Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold169
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: 2015121
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 45543 characters in sequence are not A, C, G, or T
File 9 of 14
Found at i:1257662 original size:21 final size:21
Alignment explanation
Indices: 1257595--1257662 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
1257585 AAAGATGGAA
1257595 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
* ** *
1257616 AA-G-GCCAGCTATATTGGACTTA
1 AAGGTGCCA-ATATGCT-GA-TTC
1257638 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
1257659 AAGG
1 AAGG
1257663 CCAGCTACGT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 10 0.29
22 6 0.18
23 5 0.15
24 4 0.12
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:1257866 original size:32 final size:31
Alignment explanation
Indices: 1257818--1257891 Score: 123
Period size: 32 Copynumber: 2.4 Consensus size: 31
1257808 CCAGCTATAT
1257818 TGGGC-TTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
*
1257848 TGGGCTTTAGAGAGGGTTGCCATCGACTTGTG
1 TGGGCTTTAGA-AGGGTTGCCACCGACTTGTG
1257880 TGGGCTTTAGAA
1 TGGGCTTTAGAA
1257892 AAGGTGAAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 5 0.12
31 6 0.15
32 30 0.73
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
Found at i:1257959 original size:34 final size:34
Alignment explanation
Indices: 1257878--1258571 Score: 756
Period size: 34 Copynumber: 20.3 Consensus size: 34
1257868 CATCGACTTG
** * *
1257878 TGTGGGCTTTAGAAAAGGTGAAAGATGCCACGAAGT
1 TGTGGGCTTTA-AAAA-GAAAAAGGTGCCACGGAGT
* * *
1257914 TGTGGAC-TTAAAAAGAACAAGGTGCCACAGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1257947 TGTGGGCTTTAAAAAGGAAAAAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAA-G----AAAAAG-GTGCCACGGAGT
* * *
1257987 TGTGGGC-TT-AGAAGGAAAAGAGTGCCACGTAGT
1 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
*
1258020 TGTGGGCTTT--AAAGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
* *
1258053 CGTGGAC-TT-AAAAG-----GGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
* *
1258080 TGTGGGC-TTAGAAGGAAAAGAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAG-AAA-AAGGTGCCACGGAGT
*
1258115 TGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGAAGT
1 TGTGGGCTTTAAAAA--GAAAAAG-GTGCCACGGAGT
*
1258152 TGTGGGTTTTAAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
*
1258186 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAA-AGAAAAAG-GTGCCACGGAGT
*
1258223 TGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGT
1 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
*
1258258 TGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1258292 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
* * *
1258326 TGTGGAC-TTAAAGATGAAAAAAGTGCCACGGAGT
1 TGTGGGCTTTAAA-AAGAAAAAGGTGCCACGGAGT
* *
1258360 TGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
*
1258394 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
* * *
1258428 TGTGGAC-TTAAAGATGAAAAAAGTGCCACGGAGT
1 TGTGGGCTTTAAA-AAGAAAAAGGTGCCACGGAGT
* * *
1258462 TGTAGGCTTTGAAAAGAAGAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
* *
1258496 TGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
* *
1258530 TGTGGGCTTT--AAAGGAAAAGGTGCCACGAAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1258562 TGTGGGCTTT
1 TGTGGGCTTT
1258572 GAAGAAAAAA
Statistics
Matches: 573, Mismatches: 57, Indels: 60
0.83 0.08 0.09
Matches are distributed among these distances:
27 19 0.03
28 4 0.01
32 31 0.05
33 82 0.14
34 250 0.44
35 82 0.14
36 25 0.04
37 51 0.09
38 4 0.01
39 7 0.01
40 18 0.03
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (34 bp):
TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
Found at i:1258073 original size:27 final size:27
Alignment explanation
Indices: 1258035--1258094 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1258025 GCTTTAAAGG
*
1258035 AAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
* *
1258062 AAAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
*
1258089 AGAAGG
1 AAAAGG
1258095 AAAAGAAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.38, T:0.18
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTCGTGGACTT
Found at i:1258680 original size:125 final size:126
Alignment explanation
Indices: 1258349--1258761 Score: 356
Period size: 125 Copynumber: 3.2 Consensus size: 126
1258339 ATGAAAAAAG
* * * * * *
1258349 TGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
1 TGCCACTGAGTCGTGGACTTT--AAAGAAGAAGGTGCCACGGAGTCGTGGACTTT--AAAGGAAA
* * * * * * *
1258414 AGGTGCCACGGAGTTGTGGACTTAAAGATG-AAAAAAGTGCCACGGAGTTGTAGG-CTTTGAAAA
62 AGGTGCCACTGAGTCGTGGACTT--TGA-GCAAAAAA-CGCCACTGAGTCGT-GGACTTTGAGAA
1258477 GAAGAA
122 G-AGAA
* * * * *
1258483 GGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAA
1 --TGCCACTGAGTCGTGGACTTT--AAAGAAGAAGGTGCCACGGAGTCGTGGACTTTAAAGGAAA
* *
1258548 AGGTGCCAC-GAAGTTGTGGGCTTTGAAG-AAAAAACGCCACTGAGTCGTGGACTTTGAGACA-A
62 AGGTGCCACTG-AGTCGTGGACTTTG-AGCAAAAAACGCCACTGAGTCGTGGACTTTGAGA-AGA
1258610 -AA
124 GAA
*
1258612 TGCCACTGAGTCGTGGACTTTAAAGAA-AAGGATGCCACTGAGTCGTGGACTTTAAA-GAAAAGG
1 TGCCACTGAGTCGTGGACTTTAAAGAAGAAGG-TGCCACGGAGTCGTGGACTTTAAAGGAAAAGG
* * ** *
1258675 ATGCCACTGAGTCGTGGACTTTGAGCAGAGATTGCCACTGAGTCGTGGACTTTGAGAAGAGAT
65 -TGCCACTGAGTCGTGGACTTTGAGCAAAAAACGCCACTGAGTCGTGGACTTTGAGAAGAGAA
*
1258738 TGCCACTTAGTCGTGGACTTTAAA
1 TGCCACTGAGTCGTGGACTTTAAA
1258762 AAAGGTATTT
Statistics
Matches: 246, Mismatches: 21, Indels: 30
0.83 0.07 0.10
Matches are distributed among these distances:
124 14 0.06
125 73 0.30
126 25 0.10
127 18 0.07
129 2 0.01
130 3 0.01
131 18 0.07
132 9 0.04
133 2 0.01
134 27 0.11
136 55 0.22
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.23
Consensus pattern (126 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAGAAGGTGCCACGGAGTCGTGGACTTTAAAGGAAAAGGT
GCCACTGAGTCGTGGACTTTGAGCAAAAAACGCCACTGAGTCGTGGACTTTGAGAAGAGAA
Found at i:1258714 original size:31 final size:30
Alignment explanation
Indices: 1258544--1258758 Score: 236
Period size: 31 Copynumber: 6.9 Consensus size: 30
1258534 GGCTTTAAAG
* * *
1258544 GAAAAGGTGCCAC-GAAGTTGTGGGCTTTGAA
1 GAAAAGATGCCACTG-AGTCGTGGACTTTG-A
* *
1258575 GAAAAAACGCCACTGAGTCGTGGACTTTGA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGA
*
1258605 GACAAA-ATGCCACTGAGTCGTGGACTTTAAA
1 GA-AAAGATGCCACTGAGTCGTGGACTTT-GA
*
1258636 GAAAAGGATGCCACTGAGTCGTGGACTTTAAA
1 GAAAA-GATGCCACTGAGTCGTGGACTTT-GA
1258668 GAAAAGGATGCCACTGAGTCGTGGACTTTGA
1 GAAAA-GATGCCACTGAGTCGTGGACTTTGA
* *
1258699 GCAGAGATTGCCACTGAGTCGTGGACTTTGA
1 GAAAAGA-TGCCACTGAGTCGTGGACTTTGA
* *
1258730 GAAGAGATTGCCACTTAGTCGTGGACTTT
1 GAAAAGA-TGCCACTGAGTCGTGGACTTT
1258759 AAAAAAGGTA
Statistics
Matches: 166, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
30 29 0.17
31 82 0.49
32 55 0.33
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (30 bp):
GAAAAGATGCCACTGAGTCGTGGACTTTGA
Found at i:1258744 original size:94 final size:94
Alignment explanation
Indices: 1258519--1258761 Score: 291
Period size: 94 Copynumber: 2.6 Consensus size: 94
1258509 AAGAAGAAGG
* * * * * * *
1258519 TGCCACGGAGTTGTGGGCTTTAAAGGAAAAGG-TGCCAC-GAAGTTGTGGGCTTTGAAGAAAA-A
1 TGCCACTGAGTCGTGGACTTTAAA-GAAAAGGATGCCACTG-AGTCGTGGACTTTAAAGAAAAGG
*
1258581 ACGCCACTGAGTCGTGGACTTTGAGACAAAA
64 ATGCCACTGAGTCGTGGACTTTGAGACAAAA
1258612 TGCCACTGAGTCGTGGACTTTAAAGAAAAGGATGCCACTGAGTCGTGGACTTTAAAGAAAAGGAT
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAGGATGCCACTGAGTCGTGGACTTTAAAGAAAAGGAT
*
1258677 GCCACTGAGTCGTGGACTTTGAG-CAGAGAT
66 GCCACTGAGTCGTGGACTTTGAGACA-A-AA
* * *
1258707 TGCCACTGAGTCGTGGACTTT-GAGAAGA-GATTGCCACTTAGTCGTGGACTTTAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAGGA-TGCCACTGAGTCGTGGACTTTAAA
1258762 AAAGGTATTT
Statistics
Matches: 132, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
92 7 0.05
93 49 0.37
94 54 0.41
95 22 0.17
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.24
Consensus pattern (94 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAAAGGATGCCACTGAGTCGTGGACTTTAAAGAAAAGGAT
GCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:1259981 original size:7 final size:7
Alignment explanation
Indices: 1259963--1260007 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
1259953 GCCTTTGCAC
1259963 TTTT-TT
1 TTTTGTT
1259969 TTTTGTT
1 TTTTGTT
*
1259976 TGTTGTT
1 TTTTGTT
1259983 TTTTG-T
1 TTTTGTT
1259989 TTTT-TT
1 TTTTGTT
