Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 121 of 187
Found at i:36436427 original size:20 final size:20
Alignment explanation
Indices: 36436399--36436440 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
36436389 AACTTGTAAC
*
36436399 TTAAAAAAAACTTACATATA
1 TTAAAAAAAAATTACATATA
* *
36436419 TTAATAAAAAATTATATATA
1 TTAAAAAAAAATTACATATA
36436439 TT
1 TT
36436441 TCAGATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAAAAAAAATTACATATA
Found at i:36439006 original size:76 final size:77
Alignment explanation
Indices: 36438904--36439055 Score: 234
Period size: 76 Copynumber: 2.0 Consensus size: 77
36438894 CATTTTGGTA
* *
36438904 TTTAATAAATTTTTTTTGGATTATTGTGGTAAAAGAACTACATTTTACAAATGTTAAATATATGT
1 TTTAATAAATTTTTCTTGGATTATTGTGGTAAAAGAACTACATTTTACAAATGTTAAAGATATGT
36438969 TACGTAATAAAT
66 TACGTAATAAAT
* * * *
36438981 TTTAATTAA-TTTTCTTGGATTATTGTGGTAAAAGAATTACTTTTTACAAATGTTTAAGATATGT
1 TTTAATAAATTTTTCTTGGATTATTGTGGTAAAAGAACTACATTTTACAAATGTTAAAGATATGT
*
36439045 TATGTAATAAA
66 TACGTAATAAA
36439056 AAAATTTATT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
76 60 0.88
77 8 0.12
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (77 bp):
TTTAATAAATTTTTCTTGGATTATTGTGGTAAAAGAACTACATTTTACAAATGTTAAAGATATGT
TACGTAATAAAT
Found at i:36442639 original size:24 final size:25
Alignment explanation
Indices: 36442602--36442649 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
36442592 TTTCGAGTTT
*
36442602 TTTTCTTTTAATTTTCTCTTCAATG
1 TTTTCTTTTAATTTTCTATTCAATG
* *
36442627 TTTT-TTTTGATTTTTTATTCAAT
1 TTTTCTTTTAATTTTCTATTCAAT
36442650 CTGTAAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.17, C:0.10, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTCTTTTAATTTTCTATTCAATG
Found at i:36443665 original size:44 final size:43
Alignment explanation
Indices: 36443527--36443746 Score: 124
Period size: 44 Copynumber: 5.0 Consensus size: 43
36443517 CGAGGCAAGA
*
36443527 AGGCAAGACCTGCTATCTTCAACCTGCTCCACTACAACCGAGGG
1 AGGCAAG-GCTGCTATCTTCAACCTGCTCCACTACAACCGAGGG
* * * * * * * * * *
36443571 AGACAAGGCTTG-TGTGTTCGATCTGCTTCACTGTCGA-TGCAGGA
1 AGGCAAGGC-TGCTATCTTCAACCTGCTCCACT-ACAACCG-AGGG
*
36443615 AGGCAAGTTCTGCTATCTTCAACCTGCTCCACTACAACCGAGGG
1 AGGCAAG-GCTGCTATCTTCAACCTGCTCCACTACAACCGAGGG
* * * * ** * * * *
36443659 AGGCAAGGCTTG-TGTCTTCGATCTGCTTCGTTGTCGA-TGTAGGA
1 AGGCAAGGC-TGCTATCTTCAACCTGCTCCACT-ACAACCG-AGGG
*
36443703 AGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGG
1 AGGCAAG-GCTGCTATCTTCAACCTGCTCCACTACAACCGAGGG
36443747 GATAAAGCTT
Statistics
Matches: 120, Mismatches: 44, Indels: 24
0.64 0.23 0.13
Matches are distributed among these distances:
43 33 0.28
44 54 0.45
45 33 0.28
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (43 bp):
AGGCAAGGCTGCTATCTTCAACCTGCTCCACTACAACCGAGGG
Found at i:36443797 original size:87 final size:88
Alignment explanation
Indices: 36443525--36443836 Score: 491
Period size: 88 Copynumber: 3.6 Consensus size: 88
36443515 ATCGAGGCAA
* *
36443525 GAAGGCAAGACCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGACAAGGCTTGTGTGTTC
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGACAAGGCTTGTGTCTTC
* *
36443590 GATCTGCTTCACTGTCGATGCAG
66 GATCTGCTTCGCTGTCGATGTAG
* *
36443613 GAAGGCAAGTTCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTC
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGACAAGGCTTGTGTCTTC
*
36443678 GATCTGCTTCGTTGTCGATGTAG
66 GATCTGCTTCGCTGTCGATGTAG
* * *
36443701 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGG-GATAAAGCTTGTGTCTTT
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGACAAGGCTTGTGTCTTC
* *
36443765 GATCTACTTCGCTGTTGATGTAG
66 GATCTGCTTCGCTGTCGATGTAG
* *
36443788 GAAGGCAAGATCTGCTATCTTCAACCTACTCCAGTACAACCGAGGGAGA
1 GAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGA
36443837 TAAGATCTGT
Statistics
Matches: 206, Mismatches: 17, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
87 78 0.38
88 128 0.62
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.26
Consensus pattern (88 bp):
GAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGACAAGGCTTGTGTCTTC
GATCTGCTTCGCTGTCGATGTAG
Found at i:36444284 original size:44 final size:44
Alignment explanation
Indices: 36443855--36444280 Score: 557
Period size: 44 Copynumber: 9.7 Consensus size: 44
36443845 GTAATTTTCA
* * * * *
36443855 ACCTACTCCACAGCTGCTCAGGGAGCTAGGACTTACAATTTTCT
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
* * *
36443899 ACCTATTCCACTACTGGTCAAGGAGCTAGGACTTACAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
* *
36443943 ACCTATTCCACTGCTGGTCAAGGG-GCTTGGATTTACAATCTTCC
1 ACCTATTCCACTGCTGGTC-AGGGAGCTAGGACTTACAATCTTCC
* * * *
36443987 ACCTATTCCAATGCTGTTCAGGGAGCTAGGACTTTCAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
* *
36444031 ACCTATTCCAATGCTGGTCAGGGAGCTAGGATTTACAATCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
* * * *
36444075 GCCTATTCCACTGCTGTTCAGGGAGCTAGGGCTTACAATCTTCT
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
* *
36444119 ACCTATTCCATTGCTGGTCAGGGAGCTAGGATTTACAATCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
* * * * *
36444163 ACATATTCCACAGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
* * *
36444207 ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
*
36444251 ACCTATTCCACTGCTGGTCAGGGAACTAGG
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGG
36444281 GCTTGTGATT
Statistics
Matches: 336, Mismatches: 44, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
43 4 0.01
44 329 0.98
45 3 0.01
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (44 bp):
ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
Found at i:36448111 original size:25 final size:25
Alignment explanation
Indices: 36448083--36448131 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
36448073 TTTCGAGTTT
*
36448083 TTTTCTTTTAATTTTCTCTTCAATG
1 TTTTCTTTTAATTTTCTATTCAATG
* * *
36448108 TTTTTTTTTGATTTTTTATTCAAT
1 TTTTCTTTTAATTTTCTATTCAAT
36448132 CTATAAAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.16, C:0.10, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTCTTTTAATTTTCTATTCAATG
Found at i:36448326 original size:21 final size:22
Alignment explanation
Indices: 36448288--36448329 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
36448278 GCAGGTTCGG
*
36448288 CGTATGGAGGGTGGACGTGGCA
1 CGTATGGAGGGTGCACGTGGCA
36448310 CGTATGGA-GGTGCACGTGGC
1 CGTATGGAGGGTGCACGTGGC
36448330 TGGGGAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.19
Consensus pattern (22 bp):
CGTATGGAGGGTGCACGTGGCA
Found at i:36449434 original size:46 final size:46
Alignment explanation
Indices: 36449384--36449482 Score: 162
Period size: 46 Copynumber: 2.2 Consensus size: 46
36449374 CAAGATTGTG
*
36449384 TTAATTTTGTTTGAATTAATTTATTAAACTATAACAAATGCTTGAC
1 TTAATTTTGTTTGAATTAATTTATTAAACTATAACAAAGGCTTGAC
** *
36449430 TTAATTTTGTTTTTATTAATTTATTAAACTATCACAAAGGCTTGAC
1 TTAATTTTGTTTGAATTAATTTATTAAACTATAACAAAGGCTTGAC
36449476 TTAATTT
1 TTAATTT
36449483 AAAATTTTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.48
Consensus pattern (46 bp):
TTAATTTTGTTTGAATTAATTTATTAAACTATAACAAAGGCTTGAC
Found at i:36451483 original size:45 final size:45
Alignment explanation
Indices: 36451431--36451557 Score: 191
Period size: 45 Copynumber: 2.8 Consensus size: 45
36451421 GTGCATTCAG
36451431 CACATAGCAACCACCTTATTAATCAATGATGTCCGGTGGAATCAA
1 CACATAGCAACCACCTTATTAATCAATGATGTCCGGTGGAATCAA
* *
36451476 CACATAGCAACCACCTTATTAATCAATGATGTCTGGTGGAATCAG
1 CACATAGCAACCACCTTATTAATCAATGATGTCCGGTGGAATCAA
* * * * *
36451521 CACATAGCAAACACCATACTAATTAATGATGTTCGGT
1 CACATAGCAACCACCTTATTAATCAATGATGTCCGGT
36451558 TCACATAGTA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (45 bp):
CACATAGCAACCACCTTATTAATCAATGATGTCCGGTGGAATCAA
Found at i:36451639 original size:51 final size:50
Alignment explanation
Indices: 36451554--36451749 Score: 214
Period size: 51 Copynumber: 3.9 Consensus size: 50
36451544 TAATGATGTT
* * * *
36451554 CGGTTCACATAGTAGCCTGCATATAGTACGACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATC
* * * * *
36451605 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATC
