Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004862.1 Hibiscus syriacus cultivar Beakdansim tig00010968_pilon, whole genome shotgun sequence
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: 2846896
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:1030813 original size:95 final size:94
Alignment explanation
Indices: 1030600--1030818 Score: 201
Period size: 95 Copynumber: 2.3 Consensus size: 94
1030590 GGCCCTTCAG
* * *
1030600 TATCGATACCCCTACCATAGTATCGATACTACCGAACTTTGGTATCGATACCCCTTCCAGTATCA
1 TATCGATACCCTTACCATAGTATCGATACTACCGAACTTTGGTACCGATACCCCTTACAGTATCA
* *
1030665 ATACCAAACTTAGATTCAATGTGACACAA
66 ATACAAAAATTAGATTCAATGTGACACAA
* * * * **
1030694 TATCGATACCCCATT-CTATGGTATCGATACTA-CTATA-TTATGGTACCGATACCTCTATATGG
1 TATCGATA-CCC-TTACCATAGTATCGATACTACCGA-ACTT-TGGTACCGATACCCCT-TACAG
* * * * * *
1030756 TATCGATACAAAAATTAGGTTCGATGTTACCCGA
61 TATCAATACAAAAATTAGATTCAATGTGACACAA
* *
1030790 TATCGATACCCTTACCATTGTATCAATAC
1 TATCGATACCCTTACCATAGTATCGATAC
1030819 CACTTCGTTC
Statistics
Matches: 99, Mismatches: 20, Indels: 11
0.76 0.15 0.08
Matches are distributed among these distances:
94 14 0.14
95 48 0.48
96 37 0.37
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.31
Consensus pattern (94 bp):
TATCGATACCCTTACCATAGTATCGATACTACCGAACTTTGGTACCGATACCCCTTACAGTATCA
ATACAAAAATTAGATTCAATGTGACACAA
Found at i:1040057 original size:17 final size:17
Alignment explanation
Indices: 1040032--1040075 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1040022 GCCACTTCCA
1040032 TTGCTCCGATCGACGCC
1 TTGCTCCGATCGACGCC
* *
1040049 TTTCTCCGATCGACGTC
1 TTGCTCCGATCGACGCC
1040066 TTGCTCCGAT
1 TTGCTCCGAT
1040076 ATTTTGACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.11, C:0.36, G:0.20, T:0.32
Consensus pattern (17 bp):
TTGCTCCGATCGACGCC
Found at i:1045690 original size:2 final size:2
Alignment explanation
Indices: 1045683--1045708 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1045673 GTACAAAAAC
1045683 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
1045709 TTAAATACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1046973 original size:3 final size:3
Alignment explanation
Indices: 1046965--1047040 Score: 89
Period size: 3 Copynumber: 24.0 Consensus size: 3
1046955 ATTATATATG
* *
1046965 TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA CATG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA TTA TTA TTA TTA
*
1047012 TATA TATA TTA TTA ATA TTA TTA TTA TTA
1 T-TA T-TA TTA TTA TTA TTA TTA TTA TTA
1047041 AATAATATTA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
3 53 0.83
4 11 0.17
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1047005 original size:17 final size:17
Alignment explanation
Indices: 1046966--1047050 Score: 74
Period size: 16 Copynumber: 5.3 Consensus size: 17
1046956 TTATATATGT
*
1046966 TATTATTATT-ATTA-T
1 TATTATTATTAATTACA
1046981 TATTATTATTAATTACA
1 TATTATTATTAATTACA
* *
1046998 TGTTATTATT-ATTATA
1 TATTATTATTAATTACA
*
1047014 TATATATTATTAA-TA-T
1 TAT-TATTATTAATTACA
*
1047030 TATTATTATTAAATA-A
1 TATTATTATTAATTACA
1047046 TATTA
1 TATTA
1047051 CAAAGCCCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
15 19 0.32
16 21 0.36
17 18 0.31
18 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (17 bp):
TATTATTATTAATTACA
Found at i:1047005 original size:26 final size:28
Alignment explanation
Indices: 1046950--1047048 Score: 100
Period size: 26 Copynumber: 3.6 Consensus size: 28
1046940 CTGTTTTTGT
* *
1046950 TATTAATTATATATGT-TATTATTATTAT
1 TATT-ATTATATATATATATTAATATTAT
*
1046978 TATTATTAT-TAT-TA-ATTACATGTTAT
1 TATTATTATATATATATATTA-ATATTAT
1047004 TATTATTATATATATATTATTAATATTAT
1 TATTATTATATATATA-TATTAATATTAT
*
1047033 TATTATTAAATA-ATAT
1 TATTATTATATATATAT
1047049 TACAAAGCCC
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
25 5 0.08
26 17 0.28
27 9 0.15
28 9 0.15
29 17 0.28
30 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (28 bp):
TATTATTATATATATATATTAATATTAT
Found at i:1050822 original size:14 final size:15
Alignment explanation
Indices: 1050795--1050825 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1050785 TATATACCTT
1050795 TTGCATACATTTGCA
1 TTGCATACATTTGCA
1050810 TTGCATA-ATTTGCA
1 TTGCATACATTTGCA
1050824 TT
1 TT
1050826 CTCATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (15 bp):
TTGCATACATTTGCA
Found at i:1055623 original size:249 final size:249
Alignment explanation
Indices: 1055179--1055865 Score: 1088
Period size: 249 Copynumber: 2.8 Consensus size: 249
1055169 ATCTTTTCCA
* *
1055179 AAAATAAAATTTTTGAAAAGTAAGAAGTCTCTTACTCAGTAAATTATTTATCAAGAATTTGTAAA
1 AAAATCAAATTTTTGAAAAGTAAGAAGTCTCTTACTCAGTAAATTATTTATCACGAATTTGTAAA
* *
1055244 TCCTTCGGGTCATCTGTATGTCTTTCGAGCATGATATTTAAATCCTTCGGGTCATCTGTCAGTCT
66 TCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTCAGTCT
* * **
1055309 TTCGAACCAGATGATAAGTCATTAGGATCATCCGTCAAACCTTTGGGTAGGATGTTTACATATGA
131 TTCGAGCCAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACATATGA
* *
1055374 TTTTCGCATGAAAATGAGATAGCAATTTTCAAAGTTTCTTATTTAATGTTCTAG
196 TTTTCGCATGAAAATGAGATAGCAATTTTCAAAGTTTCTCATTTAATGCTCTAG
*
1055428 AAAATCAAATTTTTGAAAAGTAAGAAGTCTCTTACTCAGAAAATTATTTATCACGAATTTGTAAA
1 AAAATCAAATTTTTGAAAAGTAAGAAGTCTCTTACTCAGTAAATTATTTATCACGAATTTGTAAA
* * * *
1055493 TCCATCGGGTCATCTGTAAGCCTTTCGATCATGATGTTTAAATCCTTCGGGTCATCTGTCAGTTT
66 TCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTCAGTCT
1055558 TTCGAGCCAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACATATGA
131 TTCGAGCCAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACATATGA
** *
1055623 TTTTCGCATGAAAATGAGATAGTGATTTTCAAAGTTTCTCGTTTAATGCTCTAG
196 TTTTCGCATGAAAATGAGATAGCAATTTTCAAAGTTTCTCATTTAATGCTCTAG
* * *
1055677 AAAATCAAATTTTTAAAAAGTAAGAAGTCTCTTACTCTGTAAATTATTTATCACGAATTTGTATA
1 AAAATCAAATTTTTGAAAAGTAAGAAGTCTCTTACTCAGTAAATTATTTATCACGAATTTGTAAA
** * *
1055742 TCCTTCAAGTCATCTTTAAGTCTTTCGAGCATGATGTTTAAATCCTTTGGGTCATCTG-CAGTCT
66 TCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTCAGTCT
* * * * * *
1055806 TTCGAGCAAAATGATAAGTCCTTAGGGCCATTCGTCAGACCTTTGGGCAGTATGTTTACA
131 TTCGAGCCAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACA
1055866 CTCTCTAATT
Statistics
Matches: 402, Mismatches: 36, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
248 59 0.15
249 343 0.85
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (249 bp):
AAAATCAAATTTTTGAAAAGTAAGAAGTCTCTTACTCAGTAAATTATTTATCACGAATTTGTAAA
TCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTCAGTCT
TTCGAGCCAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACATATGA
TTTTCGCATGAAAATGAGATAGCAATTTTCAAAGTTTCTCATTTAATGCTCTAG
Found at i:1056054 original size:3 final size:3
Alignment explanation
Indices: 1056046--1056098 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
1056036 ATTATATATG
* * * *
1056046 TTA TTA TTA TTA TTAA TTA CATG TTA TTA TTA TTA TTA ATA ATA TTA
1 TTA TTA TTA TTA TT-A TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
1056093 TTA TTA
1 TTA TTA
1056099 AATAATATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
3 38 0.90
4 4 0.10
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1056073 original size:23 final size:21
Alignment explanation
Indices: 1056021--1056098 Score: 86
Period size: 23 Copynumber: 3.6 Consensus size: 21
1056011 TAGTTCATGT
* *
1056021 ATGTTTTTGTTATTAATT-ATA
1 ATGTTATTATTATT-ATTAATA
1056042 TATGTTATTATTATTATTAATTA
1 -ATGTTATTATTATTATTAA-TA
1056065 CATGTTATTATTATTATTAATA
1 -ATGTTATTATTATTATTAATA
*
1056087 ATATTATTATTA
1 ATGTTATTATTA
1056099 AATAATATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
21 14 0.28
22 15 0.30
23 21 0.42
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (21 bp):
ATGTTATTATTATTATTAATA
Found at i:1056093 original size:15 final size:16
Alignment explanation
Indices: 1056073--1056108 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
1056063 TACATGTTAT
1056073 TATTATTATT-AATAA
1 TATTATTATTAAATAA
1056088 TATTATTATTAAATAA
1 TATTATTATTAAATAA
1056104 TATTA
1 TATTA
1056109 CAAAGCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATTATTAAATAA
Found at i:1060058 original size:24 final size:24
Alignment explanation
Indices: 1060023--1060073 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
1060013 ATCAGTAAAG
*
1060023 AAATTGAAGCACTC-AAAAGAATA
1 AAATTGAAGCACTCAAAAAGAAGA
1060046 AAATTGCAAGCACTCAAAAAGAAGA
1 AAATTG-AAGCACTCAAAAAGAAGA
1060071 AAA
1 AAA
1060074 AAAGAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.24
24 8 0.32
25 11 0.44
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (24 bp):
AAATTGAAGCACTCAAAAAGAAGA
Found at i:1077921 original size:27 final size:26
Alignment explanation
Indices: 1077891--1077976 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 26
1077881 GTATCGGCAC
1077891 TAAGTGTGCAACCCATGGAATTCATAA
1 TAAGTGTG-AACCCATGGAATTCATAA
* * * * * * *
1077918 TAAGTTTATGAA-CGATAGTATTGACAC
1 TAAG--TGTGAACCCATGGAATTCATAA
1077945 TAAGTGTGTAACCCATGGAATTCATAA
1 TAAGTGTG-AACCCATGGAATTCATAA
1077972 TAAGT
1 TAAGT
1077977 TTATGAACGA
Statistics
Matches: 41, Mismatches: 14, Indels: 8
0.65 0.22 0.13
Matches are distributed among these distances:
25 3 0.07
26 2 0.05
27 31 0.76
28 2 0.05
29 3 0.07
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (26 bp):
TAAGTGTGAACCCATGGAATTCATAA
Found at i:1078008 original size:54 final size:54
Alignment explanation
Indices: 1077458--1077993 Score: 625
Period size: 54 Copynumber: 9.9 Consensus size: 54
1077448 TTACATCACC
* *
1077458 AAGTGTACAACCCACGAAATTCATAATAAGTTTATGATCGACCGTATCGACACT
1 AAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACACT
* * * ** *
1077512 AAGTGTGCAACCCGCGAAATTCATAATATA-TTTTTGAACGAGCGTATCGGTACC
1 AAGTGTGCAACCCACGAAATTCATAATA-AGTTTATGAACGACCGTATCGACACT
* *
1077566 AAGTGTGCAACCCACAAAATTCATAATATGTTTATGAACGACCGTATCAGTACA--
1 AAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATC-G-ACACT
* *
1077620 AAGTGTGCAACACACGAAATTCATAATATA-TTTATGAACGACTGTATC-AGCACT
1 AAGTGTGCAACCCACGAAATTCATAATA-AGTTTATGAACGACCGTATCGA-CACT
* * * *
1077674 AAGTGTGCAACCCACGAAATTCATAATATGCTTATGAACGACCGCATCGGCACT
1 AAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACACT
* * * * * *
1077728 AAGTGTGCAGCCCACGGAATTCATAGTAAGTTCATGAACGACCATATCGACATT
1 AAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACACT
* * *
1077782 AAGTGTGCAATCCCCACGGAATTCATAACAAGTTTATGAACGACCGTATTGACACT
1 AAGTGTGCAA--CCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACACT
* * * *
1077838 AAGTGTGCATCCCAC-AGAATTCAAAATAAGTTTATGAACGACTGTATCGGCACT
1 AAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCGTATCGACACT
* * ** *