1259995 TTTTGTT
1 TTTTGTT
1260002 TTTTGT
1 TTTTGT
1260008 GTTTACTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 14 0.41
7 20 0.59
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTTGTT
Found at i:1259985 original size:19 final size:19
Alignment explanation
Indices: 1259963--1260007 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1259953 GCCTTTGCAC
*
1259963 TTTTTT-TTTTGTTTGTTG
1 TTTTTTGTTTTTTTTGTTG
*
1259981 TTTTTTGTTTTTTTTTTTG
1 TTTTTTGTTTTTTTTGTTG
1260000 TTTTTTGT
1 TTTTTTGT
1260008 GTTTACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (19 bp):
TTTTTTGTTTTTTTTGTTG
Found at i:1260010 original size:9 final size:10
Alignment explanation
Indices: 1259974--1260011 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
1259964 TTTTTTTTTG
1259974 TTTGTTGTTT
1 TTTGTTGTTT
1259984 TTTGTT-TTT
1 TTTGTTGTTT
*
1259993 TTTTTTGTTT
1 TTTGTTGTTT
1260003 TTTG-TGTTT
1 TTTGTTGTTT
1260012 ACTTTTGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 13 0.52
10 12 0.48
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (10 bp):
TTTGTTGTTT
Found at i:1260017 original size:19 final size:19
Alignment explanation
Indices: 1259978--1260018 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1259968 TTTTTGTTTG
* **
1259978 TTGTTTTTTGTTTTTTTTT
1 TTGTTTTTTGTGTTTACTT
1259997 TTGTTTTTTGTGTTTACTT
1 TTGTTTTTTGTGTTTACTT
1260016 TTG
1 TTG
1260019 ACTGTTCCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.80
Consensus pattern (19 bp):
TTGTTTTTTGTGTTTACTT
Found at i:1260017 original size:26 final size:26
Alignment explanation
Indices: 1259963--1260017 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1259953 GCCTTTGCAC
* **
1259963 TTTTTTTTTTGTTTGTTGTTTTTTGT
1 TTTTTTTTTTGTTTGTTGTGTTTACT
*
1259989 TTTTTTTTTTGTTTTTTGTGTTTACT
1 TTTTTTTTTTGTTTGTTGTGTTTACT
1260015 TTT
1 TTT
1260018 GACTGTTCCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.84
Consensus pattern (26 bp):
TTTTTTTTTTGTTTGTTGTGTTTACT
Found at i:1266993 original size:52 final size:52
Alignment explanation
Indices: 1266908--1267032 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
1266898 ATATGAAAAG
* *
1266908 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1266960 TTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATT-TAATAATGTATCGATACATCTGGGCAAAT
1267012 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1267033 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
52 67 0.96
53 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1267045 original size:52 final size:50
Alignment explanation
Indices: 1266908--1267052 Score: 193
Period size: 52 Copynumber: 2.8 Consensus size: 50
1266898 ATATGAAAAG
* *
1266908 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
*
1266960 TTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--A-AATAGTGTATCGATACATCTGGGCAAAT
1267012 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
1267053 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
52 80 0.94
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1267059 original size:13 final size:13
Alignment explanation
Indices: 1267041--1267065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1267031 CAAAGATCAG
1267041 TGTATCGATACAA
1 TGTATCGATACAA
1267054 TGTATCGATACA
1 TGTATCGATACA
1267066 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1267147 original size:33 final size:33
Alignment explanation
Indices: 1267105--1267174 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1267095 GGCAGTAGCT
1267105 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
1267138 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
1267171 TACA
1 TACA
1267175 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:1267148 original size:13 final size:13
Alignment explanation
Indices: 1267130--1267154 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1267120 CAAAAAAATA
1267130 TGTATCGATACAT
1 TGTATCGATACAT
1267143 TGTATCGATACA
1 TGTATCGATACA
1267155 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1267963 original size:14 final size:16
Alignment explanation
Indices: 1267934--1267965 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1267924 TTTTTATGTA
1267934 TAAAGAATATATTAAT
1 TAAAGAATATATTAAT
1267950 TAAA-AATA-ATTAAT
1 TAAAGAATATATTAAT
1267964 TA
1 TA
1267966 TGAAATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
TAAAGAATATATTAAT
Found at i:1269046 original size:28 final size:28
Alignment explanation
Indices: 1269014--1269092 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
1269004 CAAATGTCAC
*
1269014 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTAAAATATGGTGGTTT
1269042 CCTTTGTATTTGTAAAATATGGTGGTTAT
1 CCTTTGTATTTGTAAAATATGGTGGTT-T
* *
1269071 -TTTTGTA--TGTAAAAAATGGTGG
1 CCTTTGTATTTGTAAAATATGGTGG
1269093 CTTGTTGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
26 14 0.30
28 32 0.68
29 1 0.02
ACGTcount: A:0.24, C:0.06, G:0.23, T:0.47
Consensus pattern (28 bp):
CCTTTGTATTTGTAAAATATGGTGGTTT
Found at i:1269109 original size:24 final size:24
Alignment explanation
Indices: 1269073--1269118 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1269063 GTGGTTATTT
1269073 TTGTATGTAAAAAAT-GGTGGCTTG
1 TTGTATGT-AAAAATCGGTGGCTTG
* *
1269097 TTGTTTGTCAAAATCGGTGGCT
1 TTGTATGTAAAAATCGGTGGCT
1269119 AATTTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.24, C:0.09, G:0.28, T:0.39
Consensus pattern (24 bp):
TTGTATGTAAAAATCGGTGGCTTG
Found at i:1273655 original size:28 final size:28
Alignment explanation
Indices: 1273591--1273645 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
1273581 CAAATGCCAC
*
1273591 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATAGTGGTTT
1273619 CCTTTGTATTTGTCAAATATAGTGGTT
1 CCTTTGTATTTGTCAAATATAGTGGTT
1273646 ATTTTTGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATAGTGGTTT
Found at i:1273677 original size:24 final size:24
Alignment explanation
Indices: 1273650--1273695 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1273640 GTGGTTATTT
1273650 TTGTATGTAAAAAATGGTGGCTTG
1 TTGTATGTAAAAAATGGTGGCTTG
* * *
1273674 TTGTTTGTCAAAATTGGTGGCT
1 TTGTATGTAAAAAATGGTGGCT
1273696 AATTTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (24 bp):
TTGTATGTAAAAAATGGTGGCTTG
Found at i:1274080 original size:5 final size:5
Alignment explanation
Indices: 1274070--1274100 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1274060 GTTATATTTA
1274070 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T
1274101 CGATTGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAAAT
Found at i:1274149 original size:24 final size:21
Alignment explanation
Indices: 1274122--1274171 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
1274112 TAAAAAAAAT
1274122 AAAAGACAATCAATAATTATTTTC
1 AAAAGACAA--AA-AATTATTTTC
* *
1274146 AAAAGATAAAAAATTATTTTT
1 AAAAGACAAAAAATTATTTTC
1274167 AAAAG
1 AAAAG
1274172 TTTTAAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 14 0.58
22 2 0.08
24 8 0.33
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (21 bp):
AAAAGACAAAAAATTATTTTC
Found at i:1275181 original size:14 final size:14
Alignment explanation
Indices: 1275162--1275189 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1275152 CTATCGTTAA
1275162 ATTTAAATGTTTTT
1 ATTTAAATGTTTTT
1275176 ATTTAAATGTTTTT
1 ATTTAAATGTTTTT
1275190 CTCGGTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
ATTTAAATGTTTTT
Found at i:1275401 original size:21 final size:21
Alignment explanation
Indices: 1275377--1275416 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1275367 TATCGTTTAT
*
1275377 ATTTTAATAAATTAATTATTA
1 ATTTTAATAAAATAATTATTA
1275398 ATTTTAATAAAATAATTAT
1 ATTTTAATAAAATAATTAT
1275417 ATTTATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTAATAAAATAATTATTA
Found at i:1275421 original size:18 final size:19
Alignment explanation
Indices: 1275373--1275420 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 19
1275363 TTTATATCGT
*
1275373 TTATATTTTAATAAATTAA
1 TTATATTTTAATAAAATAA
1275392 TTATTAATTTTAATAAAATAA
1 TTA-T-ATTTTAATAAAATAA
1275413 TTATATTT
1 TTATATTT
1275421 ATTATACACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 7 0.27
20 2 0.08
21 17 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATATTTTAATAAAATAA
Found at i:1275630 original size:11 final size:11
Alignment explanation
Indices: 1275614--1275638 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1275604 ATAAATATAA
1275614 ATTATATAAAT