*** * * * *
36451656 CGGTACGTATAGTAGCATGCACATAGTACTATACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TC
36451706 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT
36451750 CACTTTCACT
Statistics
Matches: 115, Mismatches: 27, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.34
51 72 0.63
52 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCATC
Found at i:36451728 original size:101 final size:101
Alignment explanation
Indices: 36451562--36451745 Score: 271
Period size: 101 Copynumber: 1.8 Consensus size: 101
36451552 TTCGGTTCAC
* * *
36451562 ATAGTAGCCTGCATATAGTACGACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCAC
1 ATAGTAGCATGCACATAGTACGACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGCAC
36451627 ATAGTACTACACACGTGATCGAAACTATCCGGTACGT
65 ATAGTACTACACACGTGATCGAAACTATCCGGTACGT
* * * *
36451664 ATAGTAGCATGCACATAGTACTATACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCAC
1 ATAGTAGCATGCACATAGTACGACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTGCAC
*
36451728 ATAGTACTACACATGTGA
65 ATAGTACTACACACGTGA
36451746 CCATCACTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
100 4 0.05
101 40 0.55
102 29 0.40
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (101 bp):
ATAGTAGCATGCACATAGTACGACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCACA
TAGTACTACACACGTGATCGAAACTATCCGGTACGT
Found at i:36455967 original size:9 final size:9
Alignment explanation
Indices: 36455953--36455983 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
36455943 GTTAAACGAA
36455953 TCGAGTTAT
1 TCGAGTTAT
*
36455962 TCGAGTTAA
1 TCGAGTTAT
36455971 TCGAGTTAT
1 TCGAGTTAT
36455980 TCGA
1 TCGA
36455984 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:36456312 original size:30 final size:31
Alignment explanation
Indices: 36456276--36456335 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
36456266 AAACCTTTTA
*
36456276 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
36456306 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
36456336 TCCCACTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:36496545 original size:55 final size:55
Alignment explanation
Indices: 36496476--36496581 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 55
36496466 GTCCCAGCTC
*
36496476 GTGTCCTCACCCGTGTAACTCTATAAATAGGGTCACACAACCATGTCACACACTT
1 GTGTCATCACCCGTGTAACTCTATAAATAGGGTCACACAACCATGTCACACACTT
* * * *
36496531 GTGTCATCACCCGTGTAACTCTCTAAGTAGGGTCACACAGCCGTGTCACAC
1 GTGTCATCACCCGTGTAACTCTATAAATAGGGTCACACAACCATGTCACAC
36496582 GCCCGTCTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (55 bp):
GTGTCATCACCCGTGTAACTCTATAAATAGGGTCACACAACCATGTCACACACTT
Found at i:36504655 original size:20 final size:21
Alignment explanation
Indices: 36504627--36504669 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
36504617 TTATTTTATT
*
36504627 CTAGCAATAAAGTA-AATGAG
1 CTAGAAATAAAGTAGAATGAG
*
36504647 CTAGAAATAAATTAGAATGAG
1 CTAGAAATAAAGTAGAATGAG
36504668 CT
1 CT
36504670 CAAACGAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.23
Consensus pattern (21 bp):
CTAGAAATAAAGTAGAATGAG
Found at i:36516213 original size:23 final size:23
Alignment explanation
Indices: 36516103--36516215 Score: 70
Period size: 23 Copynumber: 4.7 Consensus size: 23
36516093 GCAAAAACAC
36516103 TTGTTTTT-TCATTTTCACACTCTTT
1 TTGTTTTTCTC-TTTT--CACTCTTT
*
36516128 TTCTTTTTCT-TTTGTCACTCTTGT
1 TTGTTTTTCTCTTT-TCACTCTT-T
** *
36516152 TT-TTTTATCACTCTCATCATTCTTT
1 TTGTTTT-T--CTCTTTTCACTCTTT
* *
36516177 TCTTTTTTTTTCTTTTCACTCTTT
1 T-TGTTTTTCTCTTTTCACTCTTT
36516201 TTGTTTTTCTCTTTT
1 TTGTTTTTCTCTTTT
36516216 TATCTTTCTC
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
23 23 0.33
24 19 0.28
25 10 0.14
26 12 0.17
27 5 0.07
ACGTcount: A:0.08, C:0.20, G:0.04, T:0.68
Consensus pattern (23 bp):
TTGTTTTTCTCTTTTCACTCTTT
Found at i:36520410 original size:11 final size:11
Alignment explanation
Indices: 36520380--36520413 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
36520370 GAAAAGCCAG
36520380 ATGGTGTGAAC
1 ATGGTGTGAAC
*
36520391 ATGG-CTGAAC
1 ATGGTGTGAAC
36520401 ATGGTGTGAAC
1 ATGGTGTGAAC
36520412 AT
1 AT
36520414 CTTTATGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.26
Consensus pattern (11 bp):
ATGGTGTGAAC
Found at i:36526178 original size:62 final size:62
Alignment explanation
Indices: 36526076--36526199 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
36526066 AAACTTAGAA
36526076 TGATACGAGTCACAAAGGCCCAACTCAAGCTCAAGAACGTGATGGGCTCAAATTACCACAAG
1 TGATACGAGTCACAAAGGCCCAACTCAAGCTCAAGAACGTGATGGGCTCAAATTACCACAAG
* * * *
36526138 TGATACGAGTCACAAAGGCCTAATTCAAGCTCAAGGACGTGATTGGCTCAAATTACCACAAG
1 TGATACGAGTCACAAAGGCCCAACTCAAGCTCAAGAACGTGATGGGCTCAAATTACCACAAG
36526200 GCCCAATAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (62 bp):
TGATACGAGTCACAAAGGCCCAACTCAAGCTCAAGAACGTGATGGGCTCAAATTACCACAAG
Found at i:36531134 original size:13 final size:13
Alignment explanation
Indices: 36531116--36531142 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
36531106 ATTCTTTAAA
36531116 TACTTAGTTTTAT
1 TACTTAGTTTTAT
36531129 TACTTAGTTTTAT
1 TACTTAGTTTTAT
36531142 T
1 T
36531143 TTTAGACTTT
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:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (13 bp):
TACTTAGTTTTAT
Found at i:36533850 original size:12 final size:12
Alignment explanation
Indices: 36533833--36533857 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36533823 AAAATCTGAT
36533833 TTCAATGTGTAA
1 TTCAATGTGTAA
36533845 TTCAATGTGTAA
1 TTCAATGTGTAA
36533857 T
1 T
36533858 GTCTATAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:36533939 original size:13 final size:13
Alignment explanation
Indices: 36533921--36533963 Score: 77
Period size: 13 Copynumber: 3.2 Consensus size: 13
36533911 CTCTTGGACT
36533921 GAATTTTTACATA
1 GAATTTTTACATA
36533934 GAATTTTTACATA
1 GAATTTTTACATA
36533947 GAAATTTTTACATA
1 G-AATTTTTACATA
36533961 GAA
1 GAA
36533964 ATTAAAACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 16 0.55
14 13 0.45
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (13 bp):
GAATTTTTACATA
Found at i:36533952 original size:14 final size:14
Alignment explanation
Indices: 36533922--36533966 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
36533912 TCTTGGACTG
36533922 AATTTTTACATAG-
1 AATTTTTACATAGA
36533935 AATTTTTACATAGA
1 AATTTTTACATAGA
36533949 AATTTTTACATAGA
1 AATTTTTACATAGA
36533963 AATT
1 AATT
36533967 AAAACTTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 13 0.42
14 18 0.58
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
AATTTTTACATAGA
Found at i:36534895 original size:33 final size:34
Alignment explanation
Indices: 36534844--36534918 Score: 125
Period size: 33 Copynumber: 2.2 Consensus size: 34
36534834 AGATTTAAAC
36534844 AAATTAATTACTAACACTTATTTAAGTTGAACTA
1 AAATTAATTACTAACACTTATTTAAGTTGAACTA
*
36534878 AAATTAATT-CTAACACTTATTTGAGTTGAACTA
1 AAATTAATTACTAACACTTATTTAAGTTGAACTA
*
36534911 AATTTAAT
1 AAATTAAT
36534919 AAACTAACTC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 30 0.77
34 9 0.23
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.40
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGTTGAACTA
Found at i:36539082 original size:20 final size:20
Alignment explanation
Indices: 36539057--36539095 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
36539047 TATTCATAAT
36539057 GTCTAAAAATTAAAACTAAA
1 GTCTAAAAATTAAAACTAAA
36539077 GTCTAAAAATTAAAACTAA
1 GTCTAAAAATTAAAACTAA
36539096 GTATTTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (20 bp):
GTCTAAAAATTAAAACTAAA
Found at i:36543955 original size:16 final size:16
Alignment explanation
Indices: 36543917--36543958 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
36543907 GTATGGGAGT
*
36543917 ATACATGAATGGCTGA
1 ATACATGGATGGCTGA
*
36543933 ATACATGGATGGCTGG
1 ATACATGGATGGCTGA
*
36543949 ATTCATGGAT
1 ATACATGGAT
36543959 ATGGCTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.29
Consensus pattern (16 bp):
ATACATGGATGGCTGA
Found at i:36548240 original size:27 final size:27
Alignment explanation