1077892 AAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGATAGTATTGACACT
1 AAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACACT
* * *
1077946 AAGTGTGTAACCCATGGAATTCATAATAAGTTTATGAACGACCGTATC
1 AAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATC
1077994 AATACTACGT
Statistics
Matches: 407, Mismatches: 61, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
51 1 0.00
52 2 0.00
54 354 0.87
55 2 0.00
56 48 0.12
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (54 bp):
AAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACACT
Found at i:1080449 original size:20 final size:20
Alignment explanation
Indices: 1080424--1080468 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1080414 TGCGGCTTTT
*
1080424 TTTTTTTACTTATAGCGGCG
1 TTTTTTTACTTATAGCGGCA
1080444 TTTTTTTACTTATAGCGGCA
1 TTTTTTTACTTATAGCGGCA
1080464 TTTTT
1 TTTTT
1080469 AAGCGCCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.56
Consensus pattern (20 bp):
TTTTTTTACTTATAGCGGCA
Found at i:1083002 original size:24 final size:21
Alignment explanation
Indices: 1082980--1083019 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1082970 AGGAGCCAAG
* *
1082980 AAATATTTTCTATTAGGATCC
1 AAATATCTTCTATTAGGAGCC
1083001 AAATATCTTCTATTAGGAG
1 AAATATCTTCTATTAGGAG
1083020 TCAAGACGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (21 bp):
AAATATCTTCTATTAGGAGCC
Found at i:1084677 original size:16 final size:16
Alignment explanation
Indices: 1084656--1084690 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1084646 CTAATCACTC
1084656 TTAAATT-ATAAAACTT
1 TTAAATTGATAAAA-TT
1084672 TTAAATTGATAAAATT
1 TTAAATTGATAAAATT
1084688 TTA
1 TTA
1084691 TGAGAGCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (16 bp):
TTAAATTGATAAAATT
Found at i:1096177 original size:14 final size:14
Alignment explanation
Indices: 1096158--1096189 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1096148 TGATTTCTGA
1096158 ATGTTTAAAAAAAT
1 ATGTTTAAAAAAAT
1096172 ATGTTTAAAAAAAT
1 ATGTTTAAAAAAAT
1096186 ATGT
1 ATGT
1096190 ATCTTTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (14 bp):
ATGTTTAAAAAAAT
Found at i:1099173 original size:18 final size:17
Alignment explanation
Indices: 1099147--1099185 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1099137 AAACCAAACA
*
1099147 CAAACATCAAAACCTTCT
1 CAAACATC-AAACCCTCT
*
1099165 CAAAGATCAAACCCTCT
1 CAAACATCAAACCCTCT
1099182 CAAA
1 CAAA
1099186 TTATCTCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.46, C:0.33, G:0.03, T:0.18
Consensus pattern (17 bp):
CAAACATCAAACCCTCT
Found at i:1099432 original size:20 final size:21
Alignment explanation
Indices: 1099407--1099445 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1099397 ATTGTTAATA
1099407 TTTTATCTA-TTTA-ATTTTTT
1 TTTTAT-TAGTTTATATTTTTT
1099427 TTTTATTAGTTTATATTTT
1 TTTTATTAGTTTATATTTT
1099446 AATCTCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 10 0.59
21 5 0.29
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (21 bp):
TTTTATTAGTTTATATTTTTT
Found at i:1103833 original size:12 final size:12
Alignment explanation
Indices: 1103816--1103843 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1103806 TGATGGTTCC
1103816 TCGACATTTAGG
1 TCGACATTTAGG
1103828 TCGACATTTAGG
1 TCGACATTTAGG
1103840 TCGA
1 TCGA
1103844 ATAAGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (12 bp):
TCGACATTTAGG
Found at i:1105641 original size:57 final size:57
Alignment explanation
Indices: 1105544--1105656 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
1105534 TTATACCTGC
* * *
1105544 AATTATTCAAATTATCATTTGTTCACATAAAACATATACTCATAGTATTTCACATAG
1 AATTACTCAAATTATCATTTATTCACATAAAACATATACTCATAGCATTTCACATAG
1105601 AATTACTCAAATTATCATTTATTCACATAGAATA-AT-TACTCATAGCATTTCACATA
1 AATTACTCAAATTATCATTTATTCACATA-AA-ACATATACTCATAGCATTTCACATA
1105657 TAGCATTTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
57 46 0.90
58 4 0.08
59 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.38
Consensus pattern (57 bp):
AATTACTCAAATTATCATTTATTCACATAAAACATATACTCATAGCATTTCACATAG
Found at i:1105661 original size:14 final size:14
Alignment explanation
Indices: 1105642--1105670 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1105632 ATAATTACTC
1105642 ATAGCATTTCACAT
1 ATAGCATTTCACAT
1105656 ATAGCATTTCACAT
1 ATAGCATTTCACAT
1105670 A
1 A
1105671 ACAAAGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (14 bp):
ATAGCATTTCACAT
Found at i:1109789 original size:15 final size:15
Alignment explanation
Indices: 1109769--1109810 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1109759 GCTAATTTGT
1109769 GGCATTTACATTATG
1 GGCATTTACATTATG
*
1109784 GGCATTTATATTATG
1 GGCATTTACATTATG
*
1109799 GGCATTTGCATT
1 GGCATTTACATT
1109811 TGAATGGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.43
Consensus pattern (15 bp):
GGCATTTACATTATG
Found at i:1110832 original size:13 final size:14
Alignment explanation
Indices: 1110798--1110834 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
1110788 CTTTCACTTT
1110798 CATATTCA--TTTA
1 CATATTCATTTTTA
1110810 CATATTCATTTTTA
1 CATATTCATTTTTA
1110824 CAT-TTCATTTT
1 CATATTCATTTT
1110835 CATAACAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 8 0.35
14 7 0.30
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.57
Consensus pattern (14 bp):
CATATTCATTTTTA
Found at i:1112488 original size:20 final size:21
Alignment explanation
Indices: 1112463--1112507 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1112453 TCCATCCCAA
1112463 TACCTC-AATAGATCCACCAT
1 TACCTCTAATAGATCCACCAT
*
1112483 TACCTCTTATAGATCCACCAT
1 TACCTCTAATAGATCCACCAT
1112504 TACC
1 TACC
1112508 ACTTAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (21 bp):
TACCTCTAATAGATCCACCAT
Found at i:1112496 original size:21 final size:21
Alignment explanation
Indices: 1112470--1112512 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1112460 CAATACCTCA
*
1112470 ATAGATCCACCATTACCTCTT
1 ATAGATCCACCATTACCACTT
1112491 ATAGATCCACCATTACCACTT
1 ATAGATCCACCATTACCACTT
1112512 A
1 A
1112513 AGTCACTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.30
Consensus pattern (21 bp):
ATAGATCCACCATTACCACTT
Found at i:1117733 original size:6 final size:6
Alignment explanation
Indices: 1117722--1117748 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1117712 AGGATGAGTA
1117722 ATTTTG ATTTTG ATTTTG ATTTTG ATT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATT
1117749 CTATTCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.67
Consensus pattern (6 bp):
ATTTTG
Found at i:1121337 original size:30 final size:30
Alignment explanation
Indices: 1121295--1121363 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
1121285 ATAAGATCAT
1121295 GTTAT-TTGTCATTAAGTTGTTTAGTGGTCA
1 GTTATGTT-TCATTAAGTTGTTTAGTGGTCA
*
1121325 GTTATGTTTCATTTAGTTGTTTAGTGGTCA
1 GTTATGTTTCATTAAGTTGTTTAGTGGTCA
*
1121355 TTTATGTTT
1 GTTATGTTT
1121364 GACACTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 34 0.94
31 2 0.06
ACGTcount: A:0.17, C:0.06, G:0.22, T:0.55
Consensus pattern (30 bp):
GTTATGTTTCATTAAGTTGTTTAGTGGTCA
Found at i:1123613 original size:175 final size:178
Alignment explanation
Indices: 1123408--1123766 Score: 517
Period size: 175 Copynumber: 2.0 Consensus size: 178
1123398 AATATGAAAG
* *
1123408 AAACAAAGTGTAGTAAATCAACATGCTTTAAAAGGAAATTTAAGTAAAGAAAAAAAGAATATAGT
1 AAACAAAGGGTAGTAAATCAACACGCTTTAAAAGGAAATTTAAGTAAAGAAAAAAAGAATATAGT
*
1123473 CAAAGGAAGCAAGCGACAAAATTAAAGGAAAATAAAAGGT-TA-GAAT-AAATATAACTAATTTT
66 CAAAGGAAGCAAACGACAAAATTAAAGGAAAATAAAAGGTATATGAATAAAATATAACTAATTTT
* * *
1123535 ATGTAATTAAGAACAAATTTGGAAAATATTAAAATAATAAATGTTAAT
131 ATGAAATTAAGAACAAACTTGGAAAATATTAAAATAATAAATGGTAAT
* * * *
1123583 AAACAAGGGGTAGTAAATCAACACGCTTTAAAAGGAAATTTAAGTAACGGAAAAAAGGATATAGT
1 AAACAAAGGGTAGTAAATCAACACGCTTTAAAAGGAAATTTAAGTAAAGAAAAAAAGAATATAGT
* *
1123648 CAAAGGAAGCAAACGACAAAATTAAAGGAAAATAAAAGGTAAAATATTAATAGAAAAATATAGCT
66 CAAAGGAAGCAAACGACAAAATTAAAGGAAAATAAAAGGT---ATATGAAT---AAAATATAACT
* *
1123713 AATTTTATGAAATTGAGAACAGACTTGGAAAATATTAAAATAATAAATGGTAAT
125 AATTTTATGAAATTAAGAACAAACTTGGAAAATATTAAAATAATAAATGGTAAT
1123767 TAAGTAAAGT
Statistics
Matches: 161, Mismatches: 14, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
175 98 0.61
179 2 0.01
180 3 0.02
184 58 0.36
ACGTcount: A:0.54, C:0.06, G:0.16, T:0.24
Consensus pattern (178 bp):
AAACAAAGGGTAGTAAATCAACACGCTTTAAAAGGAAATTTAAGTAAAGAAAAAAAGAATATAGT
CAAAGGAAGCAAACGACAAAATTAAAGGAAAATAAAAGGTATATGAATAAAATATAACTAATTTT
ATGAAATTAAGAACAAACTTGGAAAATATTAAAATAATAAATGGTAAT
Found at i:1125797 original size:59 final size:59
Alignment explanation
Indices: 1125612--1125797 Score: 273
Period size: 59 Copynumber: 3.2 Consensus size: 59
1125602 TCTTTCCATT
* * * ** *
1125612 GGAAATGTTGATCCCTCGAGTGATGCGTTGTTGATTCGAAGTGTTGTTAATCGAGCAAA
1 GGAAATGTTAACCCCTCTAGTGGGGCGTTGTTGATTCGAAGTGTTGTGAATCGAGCAAA
* * * *
1125671 GGAAATGTGAACCCCTCTAGTGGGGTGTTATTGATTCGAAGTGTTGTGAATCAAGCAAA
1 GGAAATGTTAACCCCTCTAGTGGGGCGTTGTTGATTCGAAGTGTTGTGAATCGAGCAAA
*
1125730 GGAAATGTTAACCCCTCTAGTGGGGCGTTGTTGACTCGAAGTGTTGTGAATCGAGCAAA
1 GGAAATGTTAACCCCTCTAGTGGGGCGTTGTTGATTCGAAGTGTTGTGAATCGAGCAAA
1125789 GGAAATGTT
1 GGAAATGTT
1125798 GAAAACATCC
Statistics
Matches: 112, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 112 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (59 bp):
GGAAATGTTAACCCCTCTAGTGGGGCGTTGTTGATTCGAAGTGTTGTGAATCGAGCAAA
Found at i:1126092 original size:41 final size:41
Alignment explanation
Indices: 1126029--1126153 Score: 153
Period size: 41 Copynumber: 3.0 Consensus size: 41
1126019 AAATGTTGAA
* * *
1126029 AACATCTTGCCCGAAAGTCTTATGGATGGCCCGAAGGACTT
1 AACATCTTGCTCGAAAGACTTATAGATGGCCCGAAGGACTT
* * * *
1126070 ATCATCTTACTCGAAAGACTTATAGATGACCCGAAGGATTT
1 AACATCTTGCTCGAAAGACTTATAGATGGCCCGAAGGACTT
*
1126111 AAACAT-TATGCTCGAAAGACTTATCGATGGCCCGAAGGACTT
1 -AACATCT-TGCTCGAAAGACTTATAGATGGCCCGAAGGACTT
1126153 A
1 A
1126154 CATATCAAGA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 36 0.51
42 34 0.49
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (41 bp):
AACATCTTGCTCGAAAGACTTATAGATGGCCCGAAGGACTT
Found at i:1126151 original size:228 final size:227
Alignment explanation
Indices: 1125702--1126153 Score: 699
Period size: 228 Copynumber: 2.0 Consensus size: 227
1125692 GGGGTGTTAT
* *
1125702 TGATTCGAAGTGTTGTGAATCAAGCAAAGGAAATGTTAACCCCTCTAGTGGGGCGTTGTTGACTC
1 TGATTCAAAGTGTTGTGAATCAAGCAAAGGAAATGTTAACCCCTCTAGTGGGGCGTTGCTGACTC
*
1125767 GAAGTGTTGTGAATCGAGCAAAGGAAATGTTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCC
66 GAAGTGTTGTGAATCGAGCAAAGGAAATGTTGAAAACATCCTGCCCGAAAGTCTTATAGATGGCC
* ** * * *
