATAACAATCATTT
1 CACATAGAGGCAAAACAATCATTT
1668645 TATCAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (26 bp):
CACATAGAGGCAAAACAATCATTTGC
Found at i:1669736 original size:22 final size:23
Alignment explanation
Indices: 1669711--1669786 Score: 84
Period size: 24 Copynumber: 3.3 Consensus size: 23
1669701 AATGGGGACA
* *
1669711 GGAAATAGCAAATTGGCAG-CAG
1 GGAAATAGCAAATCGGCAGAAAG
1669733 GGAAATAGC-AATCGGCAGTAAAG
1 GGAAATAGCAAATCGGCAG-AAAG
* *
1669756 GGAAATAGCAAATCGACAGTAGAG
1 GGAAATAGCAAATCGGCAG-AAAG
1669780 GGAAATA
1 GGAAATA
1669787 AAATCAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.17
22 9 0.19
23 11 0.23
24 19 0.40
ACGTcount: A:0.45, C:0.12, G:0.30, T:0.13
Consensus pattern (23 bp):
GGAAATAGCAAATCGGCAGAAAG
Found at i:1669761 original size:23 final size:24
Alignment explanation
Indices: 1669731--1669786 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
1669721 AATTGGCAGC
*
1669731 AGGGAAATAGC-AATCGGCAGTAA
1 AGGGAAATAGCAAATCGACAGTAA
*
1669754 AGGGAAATAGCAAATCGACAGTAG
1 AGGGAAATAGCAAATCGACAGTAA
1669778 AGGGAAATA
1 AGGGAAATA
1669787 AAATCAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.46, C:0.11, G:0.30, T:0.12
Consensus pattern (24 bp):
AGGGAAATAGCAAATCGACAGTAA
Found at i:1673338 original size:19 final size:18
Alignment explanation
Indices: 1673311--1673353 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1673301 TGAAATTTTG
*
1673311 ATTAGTATTATGAGAGAAA
1 ATTATTATTATGAGA-AAA
*
1673330 ATTATTATTATTAGAAAA
1 ATTATTATTATGAGAAAA
1673348 A-TATTA
1 ATTATTA
1673354 CTGTAAGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
19 13 0.59
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.40
Consensus pattern (18 bp):
ATTATTATTATGAGAAAA
Found at i:1679179 original size:43 final size:42
Alignment explanation
Indices: 1679075--1679342 Score: 195
Period size: 43 Copynumber: 6.2 Consensus size: 42
1679065 AGGATTTTCA
* * * ** *
1679075 ATATATGATTACGTGTAAGACCATGTATGGGACATCGGCATCG
1 ATATGTGATT-CGTGTAAGACCACGTCTGGGATGTTGGCATCG
* *
1679118 -TATTTGATTCGTGTAAGACCACGTCTGCGATGTTGGCATCG
1 ATATGTGATTCGTGTAAGACCACGTCTGGGATGTTGGCATCG
* ** *
1679159 ATATGTGATTACGTGTAAGACCATGTCTGGGACATCGGCATCG
1 ATATGTGATT-CGTGTAAGACCACGTCTGGGATGTTGGCATCG
* * *
1679202 -TATTTGATTCGTGTAAGTACC-CTATCTGGGACAG-TGGCATCG
1 ATATGTGATTCGTGTAAG-ACCAC-GTCTGGGA-TGTTGGCATCG
*
1679244 ATATGTGATTCCATGTAAGACCACGTCTGGGATGTTGGCATTGTACG
1 ATATGTGATT-CGTGTAAGACCACGTCTGGGATGTTGGCA---T-CG
* * ****
1679291 ATATGTG-TGTGCGAGTAAGACCACGTTTAATTTGTTGGCATCG
1 ATATGTGAT-T-CGTGTAAGACCACGTCTGGGATGTTGGCATCG
1679334 ATATGTGAT
1 ATATGTGAT
1679343 CCCGATATGT
Statistics
Matches: 179, Mismatches: 31, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
41 34 0.19
42 42 0.23
43 59 0.33
44 10 0.06
46 2 0.01
47 32 0.18
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (42 bp):
ATATGTGATTCGTGTAAGACCACGTCTGGGATGTTGGCATCG
Found at i:1679230 original size:42 final size:42
Alignment explanation
Indices: 1679075--1679275 Score: 219
Period size: 43 Copynumber: 4.7 Consensus size: 42
1679065 AGGATTTTCA
* *
1679075 ATATATGATTACGTGTAAGACCATGTATGGGACATCGGCATCG
1 ATATGTGATT-CGTGTAAGACCATGTCTGGGACATCGGCATCG
* * * ** *
1679118 -TATTTGATTCGTGTAAGACCACGTCTGCGATGTTGGCATCG
1 ATATGTGATTCGTGTAAGACCATGTCTGGGACATCGGCATCG
