Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 164 of 199
Found at i:48212259 original size:17 final size:17
Alignment explanation
Indices: 48212239--48212277 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
48212229 ATTTCAATGT
*
48212239 ATTTTTCTGATTTTCTG
1 ATTTTTCTGATTTTCGG
*
48212256 ATTTTTCTTATTTTCGG
1 ATTTTTCTGATTTTCGG
48212273 ATTTT
1 ATTTT
48212278 ATTACTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.13, C:0.10, G:0.10, T:0.67
Consensus pattern (17 bp):
ATTTTTCTGATTTTCGG
Found at i:48213012 original size:13 final size:14
Alignment explanation
Indices: 48212981--48213023 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
48212971 CCCTCCCTCT
*
48212981 TCTTTTTCTCCTTC
1 TCTTTTTCTTCTTC
*
48212995 TCTTTTTCTTTTTC
1 TCTTTTTCTTCTTC
48213009 -CTTTTTCTTCCTTC
1 TCTTTTTCTT-CTTC
48213023 T
1 T
48213024 GCGCCTCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TCTTTTTCTTCTTC
Found at i:48213045 original size:3 final size:3
Alignment explanation
Indices: 48213037--48213070 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
48213027 CCTCCTTCCC
48213037 CTT CTT CTT CTT C-T CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
48213071 CCTTTCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:48222418 original size:173 final size:173
Alignment explanation
Indices: 48222110--48222444 Score: 537
Period size: 173 Copynumber: 1.9 Consensus size: 173
48222100 CAAAGCACCC
* * *
48222110 AAGAACTTAGGCAAATGTAAACACAAATTCCTAGATGTACAAAGCATTAGCAAGATACTCCAAAA
1 AAGAACTTAGGCAAATGTAAACACAAATCCCTAGAAGTACAAAGCATTAGCAAAATACTCCAAAA
* * *
48222175 CATTATAGTAAAAACTAGTGAGACATCAGACCGAAGAAGAAACTTTATAAGGTTAAAAGAAACAA
66 CATTATAGTAAAAACTAGAGAGACATCAGACCGAAGAAGAAACTTGACAAGGTTAAAAGAAACAA
48222240 TTGAAGGGATAAAAATATAGAAGAATAAAAAAATATAATAGTA
131 TTGAAGGGATAAAAATATAGAAGAATAAAAAAATATAATAGTA
* * *
48222283 AAGAATTTAGGGAAATGTAAACACAAATCCCTAGAAGTACAAAGCATTAGGAAAATACTCC-AAA
1 AAGAACTTAGGCAAATGTAAACACAAATCCCTAGAAGTACAAAGCATTAGCAAAATACTCCAAAA
* * *
48222347 CTATTATAGTAAAGACTAGAGAGACATCAGACTGAAGAAGAAACTTGACAAGGTTAAAAGAAACT
66 C-ATTATAGTAAAAACTAGAGAGACATCAGACCGAAGAAGAAACTTGACAAGGTTAAAAGAAACA
*
48222412 ATTGAAGGGATAAAAATATAGAAGAATCAAAAA
130 ATTGAAGGGATAAAAATATAGAAGAATAAAAAA
48222445 CCACGAGTTA
Statistics
Matches: 148, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
172 4 0.03
173 144 0.97
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.20
Consensus pattern (173 bp):
AAGAACTTAGGCAAATGTAAACACAAATCCCTAGAAGTACAAAGCATTAGCAAAATACTCCAAAA
CATTATAGTAAAAACTAGAGAGACATCAGACCGAAGAAGAAACTTGACAAGGTTAAAAGAAACAA
TTGAAGGGATAAAAATATAGAAGAATAAAAAAATATAATAGTA
Found at i:48225913 original size:126 final size:126
Alignment explanation
Indices: 48225658--48226061 Score: 621
Period size: 126 Copynumber: 3.2 Consensus size: 126
48225648 GATAAAATCA
* * * * * * *
48225658 AAGCAGGATTCTTTATCAGAAGAATTTCTGAAGTCGCGCCCACATGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* *
48225723 AGGTCCTACAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
66 AGGTCCTAGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * * *
48225783 AAGCATGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGCCGCGCTTTTACTACAAT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* *
48225848 AGGTCCTAGAAGAAATAATTTCGATTTGACGTTTCTGAGCAAATAGTATAAAAAATGCTTC
66 AGGTCCTAGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
*
48225909 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * * *
48225974 AGGTCCTGGAAGAAATAATTTCGACTTGATGTTTATGAGCAAATAGTTTAAAAAACGCTTC
66 AGGTCCTAGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
48226035 AAGCAGGATGCTTTATGAGAAGAATTT
1 AAGCAGGATGCTTTATGAGAAGAATTT
48226062 AGGGTTTTTA
Statistics