Indices: 36548191--36548259 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
36548181 TTTCAATTGT
36548191 TTTTC-TT-TATTTTTC-TTCATTTTC
1 TTTTCATTCTATTTTTCATTCATTTTC
*
36548215 TTTTCATTCTATTTTTCATTCTTTTTC
1 TTTTCATTCTATTTTTCATTCATTTTC
* *
36548242 TTTTCACTCTCTTTTTCA
1 TTTTCATTCTATTTTTCA
36548260 ATAGAATCTC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
24 5 0.13
25 2 0.05
26 8 0.21
27 24 0.62
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTCATTCTATTTTTCATTCATTTTC
Found at i:36548247 original size:15 final size:15
Alignment explanation
Indices: 36548201--36548258 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 15
36548191 TTTTCTTTAT
*
36548201 TTTTC-TTCATTTTC
1 TTTTCATTCTTTTTC
*
36548215 TTTTCATTC--TAT-
1 TTTTCATTCTTTTTC
36548227 TTTTCATTCTTTTTC
1 TTTTCATTCTTTTTC
36548242 TTTTCACTCTCTTTTTC
1 TTTTCA-T-TCTTTTTC
36548259 AATAGAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
12 9 0.25
13 2 0.06
14 7 0.19
15 9 0.25
16 1 0.03
17 8 0.22
ACGTcount: A:0.09, C:0.22, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTCATTCTTTTTC
Found at i:36553962 original size:12 final size:12
Alignment explanation
Indices: 36553945--36553970 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
36553935 ATTTTAAGAG
36553945 TTCAAAATCACC
1 TTCAAAATCACC
36553957 TTCAAAATCACC
1 TTCAAAATCACC
36553969 TT
1 TT
36553971 TTGTTACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (12 bp):
TTCAAAATCACC
Found at i:36566051 original size:20 final size:20
Alignment explanation
Indices: 36565984--36566052 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
36565974 ACTCTACTTC
* *
36565984 AAGCTCACTCAGCTCAACTT
1 AAGCTCATTCAGCTCATCTT
* *
36566004 TAGCTCA-ACGAGCTCATTCTT
1 AAGCTCATTC-AGCTCA-TCTT
36566025 -AGCTCATTCAGCTCATCTT
1 AAGCTCATTCAGCTCATCTT
36566044 AAGCTCATT
1 AAGCTCATT
36566053 TTAGTTTGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.12
20 32 0.78
21 4 0.10
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (20 bp):
AAGCTCATTCAGCTCATCTT
Found at i:36567058 original size:11 final size:11
Alignment explanation
Indices: 36567042--36567067 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
36567032 GTGAGTTTGT
36567042 AAAAAAAATTG
1 AAAAAAAATTG
36567053 AAAAAAAATTG
1 AAAAAAAATTG
36567064 AAAA
1 AAAA
36567068 TTCAAAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:36575192 original size:22 final size:23
Alignment explanation
Indices: 36575144--36575192 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
36575134 TATCGGTATG
36575144 ATTAATGTGTCCTAATAAGTCGT
1 ATTAATGTGTCCTAATAAGTCGT
* *
36575167 -TTAATGTGTCTTAATAGGT-GT
1 ATTAATGTGTCCTAATAAGTCGT
36575188 ATTAA
1 ATTAA
36575193 AGAAGCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (23 bp):
ATTAATGTGTCCTAATAAGTCGT
Found at i:36595315 original size:22 final size:22
Alignment explanation
Indices: 36595285--36595328 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
36595275 TTTGGTATTT
36595285 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
36595307 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
36595329 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:36624143 original size:4 final size:4
Alignment explanation
Indices: 36624134--36624161 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
36624124 AAGTTTTATT
36624134 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
36624162 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:36625736 original size:10 final size:10
Alignment explanation
Indices: 36625721--36625782 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
36625711 TTTGAACCAT
*
36625721 TACCAATTCG
1 TACCAATTCA
*
36625731 TACCAAATACCA
1 TACC-AAT-TCA
*
36625743 TACCATTTCA
1 TACCAATTCA
36625753 TACCAATTCCA
1 TACCAATT-CA
* *
36625764 TACCATTTCG
1 TACCAATTCA
36625774 TACCAATTC
1 TACCAATTC
36625783 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:36625766 original size:21 final size:21
Alignment explanation
Indices: 36625721--36625783 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
36625711 TTTGAACCAT
* *
36625721 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
36625743 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
36625764 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
36625784 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:36629233 original size:40 final size:40
Alignment explanation
Indices: 36629189--36629266 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
36629179 TAAATAAAAG
*
36629189 AAAGTCCAATAACTCAATTACTAACTAAGATGAGTTTAAT
1 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTAAT
* * *
36629229 AAAGTCCAGCAACTCATTTATTAACTAAGATGAGTTTA
1 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTA
36629267 TTTAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (40 bp):
AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTAAT
Found at i:36635172 original size:21 final size:22
Alignment explanation
Indices: 36635127--36635176 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
36635117 AGAGAAAAAT
*
36635127 AAAAGTGAAAAAGAAGAAAATG
1 AAAAGTGAAAAAGAAGAAAAGG
**
36635149 AAAA-TGAAAAAGGCGAAAAGG
1 AAAAGTGAAAAAGAAGAAAAGG
36635170 -AAAGTGA
1 AAAAGTGA
36635177 GAGAGAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.26, T:0.08
Consensus pattern (22 bp):
AAAAGTGAAAAAGAAGAAAAGG
Found at i:36639561 original size:23 final size:23
Alignment explanation
Indices: 36639529--36639640 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
36639519 CTTTTTGAAC
* *
36639529 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
36639552 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
36639575 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
36639598 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
36639621 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
36639641 CCCAAAACCG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:36639605 original size:46 final size:46
Alignment explanation
Indices: 36639529--36639640 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
36639519 CTTTTTGAAC
* *
36639529 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
36639575 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
36639621 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
36639641 CCCAAAACCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:36647329 original size:20 final size:20
Alignment explanation
Indices: 36647304--36647386 Score: 73
Period size: 19 Copynumber: 4.1 Consensus size: 20
36647294 GCGAAAATAC
36647304 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATGAAA
* *
36647324 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATGAAA
*
36647343 AAAAGAGAATGAAAAA--AAA
1 AAAAGA-AAAGAAAAATGAAA
*
36647362 AATGAGAAAAGCAAAAGATGAAA
1 AA-AAGAAAAG-AAAA-ATGAAA
36647385 AA
1 AA
36647387 GAAAAAAGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
19 25 0.50
20 12 0.24
21 8 0.16
23 5 0.10
ACGTcount: A:0.75, C:0.02, G:0.16, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATGAAA
Found at i:36647370 original size:14 final size:15
Alignment explanation
Indices: 36647353--36647393 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
36647343 AAAAGAGAAT
36647353 GAAAA-AAAAAATGA
1 GAAAAGAAAAAATGA
*
36647367 GAAAAGCAAAAGATGA
1 GAAAAG-AAAAAATGA
36647383 -AAAAGAAAAAA
1 GAAAAGAAAAAA
36647394 GTGATTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.43
15 5 0.22
16 8 0.35
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (15 bp):
GAAAAGAAAAAATGA
Found at i:36647377 original size:15 final size:13
Alignment explanation
Indices: 36647304--36647392 Score: 55
Period size: 13 Copynumber: 6.8 Consensus size: 13
36647294 GCGAAAATAC
36647304 AAAAG-AAAA-GA
1 AAAAGAAAAATGA
36647315 AAAATGAAAAA--A
1 AAAA-GAAAAATGA
* *
36647327 AGAAAGAAAATTCA
1 A-AAAGAAAAATGA
36647341 AAAA-AAGAGAATGA
1 AAAAGAA-A-AATGA
36647355 AAAA-AAAAATGA
1 AAAAGAAAAATGA
36647367 GAAAAGCAAAAGATGA
1 -AAAAG-AAAA-ATGA
36647383 AAAAGAAAAA
1 AAAAGAAAAA
36647393 AGTGATTGAA
Statistics
Matches: 64, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
11 4 0.06
12 15 0.23
13 17 0.27
14 15 0.23
15 9 0.14
16 4 0.06