1125832 TGAAGGACTTATCATCTTGTTCGAAAGACTTTTAGATGACCTGAAGGATTTAAGCATTATGCTCG
131 CGAAGGACTTATCATCTTACTCGAAAGACTTATAGATGACCCGAAGGATTTAAACATTATGCTCG
*
1125897 AAAGATTTACTGATGGACCAAAGGACTTAAGC
196 AAAGACTTACTGATGGACCAAAGGACTTAAGC
* * * * *
1125929 TGATTCAAAGTGTTGTGAATCGAGCAATAGGAAGTGTTAACCCCTCTGGTGGGGTGTTGCTGATT
1 TGATTCAAAGTGTTGTGAATCAAGCAA-AGGAAATGTTAACCCCTCTAGTGGGGCGTTGCTGACT
* * *
1125994 TGAAGTGTTGTGAATCGAGCAAAGGAAATGTTGAAAACATCTTGCCCGAAAGTCTTATGGATGGC
65 CGAAGTGTTGTGAATCGAGCAAAGGAAATGTTGAAAACATCCTGCCCGAAAGTCTTATAGATGGC
1126059 CCGAAGGACTTATCATCTTACTCGAAAGACTTATAGATGACCCGAAGGATTTAAACATTATGCTC
130 CCGAAGGACTTATCATCTTACTCGAAAGACTTATAGATGACCCGAAGGATTTAAACATTATGCTC
* *
1126124 GAAAGACTTA-TCGATGGCCCGAAGGACTTA
195 GAAAGACTTACT-GATGGACCAAAGGACTTA
1126154 CATATCAAGA
Statistics
Matches: 203, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
227 26 0.13
228 177 0.87
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (227 bp):
TGATTCAAAGTGTTGTGAATCAAGCAAAGGAAATGTTAACCCCTCTAGTGGGGCGTTGCTGACTC
GAAGTGTTGTGAATCGAGCAAAGGAAATGTTGAAAACATCCTGCCCGAAAGTCTTATAGATGGCC
CGAAGGACTTATCATCTTACTCGAAAGACTTATAGATGACCCGAAGGATTTAAACATTATGCTCG
AAAGACTTACTGATGGACCAAAGGACTTAAGC
Found at i:1126344 original size:52 final size:52
Alignment explanation
Indices: 1126272--1126548 Score: 139
Period size: 52 Copynumber: 5.1 Consensus size: 52
1126262 TGGAAATAAT
* *
1126272 CATCAAGAAACCCATGAAAATCAGGCTTAGTTTCTAAAAAATAATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTAAAAAATAATTTGAAAA
* * * * * * *
1126324 CATCAAGAAACCCCTAAAAATTATGCTTAACTTCTTTTAAAAATTCAA-TAGAAAT
1 CATCAAGAAACCCCTAAAAATCAGGCTT-A-GT-TTCTAAAAAAT-AATTTGAAAA
* **** ** *
1126379 CTTTATCAA-AAAACCCTAAAAATCAATAATAGTTTCTAAAAGCTTATTTGAAAA
1 C---ATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTAAAAAATAATTTGAAAA
* * * ***
1126433 CATCAAGAAACCCCAAAAAATTAGGCTTAGCTTCT-TTTAATAATTCATTGAAAATCA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTAAAAAATAA-T--TTG-AAA--A
* * * *
1126490 TCATCAAGAAACCCCTAAAAACCA-GCTTAGTTTCTTTAAAAATTATTTTGAAAG
1 -CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTC--TAAAAAATAATTTGAAAA
1126544 CATCA
1 CATCA
1126549 TGTCGTTTGT
Statistics
Matches: 160, Mismatches: 46, Indels: 37
0.66 0.19 0.15
Matches are distributed among these distances:
51 7 0.04
52 45 0.28
53 7 0.04
54 18 0.11
55 19 0.12
56 6 0.04
57 28 0.17
58 25 0.16
59 2 0.01
60 3 0.02
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.30
Consensus pattern (52 bp):
CATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTAAAAAATAATTTGAAAA
Found at i:1126521 original size:109 final size:109
Alignment explanation
Indices: 1126214--1126548 Score: 372
Period size: 109 Copynumber: 3.0 Consensus size: 109
1126204 TTTCAGTTAT
* * * *
1126214 CATCAAGAAAACCCCTAAAAGTTAAGCTTAGCTTC-TTTAAAAATTCTTTGGAAATAATCATCAA
1 CATCAAG-AAACCCCTAAAAATTAAGCTTAGCTTCTTTTAAAAATTCATTGAAAATCATCATCAA
* *
1126278 GAAACCCATGAAAATCAGGCTTAGTTTCTAAAAAATAATTTGAAAA
65 GAAACCCCTAAAAATCA-GCTTAGTTTCTAAAAAATAATTTGAAAA
* * * * *
1126324 CATCAAGAAACCCCTAAAAATTATGCTTAACTTCTTTTAAAAATTCAAT-AGAAATCTTTATCAA
1 CATCAAGAAACCCCTAAAAATTAAGCTTAGCTTCTTTTAAAAATTCATTGA-AAATCATCATCAA
* * ** *
1126388 -AAAACCCTAAAAATCA-ATAATAGTTTCTAAAAGCTTATTTGAAAA
65 GAAACCCCTAAAAATCAGCT--TAGTTTCTAAAAAATAATTTGAAAA
* * *
1126433 CATCAAGAAACCCCAAAAAATTAGGCTTAGCTTCTTTTAATAATTCATTGAAAATCATCATCAAG
1 CATCAAGAAACCCCTAAAAATTAAGCTTAGCTTCTTTTAAAAATTCATTGAAAATCATCATCAAG
* * * *
1126498 AAACCCCTAAAAACCAGCTTAGTTTCTTTAAAAATTATTTTGAAAG
66 AAACCCCTAAAAATCAGCTTAGTTTC--TAAAAAATAATTTGAAAA
1126544 CATCA
1 CATCA
1126549 TGTCGTTTGT
Statistics
Matches: 185, Mismatches: 31, Indels: 17
0.79 0.13 0.07
Matches are distributed among these distances:
107 1 0.01
109 121 0.65
110 44 0.24
111 19 0.10
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (109 bp):
CATCAAGAAACCCCTAAAAATTAAGCTTAGCTTCTTTTAAAAATTCATTGAAAATCATCATCAAG
AAACCCCTAAAAATCAGCTTAGTTTCTAAAAAATAATTTGAAAA
Found at i:1133917 original size:27 final size:27
Alignment explanation
Indices: 1133887--1133945 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
1133877 TGGCAGTGAA
1133887 TGGGGCAGAGGGATGGTGGCTAAGGGT
1 TGGGGCAGAGGGATGGTGGCTAAGGGT
*
1133914 TGGGGTAGAGGGATGGTGGCTAAGGGT
1 TGGGGCAGAGGGATGGTGGCTAAGGGT
1133941 TGGGG
1 TGGGG
1133946 AAGAAGAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.05, G:0.58, T:0.20
Consensus pattern (27 bp):
TGGGGCAGAGGGATGGTGGCTAAGGGT
Found at i:1133958 original size:27 final size:27
Alignment explanation
Indices: 1133901--1133960 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1133891 GCAGAGGGAT
* * * *
1133901 GGTGGCTAAGGGTTGGGGTAGAGGGAT
1 GGTGGCTAAGGGTTGGGGAAGAAGAAG
1133928 GGTGGCTAAGGGTTGGGGAAGAAGAAG
1 GGTGGCTAAGGGTTGGGGAAGAAGAAG
1133955 GGTGGC
1 GGTGGC
1133961 CTATGGTTGG
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:0.22, C:0.05, G:0.55, T:0.18
Consensus pattern (27 bp):
GGTGGCTAAGGGTTGGGGAAGAAGAAG
Found at i:1134088 original size:18 final size:19
Alignment explanation
Indices: 1134049--1134088 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1134039 TAGGGTTTTA
*
1134049 GTTGGGTTTTTTGGGCCTG
1 GTTGGGTTTTTTGGGCCAG
*
1134068 GTTGGG-TTTTTGGTCCAG
1 GTTGGGTTTTTTGGGCCAG
1134086 GTT
1 GTT
1134089 TTAGTTTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.03, C:0.10, G:0.40, T:0.47
Consensus pattern (19 bp):
GTTGGGTTTTTTGGGCCAG
Found at i:1135373 original size:12 final size:13
Alignment explanation
Indices: 1135344--1135378 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
1135334 CTGGACTAGT
1135344 GGGCATGACTTGG
1 GGGCATGACTTGG
1135357 GGGCATGACTT-G
1 GGGCATGACTTGG
1135369 GGGCATGACT
1 GGGCATGACT
1135379 CGGATGACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.17, C:0.17, G:0.43, T:0.23
Consensus pattern (13 bp):
GGGCATGACTTGG
Found at i:1137034 original size:36 final size:36
Alignment explanation
Indices: 1136943--1137040 Score: 94
Period size: 36 Copynumber: 2.7 Consensus size: 36
1136933 CAGTCAAAAT
* *
1136943 ATTTCTATCAGTTCCAGCAACCCT-AACAGCTTCAGA
1 ATTTCTAACAGTTTCAGCAA-CCTAAACAGCTTCAGA
* * *
1136979 ATTCCTAAAAG-TTCTAGCAACCTAAACAGTTTCCAG-
1 ATTTCTAACAGTTTC-AGCAACCTAAACAGCTT-CAGA
1137015 ATTTCTAACAGTTTCAGCAACTCTAA
1 ATTTCTAACAGTTTCAGCAAC-CTAA
1137041 CTATTTCAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
35 5 0.10
36 35 0.70
37 10 0.20
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.30
Consensus pattern (36 bp):
ATTTCTAACAGTTTCAGCAACCTAAACAGCTTCAGA
Found at i:1137039 original size:18 final size:18
Alignment explanation
Indices: 1136946--1137041 Score: 56
Period size: 18 Copynumber: 5.3 Consensus size: 18
1136936 TCAAAATATT
* *
1136946 TCTATCAGTTCCAGCAAC
1 TCTAACAGTTTCAGCAAC
* * *
1136964 CCTAACAGCTTCAG-AAT
1 TCTAACAGTTTCAGCAAC
*
1136981 TCCTAAAAG-TTCTAGCAAC
1 T-CTAACAGTTTC-AGCAAC
**
1137000 -CTAAACAGTTTCCAG-ATT
1 TCT-AACAGTTT-CAGCAAC
1137018 TCTAACAGTTTCAGCAAC
1 TCTAACAGTTTCAGCAAC
1137036 TCTAAC
1 TCTAAC
1137042 TATTTCAACT
Statistics
Matches: 57, Mismatches: 13, Indels: 16
0.66 0.15 0.19
Matches are distributed among these distances:
17 10 0.18
18 38 0.67
19 8 0.14
20 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.28
Consensus pattern (18 bp):
TCTAACAGTTTCAGCAAC
Found at i:1139237 original size:3 final size:3
Alignment explanation
Indices: 1139222--1139280 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
1139212 TATTTATATA
* * **
1139222 AAT AAT AAA AAT AAT AAT AAT GA- AAT AAT AATT AA- AGC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
1139266 AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT A
1139281 TTGCAAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1139289 original size:26 final size:28
Alignment explanation
Indices: 1139230--1139291 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
1139220 TAAATAATAA
*
1139230 AAATAATAATAATGAAATAATAATTAAAGC
1 AAATAATAATAATAAAATAATAATT--AGC
1139260 -AATAATAATAATAAAATAAT-ATT-GC
1 AAATAATAATAATAAAATAATAATTAGC
1139285 AAATAAT
1 AAATAAT
1139292 GATTAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.07
26 6 0.20
28 3 0.10
29 19 0.63
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (28 bp):
AAATAATAATAATAAAATAATAATTAGC
Found at i:1139357 original size:29 final size:29
Alignment explanation
Indices: 1139308--1139369 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
1139298 AATAAAAGGA
* *
1139308 ATTAAAAATATAGTAT-TAAAATGTAAAAT
1 ATTAAAAATATAATATCAAAAATG-AAAAT
1139337 ATTAAAAATA-AATAGTCAAAAATGAAAAT
1 ATTAAAAATATAATA-TCAAAAATGAAAAT
1139366 -TTAA
1 ATTAA
1139370 TGATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 7 0.24
29 16 0.55
30 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (29 bp):
ATTAAAAATATAATATCAAAAATGAAAAT
Found at i:1140506 original size:3 final size:3
Alignment explanation
Indices: 1140498--1140573 Score: 61
Period size: 3 Copynumber: 26.0 Consensus size: 3
1140488 CCTGTTTGTA
* *
1140498 AAT AAT AAT TAT -TT AAT AAT AAT -AT AAT -AT ATAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* **
1140540 AAT ATTT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1140574 TTAAGTAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
2 7 0.12
3 46 0.79
4 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:1140561 original size:22 final size:23
Alignment explanation
Indices: 1140498--1140559 Score: 54
Period size: 25 Copynumber: 2.6 Consensus size: 23
1140488 CCTGTTTGTA
* *
1140498 AATAATAATTATTTAATAATAATAT
1 AATAATAATAATATAAT-AT-ATAT
*
1140523 AAT-ATATATAATATAATAATATTT
1 AATAATA-ATAATATAAT-ATATAT
1140547 AATAATAATAATA
1 AATAATAATAATA
1140560 ATTTTAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 15 0.47
25 17 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAATAATAATATAATATATAT
Found at i:1140825 original size:76 final size:76
Alignment explanation
Indices: 1140727--1141740 Score: 1714
Period size: 76 Copynumber: 13.4 Consensus size: 76
1140717 GAGGTCTTAA
*
1140727 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
1140792 TGGCTTTTTGG
66 AGGCTTTTTGG
* * *
1140803 AAACATCATGCACTGCAGGACTTACAGATGATCCTAAGGTTTTTAAAACATCAAAAAGCTCCAGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1140868 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
1140879 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTTAAAACATTAAAAAGCTCCTGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1140944 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1140955 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
1141020 AGGCTTTTTGA
66 AGGCTTTTTGG
*
1141031 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
1141096 AGGTTTTTTGG
66 AGGCTTTTTGG
* * *