1 ATTATATAAAT
1275625 ATTATATAAAT
1 ATTATATAAAT
1275636 ATT
1 ATT
1275639 TAAAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTATATAAAT
Found at i:1278194 original size:18 final size:17
Alignment explanation
Indices: 1278160--1278194 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1278150 TATTTTTAAT
*
1278160 TATTAAATAATAATTTA
1 TATTAAATAAAAATTTA
1278177 TATTAAATAAAAAATTTA
1 TATTAAAT-AAAAATTTA
1278195 ATCCATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATTAAATAAAAATTTA
Found at i:1279407 original size:17 final size:17
Alignment explanation
Indices: 1279381--1279426 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1279371 ATTTTAGAAT
*
1279381 AAAAGGAAATAAAAAAG
1 AAAAGTAAATAAAAAAG
*
1279398 AAAAGTAAATAAAAAAT
1 AAAAGTAAATAAAAAAG
1279415 AAAA-TAAA-AAAA
1 AAAAGTAAATAAAA
1279427 TAAATATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 4 0.15
17 19 0.70
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (17 bp):
AAAAGTAAATAAAAAAG
Found at i:1279414 original size:24 final size:24
Alignment explanation
Indices: 1279387--1279432 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1279377 GAATAAAAGG
*
1279387 AAATAAAA-AAGAAAAGTAAATAAA
1 AAATAAAATAA-AAAAATAAATAAA
1279411 AAATAAAATAAAAAAATAAATA
1 AAATAAAATAAAAAAATAAATA
1279433 TTGATATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.15
Consensus pattern (24 bp):
AAATAAAATAAAAAAATAAATAAA
Found at i:1281606 original size:39 final size:39
Alignment explanation
Indices: 1281563--1281639 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
1281553 TAAATATTAT
* *
1281563 CCCTTTAATTAAAATAATTTACACATCAAATCACTACAC
1 CCCTTGAATTAAAATAATTTACACACCAAATCACTACAC
1281602 CCCTTGAATTAAAATAATTTACACACCAAATCACTACA
1 CCCTTGAATTAAAATAATTTACACACCAAATCACTACA
1281640 TCGATGTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.29
Consensus pattern (39 bp):
CCCTTGAATTAAAATAATTTACACACCAAATCACTACAC
Found at i:1281874 original size:11 final size:11
Alignment explanation
Indices: 1281849--1281900 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
1281839 AAAATTTCAG
*
1281849 AATAAA-AAGA
1 AATAAATAATA
1281859 AATAAATAATA
1 AATAAATAATA
1281870 AATAAATAATA
1 AATAAATAATA
1281881 AA-ATAA-AATAA
1 AATA-AATAAT-A
1281892 AATAAATAA
1 AATAAATAA
1281901 GATGAATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 10 0.28
11 23 0.64
12 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (11 bp):
AATAAATAATA
Found at i:1281908 original size:28 final size:29
Alignment explanation
Indices: 1281848--1281908 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
1281838 AAAAATTTCA
1281848 GAATAAAAAGAAATAAATAATAAATAAAT
1 GAATAAAAAGAAATAAATAATAAATAAAT
1281877 -AATAAAATA-AAAT-AA-AATAAATAAGAT
1 GAATAAAA-AGAAATAAATAATAAATAA-AT
1281904 GAATA
1 GAATA
1281909 TTGATATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
26 9 0.31
27 4 0.14
28 15 0.52
29 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (29 bp):
GAATAAAAAGAAATAAATAATAAATAAAT
Found at i:1282326 original size:22 final size:22
Alignment explanation
Indices: 1282285--1282326 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1282275 TATTAAAAAA
*
1282285 ATATTTTTATATTAATATTTAT
1 ATATTTTTAAATTAATATTTAT
1282307 ATATTTTTAAAATTAA-ATTT
1 ATATTTTT-AAATTAATATTT
1282327 TAATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTTAAATTAATATTTAT
Found at i:1282908 original size:32 final size:32
Alignment explanation
Indices: 1282859--1282975 Score: 141
Period size: 32 Copynumber: 3.7 Consensus size: 32
1282849 GCTAAAACTT
* *
1282859 TTTAATAATTATTAAATTTATGAGTAATTATG
1 TTTAATATTTATCAAATTTATGAGTAATTATG
* * * *
1282891 TTTAATATTCATCAAATTTAAGAATAATTTTG
1 TTTAATATTTATCAAATTTATGAGTAATTATG
1282923 TTTAATATTTATCAAATTTATGAGT-ATTAATG
1 TTTAATATTTATCAAATTTATGAGTAATT-ATG
*
1282955 -TCAA-ATTTATCAAATTTATGA
1 TTTAATATTTATCAAATTTATGA
1282976 TCAATATGAA
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
30 17 0.23
31 6 0.08
32 50 0.68
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (32 bp):
TTTAATATTTATCAAATTTATGAGTAATTATG
Found at i:1282979 original size:21 final size:22
Alignment explanation
Indices: 1282933--1282979 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1282923 TTTAATATTT
* *
1282933 ATCAAATTTATGAGTATTAATG
1 ATCAAATTTATCAGAATTAATG
*
1282955 -TCAAATTTATCA-AATTTATG
1 ATCAAATTTATCAGAATTAATG
1282975 ATCAA
1 ATCAA
1282980 TATGAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (22 bp):
ATCAAATTTATCAGAATTAATG
Found at i:1283899 original size:21 final size:21
Alignment explanation
Indices: 1283851--1283900 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1283841 ACACAAAATC
*
1283851 ATTCAAATATTAAAAAAATAT
1 ATTCAAATTTTAAAAAAATAT
* * *
1283872 A-TAAAATTTTTAAAAATTAT
1 ATTCAAATTTTAAAAAAATAT
1283892 ATTCAAATT
1 ATTCAAATT
1283901 ATTTTTTGGC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTCAAATTTTAAAAAAATAT
Found at i:1285764 original size:14 final size:14
Alignment explanation
Indices: 1285745--1285775 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1285735 ATGAATTACG
1285745 TTGAGTTAGATTTA
1 TTGAGTTAGATTTA
1285759 TTGAGTTAGATTTA
1 TTGAGTTAGATTTA
1285773 TTG
1 TTG
1285776 GGTCAGACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (14 bp):
TTGAGTTAGATTTA
Found at i:1286004 original size:136 final size:137
Alignment explanation
Indices: 1285759--1286026 Score: 441
Period size: 136 Copynumber: 2.0 Consensus size: 137
1285749 GTTAGATTTA
* *
1285759 TTGAGTTAGATTTATTGGGTCAGACGAATTATTTGATCAGTTTTAATTAAAAAAATATCATCATA
1 TTGAGTTAGATTTATTAGGTCAGACGAATTATTTGATCAATTTTAATTAAAAAAATATCATCATA
*
1285824 AAATATAAAATAAATTTATATTAACTAGTTTAATTAGTTTGGTTTAGATTATAAAATGTTAAATT
66 AAATATAAAATAAATTTATATTAACTAGTTTAATTAGTTTGGTTTAGATTATAAAATATTAAATT
1285889 TAAGATG
131 TAAGATG
* * *
1285896 TTGAGTTAGATTTATTAGGTCAGA-GAAATTATTTGATTAATTTTAATT-AAAAAATATTATTAT
1 TTGAGTTAGATTTATTAGGTCAGACG-AATTATTTGATCAATTTTAATTAAAAAAATATCATCAT
* *
1285959 AAAATATAAAATTAATTTATATTAATTAGTTTAATTAGTTTGGTTTAGATTATAAAATATTAAAT
65 AAAATATAAAATAAATTTATATTAACTAGTTTAATTAGTTTGGTTTAGATTATAAAATATTAAAT
1286024 TTA
130 TTA
1286027 GGTATGAATT
Statistics
Matches: 122, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
136 79 0.65
137 43 0.35
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.44
Consensus pattern (137 bp):
TTGAGTTAGATTTATTAGGTCAGACGAATTATTTGATCAATTTTAATTAAAAAAATATCATCATA
AAATATAAAATAAATTTATATTAACTAGTTTAATTAGTTTGGTTTAGATTATAAAATATTAAATT
TAAGATG
Found at i:1286217 original size:15 final size:15
Alignment explanation
Indices: 1286193--1286232 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1286183 ACTTCAGCTC
* *
1286193 AAATTATAAAATATTT
1 AAATT-TAAAAAAATT
1286209 AAATTTAAAAAAATT
1 AAATTTAAAAAAATT
1286224 AAATTTAAA
1 AAATTTAAA
1286233 TATGTGTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTTAAAAAAATT
Found at i:1286225 original size:58 final size:52
Alignment explanation
Indices: 1286158--1286269 Score: 134
Period size: 58 Copynumber: 2.0 Consensus size: 52
1286148 TTTATATTAT
* *
1286158 AAAATATTAAATTTAAGTAGGTATTACTTCAGCTCAAATTATAAAATATTTAAATTTA
1 AAAAAATTAAATTTAAATAGGTATTACTTCA--T---ATTATAAAATA-TTAAATTTA
* *
1286216 AAAAAATTAAATTTAAATATGTGTTACTTCATATTATAAAATATTAAATTTA
1 AAAAAATTAAATTTAAATAGGTATTACTTCATATTATAAAATATTAAATTTA
1286268 AA
1 AA
1286270 TATAAGTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
52 11 0.22
53 11 0.22
56 1 0.02
58 27 0.54
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (52 bp):
AAAAAATTAAATTTAAATAGGTATTACTTCATATTATAAAATATTAAATTTA
Found at i:1287439 original size:34 final size:34
Alignment explanation
Indices: 1287393--1287577 Score: 266
Period size: 34 Copynumber: 5.5 Consensus size: 34
1287383 GTAAAAACCA
*
1287393 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1287427 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
1287461 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1287495 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1287529 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1287562 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1287578 TCTCCCACTT
Statistics
Matches: 137, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
33 18 0.13
34 115 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1287535 original size:102 final size:101
Alignment explanation
Indices: 1287393--1287577 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
1287383 GTAAAAACCA