ACGTcount: A:0.75, C:0.02, G:0.16, T:0.07
Consensus pattern (13 bp):
AAAAGAAAAATGA
Found at i:36652197 original size:22 final size:22
Alignment explanation
Indices: 36652155--36652197 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
36652145 TGCTCCTCAC
* *
36652155 TTTTTCTGGTTTGTTTATCTAT
1 TTTTTCTCGTTTCTTTATCTAT
36652177 TTTTCTCTCGTTTCTTT-TCTA
1 TTTT-TCTCGTTTCTTTATCTA
36652198 ATCTCAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.07, C:0.16, G:0.09, T:0.67
Consensus pattern (22 bp):
TTTTTCTCGTTTCTTTATCTAT
Found at i:36652501 original size:17 final size:16
Alignment explanation
Indices: 36652479--36652513 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
36652469 TCATCAACAT
*
36652479 TTCTTATTTTTCTTTTC
1 TTCTTATTTCT-TTTTC
36652496 TTCTTATTTCTTTTTC
1 TTCTTATTTCTTTTTC
36652512 TT
1 TT
36652514 TTGGCCTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTTATTTCTTTTTC
Found at i:36657875 original size:23 final size:23
Alignment explanation
Indices: 36657843--36657908 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
36657833 CTTTTTGAAC
* *
36657843 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
36657866 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
36657889 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
36657909 CCCAAAACCG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:36660477 original size:20 final size:21
Alignment explanation
Indices: 36660448--36660492 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
36660438 GCGAAAATAC
*
36660448 AAAAGAAAAGAAAAATGAAAA
1 AAAAGAAAAGAAAAATCAAAA
*
36660469 AAAAG-AAAGAAAATTCAAAA
1 AAAAGAAAAGAAAAATCAAAA
36660489 AAAA
1 AAAA
36660493 ATGAGAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (21 bp):
AAAAGAAAAGAAAAATCAAAA
Found at i:36660493 original size:21 final size:21
Alignment explanation
Indices: 36660448--36660493 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
36660438 GCGAAAATAC
*
36660448 AAAAGAAAAGAAAAATGAAAA
1 AAAAGAAAAGAAAAATAAAAA
*
36660469 AAAAG-AAAGAAAATTCAAAAA
1 AAAAGAAAAGAAAAAT-AAAAA
36660490 AAAA
1 AAAA
36660494 TGAGAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (21 bp):
AAAAGAAAAGAAAAATAAAAA
Found at i:36660506 original size:18 final size:19
Alignment explanation
Indices: 36660448--36660509 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
36660438 GCGAAAATAC
36660448 AAAAGAAAAGAAAAATGAAAA
1 AAAAG-AAAG-AAAATGAAAA
**
36660469 AAAAGAAAGAAAATTCAAA
1 AAAAGAAAGAAAATGAAAA
* *
36660488 AAAA-AATGAGAATGAAAA
1 AAAAGAAAGAAAATGAAAA
36660506 AAAA
1 AAAA
36660510 TGAGAAAAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
18 14 0.40
19 12 0.34
20 4 0.11
21 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.08
Consensus pattern (19 bp):
AAAAGAAAGAAAATGAAAA
Found at i:36660523 original size:18 final size:16
Alignment explanation
Indices: 36660486--36660538 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
36660476 AGAAAATTCA
*
36660486 AAAAAAAATGAGAATG
1 AAAAAAAATGAGAAAG
36660502 AAAAAAAATGAGAAA-
1 AAAAAAAATGAGAAAG
* * *
36660517 AGCAAAAGATGAAAAAG
1 A-AAAAAAATGAGAAAG
36660534 AAAAA
1 AAAAA
36660539 GTGATTGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.08
Consensus pattern (16 bp):
AAAAAAAATGAGAAAG
Found at i:36664720 original size:23 final size:23
Alignment explanation
Indices: 36664688--36664753 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
36664678 CTTTTTGAAC
* * *
36664688 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTTGTACCAAATCA
* *
36664711 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTTGTACCAAATCA
*
36664734 CATTACCATTTTGTAACAAA
1 CATTACCATTTTGTACCAAA
36664754 CCCAAAACCG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (23 bp):
CATTACCATTTTGTACCAAATCA
Found at i:36665729 original size:22 final size:21
Alignment explanation
Indices: 36665698--36665739 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
36665688 NNNNNNTTTA
36665698 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
36665719 GGAATTTGGTACGAATTGGTA
1 GGAA-TTGGTACGAAATGGTA
36665740 ATGGTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:36668574 original size:12 final size:12
Alignment explanation
Indices: 36668554--36668590 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
36668544 TAGTAGTTTC
*
36668554 TTCAAAAAAAAT
1 TTCAAAAAAAAA
*
36668566 TTGAAAAAAAAA
1 TTCAAAAAAAAA
36668578 TTCAAAAAAAAA
1 TTCAAAAAAAAA
36668590 T
1 T
36668591 GGTTTCCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:36668649 original size:14 final size:15
Alignment explanation
Indices: 36668627--36668666 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
36668617 GATATCAAGT
*
36668627 TGAAAAAAAAATTCG
1 TGAAAAAAAATTTCG
36668642 TGAAAAAAAATTTCG
1 TGAAAAAAAATTTCG
36668657 TGAAAAAAAA
1 TGAAAAAAAA
36668667 GAAGAAGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (15 bp):
TGAAAAAAAATTTCG
Found at i:36673154 original size:18 final size:18
Alignment explanation
Indices: 36673116--36673157 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
36673106 GCGAAAATAC
* *
36673116 AAAAGAAAAGAAAAATGA
1 AAAAAAAAAGAAAAATCA
*
36673134 AAAAAAAAAGAAAATTCA
1 AAAAAAAAAGAAAAATCA
36673152 AAAAAA
1 AAAAAA
36673158 GAGAATGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAGAAAAATCA
Found at i:36673207 original size:14 final size:15
Alignment explanation
Indices: 36673178--36673207 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36673168 AGAGAGCGAG
36673178 AAAAGAAAAAGATGA
1 AAAAGAAAAAGATGA
36673193 AAAAGAAAAAG-TGA
1 AAAAGAAAAAGATGA
36673207 A
1 A
36673208 TGAAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAAGATGA
Found at i:36681141 original size:27 final size:28
Alignment explanation
Indices: 36681104--36681168 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
36681094 TGTTTTTTTA
* *
36681104 CTTTCACTTTCTTTTTC-TTTTTCATTT
1 CTTTCAATTTCTTTTTCATTGTTCATTT
*
36681131 CTTTCAATTTCTTTTTCATTGTTCGTTT
1 CTTTCAATTTCTTTTTCATTGTTCATTT
*
36681159 CTCTCAATTT
1 CTTTCAATTT
36681169 TTCCACAGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.11, C:0.22, G:0.03, T:0.65
Consensus pattern (28 bp):
CTTTCAATTTCTTTTTCATTGTTCATTT
Found at i:36683321 original size:17 final size:16
Alignment explanation
Indices: 36683269--36683310 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
36683259 TCGTATACAA
36683269 TTTTTTTTCTTTTCAAT
1 TTTTTTTTCTTTT-AAT
*
36683286 TTTTTTTTCTTTTGAT
1 TTTTTTTTCTTTTAAT
36683302 TTTTTTTTC
1 TTTTTTTTC
36683311 GATTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTTTTCTTTTAAT
Found at i:36683341 original size:14 final size:14
Alignment explanation
Indices: 36683302--36683341 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
36683292 TTCTTTTGAT
*
36683302 TTTTTTTTC-G-AT
1 TTTTTTTTCAGAAA
36683314 TTTTTTTTCA-AAA
1 TTTTTTTTCAGAAA
36683327 TTTTTTTTCAGAAA
1 TTTTTTTTCAGAAA
36683341 T
1 T
36683342 CTACTTACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 9 0.38
13 11 0.46
14 4 0.17
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (14 bp):
TTTTTTTTCAGAAA
Found at i:36685436 original size:41 final size:41
Alignment explanation
Indices: 36685391--36685521 Score: 235
Period size: 41 Copynumber: 3.2 Consensus size: 41
36685381 CCTATTTTCA
*
36685391 TACATGTTATAAATATGTCTGGACGAATTTAATGCTGCCAC
1 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
*
36685432 TACATGCTATAAATATGCCTGGACGAATTTAATGCTGCCAC
1 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
*
36685473 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCTAC
1 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
36685514 TACATGTT
1 TACATGTT
36685522 TGGCCGAATT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (41 bp):
TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
Found at i:36689203 original size:23 final size:23
Alignment explanation
Indices: 36689145--36689210 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
36689135 CTTTTTGAAC
* ** *
36689145 CATTTCCATTTCAAACCAAATTC
1 CATTACCATTTCGTACCAAATTA
* *
36689168 CATTTCCATTTCGTGCCAAATTA
1 CATTACCATTTCGTACCAAATTA
36689191 CATTACCATTTCGTACCAAA
1 CATTACCATTTCGTACCAAA