1679159 ATATGTGATTACGTGTAAGACCATGTCTGGGACATCGGCATCG
1 ATATGTGATT-CGTGTAAGACCATGTCTGGGACATCGGCATCG
* * *
1679202 -TATTTGATTCGTGTAAGTACCCTATCTGGGACAGT-GGCATCG
1 ATATGTGATTCGTGTAAG-ACCATGTCTGGGACA-TCGGCATCG
* *
1679244 ATATGTGATTCCATGTAAGACCACGTCTGGGA
1 ATATGTGATT-CGTGTAAGACCATGTCTGGGA
1679276 TGTTGGCATT
Statistics
Matches: 131, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
41 34 0.26
42 44 0.34
43 46 0.35
44 7 0.05
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (42 bp):
ATATGTGATTCGTGTAAGACCATGTCTGGGACATCGGCATCG
Found at i:1679284 original size:85 final size:84
Alignment explanation
Indices: 1679075--1679275 Score: 280
Period size: 84 Copynumber: 2.4 Consensus size: 84
1679065 AGGATTTTCA
* * *
1679075 ATATATGATTACGTGTAAGACCATGTATGGGACATCGGCATCGTATTTGATTCGTGTAAGACCAC
1 ATATGTGATTACATGTAAGACCATGTCTGGGACATCGGCATCGTATTTGATTCGTGTAAGACCAC
* *
1679140 GTCTGCGATGTTGGCATCG
66 ATCTGCGAAGTTGGCATCG
*
1679159 ATATGTGATTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATTTGATTCGTGTAAGTACC-
1 ATATGTGATTACATGTAAGACCATGTCTGGGACATCGGCATCGTATTTGATTCGTGTAAG-ACCA
*
1679223 CTATCTGGGACAG-TGGCATCG
65 C-ATCTGCGA-AGTTGGCATCG
* *
1679244 ATATGTGATTCCATGTAAGACCACGTCTGGGA
1 ATATGTGATTACATGTAAGACCATGTCTGGGA
1679276 TGTTGGCATT
Statistics
Matches: 106, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
84 59 0.56
85 46 0.43
86 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (84 bp):
ATATGTGATTACATGTAAGACCATGTCTGGGACATCGGCATCGTATTTGATTCGTGTAAGACCAC
ATCTGCGAAGTTGGCATCG
Found at i:1680734 original size:13 final size:14
Alignment explanation
Indices: 1680706--1680738 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1680696 CATTTCAACC
*
1680706 ATGTTTATATTTAT
1 ATGTTTATATTGAT
1680720 ATGTTT-TATTGAT
1 ATGTTTATATTGAT
1680733 ATGTTT
1 ATGTTT
1680739 GTTTTTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (14 bp):
ATGTTTATATTGAT
Found at i:1682092 original size:48 final size:48
Alignment explanation
Indices: 1681887--1682121 Score: 146
Period size: 48 Copynumber: 4.9 Consensus size: 48
1681877 TATGCCGGAT
** * * * *
1681887 ATGGTCTTACATGGGGCCACGTATCAATGCCAATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGATCACATAACGATGCCAATGCCATGTCCCAAAC
* * * *
1681935 ATGGTCTTACATGGGATCACACTTATCGAAGCCGAT---A-G-CCC-AGC
1 ATGGTCTTACATGGGATCACA--TAACGATGCCAATGCCATGTCCCAAAC
* * * * * *
1681979 TACGGTCTTACACGATG-TGCTCATATCGATGCCAATGCCATGTCCCAGAC
1 -ATGGTCTTACATG-GGAT-CACATAACGATGCCAATGCCATGTCCCAAAC
* *
1682029 ATGGTCTTATATGGGATCACATAACGATGCCAATGCCGTG-CACCAAAC
1 ATGGTCTTACATGGGATCACATAACGATGCCAATGCCATGTC-CCAAAC
* * * *
1682077 ATGGTCTTACATGGGATCATA-AACCAATGCCGATGCCATATCCCA
1 ATGGTCTTACATGGGATCACATAA-CGATGCCAATGCCATGTCCCA
1682122 GATATGGCCT
Statistics
Matches: 142, Mismatches: 30, Indels: 30
0.70 0.15 0.15
Matches are distributed among these distances:
44 12 0.08
45 15 0.11
46 5 0.04
47 5 0.04
48 79 0.56
49 15 0.11
50 11 0.08
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (48 bp):
ATGGTCTTACATGGGATCACATAACGATGCCAATGCCATGTCCCAAAC
Found at i:1682097 original size:94 final size:92
Alignment explanation
Indices: 1681887--1682142 Score: 223
Period size: 94 Copynumber: 2.7 Consensus size: 92
1681877 TATGCCGGAT
** *
1681887 ATGGTCTTACATGGGGCCACGTATCAATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT
1 ATGGTCTTACATGGGATCA--TATCAATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGAT
* * * *
1681952 CACACTTATCGAAGCCGATAGCCCAGCTAC
64 CACAC-TAACGAAGCCAATAGCCCACCAAC
* * *
1681982 --GGTCTTACACGATGTGCTCATATCGATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGA
1 ATGGTCTT--AC-ATGGGATCATATCAATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGA
*
1682045 TCACA-TAACGATGCCAAT-GCCGTGCACCAAAC
63 TCACACTAACGAAGCCAATAGCC---CACC-AAC
* * * * * *
1682077 ATGGTCTTACATGGGATCATAAACCAATGCCGATGCCATATCCCAGATATGGCCTTATACGGGAT
1 ATGGTCTTACATGGGATCAT--ATCAATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGAT
1682142 C
64 C
1682143 TCATCAACAC
Statistics
Matches: 131, Mismatches: 19, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
91 3 0.02
92 10 0.08
93 6 0.05
94 57 0.44
95 6 0.05
96 43 0.33
97 6 0.05
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (92 bp):
ATGGTCTTACATGGGATCATATCAATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGATCA
CACTAACGAAGCCAATAGCCCACCAAC
Found at i:1684741 original size:17 final size:18
Alignment explanation
Indices: 1684714--1684749 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1684704 TCTGATTCAA
1684714 CACTCGACTCACATTGAG
1 CACTCGACTCACATTGAG
*
1684732 CACT-GACTCATATTGAG
1 CACTCGACTCACATTGAG
1684749 C
1 C
1684750 TCTCTTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.25
Consensus pattern (18 bp):
CACTCGACTCACATTGAG
Found at i:1686019 original size:81 final size:80
Alignment explanation
Indices: 1685929--1686200 Score: 346
Period size: 81 Copynumber: 3.4 Consensus size: 80
1685919 AGGGTAAATT
* * * * *
1685929 AGTCATTTTACCTTACAGGGGTATTACAGTCATTTTATCCTACAGGAGTATTACAGTCATATTAC
1 AGTCATTTTACCTTATAGGGGTATTTCAGTCATTTTATCCTACAGG-GTATTTCGGTCATTTTAC
* *
1685994 CCTATAGGGGCATTTC
65 CCTATGGGGGTATTTC
* *
1686010 AGTCATTTTACCCTATAGGGGTATTTTAGTCATTTTATCCTACAGGGGTATTTCGGTCATTTTAC
1 AGTCATTTTACCTTATAGGGGTATTTCAGTCATTTTATCCTACA-GGGTATTTCGGTCATTTTAC
*
1686075 CTTATGGGGGTATTTC
65 CCTATGGGGGTATTTC
* * * * * *
1686091 GGTCATTTTACCTTATGGGGGTATTTCAATCATTTTACCCTATGAGGGTATTTTGGTCATTTTAC
1 AGTCATTTTACCTTATAGGGGTATTTCAGTCATTTTATCCTA-CAGGGTATTTCGGTCATTTTAC
1686156 CCTATGGGGGTATTTC
65 CCTATGGGGGTATTTC
* * *
1686172 AGCCATTTTACCCTATGGGGGTATTTCAG
1 AGTCATTTTACCTTATAGGGGTATTTCAG
1686201 CCCAACATGG
Statistics
Matches: 166, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
81 163 0.98
82 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (80 bp):
AGTCATTTTACCTTATAGGGGTATTTCAGTCATTTTATCCTACAGGGTATTTCGGTCATTTTACC
CTATGGGGGTATTTC
Found at i:1686202 original size:27 final size:27
Alignment explanation
Indices: 1685929--1686200 Score: 312
Period size: 27 Copynumber: 10.1 Consensus size: 27
1685919 AGGGTAAATT
* * *
1685929 AGTCATTTTACCTTACAGGGGTATTAC
1 AGTCATTTTACCCTATAGGGGTATTTC
* * * *
1685956 AGTCATTTTATCCTACAGGAGTATTAC
1 AGTCATTTTACCCTATAGGGGTATTTC
* *
1685983 AGTCATATTACCCTATAGGGGCATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
*
1686010 AGTCATTTTACCCTATAGGGGTATTTT
1 AGTCATTTTACCCTATAGGGGTATTTC
* *
1686037 AGTCATTTTATCCTACAGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
* * *
1686064 GGTCATTTTACCTTATGGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
* * *
1686091 GGTCATTTTACCTTATGGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