1287393 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1287458 CACCCATTTAATCAACAATGGTAAGCTACCAAATCTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * *
1287495 CCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1287560 CACCATTTAATCAACAAT
66 CACCATTTAATCAACAAT
1287578 TCTCCCACTT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 16 0.20
102 63 0.80
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (101 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:1291670 original size:19 final size:19
Alignment explanation
Indices: 1291643--1291705 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1291633 TCACGTGTAC
* *
1291643 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
1291662 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
1291681 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
1291700 AGTACC
1 AGTACC
1291706 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:1292053 original size:34 final size:34
Alignment explanation
Indices: 1292007--1292190 Score: 264
Period size: 34 Copynumber: 5.4 Consensus size: 34
1291997 GTAAAAACCA
*
1292007 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1292041 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
1292075 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1292109 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1292143 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1292176 CCATTTAATCAACAA
1 CCATTTAATCAACAA
1292191 AAACAAATAA
Statistics
Matches: 136, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
33 17 0.12
34 115 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1292149 original size:102 final size:101
Alignment explanation
Indices: 1292007--1292190 Score: 323
Period size: 102 Copynumber: 1.8 Consensus size: 101
1291997 GTAAAAACCA
1292007 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1292072 CACCCATTTAATCAACAATGGTAAGCTACCAAATCTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * *
1292109 CCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1292174 CACCATTTAATCAACAA
66 CACCATTTAATCAACAA
1292191 AAACAAATAA
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 15 0.19
102 63 0.81
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (101 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:1292396 original size:10 final size:8
Alignment explanation
Indices: 1292336--1292422 Score: 61
Period size: 8 Copynumber: 10.4 Consensus size: 8
1292326 TTGTTCGAGT
1292336 TATATTTA
1 TATATTTA
* *
1292344 TTTATTTT
1 TATATTTA
1292352 TATATTATAA
1 TATATT-T-A
1292362 TTATATTTAA
1 -TATATTT-A
*
1292372 AATATTTA
1 TATATTTA
1292380 TATATTTA
1 TATATTTA
1292388 TATAAATTTA
1 TAT--ATTTA
*
1292398 -ATTTTTA
1 TATATTTA
*
1292405 TATATTTT
1 TATATTTA
1292413 TATA-TTA
1 TATATTTA
1292420 TAT
1 TAT
1292423 CATTGTTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
7 9 0.14
8 31 0.49
9 9 0.14
10 8 0.13
11 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTTA
Found at i:1292544 original size:3 final size:3
Alignment explanation
Indices: 1292536--1292561 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1292526 AAGTGAGTGA
1292536 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1292562 ATTTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1293127 original size:14 final size:14
Alignment explanation
Indices: 1293087--1293130 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1293077 TTGTTTTTTT
*
1293087 TATAATTTAGTAAA
1 TATAATTTATTAAA
*
1293101 TATAATGTATTAAA
1 TATAATTTATTAAA
*
1293115 TATAATTTTTTAAA
1 TATAATTTATTAAA
1293129 TA
1 TA
1293131 ATACTTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (14 bp):
TATAATTTATTAAA
Found at i:1295409 original size:17 final size:18
Alignment explanation
Indices: 1295389--1295435 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1295379 AATTAATTAG
*
1295389 ATAAAAATTAAAAA-ATT
1 ATAAAAATTAAAAATATA
*
1295406 ATAAAGAGACTAAAAATATA
1 ATAAA-A-ATTAAAAATATA
1295426 ATAAAAATTA
1 ATAAAAATTA
1295436 CCCCCAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 5 0.21
18 4 0.17
19 8 0.33
20 7 0.29
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (18 bp):
ATAAAAATTAAAAATATA
Found at i:1296320 original size:2 final size:2
Alignment explanation
Indices: 1296313--1296352 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1296303 CTCTTTGTTA
1296313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1296353 TCTTTTCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1297074 original size:17 final size:16
Alignment explanation
Indices: 1297035--1297074 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1297025 AATTAACATG
*
1297035 ATCTAAACTCAAAATT
1 ATCTAAACTCAAAATA
*
1297051 ATTTAAACTCAAAAATA
1 ATCTAAACTC-AAAATA
1297068 ATCTAAA
1 ATCTAAA
1297075 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (16 bp):
ATCTAAACTCAAAATA
Found at i:1299856 original size:5 final size:5
Alignment explanation
Indices: 1299843--1299920 Score: 51
Period size: 5 Copynumber: 16.8 Consensus size: 5
1299833 AGATATGATT
* * *
1299843 ATATG ATATA ATATA ATATA A-AAA AT-TA ATATA AAATA A-A-A ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * *
1299889 ATATG ATACA A-AAA ATATC ATA-A ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT
1299921 GTATATATGA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
3 2 0.04
4 14 0.25
5 40 0.71
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (5 bp):
ATATA
Found at i:1299872 original size:18 final size:19
Alignment explanation
Indices: 1299848--1299917 Score: 83
Period size: 18 Copynumber: 3.8 Consensus size: 19
1299838 TGATTATATG
1299848 ATATAATATAATATAAAAA
1 ATATAATATAATATAAAAA
*
1299867 AT-TAATATAAAAT-AAAA
1 ATATAATATAATATAAAAA
* *
1299884 ATATAATATGATACAAAAA
1 ATATAATATAATATAAAAA
*
1299903 ATATCATA-AATATAA
1 ATATAATATAATATAA
1299918 TATGTATATA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
17 6 0.14
18 23 0.55
19 13 0.31
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (19 bp):
ATATAATATAATATAAAAA
Found at i:1299995 original size:28 final size:29
Alignment explanation
Indices: 1299955--1300020 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
1299945 ATATAATTAC
1299955 ATAAAT-TATTAATATGTTGAAAAATT-TT
1 ATAAATGTATTAATAT-TTGAAAAATTATT
* *
1299983 ATAAATGTA-TAATATTTTAAATATTATT
1 ATAAATGTATTAATATTTGAAAAATTATT
1300011 ATAATATGTA
1 ATAA-ATGTA
1300021 AAAATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 8 0.24
28 18 0.55
29 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (29 bp):
ATAAATGTATTAATATTTGAAAAATTATT
Found at i:1301094 original size:24 final size:22
Alignment explanation
Indices: 1301062--1301106 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
1301052 ACAACTATAT
*
1301062 AAATATAATGTAAAATAATAATTA
1 AAATATAATAT-AAATAA-AATTA
*
1301086 AAATGTAATATAAATAAAATT
1 AAATATAATATAAATAAAATT
1301107 TTAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATATAATATAAATAAAATTA
Found at i:1301127 original size:16 final size:16
Alignment explanation
Indices: 1301106--1301153 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1301096 TAAATAAAAT
1301106 TTTAAAATTTATATAA
1 TTTAAAATTTATATAA
*
1301122 TTTAAATTATTA-AT-A
1 TTTAAAAT-TTATATAA
1301137 TATTAAAATTTATATAA
1 T-TTAAAATTTATATAA
1301154 ATAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
15 5 0.19
16 17 0.65
17 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAAAATTTATATAA
Found at i:1301134 original size:24 final size:25
Alignment explanation
Indices: 1301082--1301134 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
1301072 TAAAATAATA
1301082 ATTAAAATGTAATATAAATAAAATT
1 ATTAAAATGTAATATAAATAAAATT
* * *
1301107 -TTAAAAT-TTATATAATTTAAATT
1 ATTAAAATGTAATATAAATAAAATT
1301130 ATTAA
1 ATTAA
1301135 TATATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTAAAATGTAATATAAATAAAATT
Found at i:1301149 original size:18 final size:16
Alignment explanation
Indices: 1301107--1301169 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 16
1301097 AAATAAAATT
1301107 TTAAAATTTA-TATAA
1 TTAAAATTTATTATAA
*
1301122 TTTAAA-TTATTAATATA
1 TTAAAATTTATT-ATA-A
1301139 TTAAAATTTA-TATAA
1 TTAAAATTTATTATAA
* **
1301154 ATAAAAAATATTATAA
1 TTAAAATTTATTATAA
1301170 AATAATAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
14 3 0.08
15 14 0.37
16 11 0.29
17 7 0.18
18 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATTTATTATAA
Found at i:1301160 original size:16 final size:17