Matches: 253, Mismatches: 25, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
125 64 0.25
126 189 0.75
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (126 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTAGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
Found at i:48226084 original size:22 final size:22
Alignment explanation
Indices: 48226059--48226214 Score: 105
Period size: 22 Copynumber: 7.3 Consensus size: 22
48226049 ATGAGAAGAA
48226059 TTTAGGGTTTTTAAGTTAAGGG
1 TTTAGGGTTTTTAAGTTAAGGG
*
48226081 TTTAGGGTTTTTAAGTTAAGAG
1 TTTAGGGTTTTTAAGTTAAGGG
*
48226103 -TTA--GTGTTTAAGGTT-AGGG
1 TTTAGGGTTTTTAA-GTTAAGGG
* *
48226122 ----GGTTTTAAATTAAGTCAAGGG
1 TTTAGGGTTT---TTAAGTTAAGGG
** * *
48226143 TTTAAAGTTTTTAAGTCATGGG
1 TTTAGGGTTTTTAAGTTAAGGG
* *
48226165 TTTAGGGTTTGTAAGTTAAGTG
1 TTTAGGGTTTTTAAGTTAAGGG
* *
48226187 TTTAGGGTTTTAAAGTCAAGGG
1 TTTAGGGTTTTTAAGTTAAGGG
48226209 -TTAGGG
1 TTTAGGG
48226215 ATTAGGGTTT
Statistics
Matches: 103, Mismatches: 20, Indels: 23
0.71 0.14 0.16
Matches are distributed among these distances:
18 2 0.02
19 10 0.10
20 5 0.05
21 17 0.17
22 66 0.64
25 3 0.03
ACGTcount: A:0.26, C:0.02, G:0.31, T:0.42
Consensus pattern (22 bp):
TTTAGGGTTTTTAAGTTAAGGG
Found at i:48226253 original size:27 final size:26
Alignment explanation
Indices: 48226223--48226273 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
48226213 GGATTAGGGT
*
48226223 TTAAGGTTTAAGGTTAAGAGATTTAAA
1 TTAAGGGTTAAGGTTAAG-GATTTAAA
* *
48226250 TTAAGGGTTAGGGTTTAGGATTTA
1 TTAAGGGTTAAGGTTAAGGATTTA
48226274 GGTTTTAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.39
Consensus pattern (26 bp):
TTAAGGGTTAAGGTTAAGGATTTAAA
Found at i:48226273 original size:7 final size:7
Alignment explanation
Indices: 48226253--48226293 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
48226243 ATTTAAATTA
48226253 AGGG-TT
1 AGGGTTT
48226259 AGGGTTT
1 AGGGTTT
*
48226266 AGGATTT
1 AGGGTTT
*
48226273 AGGTTTT
1 AGGGTTT
48226280 AGGGTTT
1 AGGGTTT
48226287 AGGGTTT
1 AGGGTTT
48226294 GTCAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
6 4 0.13
7 27 0.87
ACGTcount: A:0.17, C:0.00, G:0.39, T:0.44
Consensus pattern (7 bp):
AGGGTTT
Found at i:48227532 original size:7 final size:7
Alignment explanation
Indices: 48227522--48227547 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
48227512 TTATATACAT
48227522 AATACTA
1 AATACTA
48227529 AATACTA
1 AATACTA
48227536 AATACTA
1 AATACTA
48227543 AATAC
1 AATAC
48227548 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:48227753 original size:20 final size:20
Alignment explanation
Indices: 48227716--48227753 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
48227706 ATTATTTTTA
*
48227716 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
48227736 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
48227754 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:48228731 original size:11 final size:11
Alignment explanation
Indices: 48228717--48228827 Score: 81
Period size: 11 Copynumber: 10.4 Consensus size: 11
48228707 GAGAAATTTA
48228717 AGAGGAAATTG
1 AGAGGAAATTG
*
48228728 AGAGCAAATTG
1 AGAGGAAATTG
**
48228739 AGATTAAA-T-
1 AGAGGAAATTG
* *
48228748 A-TGG-ATTTG
1 AGAGGAAATTG
48228757 AGA-GAAATTTG
1 AGAGGAAA-TTG
*
48228768 -GAAGGAATTTG
1 AG-AGGAAATTG
*
48228779 AGAGCAAATTG
1 AGAGGAAATTG
*
48228790 AGAGGAAATTA
1 AGAGGAAATTG
48228801 AGAGGAAATTG
1 AGAGGAAATTG
48228812 AGAGGAAATTTG
1 AGAGGAAA-TTG
48228824 AGAG
1 AGAG
48228828 AGGATTAGTT
Statistics
Matches: 76, Mismatches: 15, Indels: 17
0.70 0.14 0.16
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 3 0.04
10 3 0.04
11 57 0.75
12 11 0.14
ACGTcount: A:0.44, C:0.02, G:0.31, T:0.23
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:48228754 original size:51 final size:51