36689211 CCCAAACCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.35
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATTA
Found at i:36689735 original size:11 final size:11
Alignment explanation
Indices: 36689715--36689747 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
36689705 AAACTTCTAT
36689715 GAAGTTTCCTA
1 GAAGTTTCCTA
36689726 GCAA-TTTCCTA
1 G-AAGTTTCCTA
36689737 GAAGTTTCCTA
1 GAAGTTTCCTA
36689748 ACAAGCTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.10
11 16 0.80
12 2 0.10
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (11 bp):
GAAGTTTCCTA
Found at i:36691033 original size:20 final size:20
Alignment explanation
Indices: 36691008--36691055 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
36690998 TCCATGCGAT
*
36691008 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACACGAGCTCAAG
*
36691028 TCAGCTCACACGAGCTCAAT
1 TCAGCTCACACGAGCTCAAG
36691048 TCAGCTCA
1 TCAGCTCA
36691056 TTTAGCTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.35, G:0.17, T:0.21
Consensus pattern (20 bp):
TCAGCTCACACGAGCTCAAG
Found at i:36692998 original size:16 final size:16
Alignment explanation
Indices: 36692974--36693004 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36692964 TAGGTTCGTG
*
36692974 AATTGAAAAAAATTGA
1 AATTAAAAAAAATTGA
36692990 AATTAAAAAAAATTG
1 AATTAAAAAAAATTG
36693005 TATTTATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (16 bp):
AATTAAAAAAAATTGA
Found at i:36693228 original size:535 final size:533
Alignment explanation
Indices: 36692220--36693248 Score: 1689
Period size: 535 Copynumber: 1.9 Consensus size: 533
36692210 ATTAAACTGA
*
36692220 ACCTACATCTTTCTAAACCTTCCATCCATTTCAAAAATCACTTTGTAAGCTTCTGCAAACCTTAA
1 ACCTACATCTTTCTAAACCTTCCATCCATTTCAAAAATCACTTTGTAAGCTTCTGCAAACCTAAA
* * *
36692285 AGAAATTTACACCTTTTTGACTACTAGAACTTCTCCTCGTCGACGATCGGGCAAACTTTGTGAAA
66 ACAAATTTACACCTATTTGACTACTAGAACTTCTCCTCGTCGACGATCGGGCAAACTTTGTCAAA
* * *
36692350 CGACTCGATTAACCTGGGCTAGTTAGCATCATTTGGTATCAGAGCTAGAAAACAAAGAGTGCCAA
131 CGACTCGATTAACCTGGGCCAATTAGCATCATTTAGTATCAGAGCTAGAAAACAAAGAGTGCCAA
*
36692415 AGATCGAAGAAGCCAGAATAGGTTTGTGAATTGAAAAAAAAATTAAAATTAAAAAAAAAGTTGTA
196 AGATCGAAGAAGCCAGAATAGGTTCGTGAATTG-AAAAAAAATTAAAATTAAAAAAAAAGTTGTA
36692480 TTTATTTTCCTTTGTAAATCAGCATATTGTACTGAAATATTGAAAAATATATATATACGAGTATA
260 TTTATTTTCCTTTGTAAATCAGCATATTGTACTGAAATATTGAAAAATATATATATACGAGTATA
*
36692545 AAAAAAGATATAGTGAAGTTTGCAAGTTTTCAATCTCATTTCTTCTTGTTTATTCCCGATCATCG
325 AAAAAAGATATAGTGAAGCTTGCAAGTTTTCAATCTCATTTCTTCTTGTTTATTCCCGATCATCG
*
36692610 TATCCTTTTCCATTCCCAATTCTTCTACCCCAAACGCCACACACTTAACCATTTTTCTTTTATTT
390 TATCCTTTTCCATTCCCAATTCTTCTACCCCAAACACCACACACTTAACCATTTTTCTTTTATTT
*
36692675 CAGCCAAACCTACACCTAAAACATTTATCCCTTGTAACCTACACCTAAAACTTGGCTTGACCACT
455 CAGCCAAACCTACACCTAAAACATTCATCCCTTGTAACCTACACCTAAAACTTGGCTTGACCACT
36692740 ACCAAGCATCCACG
520 ACCAAGCATCCACG
36692754 ACCTACATCTTTCTAAACCTTCCATCCATTTCAAAAATCACTTTGTAAGCTT-TCGCAAACCTAA
1 ACCTACATCTTTCTAAACCTTCCATCCATTTCAAAAATCACTTTGTAAGCTTCT-GCAAACCTAA
36692818 AACAAATTTACA-C-ATTT-ACTACTAGAACTTCTCCTCGTCGACGATCGGGCAAACTTTGTCAA
65 AACAAATTTACACCTATTTGACTACTAGAACTTCTCCTCGTCGACGATCGGGCAAACTTTGTCAA
* * * ** *
36692880 ATGACTCGATTAA-CTCGGGCCAATTCGCATCATTTAGTATTAGAGCTAGAAAATGAGGAGTGCC
130 ACGACTCGATTAACCT-GGGCCAATTAGCATCATTTAGTATCAGAGCTAGAAAACAAAGAGTGCC
* * * *
36692944 GAAGATCGTAGAAGCCCGAATAGGTTCGTGAATTG-AAAAAAATTGAAATT-AAAAAAAA-TTGT
194 AAAGATCGAAGAAGCCAGAATAGGTTCGTGAATTGAAAAAAAATTAAAATTAAAAAAAAAGTTGT
36693006 ATTTATTTTCCTTTGTAAATCAGCATATTGTACTGAAATATTAAAAAAAAGAAAAA-ATATATAT
259 ATTTATTTTCCTTTGTAAATCAGCATATTGTACTGAAATATT--------GAAAAATATATATAT
36693070 ACGAGTATAAAAAAAAGATATAGTGAAGCTTGCAAGTTTTCAATCTCATTTCTTCTTGTTTATTC
316 ACGAGTAT-AAAAAAAGATATAGTGAAGCTTGCAAGTTTTCAATCTCATTTCTTCTTGTTTATTC
36693135 CCGATCATCGTATCCTTTTCCATTCCCAATTCTTCTACCCCAAACACCACACACTTAACCATTTT
380 CCGATCATCGTATCCTTTTCCATTCCCAATTCTTCTACCCCAAACACCACACACTTAACCATTTT
*
36693200 TCTTTTATTTCAGCCAAACTTACACCTAAAACATTCATCCCTTGTAACC
445 TCTTTTATTTCAGCCAAACCTACACCTAAAACATTCATCCCTTGTAACC
36693249 CATTTTGAAG
Statistics
Matches: 462, Mismatches: 22, Indels: 21
0.91 0.04 0.04
Matches are distributed among these distances:
527 46 0.10
528 8 0.02
529 14 0.03
530 2 0.00
531 127 0.27
532 3 0.01
533 2 0.00
534 88 0.19
535 172 0.37
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.32
Consensus pattern (533 bp):
ACCTACATCTTTCTAAACCTTCCATCCATTTCAAAAATCACTTTGTAAGCTTCTGCAAACCTAAA
ACAAATTTACACCTATTTGACTACTAGAACTTCTCCTCGTCGACGATCGGGCAAACTTTGTCAAA
CGACTCGATTAACCTGGGCCAATTAGCATCATTTAGTATCAGAGCTAGAAAACAAAGAGTGCCAA
AGATCGAAGAAGCCAGAATAGGTTCGTGAATTGAAAAAAAATTAAAATTAAAAAAAAAGTTGTAT
TTATTTTCCTTTGTAAATCAGCATATTGTACTGAAATATTGAAAAATATATATATACGAGTATAA
AAAAAGATATAGTGAAGCTTGCAAGTTTTCAATCTCATTTCTTCTTGTTTATTCCCGATCATCGT
ATCCTTTTCCATTCCCAATTCTTCTACCCCAAACACCACACACTTAACCATTTTTCTTTTATTTC
AGCCAAACCTACACCTAAAACATTCATCCCTTGTAACCTACACCTAAAACTTGGCTTGACCACTA
CCAAGCATCCACG
Found at i:36694969 original size:20 final size:20
Alignment explanation
Indices: 36694946--36694999 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
36694936 AGTTTTTCCC
*
36694946 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* **
36694966 AGCTTAATTTAGCTCATTTG
1 AGCTCAATTTAGCTCACATG
36694986 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
36695000 TACTTTAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:36694990 original size:30 final size:30
Alignment explanation
Indices: 36694946--36695019 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
36694936 AGTTTTTCCC
36694946 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTC-ATTTGAGCTCA-ATTGAGCTTAATTT
* *
36694976 AGCTCATTTGAGCTCAATTTAGCTTACTTT
1 AGCTCATTTGAGCTCAATTGAGCTTAATTT
* *
36695006 AGTTCGTTTGAGCT
1 AGCTCATTTGAGCT
36695020 TGGCTTAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 5 0.13
30 33 0.87
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.41
Consensus pattern (30 bp):
AGCTCATTTGAGCTCAATTGAGCTTAATTT
Found at i:36697431 original size:22 final size:22
Alignment explanation
Indices: 36697401--36697444 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
36697391 TTTGGTATTT
*
36697401 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
*
36697423 GGGATTTGGTACAAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
36697445 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.34, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACAAAATGGTAA
Found at i:36699340 original size:12 final size:12
Alignment explanation
Indices: 36699319--36699474 Score: 64
Period size: 12 Copynumber: 13.6 Consensus size: 12
36699309 AGAAAAGGAG
*
36699319 AAAGAGATTGAA
1 AAAGAAATTGAA
36699331 AAAGAAATTG--
1 AAAGAAATTGAA
**
36699341 AAAGAAA-ACAA
1 AAAGAAATTGAA
*
36699352 AAAGAAAATGAA
1 AAAGAAATTGAA
**
36699364 AAAGAAAAAGAA
1 AAAGAAATTGAA
** *
36699376 ATTGCAAA-AGAA
1 AAAG-AAATTGAA
*
36699388 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
36699400 AAAGTGAGAGAA
1 AAAGAAATTGAA
*
36699412 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
36699426 AAAGAAAATTGAA
1 AAAG-AAATTGAA
36699439 AAAGAAATTG--
1 AAAGAAATTGAA
36699449 --AG-AA-TGAA
1 AAAGAAATTGAA
36699457 AAA-AAATTGAA
1 AAAGAAATTGAA
36699468 AAAGAAA
1 AAAGAAA
36699475 AAGCGAAAAA
Statistics
Matches: 109, Mismatches: 20, Indels: 30
0.69 0.13 0.19
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 2 0.02
10 10 0.09
11 17 0.16
12 56 0.51
13 9 0.08
14 6 0.06
15 5 0.05
ACGTcount: A:0.69, C:0.02, G:0.19, T:0.11
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:36699364 original size:6 final size:6
Alignment explanation
Indices: 36699341--36699477 Score: 71
Period size: 6 Copynumber: 22.7 Consensus size: 6
36699331 AAAGAAATTG
* * ** *
36699341 AAAG-A AAACAA AAAGAA AATGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
36699388 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
** * * **
36699439 AAAGAA ATTGAG AATGAA AAA-AA ATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG
36699478 CGAAAAAAGA
Statistics
Matches: 93, Mismatches: 34, Indels: 9
0.68 0.25 0.07
Matches are distributed among these distances:
5 6 0.06
6 76 0.82
7 7 0.08