Alignment explanation
Indices: 1301109--1301174 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 17
1301099 ATAAAATTTT
* *
1301109 AAAAT-TTATATAATTT
1 AAAATATTATATAAATA
* * *
1301125 AAATTATTA-ATATATT
1 AAAATATTATATAAATA
1301141 AAAAT-TTATATAAATAA
1 AAAATATTATATAAAT-A
1301158 AAAATATTATA-AAATA
1 AAAATATTATATAAATA
1301174 A
1 A
1301175 TAAAAAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 3 0.08
16 20 0.50
17 12 0.30
18 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATATTATATAAATA
Found at i:1301161 original size:17 final size:18
Alignment explanation
Indices: 1301140--1301179 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1301130 ATTAATATAT
1301140 TAAAAT-TTATATAAATAA
1 TAAAATATTATA-AAATAA
1301158 -AAAATATTATAAAATAA
1 TAAAATATTATAAAATAA
1301175 TAAAA
1 TAAAA
1301180 AATATCTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATATTATAAAATAA
Found at i:1301179 original size:18 final size:18
Alignment explanation
Indices: 1301108--1301179 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 18
1301098 AATAAAATTT
1301108 TAAAATTTATAT-AAT--
1 TAAAATTTATATAAATAA
* *
1301123 TTAAA-TTAT-TAATATAT
1 TAAAATTTATATAA-ATAA
1301140 TAAAATTTATATAAATAA
1 TAAAATTTATATAAATAA
1301158 -AAAATATTATA-AAATAA
1 TAAAAT-TTATATAAATAA
1301175 TAAAA
1 TAAAA
1301180 AATATCTATC
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.02
14 5 0.11
15 6 0.13
17 15 0.33
18 16 0.35
19 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATTTATATAAATAA
Found at i:1301849 original size:22 final size:23
Alignment explanation
Indices: 1301824--1301870 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1301814 ATTTACAAAT
* * *
1301824 AAATTTATTT-ATATATCATTTA
1 AAATTAATTTGATAAATCACTTA
1301846 AAATTAATTTGATAAATCACTTA
1 AAATTAATTTGATAAATCACTTA
1301869 AA
1 AA
1301871 GTTTGCTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATTAATTTGATAAATCACTTA
Found at i:1303713 original size:19 final size:19
Alignment explanation
Indices: 1303675--1303721 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1303665 TCAATTGATA
*
1303675 AAAATATATAAAAATTAAATT
1 AAAAT-TAT-AAAATAAAATT
*
1303696 ATAATTATAAAATAAAATT
1 AAAATTATAAAATAAAATT
1303715 AAAATTA
1 AAAATTA
1303722 GGACTGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 3 0.13
21 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTATAAAATAAAATT
Found at i:1306086 original size:26 final size:25
Alignment explanation
Indices: 1306034--1306086 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
1306024 TTAAATTTGT
* **
1306034 ATTATCTATATTAAATTCGTATAAA
1 ATTATCTAAATTAAATTCAAATAAA
*
1306059 ATTATCTAAATTTAAATTCAAATTAA
1 ATTATCTAAA-TTAAATTCAAATAAA
1306085 AT
1 AT
1306087 GATATTATCG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTATCTAAATTAAATTCAAATAAA
Found at i:1306630 original size:17 final size:17
Alignment explanation
Indices: 1306610--1306652 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1306600 AAAAATATTC
1306610 ATATAATAATATTTTTA
1 ATATAATAATATTTTTA
** *
1306627 ATATTTTAATATTTTTG
1 ATATAATAATATTTTTA
1306644 A-ATAATAAT
1 ATATAATAAT
1306653 TTAGATTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATATAATAATATTTTTA
Found at i:1307119 original size:2 final size:2
Alignment explanation
Indices: 1307112--1307150 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1307102 TCTTTTGGAT
*
1307112 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1307151 GAGGAAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1307879 original size:34 final size:34
Alignment explanation
Indices: 1307812--1308027 Score: 292
Period size: 34 Copynumber: 6.4 Consensus size: 34
1307802 AGGTAAAAGC
* * *
1307812 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1307845 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
1307879 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
1307912 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1307946 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1307980 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1308014 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1308028 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 40 0.25
34 122 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1307993 original size:68 final size:67
Alignment explanation
Indices: 1307812--1308029 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
1307802 AGGTAAAAGC
* * * * *
1307812 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
1307877 AT
66 AT
* * * *
1307879 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
1307944 AT
66 AT
* * *
1307946 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
1308011 CAT
65 CAT
1308014 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
1308030 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:1308388 original size:19 final size:19
Alignment explanation
Indices: 1308332--1308394 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1308322 TGGTTGTCGA
**
1308332 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1308351 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1308370 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1308389 GTTACT
1 GGTACT
1308395 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1312529 original size:34 final size:34
Alignment explanation
Indices: 1312460--1312677 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
1312450 AAGTGGGAGA
* * *
1312460 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1312493 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1312527 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1312560 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1312594 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1312628 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1312662 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1312678 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1312643 original size:68 final size:67
Alignment explanation
Indices: 1312460--1312679 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
1312450 AAGTGGGAGA
* * * * *
1312460 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1312525 CC
66 CC
* * * *
1312527 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1312592 CC
66 CC
* * *
1312594 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
1312659 GCC
65 GCC
1312662 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1312680 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:1315039 original size:22 final size:22
Alignment explanation
Indices: 1315014--1315056 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1315004 TTTATATTTT
1315014 ATATATTATAGTCATTTTCATA
1 ATATATTATAGTCATTTTCATA
* *
1315036 ATATATTATGGTTATTTTCAT
1 ATATATTATAGTCATTTTCAT
1315057 CACGTAAAAA
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:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (22 bp):
ATATATTATAGTCATTTTCATA
Found at i:1315192 original size:16 final size:15
Alignment explanation
Indices: 1315157--1315212 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
1315147 TTAAATAAAC
1315157 AAAAAT-TAAGTTTT-
1 AAAAATATAA-TTTTA
1315171 AAAAATATATATTTTA
1 AAAAATATA-ATTTTA
*
1315187 AAAAATA-AATTATGA
1 AAAAATATAATT-TTA
1315202 AAAAATATAAT
1 AAAAATATAAT
1315213 ATAAGTGGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 9 0.25
15 16 0.44
16 11 0.31
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (15 bp):
AAAAATATAATTTTA
Found at i:1315448 original size:17 final size:17
Alignment explanation
Indices: 1315426--1315460 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1315416 AAAATTTTAA
1315426 TATACTTATATCAAAAT
1 TATACTTATATCAAAAT
1315443 TATACTTATATCAAAAT
1 TATACTTATATCAAAAT
1315460 T
1 T
1315461 TATGGATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (17 bp):
TATACTTATATCAAAAT
Found at i:1316809 original size:22 final size:22
Alignment explanation
Indices: 1316764--1316809 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1316754 GAAAGCTAGT
* *
1316764 TTTATATTTTTTTACAATTCAA
1 TTTATATATTTTTACAATTAAA
**
1316786 TTTATATATTTTTATTATTAAA
1 TTTATATATTTTTACAATTAAA
1316808 TT
1 TT
1316810 GTAATTTAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATATATTTTTACAATTAAA
Found at i:1322923 original size:20 final size:20
Alignment explanation
Indices: 1322898--1322941 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1322888 AAGAATTGAA
*
1322898 GAGGGATACAAGAGAAGGAT