Alignment explanation
Indices: 48228693--48228792 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
48228683 AATTATTTAA
48228693 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * * *
48228744 AAATATGGATTTGAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
48228793 GGAAATTAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.27, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:48230700 original size:21 final size:21
Alignment explanation
Indices: 48230676--48230728 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
48230666 CATTGTTTCT
*
48230676 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
48230697 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
48230718 AATCTCACCGC
1 AATCTCACCGC
48230729 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:48235243 original size:23 final size:25
Alignment explanation
Indices: 48235217--48235270 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
48235207 AAAAATTCTA
*
48235217 AAAATATAT-AAAAA-AAAGT-AGAT
1 AAAATAT-TCAAAAATAAAGTGAGAG
*
48235240 AAAAAATTCAAAAATAAAGTGAGAG
1 AAAATATTCAAAAATAAAGTGAGAG
48235265 AAAATA
1 AAAATA
48235271 AGGAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 1 0.04
23 11 0.44
24 5 0.20
25 8 0.32
ACGTcount: A:0.69, C:0.02, G:0.11, T:0.19
Consensus pattern (25 bp):
AAAATATTCAAAAATAAAGTGAGAG
Found at i:48245162 original size:11 final size:11
Alignment explanation
Indices: 48245148--48245210 Score: 67
Period size: 11 Copynumber: 5.8 Consensus size: 11
48245138 TACAATATCT
48245148 AAATAATAATA
1 AAATAATAATA
48245159 AAATAATAA-A
1 AAATAATAATA
*
48245169 AATATAATAACA
1 AA-ATAATAATA
*
48245181 AAATGATAAT-
1 AAATAATAATA
*
48245191 AAATAACAATA
1 AAATAATAATA
*
48245202 AAAAAATAA
1 AAATAATAA
48245211 GGTTAATTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
10 11 0.26
11 29 0.67
12 3 0.07
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (11 bp):
AAATAATAATA
Found at i:48249518 original size:3 final size:3
Alignment explanation
Indices: 48249510--48249538 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
48249500 TCTTAGACAG
48249510 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
48249539 CATGATGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:48257615 original size:24 final size:24
Alignment explanation
Indices: 48257579--48257632 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
48257569 GTGTTGGAAA
48257579 TTCTC-TTCTTTCTTACAT-TGCAGT
1 TTCTCTTTCTTTCTT-CATCTG-AGT
48257603 TTCTCTTTC-TTCTTCATCTGAGT
1 TTCTCTTTCTTTCTTCATCTGAGT
48257626 TT-TCTTT
1 TTCTCTTT
48257633 TAAGTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 5 0.18
23 8 0.29
24 12 0.43
25 3 0.11
ACGTcount: A:0.09, C:0.24, G:0.07, T:0.59
Consensus pattern (24 bp):
TTCTCTTTCTTTCTTCATCTGAGT
Found at i:48267224 original size:17 final size:17
Alignment explanation
Indices: 48267188--48267223 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
48267178 AATTTGGTTT
*
48267188 AAATAAAAAATTATTTA
1 AAATAAAAAATTATTAA
48267205 AAAT-AAAAATTATTAA
1 AAATAAAAAATTATTAA
48267221 AAA
1 AAA
48267224 AATTATTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATAAAAAATTATTAA
Found at i:48269528 original size:10 final size:10
Alignment explanation
Indices: 48269509--48269540 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
48269499 ATCATCAACT
*
48269509 AACTAACATC
1 AACTAGCATC
48269519 AACTAGCATC
1 AACTAGCATC
48269529 AACTAGCATC
1 AACTAGCATC
48269539 AA
1 AA
48269541 ATGATACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.47, C:0.28, G:0.06, T:0.19
Consensus pattern (10 bp):
AACTAGCATC
Found at i:48270453 original size:41 final size:41
Alignment explanation
Indices: 48270408--48270517 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 41