8 4 0.04
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.09
Consensus pattern (6 bp):
AAAGAA
Found at i:36699371 original size:18 final size:18
Alignment explanation
Indices: 36699345--36699477 Score: 90
Period size: 18 Copynumber: 7.3 Consensus size: 18
36699335 AAATTGAAAG
*
36699345 AAAACAAAAAGAAAATGA
1 AAAAGAAAAAGAAAATGA
* *
36699363 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAATGA
36699381 AAAAGAAAAAG-AAATCGA
1 AAAAGAAAAAGAAAAT-GA
** * *
36699399 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAATGA
*
36699417 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-TGA
** *
36699438 AAAAGAAATTGAGAATGA
1 AAAAGAAAAAGAAAATGA
** *
36699456 AAAA-AAATTGAAAAAGA
1 AAAAGAAAAAGAAAATGA
36699473 AAAAG
1 AAAAG
36699478 CGAAAAAAGA
Statistics
Matches: 89, Mismatches: 20, Indels: 12
0.74 0.17 0.10
Matches are distributed among these distances:
17 18 0.20
18 48 0.54
19 9 0.10
20 8 0.09
21 6 0.07
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.10
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:36699472 original size:29 final size:27
Alignment explanation
Indices: 36699409--36699475 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 27
36699399 AAAAGTGAGA
36699409 GAAAAAGAAAATGAAGAAAAGAAAATT
1 GAAAAAGAAAATGAAGAAAAGAAAATT
*
36699436 GAAAAAGAAATTGAGAATGAAAA-AAAATT
1 GAAAAAGAAAAT--GAA-GAAAAGAAAATT
36699465 GAAAAAGAAAA
1 GAAAAAGAAAA
36699476 AGCGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 11 0.31
29 19 0.54
30 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (27 bp):
GAAAAAGAAAATGAAGAAAAGAAAATT
Found at i:36699486 original size:57 final size:52
Alignment explanation
Indices: 36699319--36699495 Score: 169
Period size: 57 Copynumber: 3.2 Consensus size: 52
36699309 AGAAAAGGAG
* *
36699319 AAAGAGATTGAAAAAGAAATTGAAA-GAAAACAAAAAGAAAATGAAAAAG-AA
1 AAAGAAATTGAAAAAGAAATTGAAATGAAAA-AAAAAGAAAAAGAAAAAGAAA
* ** * * *
36699370 AAAGAAATTGCAAAAGAAAAAGAAATCGAAAAAGTGAGAGAAAAAGAAAATGAAGA
1 AAAGAAATTGAAAAAGAAATTGAAAT-GAAAAA--AAAAGAAAAAGAAAAAGAA-A
*
36699426 AAAGAAAATTGAAAAAGAAATTGAGAATGAAAAAAAATTGAAAAAGAAAAAGCGAAA
1 AAAG-AAATTGAAAAAGAAATTGA-AATGAAAAAAAA-AGAAAAAGAAAAA--GAAA
36699483 AAAGAAATTGAAA
1 AAAGAAATTGAAA
36699496 GACAGCTTGA
Statistics
Matches: 100, Mismatches: 15, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
51 21 0.21
52 1 0.01
53 5 0.05
54 13 0.13
55 2 0.02
56 25 0.25
57 27 0.27
58 6 0.06
ACGTcount: A:0.68, C:0.02, G:0.19, T:0.11
Consensus pattern (52 bp):
AAAGAAATTGAAAAAGAAATTGAAATGAAAAAAAAAGAAAAAGAAAAAGAAA
Found at i:36704145 original size:20 final size:20
Alignment explanation
Indices: 36704117--36704175 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
36704107 AGAAAAAACG
* *
36704117 AAGACGAGCTGAATGAGCTA
1 AAGATGAGCTGAATGAACTA
*
36704137 AAGATGAGCTCAATGAACTA
1 AAGATGAGCTGAATGAACTA
** *
36704157 TGGTTGAGCTGAATGAACT
1 AAGATGAGCTGAATGAACT
36704176 TGAAGTAGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (20 bp):
AAGATGAGCTGAATGAACTA
Found at i:36710906 original size:45 final size:45
Alignment explanation
Indices: 36710842--36711119 Score: 502
Period size: 45 Copynumber: 6.2 Consensus size: 45
36710832 CATGAAATTA
*
36710842 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
36710887 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
36710932 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
36710977 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
36711022 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
36711067 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
36711112 AGGAAGCA
1 AGGAAGCA
36711120 CCATGGCCGA
Statistics
Matches: 226, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 226 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:36712807 original size:29 final size:29
Alignment explanation
Indices: 36712773--36712845 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
36712763 ATGTATTAGT
* *
36712773 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
* *
36712802 TTAGGAAATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
36712831 TTAGGACATATTTAA
1 TTAGGACATATTTAA
36712846 TAATATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:36716109 original size:10 final size:9
Alignment explanation
Indices: 36716070--36716110 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
36716060 CAGGATTTCA
*
36716070 AAAAAAAAC
1 AAAAAAAAG
36716079 AAAAAAAAG
1 AAAAAAAAG
36716088 AAAAGAAAAG
1 AAAA-AAAAG
36716098 AAAAAAAGAG
1 AAAAAAA-AG
36716108 AAA
1 AAA
36716111 TTCGGAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 15 0.52
10 14 0.48
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:36722648 original size:10 final size:11
Alignment explanation
Indices: 36722619--36722647 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
36722609 CCTCTTCTAT
36722619 TTTTTTTTCAA
1 TTTTTTTTCAA
36722630 TTTTTTTTCAA
1 TTTTTTTTCAA
36722641 TTTTTTT
1 TTTTTTT
36722648 CTTTCTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:36728009 original size:18 final size:18
Alignment explanation
Indices: 36727964--36728016 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
36727954 CATTTTCATA
* *
36727964 CTCTTTCTTTTCTTTACT
1 CTCTTTATTTTCTTTTCT
*
36727982 CATC-TCATTTTCTTTTCT
1 C-TCTTTATTTTCTTTTCT
36728000 CTCTTTATTTTTCTTTT
1 CTCTTTA-TTTTCTTTT
36728017 TTTTACAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 2 0.07
18 15 0.54
19 11 0.39
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.68
Consensus pattern (18 bp):
CTCTTTATTTTCTTTTCT
Found at i:36730214 original size:10 final size:10
Alignment explanation
Indices: 36730199--36730223 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
36730189 TTTTCCCGAA
36730199 TTTCTCTTCT
1 TTTCTCTTCT
36730209 TTTCTCTTCT
1 TTTCTCTTCT
36730219 TTTCT
1 TTTCT
36730224 TTTTTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTCTCTTCT
Found at i:36739390 original size:10 final size:10
Alignment explanation
Indices: 36739352--36739390 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
36739342 ACGAGATTGT
36739352 AAAAAAAAT-
1 AAAAAAAATC
36739361 -AAAAAAATC
1 AAAAAAAATC
36739370 GAAAAAAAATC
1 -AAAAAAAATC
36739381 AAAAAAAATC
1 AAAAAAAATC
36739391 TTATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.30
10 10 0.37
11 9 0.33
ACGTcount: A:0.79, C:0.08, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:36745356 original size:19 final size:19
Alignment explanation
Indices: 36745318--36745356 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
36745308 GTTTATTTTA
*
36745318 TTTTCTTATCCTTTTACTT
1 TTTTCTTATCCTTTCACTT
*
36745337 TTTTCTTATCCTTTCCCTT
1 TTTTCTTATCCTTTCACTT
36745356 T
1 T
36745357 GTTTATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTCTTATCCTTTCACTT
Found at i:36769305 original size:21 final size:19
Alignment explanation
Indices: 36769279--36769326 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
36769269 TCTTTTTGGA
*
36769279 TTTCTTTTTCTTTTTCAATCT
1 TTTCTTTTT-TCTTTCAAT-T
36769300 TTTCTTCTTTTCTTTCAATT
1 TTTCTT-TTTTCTTTCAATT
*
36769320 TCTCTTT
1 TTTCTTT
36769327 CTCGCTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 6 0.25
21 14 0.58
22 3 0.12
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTCTTTTTTCTTTCAATT
Found at i:36770403 original size:16 final size:15
Alignment explanation
Indices: 36770363--36770405 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
36770353 CTCACAAGAC
*
36770363 TTTTCACTTCTTTTT
1 TTTTCACTTCATTTT
*
36770378 TTTTATACTTCGATTTT
1 TTTT-CACTTC-ATTTT
36770395 TTTTCACTTCA
1 TTTTCACTTCA
36770406 AATACAATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 8 0.35
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTTCACTTCATTTT
Found at i:36770516 original size:13 final size:13
Alignment explanation
Indices: 36770459--36770519 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
36770449 TCCTCTTCTC
*
36770459 TTTTTTTTCAATT
1 TTTTTTTTCACTT
*
36770472 TTTTCTTTCTCTCTT
1 TTTT-TTT-TCACTT
* * **
36770487 TTTTTTTGCTCGA
1 TTTTTTTTCACTT
36770500 TTTTTTTTCACTT
1 TTTTTTTTCACTT
36770513 TTTTTTT
1 TTTTTTT
36770520 GAATTTTTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