1 GAGGGATACAAGAGAAGGAG
**
1322918 GAGGGATACTTGAGAAGGAG
1 GAGGGATACAAGAGAAGGAG
1322938 GAGG
1 GAGG
1322942 AAGCCTCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.45, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAAGGAG
Found at i:1327515 original size:20 final size:20
Alignment explanation
Indices: 1327472--1327515 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1327462 AAGAATTGAA
*
1327472 GAGGGATACAAGAGAAGGAT
1 GAGGGATACAAGAGAAGGAG
** *
1327492 GAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAAGGAG
1327512 GAGG
1 GAGG
1327516 AAGCCTCTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.48, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAAGGAG
Found at i:1328114 original size:27 final size:27
Alignment explanation
Indices: 1328084--1328173 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 27
1328074 GTACAATCAT
1328084 ATATACATGTATATTATATATATACTA
1 ATATACATGTATATTATATATATACTA
* *
1328111 ATATAC-GGTACAGTCATATATATATACTAATAA
1 ATATACATGT--A-T-AT-TATATATA-TACT-A
1328144 TATATACATGTATATTATATATAATACTA
1 -ATATACATGTATATTATATAT-ATACTA
1328173 A
1 A
1328174 ACAAAATCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 19
0.68 0.06 0.26
Matches are distributed among these distances:
26 2 0.04
27 6 0.12
28 2 0.04
29 2 0.04
30 12 0.24
31 11 0.22
32 4 0.08
33 2 0.04
34 6 0.12
35 2 0.04
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (27 bp):
ATATACATGTATATTATATATATACTA
Found at i:1328151 original size:29 final size:30
Alignment explanation
Indices: 1328098--1328169 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
1328088 ACATGTATAT
*
1328098 TATATATATACTAAT-ATACGGTACA-GTCA
1 TATATATATACTAATAATACGATACATGT-A
*
1328127 TATATATATACTAATAATA-TATACATGTA
1 TATATATATACTAATAATACGATACATGTA
1328156 TAT-TATATA-TAATA
1 TATATATATACTAATA
1328170 CTAAACAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.13
28 6 0.15
29 23 0.59
30 5 0.13
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (30 bp):
TATATATATACTAATAATACGATACATGTA
Found at i:1329663 original size:20 final size:20
Alignment explanation
Indices: 1329638--1329687 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1329628 TATTTGTATT
*
1329638 ATTTTTTTATATATTT-TTTA
1 ATTTTTTTATA-ATTTATTAA
*
1329658 ATTTTTTGATAATTTATTAA
1 ATTTTTTTATAATTTATTAA
*
1329678 ATTTTATTAT
1 ATTTTTTTAT
1329688 TTAAAAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
ATTTTTTTATAATTTATTAA
Found at i:1330786 original size:232 final size:232
Alignment explanation
Indices: 1330361--1330828 Score: 731
Period size: 232 Copynumber: 2.0 Consensus size: 232
1330351 ACTAAAGCTG
* * * * * * *
1330361 TCAAGTAGGTATATTGTGCTCCTCTCGACGTAATGCTATGATCAGTTCTTTGTAATAATCTAAAG
1 TCAAATAGGTAAATTGTGCTCCTCTCCAAGTAATGCCATGATCAGTTCTTTGCAAAAATCTAAAG
** * *
1330426 GTAGTGGCCTTCATCTTGAGCAACTTCTTCACGCACCATCTACTATTGTGATAGATTGAGACTTT
66 ACAGTGACCTTCATCTTGAGCAACTTCTTCACGCACCATCTACTATTGTGAGAGATTGAGACTTT
* * *
1330491 CTATAGATCACCTCTTAAAGATGTATGATTGAGTCCATATAATCCATAAAAATCCAGCTTGAAAA
131 CTATAGATCACCCCTTAAAGATGTATGATTAAGTCCATATAATCCATAAAAATCCAACTTGAAAA
1330556 AACAAAGATCACAAATAACGTAGGATCAAGCTTGATT
196 AACAAAGATCACAAATAACGTAGGATCAAGCTTGATT
*
1330593 TCAAATAGGTAAATTGTGCTCCTCTCCAAGTAATGCCATGATCAGTTCTTTGCAAAAATCTAATG
1 TCAAATAGGTAAATTGTGCTCCTCTCCAAGTAATGCCATGATCAGTTCTTTGCAAAAATCTAAAG
* * * *
1330658 ACAGTGACCTTCATCTTGAGCAACTTTTTCATGCACCATCTATTATTGTGAGAGATTGGGACTTT
66 ACAGTGACCTTCATCTTGAGCAACTTCTTCACGCACCATCTACTATTGTGAGAGATTGAGACTTT
1330723 -TCATAGATCACCCCTTAAAGATGTATGATTAAGTCCATATAATCCATAAAAATCCAACTTGAAA
131 CT-ATAGATCACCCCTTAAAGATGTATGATTAAGTCCATATAATCCATAAAAATCCAACTTGAAA
* *
1330787 AAACAAAGATCGCAAATGACGTAGGATCAAGCTTGATT
195 AAACAAAGATCACAAATAACGTAGGATCAAGCTTGATT
1330825 TCAA
1 TCAA
1330829 GAATGAATGT
Statistics
Matches: 214, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
231 1 0.00
232 213 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (232 bp):
TCAAATAGGTAAATTGTGCTCCTCTCCAAGTAATGCCATGATCAGTTCTTTGCAAAAATCTAAAG
ACAGTGACCTTCATCTTGAGCAACTTCTTCACGCACCATCTACTATTGTGAGAGATTGAGACTTT
CTATAGATCACCCCTTAAAGATGTATGATTAAGTCCATATAATCCATAAAAATCCAACTTGAAAA
AACAAAGATCACAAATAACGTAGGATCAAGCTTGATT
Found at i:1331112 original size:34 final size:34
Alignment explanation
Indices: 1331069--1331164 Score: 165
Period size: 34 Copynumber: 2.8 Consensus size: 34
1331059 AAGTGTGTTA
1331069 GGTGAAGAATGTTAGGTGTGTTAGGTGATGTATTT
1 GGTG-AGAATGTTAGGTGTGTTAGGTGATGTATTT
* *
1331104 GGTGAGAATATTAGGTGTGTTAGGTGATGTGTTT
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
1331138 GGTGAGAATGTTAGGTGTGTTAGGTGA
1 GGTGAGAATGTTAGGTGTGTTAGGTGA
1331165 GAATGTTAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
34 54 0.93
35 4 0.07
ACGTcount: A:0.22, C:0.00, G:0.40, T:0.39
Consensus pattern (34 bp):
GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
Found at i:1331163 original size:22 final size:22
Alignment explanation
Indices: 1331131--1331186 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
1331121 TGTTAGGTGA
*
1331131 TGTGTTTGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
1331153 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
1331175 TGTGTTAGGTGA
1 TGTGTTAGGTGA
1331187 TGTATTTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (22 bp):
TGTGTTAGGTGAGAATGTTAGG
Found at i:1331174 original size:56 final size:56
Alignment explanation
Indices: 1331104--1331215 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
1331094 TGATGTATTT
* *
1331104 GGTGAGAATATTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATATTAGGTGTGTTAGGTGATGTATTTAGTGAGAATGTTAGGTGTGTTA
*
1331160 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTAGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATATTAGGTGTGTTAGGTGATGTATTTAGTGAGAATGTTAGGTGTGTTA
1331216 ACATGTATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.39
Consensus pattern (56 bp):
GGTGAGAATATTAGGTGTGTTAGGTGATGTATTTAGTGAGAATGTTAGGTGTGTTA
Found at i:1331195 original size:22 final size:23
Alignment explanation
Indices: 1331055--1331188 Score: 102
Period size: 22 Copynumber: 5.9 Consensus size: 23
1331045 TTAATTTCTT
* *
1331055 TGTTAAGTGTGTTAGGTGAAGAA
1 TGTTAGGTGTGTTAGGTGATGAA
*
1331078 TGTTAGGTGTGTTAGGTGATGTA
1 TGTTAGGTGTGTTAGGTGATGAA
* *
1331101 T-TT-GGTGAGAATATTAGGTG-TG-T
1 TGTTAGGT--G--TGTTAGGTGATGAA
* * *
1331124 TAGGT-GATGTGTTTGGTGA-GAA
1 T-GTTAGGTGTGTTAGGTGATGAA
1331146 TGTTAGGTGTGTTAGGTGA-GAA
1 TGTTAGGTGTGTTAGGTGATGAA
1331168 TGTTAGGTGTGTTAGGTGATG
1 TGTTAGGTGTGTTAGGTGATG
1331189 TATTTAGTGA
Statistics
Matches: 88, Mismatches: 13, Indels: 20
0.73 0.11 0.17
Matches are distributed among these distances:
21 13 0.15
22 37 0.42
23 25 0.28
24 2 0.02
25 11 0.12
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.40
Consensus pattern (23 bp):
TGTTAGGTGTGTTAGGTGATGAA
Found at i:1332384 original size:51 final size:51
Alignment explanation
Indices: 1332308--1332409 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
1332298 AACAAAAGAA
1332308 GAAATCAATCTCGTGGTCAGAACAGAGAAAATACACGAGAGAATACCCAAT
1 GAAATCAATCTCGTGGTCAGAACAGAGAAAATACACGAGAGAATACCCAAT
1332359 GAAATCAATCTCGTGGTCAGAACAGAGAAAATACACGAGAGAATACCCAAT
1 GAAATCAATCTCGTGGTCAGAACAGAGAAAATACACGAGAGAATACCCAAT
1332410 ATAGGGGAGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.16
Consensus pattern (51 bp):
GAAATCAATCTCGTGGTCAGAACAGAGAAAATACACGAGAGAATACCCAAT
Found at i:1335909 original size:34 final size:34
Alignment explanation
Indices: 1335866--1335961 Score: 165
Period size: 34 Copynumber: 2.8 Consensus size: 34
1335856 AAGTGTGTTA
1335866 GGTGAAGAATGTTAGGTGTGTTAGGTGATGTATTT
1 GGTG-AGAATGTTAGGTGTGTTAGGTGATGTATTT
* *
1335901 GGTGAGAATATTAGGTGTGTTAGGTGATGTGTTT
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
1335935 GGTGAGAATGTTAGGTGTGTTAGGTGA
1 GGTGAGAATGTTAGGTGTGTTAGGTGA
1335962 GAATGTTAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
34 54 0.93
35 4 0.07
ACGTcount: A:0.22, C:0.00, G:0.40, T:0.39
Consensus pattern (34 bp):
GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTT
Found at i:1335960 original size:22 final size:22
Alignment explanation
Indices: 1335928--1335983 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
1335918 TGTTAGGTGA
*
1335928 TGTGTTTGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
1335950 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
1335972 TGTGTTAGGTGA
1 TGTGTTAGGTGA
1335984 TGTATTTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (22 bp):