48270398 CACCGAAACA
*
48270408 AAGCTTGCTAGGCACAAAGTCTGATATAAATCACCGGCATG
1 AAGCTTGCTAGGCACAAAGTCTGATATAAATCACCAGCATG
*
48270449 AAGCTTGCTAGGCACAGAG-CTTGATATAAATCACCAGCATG
1 AAGCTTGCTAGGCACAAAGTC-TGATATAAATCACCAGCATG
* * * * *
48270490 AAGCATACTAGACTCAAAGTCCGATATA
1 AAGCTTGCTAGGCACAAAGTCTGATATA
48270518 TTATCTCAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 1 0.02
41 57 0.97
42 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (41 bp):
AAGCTTGCTAGGCACAAAGTCTGATATAAATCACCAGCATG
Found at i:48280542 original size:11 final size:13
Alignment explanation
Indices: 48280518--48280549 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
48280508 TAGTTTATTA
48280518 ATATTTTAATATG
1 ATATTTTAATATG
48280531 AT-TTTTAA-ATG
1 ATATTTTAATATG
48280542 ATATTTTA
1 ATATTTTA
48280550 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:48282778 original size:30 final size:27
Alignment explanation
Indices: 48282716--48282784 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 27
48282706 TCAATTCAAA
48282716 AAAATCAA-TCAATCAATTCATAATAT
1 AAAATCAATTCAATCAATTCATAATAT
* *
48282742 -ATATCAATTCAATCAATTCCCATCAATTT
1 AAAATCAATTCAATCAATT--CAT-AATAT
48282771 AAAATCAATTCAAT
1 AAAATCAATTCAAT
48282785 ATGAAAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 6 0.17
26 10 0.29
28 3 0.09
29 4 0.11
30 12 0.34
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAATCAATTCAATCAATTCATAATAT
Found at i:48283193 original size:50 final size:50
Alignment explanation
Indices: 48283137--48283238 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
48283127 TTTAACTCCC
48283137 TAATTTCACTTAAATCCCTAAATTTTGAATTTTCACAATTTAATCCCTAT
1 TAATTTCACTTAAATCCCTAAATTTTGAATTTTCACAATTTAATCCCTAT
48283187 TAATTTCACTTAAATCCCTAAATTTTGAATTTTCACAATTTAATCCCTAT
1 TAATTTCACTTAAATCCCTAAATTTTGAATTTTCACAATTTAATCCCTAT
48283237 TA
1 TA
48283239 CTCAAAATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.34, C:0.20, G:0.02, T:0.44
Consensus pattern (50 bp):
TAATTTCACTTAAATCCCTAAATTTTGAATTTTCACAATTTAATCCCTAT
Found at i:48283592 original size:7 final size:7
Alignment explanation
Indices: 48283575--48283635 Score: 99
Period size: 7 Copynumber: 8.9 Consensus size: 7
48283565 TTCTTTGTTT
48283575 TATATTAA
1 TATA-TAA
48283583 TATATAA
1 TATATAA
48283590 TATATAA
1 TATATAA
48283597 TATATAA
1 TATATAA
48283604 TATAT-A
1 TATATAA
48283610 -ATATAA
1 TATATAA
48283616 TATATAA
1 TATATAA
48283623 TATATAA
1 TATATAA
48283630 TATATA
1 TATATA
48283636 TACTTAAACA
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
5 4 0.08
6 2 0.04
7 41 0.80
8 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATATAA
Found at i:48283616 original size:26 final size:26
Alignment explanation
Indices: 48283584--48283635 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
48283574 TTATATTAAT
48283584 ATATAATATATAATATATAATATATA
1 ATATAATATATAATATATAATATATA
48283610 ATATAATATATAATATATAATATATA
1 ATATAATATATAATATATAATATATA
48283636 TACTTAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATATAATATATAATATATAATATATA
Found at i:48283633 original size:12 final size:12
Alignment explanation
Indices: 48283580--48283626 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
48283570 TGTTTTATAT
48283580 TAATATATAATA
1 TAATATATAATA
48283592 T-ATA-AT-ATA
1 TAATATATAATA
48283601 TAATATATAATA
1 TAATATATAATA
48283613 TAATATATAATA
1 TAATATATAATA
48283625 TA
1 TA
48283627 TAATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.12
10 5 0.16
11 5 0.16
12 18 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATATATAATA
Found at i:48283699 original size:44 final size:45
Alignment explanation
Indices: 48283608--48283709 Score: 111
Period size: 46 Copynumber: 2.3 Consensus size: 45