1141107 AAACATCATGTACTGCAGGACTTACAGATGACCCTAAGGTTTTTAAAACATCAAAAAGTTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1141172 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1141183 AAACATCATGCACTGCAGGACATAC--A--ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1141244 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1141255 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1141320 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
1141331 AAACATCATGCACTGCAGGACTTACTGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
1141396 AGGCTTTTTAG
66 AGGCTTTTTGG
1141407 AAACATCATGCACTGCAGGACTTACAGATGACCCTAA-GTCTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGT-TTTGAAAACATCAAAAAGCTCCCG
1141471 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
1141483 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1141548 AGGCTTTTTGG
66 AGGCTTTTTGG
1141559 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
1141624 AGGCTTTTTTG
66 AGGCTTTTTGG
* * *
1141635 AAACATCATGCACTGCATGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1141700 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1141711 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
1141741 TGAGAAATAG
Statistics
Matches: 882, Mismatches: 50, Indels: 12
0.93 0.05 0.01
Matches are distributed among these distances:
72 67 0.08
74 2 0.00
75 1 0.00
76 810 0.92
77 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1142441 original size:22 final size:22
Alignment explanation
Indices: 1142416--1142514 Score: 171
Period size: 22 Copynumber: 4.5 Consensus size: 22
1142406 AATAAAGCTT
1142416 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1142438 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1142460 TCTTCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1142482 TCATCTTTGAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1142504 TCATCTTTGAA
1 TCATCTTTGAA
1142515 GAGTGTAGAT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 72 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1142969 original size:54 final size:54
Alignment explanation
Indices: 1142882--1143037 Score: 224
Period size: 54 Copynumber: 2.9 Consensus size: 54
1142872 GACAACACTA
* *
1142882 GTTCGTAAAACATTTGACAGCGCATTCATCCTTTCTTGTGGTTTCTGCTCAGAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTGCTCAGAC
* * *
1142936 GTTTGTAAAACATTTGACAACACATTCAGCCTTTCTTGTGGTTTATGCTCAGAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTGCTCAGAC
* * *
1142990 GTTCGTAAAGCGTTTGACAACACATTCATCCTTT-TCTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCT-TGTGGTTTCTGC
1143038 CAAGATTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.01
54 89 0.99
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTGCTCAGAC
Found at i:1145294 original size:114 final size:114
Alignment explanation
Indices: 1145094--1145310 Score: 353
Period size: 114 Copynumber: 1.9 Consensus size: 114
1145084 GATCATGCAG
* **
1145094 TTCATCTTTCAATTCCAATGATTGGTTCTAGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTAATACCGAACCAGATCAGATAACTCAAAGA
*
1145159 ACACTTCCAGAAGATGCTATTGGGCCTCTTTATTTCTATTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTATTATGAGCAAA
* * * *
1145208 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTAATACCGAACCAGATCAGATAACTCATAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTAATACCGAACCAGATCAGATAACTCAAAGA
*
1145273 ATACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTA
66 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTA
1145311 CAACGAGAAT
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 94 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTAATACCGAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTATTATGAGCAAA
Found at i:1152499 original size:25 final size:25
Alignment explanation
Indices: 1152471--1152524 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1152461 TATTTATATA
1152471 AATAATAAAAAT-ATAATAATGAAAT
1 AATAATAAAAATAATAATAAT-AAAT
* *
1152496 AATAATTAAAGTAATAATAATAAAT
1 AATAATAAAAATAATAATAATAAAT
1152521 AATA
1 AATA
1152525 TTGCAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (25 bp):
AATAATAAAAATAATAATAATAAAT
Found at i:1152513 original size:15 final size:13
Alignment explanation
Indices: 1152471--1152524 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 13
1152461 TATTTATATA
1152471 AATAATAA-AAAT
1 AATAATAATAAAT
1152483 -ATAATAATGAAAT
1 AATAATAAT-AAAT
1152496 AATAAT--TAAAGT
1 AATAATAATAAA-T
1152508 AATAATAATAAAT
1 AATAATAATAAAT
1152521 AATA
1 AATA
1152525 TTGCAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
11 10 0.28
12 8 0.22
13 9 0.25
14 9 0.25
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:1152513 original size:37 final size:37
Alignment explanation
Indices: 1152471--1152542 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
1152461 TATTTATATA
1152471 AATAATAAAAATATAATAATG-AAATAATAATTAAAGT
1 AATAATAAAAA-ATAATAATGCAAATAATAATTAAAGT
* * *
1152508 AATAATAATAAATAATATTGCAAATAATGATTAAA
1 AATAATAAAAAATAATAATGCAAATAATAATTAAA
1152543 ATAAAAGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 8 0.26
37 23 0.74
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (37 bp):
AATAATAAAAAATAATAATGCAAATAATAATTAAAGT
Found at i:1152535 original size:25 final size:25
Alignment explanation
Indices: 1152470--1152524 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 25
1152460 TTATTTATAT
1152470 AAATAATAA--AAAT-ATAATAATG
1 AAATAATAATTAAATAATAATAATG
1152492 AAATAATAATTAAAGTAATAATAAT-
1 AAATAATAATTAAA-TAATAATAATG
1152517 AAATAATA
1 AAATAATA
1152525 TTGCAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 9 0.31
24 3 0.10
25 9 0.31
26 8 0.28
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (25 bp):
AAATAATAATTAAATAATAATAATG
Found at i:1152544 original size:12 final size:12
Alignment explanation
Indices: 1152470--1152546 Score: 54
Period size: 12 Copynumber: 6.5 Consensus size: 12
1152460 TTATTTATAT
1152470 AAATAATAA--A
1 AAATAATAATTA
*
1152480 AATATAATAA-TG
1 AA-ATAATAATTA
1152492 AAATAATAATTA
1 AAATAATAATTA
* *
1152504 AAGTAATAATAA
1 AAATAATAATTA
*
1152516 TAAATAAT-ATTGC
1 -AAATAATAATT-A
*
1152529 AAATAATGATTA
1 AAATAATAATTA
1152541 AAATAA
1 AAATAA
1152547 AAGGAATTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
10 2 0.04
11 14 0.26
12 28 0.53
13 9 0.17
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (12 bp):
AAATAATAATTA
Found at i:1152769 original size:2 final size:2
Alignment explanation
Indices: 1152762--1152811 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1152752 TTACCTAAAA
1152762 AT 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 AT
1152804 AT AT AT AT
1 AT AT AT AT
1152812 GCTGATAAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1153786 original size:3 final size:3
Alignment explanation
Indices: 1153778--1153853 Score: 52
Period size: 3 Copynumber: 26.0 Consensus size: 3
1153768 CCTGTTTGTA
* * *
1153778 AAT AAT AAT TAT -TT AAT AAT AAT -AT AAT -AT ATAT AAT -CT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* **
1153820 AAT ATTT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1153854 TTAAGTAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
2 6 0.11
3 45 0.80
4 5 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:1153804 original size:22 final size:23
Alignment explanation
Indices: 1153779--1153838 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
1153769 CTGTTTGTAA
*
1153779 ATAATAAT-T-ATTTAATAATAAT
1 ATAATAATATAATCTAATAAT-AT
1153801 ATAATATATATAATCTAATAATAT
1 ATAATA-ATATAATCTAATAATAT
*
1153825 TTAATAATAATAAT
1 ATAATAAT-ATAAT
1153839 AATTTTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 6 0.19
23 4 0.12
24 13 0.41
25 9 0.28
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAATAATATAATCTAATAATAT
Found at i:1157098 original size:35 final size:35
Alignment explanation
Indices: 1157008--1157098 Score: 101
Period size: 35 Copynumber: 2.6 Consensus size: 35
1156998 GTTAAAATAA
* *
1157008 CTTGTTGCTCAACTCATTGCTCGTTGCTCATTAAG
1 CTTGTTGCTCGACTCATTGCTCATTGCTCATTAAG
* * * ** *
1157043 CTCGCTACTCGACTTGTTGCTCATTGCTCGTTAAG
1 CTTGTTGCTCGACTCATTGCTCATTGCTCATTAAG
*
1157078 CTTGTTGCTTGACTCATTGCT
1 CTTGTTGCTCGACTCATTGCT
1157099 TGTTAAACTC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.41
Consensus pattern (35 bp):
CTTGTTGCTCGACTCATTGCTCATTGCTCATTAAG
Found at i:1158794 original size:44 final size:43
Alignment explanation
Indices: 1158746--1158888 Score: 125
Period size: 44 Copynumber: 3.3 Consensus size: 43
1158736 GACAATTTTA
*
1158746 TAGTGGCGTTTTTAGTCATAAACGTCGTAAATTATCTAACACTT
1 TAGTGGCATTTTTAGTCATAAACGTCGTAAATTATCTAA-ACTT
* * **
1158790 TAGTGGCATTTTCATAGT-A-AAACGCCGT-TATTGA-C-AATTTT
1 TAGTGGCATTTT--TAGTCATAAACGTCGTAAATT-ATCTAAACTT
*
1158831 ATAGTGGCATTTTTAGTCATAAACGTCGTAAAATATCTAAAACTT
1 -TAGTGGCATTTTTAGTCATAAACGTCGTAAATTATCT-AAACTT
* *
1158876 TAGTAGCTTTTTT
1 TAGTGGCATTTTT
1158889 TTAAAACGCC
Statistics
Matches: 77, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
40 4 0.05
41 3 0.04
42 23 0.30
43 7 0.09
44 31 0.40
45 5 0.06
46 4 0.05
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (43 bp):
TAGTGGCATTTTTAGTCATAAACGTCGTAAATTATCTAAACTT
Found at i:1158855 original size:42 final size:43
Alignment explanation
Indices: 1158732--1158860 Score: 124
Period size: 42 Copynumber: 3.0 Consensus size: 43
1158722 AAAATGCCAC
* *
1158732 TATTGACAATTTTATAGTGGCGTTTTTAGTCATAAACGTCGTA
1 TATTGACAATTTTATAGTGGCATTTTTAGTCATAAACGCCGTA
* **
1158775 AATT-ATCTAACACTT-TAGTGGCATTTTCATAGT-A-AAACGCCGT-
1 TATTGA-C-AA-TTTTATAGTGGCATTTT--TAGTCATAAACGCCGTA
*
1158818 TATTGACAATTTTATAGTGGCATTTTTAGTCATAAACGTCGTA
1 TATTGACAATTTTATAGTGGCATTTTTAGTCATAAACGCCGTA
1158861 AAATATCTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
40 4 0.06
41 3 0.04
42 23 0.34
43 8 0.12
44 22 0.33
45 3 0.04
46 4 0.06
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (43 bp):
TATTGACAATTTTATAGTGGCATTTTTAGTCATAAACGCCGTA
Found at i:1158907 original size:86 final size:85
Alignment explanation
Indices: 1158732--1158900 Score: 261
Period size: 86 Copynumber: 2.0 Consensus size: 85
1158722 AAAATGCCAC
* * * *
1158732 TATTGACAATTTTATAGTGGCGTTTTTAGTCATAAACGTCGTAAATTATCTAACACTTTAGTGGC
1 TATTGACAATTTTATAGTGGCATTTTTAGTCATAAACGTCGTAAAATATCTAAAACTTTAGTAGC
1158797 ATTTTCATAGTAAAACGCCGT
66 ATTTT-ATAGTAAAACGCCGT
1158818 TATTGACAATTTTATAGTGGCATTTTTAGTCATAAACGTCGTAAAATATCTAAAACTTTAGTAGC
1 TATTGACAATTTTATAGTGGCATTTTTAGTCATAAACGTCGTAAAATATCTAAAACTTTAGTAGC
**
1158883 -TTTT-TTTTAAAACGCCGT
66 ATTTTATAGTAAAACGCCGT
1158901 ATTTATTATG
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
83 12 0.16
85 4 0.05
86 61 0.79