TGTGTTAGGTGAGAATGTTAGG
Found at i:1335971 original size:56 final size:56
Alignment explanation
Indices: 1335901--1336012 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
1335891 TGATGTATTT
*
1335901 GGTGAGAATATTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATATTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
*
1335957 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATATTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1336013 ACATGTATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (56 bp):
GGTGAGAATATTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
Found at i:1338445 original size:25 final size:24
Alignment explanation
Indices: 1338417--1338541 Score: 106
Period size: 27 Copynumber: 4.9 Consensus size: 24
1338407 AAGCCACCCA
1338417 TTTGTTTGTCAAAAATGGTGGTTATT
1 TTTGTTTGTCAAAAATGGTGG-T-TT
1338443 TTGTGTTTGTCAAAAATGGTGGTTT
1 TT-TGTTTGTCAAAAATGGTGGTTT
* * *
1338468 CCTTTGTATTTGTCAAATATGGAGGCTTG
1 --TTTG--TTTGTCAAAAATGGTGG-TTT
* * *
1338497 TTTATTTGTCAAAATTGGTGGCTT
1 TTTGTTTGTCAAAAATGGTGGTTT
* *
1338521 GTTGTTTGTCAAAATTGGTGG
1 TTTGTTTGTCAAAAATGGTGG
1338542 CTAATTTTTA
Statistics
Matches: 82, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
24 20 0.24
25 16 0.20
26 5 0.06
27 24 0.29
28 15 0.18
29 2 0.02
ACGTcount: A:0.21, C:0.07, G:0.26, T:0.46
Consensus pattern (24 bp):
TTTGTTTGTCAAAAATGGTGGTTT
Found at i:1338528 original size:24 final size:25
Alignment explanation
Indices: 1338474--1338543 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
1338464 GTTTCCTTTG
*
1338474 TATTTGTC-AAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGTGGCTTGTT
1338499 TATTTGTCAAAATTGGTGGCTTG-T
1 TATTTGTCAAAATTGGTGGCTTGTT
*
1338523 TGTTTGTCAAAATTGGTGGCT
1 TATTTGTCAAAATTGGTGGCT
1338544 AATTTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 17 0.40
26 4 0.10
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (25 bp):
TATTTGTCAAAATTGGTGGCTTGTT
Found at i:1343039 original size:25 final size:24
Alignment explanation
Indices: 1343011--1343135 Score: 106
Period size: 27 Copynumber: 4.9 Consensus size: 24
1343001 AAGCCACCCA
1343011 TTTGTTTGTCAAAAATGGTGGTTATT
1 TTTGTTTGTCAAAAATGGTGG-T-TT
1343037 TTGTGTTTGTCAAAAATGGTGGTTT
1 TT-TGTTTGTCAAAAATGGTGGTTT
* * *
1343062 CCTTTGTATTTGTCAAATATGGAGGCTTG
1 --TTTG--TTTGTCAAAAATGGTGG-TTT
* * *
1343091 TTTATTTGTCAAAATTGGTGGCTT
1 TTTGTTTGTCAAAAATGGTGGTTT
* *
1343115 GTTGTTTGTCAAAATTGGTGG
1 TTTGTTTGTCAAAAATGGTGG
1343136 CTAATTTTTA
Statistics
Matches: 82, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
24 20 0.24
25 16 0.20
26 5 0.06
27 24 0.29
28 15 0.18
29 2 0.02
ACGTcount: A:0.21, C:0.07, G:0.26, T:0.46
Consensus pattern (24 bp):
TTTGTTTGTCAAAAATGGTGGTTT
Found at i:1343122 original size:24 final size:25
Alignment explanation
Indices: 1343068--1343137 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
1343058 GTTTCCTTTG
*
1343068 TATTTGTC-AAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGTGGCTTGTT
1343093 TATTTGTCAAAATTGGTGGCTTG-T
1 TATTTGTCAAAATTGGTGGCTTGTT
*
1343117 TGTTTGTCAAAATTGGTGGCT
1 TATTTGTCAAAATTGGTGGCT
1343138 AATTTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 17 0.40
26 4 0.10
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (25 bp):
TATTTGTCAAAATTGGTGGCTTGTT
Found at i:1344967 original size:26 final size:26
Alignment explanation
Indices: 1344916--1344967 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1344906 ATAAAATTAT
*
1344916 ATATATTAATTTTAAAAATATTTTTA
1 ATATATTAATTTTAAAAATATATTTA
* *
1344942 ATATTTTAATTTTTAATAATA-ATTTA
1 ATATATTAA-TTTTAAAAATATATTTA
1344968 GATTTATAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATATATTAATTTTAAAAATATATTTA
Found at i:1345448 original size:2 final size:2
Alignment explanation
Indices: 1345443--1345467 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1345433 TTATATAGGT
1345443 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1345468 GAAAAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1345789 original size:16 final size:18
Alignment explanation
Indices: 1345770--1345803 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1345760 AAATCTAACA
1345770 ATTAATT-TAT-TAATAT
1 ATTAATTATATATAATAT
1345786 ATTAATTATATATAATAT
1 ATTAATTATATATAATAT
1345804 TATAAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAATTATATATAATAT
Found at i:1346328 original size:21 final size:21
Alignment explanation
Indices: 1346304--1346343 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1346294 TTTAAAAAAT
1346304 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
1346325 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
1346344 AATAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:1347207 original size:34 final size:34
Alignment explanation
Indices: 1347154--1347368 Score: 218
Period size: 34 Copynumber: 6.4 Consensus size: 34
1347144 TAATTTATTG
** *
1347154 TTGATTAAAT-GGTGATTTGGTAATTTATCATTA
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTA
* * ** *
1347187 TTGATTAAATGGGTGATTTGGTGGTTTGTCATTG
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTA
* * *
1347221 TTGACTAAATGGGAGATTTGGTAGCTTACCATTG
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTA
****
1347255 TTGATTAAATGAAAAATTTGGTAGCTTACCATTA
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTA
* *
1347289 TTGATTAAATAGGTGATTTGGTGGCTTACCATTA
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTA
* * * *
1347323 TTGACTAAAT-GGTAGATTTGGTAGGTTGCCATTG
1 TTGATTAAATGGGT-GATTTGGTAGCTTACCATTA
1347357 TTGATTAAATGG
1 TTGATTAAATGG
1347369 TGGTTTTTAC
Statistics
Matches: 152, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
33 13 0.09
34 138 0.91
35 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (34 bp):
TTGATTAAATGGGTGATTTGGTAGCTTACCATTA
Found at i:1347327 original size:102 final size:101
Alignment explanation
Indices: 1347150--1347367 Score: 301
Period size: 102 Copynumber: 2.1 Consensus size: 101
1347140 TTAATAATTT
*** * * * * *
1347150 ATTGTTGATTAAATGGTGATTTGGTAATTTATCATTATTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGAAAATTTGGTAACTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTA
* *
1347215 TCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTATTGACTAAATGGGAGATTTGGTAGCTTACC
*
1347251 ATTGTTGATTAAATGAAAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-AAAATTTGGTAACTTACCATTATTGATTAAATAGGTGATTTGGTGGCTT
* * *
1347316 ACCATTATTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTATTGACTAAATGGGAGATTTGGTAGCTTACC
1347353 ATTGTTGATTAAATG
1 ATTGTTGATTAAATG
1347368 GTGGTTTTTA
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
101 15 0.15
102 87 0.85
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.42
Consensus pattern (101 bp):
ATTGTTGATTAAATGAAAATTTGGTAACTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTA
CCATTATTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1351833 original size:34 final size:34
Alignment explanation
Indices: 1351776--1351994 Score: 271
Period size: 34 Copynumber: 6.5 Consensus size: 34
1351766 AAATGGGAGA
*
1351776 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1351809 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1351843 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* ** *
1351877 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACT
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1351911 ATTATTGATTAAATAGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1351945 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1351979 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1351995 TGGTTTTTAC
Statistics
Matches: 159, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
33 17 0.11
34 141 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1351930 original size:102 final size:101
Alignment explanation
Indices: 1351776--1351994 Score: 330
Period size: 102 Copynumber: 2.2 Consensus size: 101
1351766 AAATGGGAGA
** * * * * *
1351776 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTA
1351841 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
1351877 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACTATTATTGATTAAATAGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTT
* * *
1351942 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1351979 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1351995 TGGTTTTTAC
Statistics