* *
1686118 AATCATTTTACCCTAT-GAGGGTATTTT
1 AGTCATTTTACCCTATAG-GGGTATTTC
* *
1686145 GGTCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
* *
1686172 AGCCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
1686199 AG
1 AG
1686201 CCCAACATGG
Statistics
Matches: 214, Mismatches: 29, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
26 1 0.00
27 212 0.99
28 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (27 bp):
AGTCATTTTACCCTATAGGGGTATTTC
Found at i:1689174 original size:38 final size:38
Alignment explanation
Indices: 1689123--1689201 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
1689113 ATTATGCAAC
1689123 ATGTACCATTGTAAAACCCCAAACCCGGCCTAGATGTT
1 ATGTACCATTGTAAAACCCCAAACCCGGCCTAGATGTT
1689161 ATGTACCATTGTAAAACCCCAAACCCGGCCTAGATGTT
1 ATGTACCATTGTAAAACCCCAAACCCGGCCTAGATGTT
1689199 ATG
1 ATG
1689202 GCCAAATTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (38 bp):
ATGTACCATTGTAAAACCCCAAACCCGGCCTAGATGTT
Found at i:1689807 original size:34 final size:34
Alignment explanation
Indices: 1689735--1689807 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
1689725 AGTAACAGTC
* *
1689735 CAGTATCAGTTTGGGCCTTAGCCCATTACAGTAT
1 CAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
* * *
1689769 CAGTATCTGTGTGGGCCTTAGCCCATTTCATTAA
1 CAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
1689803 CAGTA
1 CAGTA
1689808 ACAGAAATGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (34 bp):
CAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
Found at i:1692198 original size:44 final size:44
Alignment explanation
Indices: 1692147--1692231 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
1692137 TATGTAATCT
* * * *
1692147 GAACTCATTGAGTTGTGTTTGAGTTCATGATATATGTGACAGCA
1 GAACTCATTGAGTTATGGTCGAGTTCATGATATATATGACAGCA
*
1692191 GAACTCATTGAGTTATGGTCGAGTTCGTGATATATATGACA
1 GAACTCATTGAGTTATGGTCGAGTTCATGATATATATGACA
1692232 CATGTTTTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (44 bp):
GAACTCATTGAGTTATGGTCGAGTTCATGATATATATGACAGCA
Found at i:1695859 original size:79 final size:81
Alignment explanation
Indices: 1695723--1695907 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
1695713 TTGAATGATG
*
1695723 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
1695787 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
1695802 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
1695864 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
1695882 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1695908 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:1695914 original size:40 final size:39
Alignment explanation
Indices: 1695724--1695907 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 39
1695714 TGAATGATGT
* * * *
1695724 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* * *
1695764 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
1695804 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
1695842 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
1695883 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
1695908 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:1695929 original size:79 final size:79
Alignment explanation
Indices: 1695776--1695940 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