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (85 bp):
TATTGACAATTTTATAGTGGCATTTTTAGTCATAAACGTCGTAAAATATCTAAAACTTTAGTAGC
ATTTTATAGTAAAACGCCGT
Found at i:1159045 original size:21 final size:21
Alignment explanation
Indices: 1159020--1159065 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1159010 TACTATTATC
1159020 CAACAAACATGACA-TCTATAA
1 CAACAAACATGA-ATTCTATAA
* *
1159041 CAACAAACTTTAATTCTATAA
1 CAACAAACATGAATTCTATAA
1159062 CAAC
1 CAAC
1159066 CAACTTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
CAACAAACATGAATTCTATAA
Found at i:1160953 original size:18 final size:18
Alignment explanation
Indices: 1160930--1160977 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
1160920 GTTGACTACT
1160930 TCATCTTCATCATTGGAA
1 TCATCTTCATCATTGGAA
1160948 TCATCTTCATCATTGGAA
1 TCATCTTCATCATTGGAA
1160966 TCATCTTCATCA
1 TCATCTTCATCA
1160978 CTCCAAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (18 bp):
TCATCTTCATCATTGGAA
Found at i:1162728 original size:21 final size:20
Alignment explanation
Indices: 1162684--1162734 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1162674 GCAGCCTTCG
*
1162684 TGCATGGATGCACGACAGGA
1 TGCATCGATGCACGACAGGA
* * *
1162704 TGCATTGATGCACAGCCATGA
1 TGCATCGATGCAC-GACAGGA
1162725 TGCATCGATG
1 TGCATCGATG
1162735 AATTAATTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCACGACAGGA
Found at i:1162805 original size:22 final size:23
Alignment explanation
Indices: 1162772--1162814 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1162762 ATAGATGCAC
1162772 TGCATTGTGCATGGATGCACTAG
1 TGCATTGTGCATGGATGCACTAG
*
1162795 TGCA-TGTGCATGGATTCACT
1 TGCATTGTGCATGGATGCACT
1162815 GCAGGGGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (23 bp):
TGCATTGTGCATGGATGCACTAG
Found at i:1162936 original size:29 final size:29
Alignment explanation
Indices: 1162915--1162972 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1162905 AAACTTTGAA
1162915 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
*
1162944 TAAATTCAATTCAAGTCTAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
1162973 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:1162966 original size:30 final size:30
Alignment explanation
Indices: 1162915--1162974 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1162905 AAACTTTGAA
1162915 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
*
1162944 TAAATTCAATTCAAGTCTAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1162975 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1164312 original size:12 final size:12
Alignment explanation
Indices: 1164297--1164321 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1164287 GAAAAATTCC
1164297 TGGATAAATTTG
1 TGGATAAATTTG
1164309 TGGATAAATTTG
1 TGGATAAATTTG
1164321 T
1 T
1164322 ACATGGGATT
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:0.00, G:0.24, T:0.44
Consensus pattern (12 bp):
TGGATAAATTTG
Found at i:1167287 original size:83 final size:81
Alignment explanation
Indices: 1167163--1167407 Score: 267
Period size: 83 Copynumber: 3.0 Consensus size: 81
1167153 GTCTGTTAGA
* * * ** *
1167163 AAAACGCCACTA-AGAACGAACTCTATTCCGATATTTCTACAAAAACACAGCTAAAGTACTACTC
1 AAAACGCCACTATA-AACAAACCCTATTACGGCATTTATACAAAAACACAGCTAAAGTACTACTC
1167227 TATCGCGACGTTTATTGG
65 TATCGC-ACGTTTATTGG
* *
1167245 AAAAACGCCACTATAAACAAACCCTATTATGGCATTTTTACAAAAACACAGCTAAAGTACTACTC
1 -AAAACGCCACTATAAACAAACCCTATTACGGCATTTATACAAAAACACAGCTAAAGTACTACTC
*
1167310 TATCGCAGCATTTATTGG
65 TATCGCA-CGTTTATTGG
* * * ** * ** * *
1167328 AAAATGCCACTATAAACTAACCCTATTGCGGTGTTTATATAAAAACACCTCAAAATTACTACTCT
1 AAAACGCCACTATAAACAAACCCTATTACGGCATTTATACAAAAACACAGCTAAAGTACTACTCT
1167393 ATCGCTACGTTTATT
66 ATCGC-ACGTTTATT
1167408 TAAGAAACGT
Statistics
Matches: 138, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
82 66 0.48
83 71 0.51
84 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (81 bp):
AAAACGCCACTATAAACAAACCCTATTACGGCATTTATACAAAAACACAGCTAAAGTACTACTCT
ATCGCACGTTTATTGG
Found at i:1168086 original size:2 final size:2
Alignment explanation
Indices: 1168079--1168126 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1168069 TTTATTGTTA
1168079 AT 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 AT
*
1168121 TT AT AT
1 AT AT AT
1168127 TCCATATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1175428 original size:8 final size:8
Alignment explanation
Indices: 1175415--1175473 Score: 52
Period size: 8 Copynumber: 7.1 Consensus size: 8
1175405 ATGTTCATTA
1175415 ATTTTAAT
1 ATTTTAAT
1175423 ATTTT-AT
1 ATTTTAAT
1175430 AATTTTAAT
1 -ATTTTAAT
1175439 A-TTTAAT
1 ATTTTAAT
1175446 ATTATTATAAT
1 A-T-TT-TAAT
1175457 ATATTT-AT
1 AT-TTTAAT
1175465 ATTTTAAT
1 ATTTTAAT
1175473 A
1 A
1175474 CCTAAAATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
7 12 0.27
8 18 0.41
9 3 0.07
10 6 0.14
11 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTTTAAT
Found at i:1175434 original size:16 final size:16
Alignment explanation
Indices: 1175413--1175473 Score: 70
Period size: 16 Copynumber: 3.7 Consensus size: 16
1175403 TTATGTTCAT
1175413 TAATTTTAATATTTTA
1 TAATTTTAATATTTTA
1175429 TAATTTTAATATTTAATA
1 TAATTTTAATATTT--TA
* *
1175447 TTATTATAATATATTTA
1 TAATTTTAATAT-TTTA
1175464 T-ATTTTAATA
1 TAATTTTAATA
1175474 CCTAAAATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
16 22 0.56
17 3 0.08
18 12 0.31
19 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTTAATATTTTA
Found at i:1176590 original size:19 final size:19
Alignment explanation
Indices: 1176566--1176616 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
1176556 TGAGCCTAGA
* *
1176566 GTGCATCGATGCATGATCT
1 GTGCATCGATACATGATAT
*
1176585 GTGCATCGGTACATGATAT
1 GTGCATCGATACATGATAT
*
1176604 GTGCATCGGTACA
1 GTGCATCGATACA
1176617 CAAAATGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (19 bp):
GTGCATCGATACATGATAT
Found at i:1176651 original size:84 final size:84
Alignment explanation
Indices: 1176520--1176681 Score: 211
Period size: 84 Copynumber: 1.9 Consensus size: 84
1176510 TACACTAGGG
* * * *
1176520 GTGCATCGGTACACTAATTACATTCAATGTTTCAAATGAGCCTAGAGTGCATCGATGCAT-GATC
1 GTGCATCGGTACACAAAATACATTCAATGTTTCAAATGAGCCAAGAGTGCATCGATGCATGGCT-
*
1176584 TGTGCATCGGTACATGATAT
65 TGTGCATCGCTACATGATAT
* * **
1176604 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAT-ATTCAAGAGTGCATCGATGCATGGCT
1 GTGCATCGGTACACAAAATACATTCAATGTTTC-AAATGAGCCAAGAGTGCATCGATGCATGGCT
1176668 TGTGCATCGCTACA
65 TGTGCATCGCTACA
1176682 CAAAATGCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 61 0.91
85 6 0.09
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (84 bp):
GTGCATCGGTACACAAAATACATTCAATGTTTCAAATGAGCCAAGAGTGCATCGATGCATGGCTT
GTGCATCGCTACATGATAT
Found at i:1177099 original size:27 final size:28
Alignment explanation
Indices: 1177049--1177103 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1177039 GAAAATCATT
* *
1177049 TTTGAAAAATAATTTTGTAAAATTACTC
1 TTTGAAAAACAAATTTGTAAAATTACTC
1177077 TTTGAAAAACAAATTT-TAAAATTACTC
1 TTTGAAAAACAAATTTGTAAAATTACTC
1177104 CCCTTACTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40
Consensus pattern (28 bp):
TTTGAAAAACAAATTTGTAAAATTACTC
Found at i:1179465 original size:44 final size:43
Alignment explanation
Indices: 1179410--1179502 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 43
1179400 AGAGTGCATT
* * * *
1179410 GATGCACATTCAA-GGAGTGCATCGGTGCACCTTTATGGTGTATC
1 GATGCACATTCAAGGGA-TGCATCGATG-AACTATATAGTGTATC
*
1179454 GATGTACATTCAAGGGATGCATCGATGAACTATATAGTGTATC
1 GATGCACATTCAAGGGATGCATCGATGAACTATATAGTGTATC
1179497 GATGCA
1 GATGCA
1179503 TTATGCACAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
43 18 0.43
44 21 0.50
45 3 0.07
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (43 bp):
GATGCACATTCAAGGGATGCATCGATGAACTATATAGTGTATC
Found at i:1185352 original size:65 final size:65
Alignment explanation
Indices: 1185258--1185414 Score: 174
Period size: 65 Copynumber: 2.4 Consensus size: 65
1185248 TACACTAGGG
* * * * **
1185258 GTGCATCAGTACACTAATTACATTCGATGTTTC-AAATGAGCCTGGAGTGCATCGATGCAT-GAT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAT-AGCCAAGAGTGCATCGATGCATGGAT
1185321 AT
65 -T
* * ** *
1185323 GTGCATTGGTACACAAAATGCATTTGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATAGCCAAGAGTGCATCGATGCATGGATT
*
1185388 GTGCATCGGTACTCAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
1185415 AATGGGTGTG
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
65 70 0.92
66 6 0.08
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATAGCCAAGAGTGCATCGATGCATGGATT
Found at i:1191319 original size:41 final size:40
Alignment explanation
Indices: 1191267--1191411 Score: 191
Period size: 41 Copynumber: 3.6 Consensus size: 40
1191257 AAGAAAATAC
* * *
1191267 TGGGGCATGCTGAAGGTCCATTTTAATCAGAAATAGAATG
1 TGGGACATGCTGAAAGCCCATTTTAATCAGAAATAGAATG
*
1191307 ATGGGACTTGCTGAAAGCCCATTTTAATCAGAAATAGAATG
1 -TGGGACATGCTGAAAGCCCATTTTAATCAGAAATAGAATG
*
1191348 TTGGGACATGCTGAAAGCCCATTTTAACCAGAAATAGAATG
1 -TGGGACATGCTGAAAGCCCATTTTAATCAGAAATAGAATG
* ** *
1191389 TGGGGCATTTTGAAAGCTCATTT
1 TGGGACATGCTGAAAGCCCATTT
1191412 CAGGCAAAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 19 0.20
41 74 0.80
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.28
Consensus pattern (40 bp):
TGGGACATGCTGAAAGCCCATTTTAATCAGAAATAGAATG
Found at i:1192879 original size:20 final size:20
Alignment explanation
Indices: 1192853--1192982 Score: 140
Period size: 20 Copynumber: 6.5 Consensus size: 20
1192843 ATTTCCCATG
* *
1192853 AATTTGTAAAAGCTCTGGAT
1 AATTTGTAAAACCTCTGGGT
* *
1192873 GATTTGTAAAAGCTCTGGGT
1 AATTTGTAAAACCTCTGGGT
1192893 AATTTGTAAAATCCTC-GGGT
1 AATTTGTAAAA-CCTCTGGGT
*
1192913 TATTTGTAAAACCTTCT-GGT
1 AATTTGTAAAACC-TCTGGGT
* *
1192933 TATTTGTAAGACCGT-TGGGT
1 AATTTGTAAAACC-TCTGGGT
*
1192953 CATTTGTAAAACCTCTGGGT
1 AATTTGTAAAACCTCTGGGT
1192973 AATTTGTAAA
1 AATTTGTAAA
1192983 TCCTTCAGGT
Statistics
Matches: 95, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.04
20 88 0.93
21 3 0.03
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (20 bp):
AATTTGTAAAACCTCTGGGT
Found at i:1192897 original size:40 final size:40
Alignment explanation
Indices: 1192853--1192999 Score: 149
Period size: 40 Copynumber: 3.7 Consensus size: 40
1192843 ATTTCCCATG
* * * *
1192853 AATTTGTAAAAGCTCTGGATGATTTGTAAAAGCTCTGGGT
1 AATTTGTAAAACCTCTGGGTCATTTGTAAAACCTCTGGGT
*
1192893 AATTTGTAAAATCCTC-GGGTTATTTGTAAAACCTTCT-GGT
1 AATTTGTAAAA-CCTCTGGGTCATTTGTAAAACC-TCTGGGT
* *
1192933 TATTTGTAAGACCGT-TGGGTCATTTGTAAAACCTCTGGGT
1 AATTTGTAAAACC-TCTGGGTCATTTGTAAAACCTCTGGGT
* *
1192973 AATTTGTAAATCCT-TCAGGTCATTTGT
1 AATTTGTAAAACCTCT-GGGTCATTTGT
1193000 CAGTCTTCGA