Matches: 106, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 16 0.15
102 90 0.85
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1353629 original size:16 final size:16
Alignment explanation
Indices: 1353608--1353648 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1353598 ATTAAGCTTC
* *
1353608 AAAATATATATTTTAA
1 AAAATATAAATTATAA
1353624 AAAATATAAATTATAA
1 AAAATATAAATTATAA
1353640 AAAATATAA
1 AAAATATAA
1353649 TATATGCGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATATAAATTATAA
Found at i:1353904 original size:19 final size:18
Alignment explanation
Indices: 1353865--1353905 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1353855 TAAAAAAAAT
1353865 TAAT-ATATTTATATCAA
1 TAATCATATTTATATCAA
*
1353882 -AATCATATTTATTTTCAA
1 TAATCATATTTA-TATCAA
1353900 TAATCA
1 TAATCA
1353906 CCTTGAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 7 0.35
18 5 0.25
19 5 0.25
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATCATATTTATATCAA
Found at i:1355273 original size:22 final size:22
Alignment explanation
Indices: 1355225--1355266 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1355215 AAGTTATTTT
*
1355225 TATATTTTTATAATTAAATCTA
1 TATATTTTTATAATTAAATATA
* *
1355247 TATATTTTTATTATTCAATA
1 TATATTTTTATAATTAAATA
1355267 ATAATATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATTTTTATAATTAAATATA
Found at i:1356726 original size:2 final size:2
Alignment explanation
Indices: 1356721--1356777 Score: 57
Period size: 2 Copynumber: 29.5 Consensus size: 2
1356711 TAGTACAATC
* *
1356721 AT AT AT AT AT AC ACT A- AT AT -T AT AT AT AT AC AT AT AT AT -T
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1356761 TT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1356778 CTAAAAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
1 3 0.07
2 42 0.91
3 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1356744 original size:19 final size:19
Alignment explanation
Indices: 1356722--1356777 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1356712 AGTACAATCA
1356722 TATATATATACACTA-ATAT
1 TATATATATACA-TATATAT
1356741 TATATATATACATATATAT
1 TATATATATACATATATAT
* *
1356760 TTTATATATATATATATA
1 TATATATATACATATATA
1356778 CTAAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 2 0.06
19 32 0.94
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATATATACATATATAT
Found at i:1356991 original size:18 final size:17
Alignment explanation
Indices: 1356948--1356995 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1356938 TCCAAATCTG
* *
1356948 TTTAAAAAATTATTTAT
1 TTTAAAAAATTATTAAA
*
1356965 TTCTTAAAAATTATATAAA
1 TT-TAAAAAATTAT-TAAA
1356984 TTTAAAAAATTA
1 TTTAAAAAATTA
1356996 CTCACTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 2 0.08
18 19 0.76
19 4 0.16
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAAAAATTATTAAA
Found at i:1358477 original size:21 final size:21
Alignment explanation
Indices: 1358440--1358479 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1358430 ATTGCTTAAT
*
1358440 AAAATATTTATATTTTTTTTC
1 AAAATATTTATAATTTTTTTC
1358461 AAAAT-TTTAATAATTTTTT
1 AAAATATTT-ATAATTTTTT
1358480 ATTTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
AAAATATTTATAATTTTTTTC
Found at i:1359557 original size:28 final size:29
Alignment explanation
Indices: 1359503--1359562 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
1359493 AAAAGTCAAC
1359503 TATTTATTATAAAAATTATTAAAATAA-A
1 TATTTATTATAAAAATTATTAAAATAATA
* *
1359531 TATTTATTAT-TAAATTATTACATATAATA
1 TATTTATTATAAAAATTATTA-AAATAATA
1359560 TAT
1 TAT
1359563 AATAAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 9 0.32
28 15 0.54
29 4 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
TATTTATTATAAAAATTATTAAAATAATA
Found at i:1359988 original size:23 final size:22
Alignment explanation
Indices: 1359941--1359988 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1359931 TAACATCAAA
* * *
1359941 TATTTTAAAAAAATTAATTATT
1 TATTATAAAAAAATTAATAAAT
1359963 TATTATAAAAATAATTAATAAAT
1 TATTATAAAAA-AATTAATAAAT
1359986 TAT
1 TAT
1359989 CGAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTATAAAAAAATTAATAAAT
Found at i:1362419 original size:15 final size:15
Alignment explanation
Indices: 1362399--1362428 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1362389 AGGTCTAGAA
1362399 CGTTAATCTTAGTAT
1 CGTTAATCTTAGTAT
1362414 CGTTAATCTTAGTAT
1 CGTTAATCTTAGTAT
1362429 ACATATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
CGTTAATCTTAGTAT
Found at i:1362796 original size:20 final size:20
Alignment explanation
Indices: 1362771--1362818 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1362761 TTAATAAAAA
* * *
1362771 AATTAATTTTTTATTTTTAT
1 AATTAAATTTATATCTTTAT
1362791 AATTAAATTTATATCTTTAT
1 AATTAAATTTATATCTTTAT
*
1362811 TATTAAAT
1 AATTAAAT
1362819 AATAATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTAAATTTATATCTTTAT
Found at i:1362982 original size:34 final size:34
Alignment explanation
Indices: 1362915--1363130 Score: 292
Period size: 34 Copynumber: 6.4 Consensus size: 34
1362905 AATTCAATCC
* * *
1362915 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1362948 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
1362982 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
1363015 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1363049 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1363083 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1363117 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1363131 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 40 0.25
34 122 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1363096 original size:68 final size:67
Alignment explanation
Indices: 1362915--1363132 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
1362905 AATTCAATCC
* * * * *
1362915 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
1362980 AT
66 AT
* * * *
1362982 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
1363047 AT
66 AT
* * *
1363049 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
1363114 CAT
65 CAT
1363117 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
1363133 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:1363488 original size:19 final size:19
Alignment explanation
Indices: 1363432--1363494 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1363422 TGGTTGTCGA
**
1363432 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1363451 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1363470 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1363489 GTTACT
1 GGTACT
1363495 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1367629 original size:34 final size:34
Alignment explanation
Indices: 1367560--1367777 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
1367550 AAGTGGGAGA
* * *
1367560 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1367593 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1367627 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1367660 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1367694 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1367728 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1367762 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1367778 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1367743 original size:68 final size:67
Alignment explanation
Indices: 1367560--1367779 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
1367550 AAGTGGGAGA
* * * * *
1367560 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1367625 CC
66 CC
* * * *
1367627 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1367692 CC
66 CC
* * *
1367694 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
1367759 GCC
65 GCC
1367762 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1367780 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:1369481 original size:27 final size:27
Alignment explanation
Indices: 1369442--1369508 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
1369432 CATCTCTTTT
* *
1369442 ATATTTTAT-TATATAT-AGTACAATC
1 ATATTATATATATATATAAGTACAATA
* *
1369467 ATATATATATATATATATAAGTAGATTA
1 ATAT-TATATATATATATAAGTACAATA
1369495 ATATTATATATATA
1 ATATTATATATATA
1369509 CTAAGGAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 4 0.11
26 4 0.11
27 17 0.49
28 10 0.29
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (27 bp):
ATATTATATATATATATAAGTACAATA
Done.