1695766 GGACTAAGAT
* **
1695776 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
1695841 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
1695855 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
** *
1695918 TATTTCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
1695934 CCGAAGG
1 CCGAAGG
1695941 TATGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:1696766 original size:13 final size:13
Alignment explanation
Indices: 1696748--1696774 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1696738 TAGGAAAGTA
1696748 ACGAAACAATCAT
1 ACGAAACAATCAT
1696761 ACGAAACAATCAT
1 ACGAAACAATCAT
1696774 A
1 A
1696775 TGGACAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (13 bp):
ACGAAACAATCAT
Found at i:1703959 original size:40 final size:40
Alignment explanation
Indices: 1703681--1703945 Score: 349
Period size: 40 Copynumber: 6.7 Consensus size: 40
1703671 TTGAATGATG
* * * * *
1703681 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
1703721 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
1703761 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1703800 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
1703840 TCCGGGTTAAGGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1703880 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
1703921 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
1703946 AACGAGTAGC
Statistics
Matches: 203, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
39 34 0.17
40 159 0.78
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:1710797 original size:47 final size:47
Alignment explanation
Indices: 1710665--1711080 Score: 688
Period size: 47 Copynumber: 8.8 Consensus size: 47
1710655 NNNNNNNNNN
* *
1710665 TTAGGCCTTATCACATATATACACGTTCACATTCATCACATTGGCCA
1 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
*
1710712 TTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCA
1 TTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCA
*
1710761 TTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
1 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
*
1710808 TTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCTA
1 TTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCA
* *
1710857 TTAGGCCTTATCACATATATACACTTTCACATTTATCACATCGGTCA
1 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
1710904 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
1 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
* *
1710951 TTAGGCCTTATCACATATATACACGTTCACATTCATCACATTGGCCA
1 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
* *
1710998 TTAGGCCTTATCACATATATACACGTTCACATTCATCACATTGGCCA
1 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
*
1711045 TTAGGCCTTATCACATATATACACGTTCACATTCAT
1 TTAGGCCTTATCACATATATACACTTTCACATTCAT
1711081 TATTCAAATA
Statistics
Matches: 353, Mismatches: 12, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
47 262 0.74
49 91 0.26
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (47 bp):
TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
Found at i:1714801 original size:39 final size:39
Alignment explanation
Indices: 1714753--1714880 Score: 202
Period size: 39 Copynumber: 3.3 Consensus size: 39
1714743 TTTAACCCGA
* ** *