Statistics
Matches: 90, Mismatches: 11, Indels: 12
0.80 0.10 0.11
Matches are distributed among these distances:
39 7 0.08
40 77 0.86
41 6 0.07
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.39
Consensus pattern (40 bp):
AATTTGTAAAACCTCTGGGTCATTTGTAAAACCTCTGGGT
Found at i:1192938 original size:60 final size:60
Alignment explanation
Indices: 1192853--1192999 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 60
1192843 ATTTCCCATG
* * *
1192853 AATTTGTAAAAGC-TCTGGATGATTTGTAAAAGC-TCTGGGTAATTTGTAAAATCCTC-GGGT
1 AATTTGTAAAACCTTCTGG-TCATTTGTAAAACCGT-TGGGTAATTTGTAAAA-CCTCTGGGT
* * * *
1192913 TATTTGTAAAACCTTCTGGTTATTTGTAAGACCGTTGGGTCATTTGTAAAACCTCTGGGT
1 AATTTGTAAAACCTTCTGGTCATTTGTAAAACCGTTGGGTAATTTGTAAAACCTCTGGGT
* *
1192973 AATTTGTAAATCCTTCAGGTCATTTGT
1 AATTTGTAAAACCTTCTGGTCATTTGT
1193000 CAGTCTTCGA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 4 0.05
60 64 0.86
61 6 0.08
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.39
Consensus pattern (60 bp):
AATTTGTAAAACCTTCTGGTCATTTGTAAAACCGTTGGGTAATTTGTAAAACCTCTGGGT
Found at i:1192997 original size:20 final size:20
Alignment explanation
Indices: 1192874--1192999 Score: 107
Period size: 20 Copynumber: 6.3 Consensus size: 20
1192864 GCTCTGGATG
* *
1192874 ATTTGTAAAAGC-TCTGGGTA
1 ATTTGTAAAACCTTC-GGGTC
*
1192894 ATTTGTAAAATCC-TCGGGTT
1 ATTTGTAAAA-CCTTCGGGTC
* *
1192914 ATTTGTAAAACCTTCTGGTT
1 ATTTGTAAAACCTTCGGGTC
*
1192934 ATTTGTAAGACCGTT-GGGTC
1 ATTTGTAAAACC-TTCGGGTC
*
1192954 ATTTGTAAAACC-TCTGGGTA
1 ATTTGTAAAACCTTC-GGGTC
* *
1192974 ATTTGTAAATCCTTCAGGTC
1 ATTTGTAAAACCTTCGGGTC
1192994 ATTTGT
1 ATTTGT
1193000 CAGTCTTCGA
Statistics
Matches: 89, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 79 0.89
21 7 0.08
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTTGTAAAACCTTCGGGTC
Found at i:1193315 original size:36 final size:36
Alignment explanation
Indices: 1193264--1193402 Score: 190
Period size: 36 Copynumber: 3.8 Consensus size: 36
1193254 TTTCGATTAA
* *
1193264 ATCATGTTCAAACCTTCACGAAAGAGTAGTGAAGTCG
1 ATCATTTTC-AACCTTCACGGAAGAGTAGTGAAGTCG
*
1193301 ATCATTTTCGACCTTCACGGAAGAGTAGTGAAGTCG
1 ATCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCG
*
1193337 ATCATTTTCAACCTTCACGGAAGAGTAGTGAAGTTG
1 ATCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCG
* * *
1193373 ATCATTGTT-AACATCCACGGAAGAATAGTG
1 ATCATT-TTCAACCTTCACGGAAGAGTAGTG
1193403 GAAGCAAAAG
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
36 83 0.89
37 10 0.11
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (36 bp):
ATCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCG
Found at i:1195056 original size:26 final size:23
Alignment explanation
Indices: 1195000--1195043 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1194990 ATTATGTTCA
1195000 TTAAT-TTTAATATTTTATAATT
1 TTAATATTTAATATTTTATAATT
1195022 TTAATATTTAATATTATTATAA
1 TTAATATTTAATATT-TTATAA
1195044 GATATTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTAATATTTAATATTTTATAATT
Found at i:1200223 original size:29 final size:30
Alignment explanation
Indices: 1200180--1200260 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
1200170 GTTGGTGACT
* * * *
1200180 AAAATTTAAGTTTTAAAAGTTTTATGACC-
1 AAAATATAAATTTTAAAAGTTTAAGGACCA
*
1200209 AAAGTATAAATTTTAAAAAGTTTAAGGACCA
1 AAAATATAAATTTT-AAAAGTTTAAGGACCA
* *
1200240 AAAATGTAATTTTTAAAAGTT
1 AAAATATAAATTTTAAAAGTT
1200261 ATAAATTTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 11 0.26
30 20 0.48
31 11 0.26
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (30 bp):
AAAATATAAATTTTAAAAGTTTAAGGACCA
Found at i:1202809 original size:27 final size:27
Alignment explanation
Indices: 1202771--1202828 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
1202761 TCTCAAGGTA
*
1202771 ATTTCACTATCAGGGTCAGTTCGGACC
1 ATTTCACTATCAGGGTCAGTTCAGACC
1202798 ATTTCACTATCAGGGTCAGTTCAGACC
1 ATTTCACTATCAGGGTCAGTTCAGACC
1202825 ATTT
1 ATTT
1202829 TTACCTCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (27 bp):
ATTTCACTATCAGGGTCAGTTCAGACC
Found at i:1203502 original size:20 final size:19
Alignment explanation
Indices: 1203479--1203517 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1203469 AGGTCAGACC
1203479 GGTTCGGGTTGACTCAGGTT
1 GGTTCGGGTTGACTC-GGTT
*
1203499 GGTTCGGGTTTACTCGGTT
1 GGTTCGGGTTGACTCGGTT
1203518 CAGTCTGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.08, C:0.15, G:0.38, T:0.38
Consensus pattern (19 bp):
GGTTCGGGTTGACTCGGTT
Found at i:1206055 original size:25 final size:25
Alignment explanation
Indices: 1206021--1206070 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1206011 GACATATCTT
1206021 GTGATCCTAGTGATTCAAAGGCAAA
1 GTGATCCTAGTGATTCAAAGGCAAA
**
1206046 GTGATCCTAGTGATTTGAAGGCAAA
1 GTGATCCTAGTGATTCAAAGGCAAA
1206071 TGACAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (25 bp):
GTGATCCTAGTGATTCAAAGGCAAA
Found at i:1209742 original size:30 final size:30
Alignment explanation
Indices: 1209700--1209768 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
1209690 ATAAGATCAT
1209700 GTTAT-TTGTCATTAAGTTGTTTAGTGGTCA
1 GTTATGTT-TCATTAAGTTGTTTAGTGGTCA
*
1209730 GTTATGTTTCATTCAGTTGTTTAGTGGTCA
1 GTTATGTTTCATTAAGTTGTTTAGTGGTCA
*
1209760 TTTATGTTT
1 GTTATGTTT
1209769 GACACTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 34 0.94
31 2 0.06
ACGTcount: A:0.17, C:0.07, G:0.22, T:0.54
Consensus pattern (30 bp):
GTTATGTTTCATTAAGTTGTTTAGTGGTCA
Found at i:1216182 original size:3 final size:3
Alignment explanation
Indices: 1216174--1216223 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
1216164 CTACAAAAAC
1216174 ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1216221 ATT
1 ATT
1216224 TTGATTACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1217072 original size:2 final size:2
Alignment explanation
Indices: 1217065--1217101 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1217055 GGTTTTGGGC
1217065 TA TA TA TA 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 T
1217102 TTTAAACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1222581 original size:4 final size:4
Alignment explanation
Indices: 1222572--1224853 Score: 3499
Period size: 4 Copynumber: 581.0 Consensus size: 4
1222562 ATTGAGAAAA
*
1222572 ACAT ACAT ACAA ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1222620 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1222667 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1222715 ACAT ACAT CCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1222762 ACA- ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACCT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1222807 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1222855 AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1222902 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1222950 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
1222998 ACAT ACAT ACAT ACAT ACAT ACAT ACAG ACAC ACAT ACAT ACAG ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
1223046 ACAC ACAC ACAT ACAT ACAT ACAC ACAT ACAT ACAT ACAT ACAT ACAA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
1223094 ACAT ACAT ACAT ACAC ACAC ACAT ACAT ACAC ACAC ACAT ACAT AC--
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
1223140 ACAC ACAT ACAT ACAT AC-- ACAT ACAC ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1223186 AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAG ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1223233 ACAT -CAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1223279 ACAT ACAT ACTAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1223328 ACAT ACA- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1223375 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1223422 -CAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1223467 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1223514 ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-AT ACAT ACAT
1223561 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1223609 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1223657 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1223703 ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAC ATCAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-CAT ACAT ACAT
* * * * * *
1223750 ACAT ACAT ACAT ACAT ACAT ACAT ACAG ACAG ACAG ACAG ACAC ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * * * * * * *
1223798 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * * * * * * *
1223846 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACACC ACAC ACA- ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA-T ACAT ACAT ACAT
* * * * * * * * * * *
1223894 ACA- ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACCAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-CAT
* * * * * * * * * *
1223942 ACAC ACAC ACAC ACAC ACAC ACAC ACAT ACAT ACAC ACAC ACAC ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1223990 ACAC ACAT ACAT -CAT ACAT ACAT ACAT ACAT ACAT ACCAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-CAT ACAT ACAT
1224038 ACA- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224083 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224130 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224178 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-AT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
1224225 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT GCAT GCAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1224272 GCAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224318 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224366 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224414 AC-- ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACA-
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224458 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224505 ACAT ACAT ACAT ACAT -CAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224551 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224599 ACA- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224646 ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224692 ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1224739 ACAT ACAT -CCT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1224786 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1224834 ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT
1224854 GACACATGAA
Statistics
Matches: 2185, Mismatches: 39, Indels: 108
0.94 0.02 0.05
Matches are distributed among these distances:
2 22 0.01
3 77 0.04
4 2063 0.94
5 23 0.01