48283598 ATATAATATA
*
48283608 TAATATAATATATAATATATAATATATATACTTAAACATTAAGTTT
1 TAATATAATATATAATATATAATATATATA-TTAAACATTAAATTT
* ** *
48283654 TAATATTATAT-TAATATTATAATATATAT-TTTTACTTTAAATTT
1 TAATATAATATATAATA-TATAATATATATATTAAACATTAAATTT
48283698 T-ATAATAATATA
1 TAAT-ATAATATA
48283710 CTTATGCCGC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
43 2 0.04
44 18 0.38
45 5 0.11
46 22 0.47
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (45 bp):
TAATATAATATATAATATATAATATATATATTAAACATTAAATTT
Found at i:48285362 original size:15 final size:15
Alignment explanation
Indices: 48285342--48285371 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
48285332 TTTCTAATAA
48285342 AATCAAGACTCCAAC
1 AATCAAGACTCCAAC
48285357 AATCAAGACTCCAAC
1 AATCAAGACTCCAAC
48285372 TTTCATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.33, G:0.07, T:0.13
Consensus pattern (15 bp):
AATCAAGACTCCAAC
Found at i:48285883 original size:23 final size:23
Alignment explanation
Indices: 48285811--48285878 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
48285801 GTGATAATTC
*
48285811 GTGATTTCAACACTTTGGTGCTA
1 GTGATTTCAACACTTTAGTGCTA
* *
48285834 GTGATTTCAGCACTTCAGTGCTA
1 GTGATTTCAACACTTTAGTGCTA
*
48285857 GTG-TTTCCAACACTTTTGTGCT
1 GTGATTT-CAACACTTTAGTGCT
48285879 CGTGTATCGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 3 0.08
23 35 0.92
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (23 bp):
GTGATTTCAACACTTTAGTGCTA
Found at i:48286396 original size:61 final size:61
Alignment explanation
Indices: 48286322--48286443 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
48286312 GAATATAATG
* *
48286322 AAAGCTCAGAAGTGTTTTTAAGAAAATGTATGAAATAATTAAGCTCTAGGTTGTTTTGATT
1 AAAGCTCACAAGTGTTTATAAGAAAATGTATGAAATAATTAAGCTCTAGGTTGTTTTGATT
48286383 AAAGCTCACAAGTGTTTATAAGAAAATGTATGAAATAATTAAGCTCTAGGTTGTTTTGATT
1 AAAGCTCACAAGTGTTTATAAGAAAATGTATGAAATAATTAAGCTCTAGGTTGTTTTGATT
48286444 GATCTTTAAG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (61 bp):
AAAGCTCACAAGTGTTTATAAGAAAATGTATGAAATAATTAAGCTCTAGGTTGTTTTGATT
Found at i:48287074 original size:26 final size:27
Alignment explanation
Indices: 48287038--48287099 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
48287028 CGGCCCGCCC
* * * *
48287038 ATTTTTAAAAT-AAACATTAAAAAATT
1 ATTTTAAAAATAAAAAAATAAAAAAAT
48287064 ATTTTAAAAATAAAAAAATAAAAAAAT
1 ATTTTAAAAATAAAAAAATAAAAAAAT
48287091 ATTTTAAAA
1 ATTTTAAAA
48287100 GTATTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
ATTTTAAAAATAAAAAAATAAAAAAAT
Found at i:48290746 original size:24 final size:23
Alignment explanation
Indices: 48290690--48290743 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
48290680 GAGAATGGTT
* *
48290690 TATTAAATAAAAATAAAATAATAT
1 TATTAAATTAAAATAAAATAA-AA
* *
48290714 TTTTTAATTAAAATAAAATAAAA
1 TATTAAATTAAAATAAAATAAAA
48290737 TATTAAA
1 TATTAAA
48290744 ATTTCTTGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TATTAAATTAAAATAAAATAAAA
Found at i:48291516 original size:11 final size:11
Alignment explanation
Indices: 48291500--48291548 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
48291490 TGCTCCCACT
*
48291500 TTTTGCTATTA
1 TTTTGCTACTA
48291511 TTTTGCTACTA
1 TTTTGCTACTA
** *
48291522 TTTCACTATTA
1 TTTTGCTACTA
*
48291533 TGTTGCTACTA
1 TTTTGCTACTA
48291544 TTTTG
1 TTTTG
48291549 TTGTTAATGT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.10, T:0.57
Consensus pattern (11 bp):
TTTTGCTACTA
Found at i:48291533 original size:22 final size:22
Alignment explanation
Indices: 48291505--48291546 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
48291495 CCACTTTTTG
*
48291505 CTATTATTTTGCTACTATTTCA
1 CTATTATGTTGCTACTATTTCA
48291527 CTATTATGTTGCTACTATTT
1 CTATTATGTTGCTACTATTT