1714753 ATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGG
1 ATATATTTCCAGCATATAGCCTGCGGACCTCATGTCCGG
*
1714792 ATATATTTCCGGCATATAGCCTGCGGACCTCATGTCCGG
1 ATATATTTCCAGCATATAGCCTGCGGACCTCATGTCCGG
*
1714831 ATATGTTTCCAGCATATAGCCTGCGGACCTCATGTCCGG
1 ATATATTTCCAGCATATAGCCTGCGGACCTCATGTCCGG
1714870 ATATATTTCCA
1 ATATATTTCCA
1714881 ATCTCATATA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (39 bp):
ATATATTTCCAGCATATAGCCTGCGGACCTCATGTCCGG
Found at i:1717253 original size:43 final size:43
Alignment explanation
Indices: 1717205--1717369 Score: 178
Period size: 43 Copynumber: 3.9 Consensus size: 43
1717195 ACTGAGATGA
1717205 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGCATTAT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGCATTAT
1717248 GATTACATGTAAGACCATGTCTGGGACATTGGCA-T-CATTAAT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGCATT-AT
* ** * * *
1717290 CGTTTATGTGTAAGACCCTGTCTGGGATATTGGCATCG-A-TAT
1 -GATTACATGTAAGACCATGTCTGGGACATTGGCATTGCATTAT
* * *
1717332 GTAATGACATGTAAGACCATATCTGGGATA-TGGCATTG
1 G--ATTACATGTAAGACCATGTCTGGGACATTGGCATTG
1717370 TACGAGCTAT
Statistics
Matches: 103, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
41 5 0.05
42 12 0.12
43 85 0.83
44 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATTGCATTAT
Found at i:1719834 original size:45 final size:44
Alignment explanation
Indices: 1719704--1719836 Score: 112
Period size: 45 Copynumber: 3.0 Consensus size: 44
1719694 ATGCTATCTC
* * *
1719704 ATATCGATGCCACTGTCCCAGATAG-GGTCTTACACGAATCA-A-
1 ATATCGATGCCAATGTCCCAGA-CGTGGTCTTACACGAAACACAT
* * * * * * * *
1719746 AT-CCGATGTCGATGTCCCAAACATGGTCGTACTCGTAACCACAT
1 ATATCGATGCCAATGTCCCAGACGTGGTCTTACACG-AAACACAT
1719790 ATATCGATGCCAATGTCCCAGACGTGGTCTTACACGAGAACACAT
1 ATATCGATGCCAATGTCCCAGACGTGGTCTTACACGA-AACACAT
1719835 AT
1 AT
1719837 CGAAAATCCT
Statistics
Matches: 67, Mismatches: 18, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
41 23 0.34
42 6 0.09
43 1 0.01
44 3 0.04
45 34 0.51
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (44 bp):
ATATCGATGCCAATGTCCCAGACGTGGTCTTACACGAAACACAT
Found at i:1720156 original size:20 final size:20
Alignment explanation
Indices: 1720131--1720172 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1720121 TCTTTGGTTC
1720131 TTGATCTAAAAAAATTCAAA
1 TTGATCTAAAAAAATTCAAA
1720151 TTGATCTAAAAAAATTCAAA
1 TTGATCTAAAAAAATTCAAA
1720171 TT
1 TT
1720173 AAACTTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (20 bp):
TTGATCTAAAAAAATTCAAA
Found at i:1727693 original size:45 final size:45
Alignment explanation
Indices: 1727563--1727694 Score: 118
Period size: 44 Copynumber: 3.0 Consensus size: 45
1727553 ATGCTATCTC
* *
1727563 ATATCAATGCCACTGTCCCAGACAG-GGTCTTACAC--GAATCA-A-
1 ATATCGATGCCAATGTCCCAGAC-GTGGTCTTACACAAGAA-CACAT
** * * *
1727605 ATAT-GATGCTGATGTCCCAGACAT-GTCTTACTCATA-ACCACAT
1 ATATCGATGCCAATGTCCCAGACGTGGTCTTACACA-AGAACACAT
1727648 ATATCGATGCCAATGTCCCAGACGTGGTCTTACACAAGAACACAT
1 ATATCGATGCCAATGTCCCAGACGTGGTCTTACACAAGAACACAT
1727693 AT
1 AT
1727695 CAGAAATCCT
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
40 8 0.12
41 16 0.23
42 6 0.09
43 4 0.06
44 18 0.26
45 17 0.25
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (45 bp):
ATATCGATGCCAATGTCCCAGACGTGGTCTTACACAAGAACACAT
Done.