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:1223797 original size:2 final size:2
Alignment explanation
Indices: 1223790--1223996 Score: 368
Period size: 2 Copynumber: 105.5 Consensus size: 2
1223780 AGACAGACAG
1223790 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1223832 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1223874 AC AC AC AC -C AC AC AC A- AC AC AC A- AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1223913 AC AC AC AC AC AC AC AC AC AC AC AC AC -C AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* *
1223954 AC AC AC AC AC AC AC AT AC AT AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1223996 A
1 A
1223997 TACATCATAC
Statistics
Matches: 197, Mismatches: 4, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
1 4 0.02
2 193 0.98
ACGTcount: A:0.50, C:0.49, G:0.00, T:0.01
Consensus pattern (2 bp):
AC
Found at i:1225940 original size:130 final size:130
Alignment explanation
Indices: 1225702--1226002 Score: 381
Period size: 130 Copynumber: 2.3 Consensus size: 130
1225692 GAAATAAATC
* **
1225702 CCCTAGATAACCAACCGTCTTCATCACGTAGGAACCGTGTTATCATCCCTAAAAATGGCATGCCA
1 CCCTAGATAACCAACCGTCCTCATCACGTACAAACCGTGTTATCATCCCTAAAAATGGCATGCCA
* *
1225767 TCCTCATCACGTAGGAACTGTGTCATCCACTGACCAGACCTCCTCATCACATAGGAGCCGTGTCA
66 TCCTCATCACGTAGGAACCGTGTCATCCACTGAACAGACCTCCTCATCACATAGGAGCCGTGTCA
* * *
1225832 CCCTCAGATAACCAGCCGTCCTCATCACGTACAAATCGTGTTATC-TCCCTAAAGATGGTC-TGC
1 CCCT-AGATAACCAACCGTCCTCATCACGTACAAACCGTGTTATCATCCCTAAAAATGG-CATGC
* * * * *
1225895 TATCCTCATCACGTAGGAACCGTGTCATCCCCTGAACAGGCCTCCTCATCATATAGGAGTCGTGT
64 CATCCTCATCACGTAGGAACCGTGTCATCCACTGAACAGACCTCCTCATCACATAGGAGCCGTGT
1225960 CA
129 CA
* *** * **
1225962 TCCTTAGATAACCTTTCGTCCTCATCAAGTAGGAACCGTGT
1 -CCCTAGATAACCAACCGTCCTCATCACGTACAAACCGTGT
1226003 CATCCCATGA
Statistics
Matches: 147, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
130 108 0.73
131 39 0.27
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (130 bp):
CCCTAGATAACCAACCGTCCTCATCACGTACAAACCGTGTTATCATCCCTAAAAATGGCATGCCA
TCCTCATCACGTAGGAACCGTGTCATCCACTGAACAGACCTCCTCATCACATAGGAGCCGTGTCA
Found at i:1226035 original size:40 final size:40
Alignment explanation
Indices: 1225897--1226049 Score: 123
Period size: 40 Copynumber: 3.8 Consensus size: 40
1225887 TGGTCTGCTA
* * *
1225897 TCCTCATCACGTAGGAACCGTGTCATCCCCTGAACAGGCC
1 TCCTCATCACGTAGGAACCGTGTCATCCCATGAAAAGACC
** ** * * *
1225937 TCCTCATCATATAGGAGTCGTGTCAT-CCTTAGATAA-CCTTTC
1 TCCTCATCACGTAGGAACCGTGTCATCCCAT-GAAAAGAC---C
*
1225979 GTCCTCATCAAGTAGGAACCGTGTCATCCCATGAAAAGACC
1 -TCCTCATCACGTAGGAACCGTGTCATCCCATGAAAAGACC
* *
1226020 TCCTCATCACGTAGGAGCCATGTCA-CCCAT
1 TCCTCATCACGTAGGAACCGTGTCATCCCAT
1226050 ATATAACCAG
Statistics
Matches: 88, Mismatches: 18, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
39 9 0.10
40 47 0.53
41 1 0.01
42 1 0.01
43 26 0.30
44 4 0.05
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCATGAAAAGACC
Found at i:1226056 original size:83 final size:83
Alignment explanation
Indices: 1225897--1226057 Score: 223
Period size: 83 Copynumber: 1.9 Consensus size: 83
1225887 TGGTCTGCTA
* * * * * * *
1225897 TCCTCATCACGTAGGAACCGTGTCATCCCCTGAACAGGCCTCCTCATCATATAGGAGTCGTGTCA
1 TCCTCATCAAGTAGGAACCGTGTCATCCCATGAAAAGACCTCCTCATCACATAGGAGCCATGTCA
* *
1225962 TCCTTAGATAACCTTTCG
66 CCCATAGATAACCTTTCG
*
1225980 TCCTCATCAAGTAGGAACCGTGTCATCCCATGAAAAGACCTCCTCATCACGTAGGAGCCATGTCA
1 TCCTCATCAAGTAGGAACCGTGTCATCCCATGAAAAGACCTCCTCATCACATAGGAGCCATGTCA
*
1226045 CCCATATATAACC
66 CCCATAGATAACC
1226058 AGCCGTCCTC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.25
Consensus pattern (83 bp):
TCCTCATCAAGTAGGAACCGTGTCATCCCATGAAAAGACCTCCTCATCACATAGGAGCCATGTCA
CCCATAGATAACCTTTCG
Found at i:1226177 original size:40 final size:40
Alignment explanation
Indices: 1226117--1226219 Score: 109
Period size: 43 Copynumber: 2.5 Consensus size: 40
1226107 CCAGAACTCT
** * *
1226117 TCATCACGTATGAGATGTGTCATCC-ACTGACGAGATCTCC
1 TCATCACGTATGAGCCGTGTCACCCAAC-GACGAGACCTCC
* *
1226157 TCATCACGTATGAGCCGTGTCACCCTTAAACGACTAGACCTCT
1 TCATCACGTATGAGCCGTGTCACCC---AACGACGAGACCTCC
1226200 TCATCACGTATGAGCCGTGT
1 TCATCACGTATGAGCCGTGT
1226220 TGTCCCCCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
40 22 0.42
43 29 0.55
44 2 0.04
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (40 bp):
TCATCACGTATGAGCCGTGTCACCCAACGACGAGACCTCC
Found at i:1227873 original size:30 final size:29
Alignment explanation
Indices: 1227768--1227911 Score: 136
Period size: 30 Copynumber: 5.0 Consensus size: 29
1227758 GCCCTTCAAA
1227768 TTTCT-TTTTAGCTATTTTAGTCCTTTAAG
1 TTTCTGTTTT-GCTATTTTAGTCCTTTAAG
*
1227797 TTTCTGTTTT-CTATTTT-GTCCTTTAAA
1 TTTCTGTTTTGCTATTTTAGTCCTTTAAG
* * *
1227824 TTCCTGTTGTTGTTGTTTTAG-CCTTTTAAG
1 TTTCTGTT-TTGCTATTTTAGTCC-TTTAAG
* *
1227854 TTTATGTTTATGCTATTTTAG-CCCTTAAG
1 TTTCTGTTT-TGCTATTTTAGTCCTTTAAG
* *
1227883 TTTCTATTTTTACTATTTTAGTCCTTTAA
1 TTTCT-GTTTTGCTATTTTAGTCCTTTAA
1227912 ATTCTTGTTT
Statistics
Matches: 93, Mismatches: 14, Indels: 15
0.76 0.11 0.12
Matches are distributed among these distances:
27 16 0.17
28 9 0.10
29 32 0.34
30 36 0.39
ACGTcount: A:0.17, C:0.14, G:0.11, T:0.58
Consensus pattern (29 bp):
TTTCTGTTTTGCTATTTTAGTCCTTTAAG
Found at i:1227885 original size:29 final size:29
Alignment explanation
Indices: 1227839--1227908 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
1227829 GTTGTTGTTG
* * *
1227839 TTTTAGCCTTTTAAGTTTATGTTTATGCTA
1 TTTTAGCC-CTTAAGTTTATATTTATACTA
* *
1227869 TTTTAGCCCTTAAGTTTCTATTTTTACTA
1 TTTTAGCCCTTAAGTTTATATTTATACTA
*
1227898 TTTTAGTCCTT
1 TTTTAGCCCTT
1227909 TAAATTCTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 26 0.76
30 8 0.24
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (29 bp):
TTTTAGCCCTTAAGTTTATATTTATACTA
Found at i:1227929 original size:30 final size:29
Alignment explanation
Indices: 1227779--1227931 Score: 97
Period size: 30 Copynumber: 5.2 Consensus size: 29
1227769 TTCTTTTTAG
* *
1227779 CTATTTTAGTCCTTTAAGTT-TCTGTTTT
1 CTATTTTAGTCCTTTAAATTCTATGTTTT
*
1227807 CTATTTT-GTCCTTTAAATTC-CTGTTGTT
1 CTATTTTAGTCCTTTAAATTCTATGTT-TT
* * *
1227835 GTTGTTTTAG-CCTTTTAAGTT-TATGTTTAT
1 -CTATTTTAGTCC-TTTAAATTCTATGTTT-T
* *
1227865 GCTATTTTAG-CCCTTAAGTTTCTAT-TTTT
1 -CTATTTTAGTCCTTTAA-ATTCTATGTTTT
1227894 ACTATTTTAGTCCTTTAAATTCT-TGTTTGT
1 -CTATTTTAGTCCTTTAAATTCTATGTTT-T
1227924 ACTATTTT
1 -CTATTTT
1227932 TGGTCCTTGT
Statistics
Matches: 101, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
27 16 0.16
28 10 0.10
29 29 0.29
30 43 0.43
31 3 0.03
ACGTcount: A:0.17, C:0.14, G:0.11, T:0.58
Consensus pattern (29 bp):
CTATTTTAGTCCTTTAAATTCTATGTTTT
Found at i:1229128 original size:29 final size:29
Alignment explanation
Indices: 1229093--1229163 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
1229083 TATTGCTGAG
1229093 CTCGACTCAAACTTTAAAAGTAAGCTCAA
1 CTCGACTCAAACTTTAAAAGTAAGCTCAA
1229122 CTCGACTCAAACTTTAAAAGTAAGCTCAA
1 CTCGACTCAAACTTTAAAAGTAAGCTCAA
*
1229151 CTCAACTCAAACT
1 CTCGACTCAAACT
1229164 CAAACTCACG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (29 bp):
CTCGACTCAAACTTTAAAAGTAAGCTCAA
Found at i:1238632 original size:21 final size:22
Alignment explanation
Indices: 1238584--1238642 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
1238574 TAGAACAGAG
*
1238584 AAGGGATCAATCA-TTTCTTTC
1 AAGGGATCAATCATTTTCTTAC
* *
1238605 AAAGGATCTATCATTTTC-TAC
1 AAGGGATCAATCATTTTCTTAC
* *
1238626 AAGGGATCGATCCTTTT
1 AAGGGATCAATCATTTT
1238643 GAAAAGGGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (22 bp):
AAGGGATCAATCATTTTCTTAC
Found at i:1238651 original size:20 final size:20
Alignment explanation
Indices: 1238626--1238702 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
1238616 CATTTTCTAC
1238626 AAGGGATCGATCCTTTTGAA
1 AAGGGATCGATCCTTTTGAA
* * ***
1238646 AAGGGATCCATACTTTCTCCC
1 AAGGGATCGATCCTTT-TGAA
*
1238667 AAGGAATCGATCCTTTTGAA
1 AAGGGATCGATCCTTTTGAA
* *
1238687 AAAGGATCGACCCTTT
1 AAGGGATCGATCCTTT
1238703 GCTGTACATA
Statistics
Matches: 42, Mismatches: 14, Indels: 2
0.72 0.24 0.03
Matches are distributed among these distances:
20 28 0.67
21 14 0.33
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (20 bp):
AAGGGATCGATCCTTTTGAA
Found at i:1246482 original size:21 final size:21
Alignment explanation
Indices: 1246449--1246490 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1246439 CAATTGGAAA
*
1246449 CATCCTGCCCGAAGGACTTAT
1 CATCCTGCCCGAAAGACTTAT
* *
1246470 CATCTTGCTCGAAAGACTTAT
1 CATCCTGCCCGAAAGACTTAT
1246491 AGATAACCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (21 bp):
CATCCTGCCCGAAAGACTTAT
Found at i:1247064 original size:235 final size:236
Alignment explanation
Indices: 1246481--1247074 Score: 777
Period size: 243 Copynumber: 2.5 Consensus size: 236
1246471 ATCTTGCTCG
* * * *
1246481 AAAGACTTATAGATAACCCAAAGGATTTAAACATCATGCTCAAAAGACTTACTGATAGCCAAAGG
1 AAAGACTTATAGATGACCCAAAGGATTTAAACATCATGCTCAAAAGACTTACTAATGGCCGAAGG
* * *
1246546 ACTTAGTCAGTAAGAAATTTTGGAAATCGTTTTCTTACTCTTTCAAG--AAAAACCAATCTTTAG
66 ACTTACTCAGTAAGAAACTTTGGAAATCGCTTTCTTACT-TTTCAAGAAAAAAACCAATCTTTAG
* * * *
1246609 AAAAGGTTTAAATGAGAAACTTTAGAAATTGCTTTCTCATTTTCCAAAATTATGTGAAAATATCA
130 AAAAGGTTTAAATGAGAAACTTTAGAAATCGCTTTCTCATTTTCCAAAATAATATGAAAACATCA
* * *
1246674 TACCCAAAGGTCTTATGGATTGCCTGAAGGACTTATCATCCTGCTCG
195 TACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCA-----CTCA
* **
1246721 AAAGACTTATAGATGACCCGAAGGATTTAAACATCATGCTTGAAAGACTTACTAATGGCCCGAAG
1 AAAGACTTATAGATGACCCAAAGGATTTAAACATCATGCTCAAAAGACTTACTAATGG-CCGAAG
* * *
1246786 GACTTACTCAGTAAGAAACTTTAGAAATCGCTTTCTTACTTTTCAAGAAAAAAACCATTCTTTCT
65 GACTTACTCAGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAGAAAAAAACCAATCTTT-A
* * *
1246851 GAAAA-GTTTCAAATTAGAAACTTTGGAAATCGCTTTCTCATTTTCGAAAATAATATGAAAACAT
129 GAAAAGGTTT-AAATGAGAAACTTTAGAAATCGCTTTCTCATTTTCCAAAATAATATGAAAACAT
* * * * *
1246915 CTTGCTCGAAGGTTTTATGGATGGCCCGAAGGACTTATCA-TCA
193 CATACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCACTCA
*
1246958 AAAGACTTATATATGACCCAAAGG-TTTAAACATCATGCTCAAAAGACTTACT-ATGGCTCGAAG
1 AAAGACTTATAGATGACCCAAAGGATTTAAACATCATGCTCAAAAGACTTACTAATGGC-CGAAG
**
1247021 GACTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAGAAAAAAA
65 GACTTACTCAGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAGAAAAAAA
1247075 ATCAATATCG
Statistics
Matches: 313, Mismatches: 35, Indels: 17
0.86 0.10 0.05
Matches are distributed among these distances:
234 1 0.00
235 60 0.19
236 26 0.08
237 24 0.08
240 59 0.19
241 41 0.13
242 17 0.05
243 85 0.27
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (236 bp):
AAAGACTTATAGATGACCCAAAGGATTTAAACATCATGCTCAAAAGACTTACTAATGGCCGAAGG
ACTTACTCAGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAGAAAAAAACCAATCTTTAGA
AAAGGTTTAAATGAGAAACTTTAGAAATCGCTTTCTCATTTTCCAAAATAATATGAAAACATCAT
ACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCACTCA
Found at i:1247211 original size:271 final size:275
Alignment explanation
Indices: 1246812--1247308 Score: 666
Period size: 271 Copynumber: 1.8 Consensus size: 275
1246802 AACTTTAGAA
* * * *
1246812 ATCGCTTTCTTACTTTTCAAGAAAAAAACCATTCTTTCTGAAAAGTTTCAAATTAGAAACTTTGG
1 ATCGCTTTCTTACTTTTCAAGAAAAAAACCAATCTTTCAGAAAAGTTTCAAATGAGAAAATTTGG
* * * *
1246877 AAATCGCTTTCTCATTTTCGAAAATAATATGAAAACATCTTGCTCGAAGGTTTTATGGATGGCCC
66 AAATCGCTTTCTCATTTTCGAAAATAATATGAAAACATCCTACCCGAAGGTCTTATGGATGGCCC
* *
1246942 GAAGGAC-TT-ATC-ATC-AAAAGACTTATATATGACCCAAAGG-TTTAAACATCATGCTCAAAA
131 GAAGAACTTTCATCTATCTAAAAGACTTATAAATGACCCAAAGGATTTAAACATCATGCTCAAAA
*
1247002 GACTTACT-ATGGCTCGAAGGACTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCA
196 GACTTACTGATGGCCCGAAGGACTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCA
1247066 AGAAAAAAAATCAAT
261 AGAAAAAAAATCAAT
* **
1247081 ATCGCTTTCTTGCTTTTCAAGAAAAAAATTAATCTTTCAGAAAAGATTT-AAATGAGAAAAATTT
1 ATCGCTTTCTTACTTTTCAAGAAAAAAACCAATCTTTCAGAAAAG-TTTCAAATGAG-AAAATTT
* * * * *
1247145 GGAAATCGCTTTCTTATTTTTTGGAAATCATATGAAAATATCCTACCCGAAGGTCTTATGGATGG
64 GGAAATCGCTTTCTCA-TTTTCGAAAATAATATGAAAACATCCTACCCGAAGGTCTTATGGATGG
* * * * *
1247210 CCCGAAGAACTTTTTCATCTTTCTTAAAAGACTTATAAATTACCCGAAGGATTTAATCTTCATGC
128 CCCGAAGAAC--TTTCATCTATC-TAAAAGACTTATAAATGACCCAAAGGATTTAAACATCATGC
*
1247275 TCGAAAGACTTACTGATGGCCCGAAGGACTTACT
190 TCAAAAGACTTACTGATGGCCCGAAGGACTTACT
1247309 CATCAAGAAA
Statistics
Matches: 191, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
269 46 0.24
270 24 0.13
271 49 0.26
274 2 0.01
275 3 0.02
276 2 0.01
278 22 0.12
279 25 0.13
280 18 0.09
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (275 bp):
ATCGCTTTCTTACTTTTCAAGAAAAAAACCAATCTTTCAGAAAAGTTTCAAATGAGAAAATTTGG
AAATCGCTTTCTCATTTTCGAAAATAATATGAAAACATCCTACCCGAAGGTCTTATGGATGGCCC
GAAGAACTTTCATCTATCTAAAAGACTTATAAATGACCCAAAGGATTTAAACATCATGCTCAAAA
GACTTACTGATGGCCCGAAGGACTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCA
AGAAAAAAAATCAAT
Found at i:1247458 original size:57 final size:58
Alignment explanation
Indices: 1247365--1247541 Score: 230
Period size: 58 Copynumber: 3.1 Consensus size: 58
1247355 ATTTACAATT
* * * * * * * *
1247365 ATCATTAAGAAACCCCTAAAAAATTAGGCTTGGCTTC-TTTAAAAATTTATTGGAAATA
1 ATCATCAAAAAACCCCT-GAAAATCAGACTTAGCTTCTTTTAAAAGTTCATTGGAAATA
*
1247423 ATTATCAAAAAACCCCTGAAAATCAGACTTAGCTTCTTTTAAAAGTTCATTGGAAATA
1 ATCATCAAAAAACCCCTGAAAATCAGACTTAGCTTCTTTTAAAAGTTCATTGGAAATA
* * *
1247481 ATCATCAAGAAACCCTTGAAAATCAGACTTAGCTTCTTTTAAAAGTTCATTAGAAATA
1 ATCATCAAAAAACCCCTGAAAATCAGACTTAGCTTCTTTTAAAAGTTCATTGGAAATA
1247539 ATC
1 ATC
1247542 TTTAAGAAAC
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
57 15 0.14
58 90 0.86
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (58 bp):
ATCATCAAAAAACCCCTGAAAATCAGACTTAGCTTCTTTTAAAAGTTCATTGGAAATA
Found at i:1247549 original size:58 final size:58
Alignment explanation
Indices: 1247397--1247575 Score: 236
Period size: 58 Copynumber: 3.1 Consensus size: 58
1247387 ATTAGGCTTG
* * * *
1247397 GCTTC-TTTAAAAATTTATTGGAAATAAT-TATCAAAAAACCCCTGAAAATCAGACTTA
1 GCTTCTTTTAAAAGTTCATTGGAAATAATCT-TCAAGAAACCCTTGAAAATCAGACTTA
*
1247454 GCTTCTTTTAAAAGTTCATTGGAAATAATCATCAAGAAACCCTTGAAAATCAGACTTA
1 GCTTCTTTTAAAAGTTCATTGGAAATAATCTTCAAGAAACCCTTGAAAATCAGACTTA
* * * * *
1247512 GCTTCTTTTAAAAGTTCATTAGAAATAATCTTTAAGAAACACTTGGAAATCAGGCTTA
1 GCTTCTTTTAAAAGTTCATTGGAAATAATCTTCAAGAAACCCTTGAAAATCAGACTTA
*
1247570 GTTTCT
1 GCTTCT
1247576 AAAAAAACCT
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
57 5 0.05
58 103 0.95
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.34
Consensus pattern (58 bp):
GCTTCTTTTAAAAGTTCATTGGAAATAATCTTCAAGAAACCCTTGAAAATCAGACTTA
Found at i:1251444 original size:84 final size:84
Alignment explanation
Indices: 1251303--1251470 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
1251293 GTAAGTAAGA
1251303 TGGGCACTAAACTTAGCTCTCTCGCGTCTAAGTTTTCATGGGATAGCTCACCAACATTTATTCCC
1 TGGGCACTAAACTTAGCTCTCTCGCGTCTAAGTTTTCATGGGATAGCTCACCAACATTTATTCCC
1251368 TTAATCGATTTTCTAACTG
66 TTAATCGATTTTCTAACTG
1251387 TGGGCACTAAACTTAGCTCTCTCGCGTCTAAGTTTTCATGGGATAGCTCACCAACATTTATTCCC
1 TGGGCACTAAACTTAGCTCTCTCGCGTCTAAGTTTTCATGGGATAGCTCACCAACATTTATTCCC
1251452 TTAATCGATTTTCTAACTG
66 TTAATCGATTTTCTAACTG
1251471 CTTAATATTT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (84 bp):
TGGGCACTAAACTTAGCTCTCTCGCGTCTAAGTTTTCATGGGATAGCTCACCAACATTTATTCCC
TTAATCGATTTTCTAACTG
Found at i:1254242 original size:66 final size:66
Alignment explanation
Indices: 1254136--1254270 Score: 270
Period size: 66 Copynumber: 2.0 Consensus size: 66
1254126 GTATTGTTTT
1254136 TCAAGAACCTTCTAAAAGATAGGTTATTTAAGGGATCAATACCTTTGAAGGACATGTCAGGATAT
1 TCAAGAACCTTCTAAAAGATAGGTTATTTAAGGGATCAATACCTTTGAAGGACATGTCAGGATAT
1254201 G
66 G
1254202 TCAAGAACCTTCTAAAAGATAGGTTATTTAAGGGATCAATACCTTTGAAGGACATGTCAGGATAT
1 TCAAGAACCTTCTAAAAGATAGGTTATTTAAGGGATCAATACCTTTGAAGGACATGTCAGGATAT
1254267 G
66 G
1254268 TCA
1 TCA
1254271 TGTTCATGAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (66 bp):
TCAAGAACCTTCTAAAAGATAGGTTATTTAAGGGATCAATACCTTTGAAGGACATGTCAGGATAT
G
Found at i:1258223 original size:21 final size:21
Alignment explanation
Indices: 1258197--1258295 Score: 85
Period size: 21 Copynumber: 4.8 Consensus size: 21
1258187 CAGAACAGAG
* *
1258197 AAGGATCGATCCTTTTTTTCA
1 AAGGATCGATCCTTTTCTCCA
* *
1258218 AAGGATTGGTCCTTTTCTCCA
1 AAGGATCGATCCTTTTCTCCA
* ***
1258239 AGGGATCGATCCTTTT-GAAA
1 AAGGATCGATCCTTTTCTCCA
*
1258259 AAGGATCGAT-CTTTTCTCCC
1 AAGGATCGATCCTTTTCTCCA
*
1258279 AAGGAATCAATCCTTTT
1 AAGG-ATCGATCCTTTT
1258296 GAAAAGGGAT
Statistics
Matches: 59, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
19 5 0.08
20 14 0.24
21 35 0.59
22 5 0.08
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.36
Consensus pattern (21 bp):
AAGGATCGATCCTTTTCTCCA
Found at i:1258281 original size:41 final size:40
Alignment explanation
Indices: 1258229--1258306 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 40
1258219 AGGATTGGTC
* *
1258229 CTTTTCTCCAAGGGATCGATCCTTTTGAAAAAGGATCGAT
1 CTTTTCTCCAAGGAATCAATCCTTTTGAAAAAGGATCGAT
*
1258269 CTTTTCTCCCAAGGAATCAATCCTTTTGAAAAGGGATC
1 CTTTTCT-CCAAGGAATCAATCCTTTTGAAAAAGGATC
1258307 AATCATTTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 7 0.21
41 27 0.79
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (40 bp):
CTTTTCTCCAAGGAATCAATCCTTTTGAAAAAGGATCGAT
Found at i:1260396 original size:24 final size:24
Alignment explanation
Indices: 1260362--1260428 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
1260352 AGTCACTTCC
1260362 TTAT-TTC-TTATTATTATTATTA
1 TTATATTCTTTATTATTATTATTA
1260384 TTATATTCTTTATTATTATTATTA
1 TTATATTCTTTATTATTATTATTA
1260408 TTATTATT-TTTATTATTATTA
1 TTA-TATTCTTTATTATTATTA
1260429 ACACTTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.10
23 3 0.07
24 31 0.74
25 4 0.10
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (24 bp):
TTATATTCTTTATTATTATTATTA
Found at i:1260398 original size:21 final size:21
Alignment explanation
Indices: 1260372--1260445 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
1260362 TTATTTCTTA
1260372 TTATTATTATTATTATATTCT
1 TTATTATTATTATTATATTCT
*
1260393 TTATTATTATTATTATTATTAT
1 TTATTATTATTATTA-TATTCT
**
1260415 TT-TTATTATTATTA-ACACT
1 TTATTATTATTATTATATTCT
*
1260434 TTTTTATTATTA
1 TTATTATTATTA
1260446 ATTTAATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 4 0.09
20 9 0.19
21 27 0.57
22 7 0.15
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATTATTATTATTATATTCT
Found at i:1260445 original size:3 final size:3
Alignment explanation
Indices: 1260369--1260428 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
1260359 TCCTTATTTC
*
1260369 TTA TTA TTA TTA TTA TTA -TA TTCT TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
*
1260414 TTT TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1260429 ACACTTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.92
4 2 0.04
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1260457 original size:21 final size:20
Alignment explanation
Indices: 1260375--1260457 Score: 62
Period size: 21 Copynumber: 4.0 Consensus size: 20
1260365 TTTCTTATTA
*
1260375 TTATTATTA-TTATATTCTTTA
1 TTATTATTATTTA-ATT-TTTT
* *
1260396 TTATTATTATTATTATTATTT
1 TTATTATTATT-TAATTTTTT
**
1260417 TTATTATTA-TTAACACTTTT
1 TTATTATTATTTAA-TTTTTT
1260437 TTATTATTAATTTAATTTTTT
1 TTATTATT-ATTTAATTTTTT
1260458 ATTTTATATA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.04
20 12 0.25
21 25 0.52
22 8 0.17
23 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTATTATTTAATTTTTT
Found at i:1260487 original size:24 final size:24
Alignment explanation
Indices: 1260460--1260516 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 24
1260450 AATTTTTTAT
1260460 TTTATATAAAAACATATGAACTCA
1 TTTATATAAAAACATATGAACTCA
***
1260484 TTTATATTTTTTAACATATGAACTCA
1 TTTATA--TAAAAACATATGAACTCA
1260510 TTTATAT
1 TTTATAT
1260517 TATTCACATC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 7 0.25
26 21 0.75
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.46
Consensus pattern (24 bp):
TTTATATAAAAACATATGAACTCA
Found at i:1261253 original size:35 final size:35
Alignment explanation
Indices: 1261214--1261288 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1261204 TGTCACGAAC
*
1261214 AGTAAGGCCCTGAGCAAAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTGAGCAAAAAGCCGAGGAGCCTCCA
* *
1261249 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCAAAAAGCCGAGGAGCCTCCA
1261284 AGTAA
1 AGTAA
1261289 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.28, G:0.29, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCAAAAAGCCGAGGAGCCTCCA
Found at i:1261376 original size:24 final size:23
Alignment explanation
Indices: 1261349--1261459 Score: 98
Period size: 24 Copynumber: 4.7 Consensus size: 23
1261339 TATAGCAAAA
* *
1261349 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAATCAGAATTCAAGTCAA-T
* * *
1261373 ATCATATCAGAATTCAGGTCATGT
1 ATCAAATCAGAATTCAAGTCA-AT
* * *
1261397 ATCAGATCAGAATCCATGTCAAT
1 ATCAAATCAGAATTCAAGTCAAT
* *
1261420 ATCAAATCAGAATCCAGGTCAAT
1 ATCAAATCAGAATTCAAGTCAAT
1261443 ATCATAA-CAGAATTCAA
1 ATCA-AATCAGAATTCAA
1261460 ATTTGAAATC
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
23 34 0.47
24 38 0.53
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (23 bp):
ATCAAATCAGAATTCAAGTCAAT
Done.