48291547 TGTTGTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.55
Consensus pattern (22 bp):
CTATTATGTTGCTACTATTTCA
Found at i:48292290 original size:10 final size:11
Alignment explanation
Indices: 48292251--48292289 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
48292241 CCGGATAGAG
48292251 AATAAAAA-A-
1 AATAAAAACAT
48292260 AACTAAAAACAT
1 AA-TAAAAACAT
48292272 AATAAAAACAT
1 AATAAAAACAT
48292283 AATAAAA
1 AATAAAA
48292290 CTGCATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.07
10 6 0.22
11 17 0.63
12 2 0.07
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AATAAAAACAT
Found at i:48296112 original size:22 final size:22
Alignment explanation
Indices: 48296086--48296155 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
48296076 TTGATTTTAT
*
48296086 AAATAAAATATTTAAAAATAAA
1 AAATAAAATAATTAAAAATAAA
* *
48296108 AAATACATTAATTAAAAAT-AA
1 AAATAAAATAATTAAAAATAAA
*
48296129 AAATAAACATTAATTAAAAAGAAA
1 AAATAAA-A-TAATTAAAAATAAA
48296153 AAA
1 AAA
48296156 GCTTGAAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 8 0.21
22 16 0.41
23 10 0.26
24 5 0.13
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.24
Consensus pattern (22 bp):
AAATAAAATAATTAAAAATAAA
Found at i:48296131 original size:23 final size:22
Alignment explanation
Indices: 48296097--48296155 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 22
48296087 AATAAAATAT
*
48296097 TTAAAAATAAAAAATACATTAA
1 TTAAAAATAAAAAAAACATTAA
48296119 TTAAAAATAAAAATAAACATTAA
1 TTAAAAATAAAAA-AAACATTAA
*
48296142 TTAAAAAGAAAAAA
1 TTAAAAATAAAAAA
48296156 GCTTGAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (22 bp):
TTAAAAATAAAAAAAACATTAA
Found at i:48296506 original size:142 final size:133
Alignment explanation
Indices: 48296215--48296557 Score: 384
Period size: 142 Copynumber: 2.5 Consensus size: 133
48296205 ATGGAACCTC
** * **
48296215 AGACTCAAGGATGTAAGCGCAATTATCTAATCATCTAACAAAAGGAGTTAATATGTTAAAAATAT
1 AGACTCAA-GATGTAATTGCAATTATCTAACCATCTAACAAAA-GAACTAATATGTTAAAAATAT
* * *
48296280 TAATTAAAAAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATGTGAGTAGTAGAGGAATTGA
64 TAATTAAAAAAAAGCTTAAAGCAACATGAAATAAAAAATACAAATATGAGTAGAAGAGGAATTGA
*
48296345 ATTTG
129 ATATG
* * * * *
48296350 GGATTCAATGATGTAATTACAACTATCTAACCATCTAACGAAAGAACTAATATGTTAACAAATAT
1 AGACTCAA-GATGTAATTGCAATTATCTAACCATCTAACAAAAGAACTAATATGTTAA-AAATAT
*
48296415 TAATTAAAAATTTAAAAAGCTTAAAGCAACATGAAATAAAAAAAATATAAATATGAGTAGAAGAG
64 TAATT--AAA---AAAAAGCTTAAAGCAACATGAAAT--AAAAAATACAAATATGAGTAGAAGAG
*
48296480 GAATTTAACTAT-
122 GAATTGAA-TATG
** *
48296492 AGACTCAAGAATGTAATTGCAATTATCTAACCATCTAATTAAAGAACTAATATATTAAAAAT-TT
1 AGACTCAAG-ATGTAATTGCAATTATCTAACCATCTAACAAAAGAACTAATATGTTAAAAATATT
48296556 AA
65 AA
48296558 AAAGCTTAAA
Statistics
Matches: 174, Mismatches: 24, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
134 13 0.07
135 45 0.26
137 3 0.02
140 27 0.16
141 5 0.03
142 79 0.45
143 2 0.01
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.28
Consensus pattern (133 bp):
AGACTCAAGATGTAATTGCAATTATCTAACCATCTAACAAAAGAACTAATATGTTAAAAATATTA
ATTAAAAAAAAGCTTAAAGCAACATGAAATAAAAAATACAAATATGAGTAGAAGAGGAATTGAAT
ATG
Found at i:48298139 original size:21 final size:20
Alignment explanation
Indices: 48298110--48298163 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 20
48298100 TGCCTTAAAG
*
48298110 TCTTTTAAAATTTTAAAAAT
1 TCTTTTAAAACTTTAAAAAT
*
48298130 TCTTATTAAACCTTT-AAAA-
1 TCTT-TTAAAACTTTAAAAAT
48298149 --TTTTAAAACTTTAAA
1 TCTTTTAAAACTTTAAA
48298164 TTAAATCTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 9 0.31
17 4 0.14
20 8 0.28
21 8 0.28
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.46
Consensus pattern (20 bp):
TCTTTTAAAACTTTAAAAAT