13 23 0.62
14 6 0.16
15 8 0.22
ACGTcount: A:0.07, C:0.15, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTTTTTTCACTT
Found at i:36770535 original size:10 final size:10
Alignment explanation
Indices: 36770498--36770548 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
36770488 TTTTTTGCTC
36770498 GATTTTTTTT
1 GATTTTTTTT
*
36770508 CACTTTTTTTTT
1 GA--TTTTTTTT
36770520 GAATTTTTTTT
1 G-ATTTTTTTT
*
36770531 GATTTTCTTT
1 GATTTTTTTT
36770541 -ATTTTTTT
1 GATTTTTTT
36770549 AATCCAATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
9 7 0.21
10 9 0.26
11 9 0.26
12 8 0.24
13 1 0.03
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (10 bp):
GATTTTTTTT
Found at i:36784560 original size:20 final size:20
Alignment explanation
Indices: 36784535--36784577 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
36784525 GAGTAAAAGA
36784535 CATGCCCGATGGGTAGAATT
1 CATGCCCGATGGGTAGAATT
36784555 CATGCCCGATGGGTAGAATT
1 CATGCCCGATGGGTAGAATT
36784575 CAT
1 CAT
36784578 TGAAACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (20 bp):
CATGCCCGATGGGTAGAATT
Found at i:36788679 original size:20 final size:20
Alignment explanation
Indices: 36788656--36788702 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
36788646 GGGTTGAGGT
36788656 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
36788676 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
36788696 TGAGCTG
1 TGAGCTG
36788703 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:36790572 original size:12 final size:12
Alignment explanation
Indices: 36790557--36790582 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
36790547 TTTTTCAATC
36790557 TCAATTTCCTTT
1 TCAATTTCCTTT
36790569 TCAATTTCCTTT
1 TCAATTTCCTTT
36790581 TC
1 TC
36790583 TTCATTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (12 bp):
TCAATTTCCTTT
Found at i:36791697 original size:13 final size:12
Alignment explanation
Indices: 36791663--36791699 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
36791653 TTTTTTTTCC
36791663 TTTTTTTCG-AT
1 TTTTTTTCGAAT
36791674 TTTTTTT-GAAT
1 TTTTTTTCGAAT
36791685 TTTTTTTCCGAAT
1 TTTTTTT-CGAAT
36791698 TT
1 TT
36791700 CTTCTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.04
11 16 0.70
13 6 0.26
ACGTcount: A:0.14, C:0.08, G:0.08, T:0.70
Consensus pattern (12 bp):
TTTTTTTCGAAT
Found at i:36793067 original size:20 final size:20
Alignment explanation
Indices: 36793044--36793090 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
36793034 GGGTTGAGGT
36793044 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
36793064 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
36793084 TGAGCTG
1 TGAGCTG
36793091 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:36793507 original size:52 final size:52
Alignment explanation
Indices: 36793419--36793519 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
36793409 TAAGGAAACG
* * * *
36793419 TAATGGACAGTAGCTTAAGATCTCATTTCTATCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
36793471 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
36793520 TATGTGCATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:36801245 original size:21 final size:21
Alignment explanation
Indices: 36801219--36801281 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
36801209 TTGGTATTTG
*
36801219 GGAATTGGTACGAACTGGTAT
1 GGAATTGGTACGAAATGGTAT
*
36801240 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
36801261 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
36801282 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:36802472 original size:30 final size:30
Alignment explanation
Indices: 36802414--36802472 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
36802404 TTGAAAAGGT
* *
36802414 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
36802444 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
36802473 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:36804890 original size:29 final size:29
Alignment explanation
Indices: 36804856--36804928 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
36804846 TTAGATATTA
* *
36804856 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
36804885 TTAAATATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
36804914 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
36804929 ACTAATACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:36809432 original size:20 final size:20
Alignment explanation
Indices: 36809407--36809453 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
36809397 AAGCTAACTT
*
36809407 TAGCTCAATTTCAACTCCCA
1 TAGCTCAATTTCAACTCCAA
*
36809427 TAGCTC-ATTTCAGCTCCAA
1 TAGCTCAATTTCAACTCCAA
36809446 TCAGCTCA
1 T-AGCTCA
36809454 CTTCAGCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.28, C:0.34, G:0.09, T:0.30
Consensus pattern (20 bp):
TAGCTCAATTTCAACTCCAA
Found at i:36809438 original size:19 final size:19
Alignment explanation
Indices: 36809407--36809458 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
36809397 AAGCTAACTT
*
36809407 TAGCTCAATTTCAACTCCCA
1 TAGCTC-ATTTCAACTCCAA
*
36809427 TAGCTCATTTCAGCTCCAA
1 TAGCTCATTTCAACTCCAA
*
36809446 TCAGCTCACTTCA
1 T-AGCTCATTTCA
36809459 GCTCAATTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.27, C:0.35, G:0.08, T:0.31
Consensus pattern (19 bp):
TAGCTCATTTCAACTCCAA
Found at i:36812293 original size:21 final size:21
Alignment explanation
Indices: 36812267--36812329 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
36812257 TTGGTATTTG
36812267 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
36812288 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
36812309 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
36812330 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:36813366 original size:45 final size:45
Alignment explanation
Indices: 36813302--36813534 Score: 403
Period size: 45 Copynumber: 5.2 Consensus size: 45
36813292 CATGAAATTA
*
36813302 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
36813347 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
36813392 AGGAAGCATTTGACCAACATCATACATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
36813437 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
36813482 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
36813527 AGGAAGCA
1 AGGAAGCA
36813535 CCATGGCCGA
Statistics
Matches: 179, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 179 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:36819678 original size:45 final size:45
Alignment explanation
Indices: 36819614--36819846 Score: 403
Period size: 45 Copynumber: 5.2 Consensus size: 45
36819604 CATGAAATTA
*
36819614 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
36819659 AGGAACCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
36819704 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
36819749 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
36819794 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
36819839 AGGAAGCA
1 AGGAAGCA
36819847 CCATGGCCGA
Statistics
Matches: 179, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 179 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:36821540 original size:29 final size:29
Alignment explanation
Indices: 36821506--36821578 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
36821496 ATGTATTAGT
* *
36821506 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
* *
36821535 TTAGGAAATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
36821564 TTAGGACATATTTAA
1 TTAGGACATATTTAA
36821579 TAATATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:36826733 original size:29 final size:29
Alignment explanation
Indices: 36826700--36826772 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
36826690 ATGTATTAGT
* *
36826700 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
36826729 TTAGGACATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
36826758 TTAGGACATATTTAA
1 TTAGGACATATTTAA
36826773 TAATATCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:36827340 original size:22 final size:21
Alignment explanation