Found at i:48298547 original size:20 final size:22
Alignment explanation
Indices: 48298522--48298562 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
48298512 AAGAGAGAAA
48298522 GAAAAC-TCTT-AAAATTTGGG
1 GAAAACGTCTTGAAAATTTGGG
*
48298542 GAAAACGTTTTGAAAATTTGG
1 GAAAACGTCTTGAAAATTTGG
48298563 ATTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (22 bp):
GAAAACGTCTTGAAAATTTGGG
Found at i:48322344 original size:13 final size:13
Alignment explanation
Indices: 48322326--48322369 Score: 88
Period size: 13 Copynumber: 3.4 Consensus size: 13
48322316 GCCTTAAAAA
48322326 TAATTATAATATT
1 TAATTATAATATT
48322339 TAATTATAATATT
1 TAATTATAATATT
48322352 TAATTATAATATT
1 TAATTATAATATT
48322365 TAATT
1 TAATT
48322370 TAGAATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATTATAATATT
Found at i:48323462 original size:18 final size:18
Alignment explanation
Indices: 48323418--48323465 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
48323408 TAAATATGAG
* *
48323418 AAATGATGCTCACATTTT
1 AAATGATGTTCACATTTC
48323436 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
48323454 AAATGATGTTCA
1 AAATGATGTTCA
48323466 AATTGATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:48323991 original size:72 final size:73
Alignment explanation
Indices: 48323888--48324060 Score: 237
Period size: 72 Copynumber: 2.4 Consensus size: 73
48323878 AACAACAATG
* * * *
48323888 CTAAA-CTAGTTTTATCAATAGTTATTCATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTT
1 CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTT
48323952 ATTTATGT-
66 ATTT-TGTA
* * *
48323960 GT-AATCTAGTTTTATTAATAGTTGTTTATGTTTGGTCTTTAGATGTTGAATTTATGTTCTACTT
1 CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTT
*
48324024 ATTTTTTA
66 ATTTTGTA
48324032 CTAAAT-TAGTTTTATCAATAGTTGTTTAT
1 CTAAATCTAGTTTTATCAATAGTTGTTTAT
48324061 ATGTGATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
71 4 0.05
72 81 0.92
73 3 0.03
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (73 bp):
CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTT
ATTTTGTA
Found at i:48330241 original size:156 final size:153
Alignment explanation
Indices: 48329960--48330241 Score: 413
Period size: 156 Copynumber: 1.8 Consensus size: 153
48329950 CATTTATTCA
* * *
48329960 TATTTTTTTTCAAATTTTATTACTTTAAAAAATATATTATTTTGTAATTTTATTATTTTATATTA
1 TATTTTTTTCCAAATTTTATTACTTTAAAAAATATATTATTTTCTAATTTTATTATTTTAAATTA
* * * * *
48330025 TTTTAGTACATTATTTTTGAAATGTATTCATTTAGTTTGATTTTTCAATAAATTTAAAAAAAAAA
66 TTTTAGTACATTATGTTTGAAATGTATTAATTTACTATGATTTTTAAATAAATTTAAAAAAAAAA
48330090 CTCTTATTTCGTCCCTTTGTTCG
131 CTCTTATTTCGTCCCTTTGTTCG
* *
48330113 TATTTTTTTCCTAGATTTTCTTACTTTCAATAAAATATATTATTTTCCT-ATTTTATTATTTTAA
1 TATTTTTTTCC-AAATTTTATTACTTT-AA-AAAATATATTATTTT-CTAATTTTATTATTTTAA
* *
48330177 ATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTATGTTTTTTAAATAAATTTTAAAAA
62 ATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTATGATTTTTAAATAAATTTAAAAAA
48330242 NNNNNNNNNN
Statistics
Matches: 113, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
153 10 0.09
154 13 0.12
155 2 0.02
156 87 0.77
157 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (153 bp):
TATTTTTTTCCAAATTTTATTACTTTAAAAAATATATTATTTTCTAATTTTATTATTTTAAATTA
TTTTAGTACATTATGTTTGAAATGTATTAATTTACTATGATTTTTAAATAAATTTAAAAAAAAAA
CTCTTATTTCGTCCCTTTGTTCG
Found at i:48330674 original size:152 final size:152
Alignment explanation
Indices: 48330398--48330695 Score: 442
Period size: 152 Copynumber: 2.0 Consensus size: 152
48330388 AATAAGGGTT
* * * *
48330398 TTTTTAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATG
1 TTTTTAAATTTATTTAAAAAACAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATG
** *
48330463 TAAAATAATAAAATACAAAAATAATATATTTTTACTGGAAGTAATAAAATCCGGGAAAAAAATGC