Indices: 36827308--36827349 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
36827298 TTGGTATTTA
36827308 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
36827329 GGAATTTGGTACGAATTGGTA
1 GGAA-TTGGTACGAAATGGTA
36827350 ATGGTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:36828460 original size:9 final size:10
Alignment explanation
Indices: 36828425--36828461 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
36828415 ATTTGCAAGC
36828425 TTTGAGCTAA
1 TTTGAGCTAA
36828435 TTTGAGCTAA
1 TTTGAGCTAA
*
36828445 TTTGAGCTCA
1 TTTGAGCTAA
36828455 -TTGAGCT
1 TTTGAGCT
36828462 TGAAAGGAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (10 bp):
TTTGAGCTAA
Found at i:36840520 original size:16 final size:16
Alignment explanation
Indices: 36840499--36840538 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
36840489 AAAAAATCAG
36840499 TAGAAAAAGT-CAAAAT
1 TAGAAAAA-TACAAAAT
*
36840515 TAGAAAAATACGAAAT
1 TAGAAAAATACAAAAT
36840531 TAGAAAAA
1 TAGAAAAA
36840539 AATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.17
Consensus pattern (16 bp):
TAGAAAAATACAAAAT
Found at i:36848647 original size:61 final size:61
Alignment explanation
Indices: 36848547--36848663 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
36848537 GCATCTCCAC
* ** * *
36848547 GATATGGGGTTGCGCGTGGACCAAGATCGAGTTGTCAAGTCACGGGAAAGTCCTACAAGAT
1 GATACGGGGTTGCGCACGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACAAGAT
36848608 GATACGGGGTTGCGCACGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTAC
1 GATACGGGGTTGCGCACGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTAC
36848664 GAAAAACCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.27, C:0.22, G:0.32, T:0.19
Consensus pattern (61 bp):
GATACGGGGTTGCGCACGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACAAGAT
Found at i:36849449 original size:4 final size:4
Alignment explanation
Indices: 36849440--36849466 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
36849430 AAACTAAGTA
36849440 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
36849467 AACTTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:36853507 original size:19 final size:19
Alignment explanation
Indices: 36853483--36853521 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
36853473 TGAAACCCGA
36853483 AAACCCAAAAAAACTGCGG
1 AAACCCAAAAAAACTGCGG
*
36853502 AAACCCGAAAAAACTGCGG
1 AAACCCAAAAAAACTGCGG
36853521 A
1 A
36853522 GTAACTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.26, G:0.18, T:0.05
Consensus pattern (19 bp):
AAACCCAAAAAAACTGCGG
Found at i:36860765 original size:40 final size:40
Alignment explanation
Indices: 36860721--36860798 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
36860711 TAAATAAAAG
*
36860721 AAAGTCCAATAACTCAATTACTAACTAAGATGAGTTTAAT
1 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTAAT
* * * * *
36860761 AAAGTCGAGCAAGTCATTTATTAACTAAGATGAGTTTA
1 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTA
36860799 TTTAAATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (40 bp):
AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTAAT
Found at i:36862437 original size:22 final size:22
Alignment explanation
Indices: 36862412--36862456 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
36862402 TAGCTGATTC
36862412 AAATTCAGCTCCCAGCAAATTG
1 AAATTCAGCTCCCAGCAAATTG
36862434 AAATTCAGCTCCCAGCAAATTG
1 AAATTCAGCTCCCAGCAAATTG
36862456 A
1 A
36862457 GATTGCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (22 bp):
AAATTCAGCTCCCAGCAAATTG
Found at i:36864450 original size:20 final size:20
Alignment explanation
Indices: 36864427--36864473 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
36864417 GGGTTAAAAT
*
36864427 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
36864447 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
36864467 TGAGCTG
1 TGAGCTG
36864474 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:36866369 original size:12 final size:12
Alignment explanation
Indices: 36866341--36866380 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
36866331 ACTCGATTTC
*
36866341 TTTTCAAGCTCT
1 TTTTCAATCTCT
* *
36866353 CTTTCAATTTCT
1 TTTTCAATCTCT
36866365 TTTTCAATCTCT
1 TTTTCAATCTCT
36866377 TTTT
1 TTTT
36866381 GCTTTTCACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.60
Consensus pattern (12 bp):
TTTTCAATCTCT
Found at i:36866433 original size:15 final size:15
Alignment explanation
Indices: 36866410--36866456 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
36866400 TTTTGAAATC
36866410 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
36866425 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
36866440 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
36866456 T
1 T
36866457 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:36867328 original size:52 final size:52
Alignment explanation
Indices: 36867240--36867340 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
36867230 TAAGGAAACG
* * * *
36867240 TAATGGACAGTAGCTTAAGATCTCATTTCTATCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
36867292 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
36867341 TATGTGCATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:36868190 original size:20 final size:20
Alignment explanation
Indices: 36868167--36868213 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
36868157 GGGTTAAAAT
*
36868167 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
36868187 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
36868207 TGAGCTG
1 TGAGCTG
36868214 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:36871958 original size:20 final size:21
Alignment explanation
Indices: 36871935--36871996 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 21
36871925 AACAAGTGAT
*
36871935 AGAAAAAGAAAA-GAGAAAGA
1 AGAAAAAGAAAAGGAAAAAGA
*
36871955 AGAAAAATAAAAGTGAAAAAGA
1 AGAAAAAGAAAAG-GAAAAAGA
* *
36871977 AGAAAATGAAAATGAAAAAG
1 AGAAAAAGAAAAGGAAAAAG
36871997 GCGAAAAGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 11 0.31
21 7 0.20
22 17 0.49
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (21 bp):
AGAAAAAGAAAAGGAAAAAGA
Found at i:36871992 original size:21 final size:21
Alignment explanation
Indices: 36871935--36871996 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
36871925 AACAAGTGAT
* *
36871935 AGAAAAAGAAAA-GAGAAAGA
1 AGAAAATGAAAATGAAAAAGA
36871955 AGAAAAAT-AAAAGTGAAAAAGA
1 AG-AAAATGAAAA-TGAAAAAGA
36871977 AGAAAATGAAAATGAAAAAG
1 AGAAAATGAAAATGAAAAAG
36871997 GCGAAAAGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 6 0.17
21 17 0.47
22 13 0.36
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (21 bp):
AGAAAATGAAAATGAAAAAGA
Found at i:36872008 original size:21 final size:22
Alignment explanation
Indices: 36871950--36872012 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 22
36871940 AAGAAAAGAG
**
36871950 AAAGAAGAAAAATAAAAGTGAA
1 AAAGAAGAAAAGGAAAAGTGAA
*
36871972 AAAGAAGAAAATGAAAA-TGAA
1 AAAGAAGAAAAGGAAAAGTGAA
**
36871993 AAAGGCGAAAAGG-AAAGTGA
1 AAAGAAGAAAAGGAAAAGTGA
36872013 GAGAGAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 3 0.09
21 17 0.49
22 15 0.43
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.08
Consensus pattern (22 bp):
AAAGAAGAAAAGGAAAAGTGAA
Found at i:36873643 original size:16 final size:16
Alignment explanation
Indices: 36873605--36873635 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
36873595 GTATGGGAGT
36873605 ATACATGAATGGTTGA
1 ATACATGAATGGTTGA
36873621 ATACATGAATGGTTG
1 ATACATGAATGGTTG
36873636 GATTCATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (16 bp):
ATACATGAATGGTTGA
Found at i:36876237 original size:27 final size:28
Alignment explanation
Indices: 36876200--36876264 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
36876190 TGTTTTTTTA
* *
36876200 CTTTCACTTTCTTTTTC-TTTTTCATTT
1 CTTTCAATTTCTTTTTCATTGTTCATTT
*
36876227 CTTTCAATTTCTTTTTCATTGTTCGTTT
1 CTTTCAATTTCTTTTTCATTGTTCATTT
*
36876255 CTCTCAATTT
1 CTTTCAATTT
36876265 TTCCATAGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.11, C:0.22, G:0.03, T:0.65
Consensus pattern (28 bp):
CTTTCAATTTCTTTTTCATTGTTCATTT
Done.