66 TAAAATAATAAAATACAAAAATAATATATTTTTA-TAAAAGTAATAAAATCCGGGAAAAAAATAC
48330528 GAACAAAGGGTCGAAATAATTTG
130 GAACAAAGGGTCGAAATAATTTG
48330551 TTTTT-AATTTATTTAAAAATA-AAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAAT
1 TTTTTAAATTTATTTAAAAA-ACAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAAT
* *
48330614 GTAAAATAATAAAATTA-GAAAATAATATATTTTT-TAAAAGTAATAAAATCTGGGAAAAAAATA
65 GTAAAATAATAAAA-TACAAAAATAATATATTTTTATAAAAGTAATAAAATCCGGGAAAAAAATA
* *
48330677 CGAACAAATGGTTGAAATA
129 CGAACAAAGGGTCGAAATA
48330696 CGAACATGTT
Statistics
Matches: 132, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
150 42 0.32
152 82 0.62
153 8 0.06
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (152 bp):
TTTTTAAATTTATTTAAAAAACAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATG
TAAAATAATAAAATACAAAAATAATATATTTTTATAAAAGTAATAAAATCCGGGAAAAAAATACG
AACAAAGGGTCGAAATAATTTG
Found at i:48331003 original size:16 final size:18
Alignment explanation
Indices: 48330964--48330997 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48330954 TAATTTTATA
48330964 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
48330981 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
48330998 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:48332055 original size:9 final size:8
Alignment explanation
Indices: 48332035--48332152 Score: 55
Period size: 9 Copynumber: 13.8 Consensus size: 8
48332025 ATTAAAATCA
48332035 ATAAAATCT
1 ATAAAAT-T
48332044 ATAAATATT
1 ATAAA-ATT
48332053 ATAAAATT
1 ATAAAATT
*
48332061 -T-TAATT
1 ATAAAATT
*
48332067 AAAAATATT
1 ATAAA-ATT
48332076 A-AAAATT
1 ATAAAATT
48332083 A-AAAATTT
1 ATAAAA-TT
48332091 ATTAAAAATT
1 A-T-AAAATT
*
48332101 AGAAAAATT
1 A-TAAAATT
48332110 ATAAAAATCGT
1 AT-AAAAT--T
*
48332121 AAAAAATTT
1 ATAAAA-TT
48332130 ATAAAATAT
1 ATAAAAT-T
*
48332139 ATAGAATT
1 ATAAAATT
48332147 ATAAAA
1 ATAAAA
48332153 AAAAATTAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 27
0.70 0.08 0.22
Matches are distributed among these distances:
6 4 0.05
7 9 0.10
8 17 0.20
9 40 0.47
10 9 0.10
11 7 0.08
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (8 bp):
ATAAAATT
Found at i:48332095 original size:18 final size:17
Alignment explanation
Indices: 48332063--48332135 Score: 76
Period size: 18 Copynumber: 4.1 Consensus size: 17
48332053 ATAAAATTTT
*
48332063 AATTAAAAATAT-TAAA
1 AATTAAAAATTTATAAA
48332079 AATTAAAAATTTATTAAA
1 AATTAAAAATTTA-TAAA
*
48332097 AATTAGAAAAATTATAAA
1 AATTA-AAAATTTATAAA
48332115 AATCGTAAAAAATTTATAAA
1 AAT--T-AAAAATTTATAAA
48332135 A
1 A
48332136 TATATAGAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
16 11 0.23
18 16 0.33
19 7 0.15
20 13 0.27
21 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (17 bp):
AATTAAAAATTTATAAA
Found at i:48332296 original size:20 final size:19
Alignment explanation
Indices: 48332272--48332322 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
48332262 TTTTTTTATG
48332272 ATTTTTATAAAATTTTACA
1 ATTTTTATAAAATTTTACA
* ***
48332291 ATTTTTTTTATTTTTTTACA
1 A-TTTTTATAAAATTTTACA
48332311 ATTTTTATAAAA
1 ATTTTTATAAAA
48332323 AAATCTAATT
Statistics
Matches: 23, Mismatches: 8, Indels: 2
0.70 0.24 0.06
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTTATAAAATTTTACA
Found at i:48332363 original size:30 final size:30
Alignment explanation
Indices: 48332329--48332400 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
48332319 AAAAAAATCT
*
48332329 AATTTTAATAAATTT-TAATATTTTTTTCTA
1 AATTTTAATAAATTTATAAT-TTCTTTTCTA
** *
48332359 AATTTTTTTATTATTTATAATTTCTTTTCTA
1 AATTTTAATA-AATTTATAATTTCTTTTCTA
*
48332390 ATTTTTAATAA
1 AATTTTAATAA
48332401 GAGGAGGGGC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
30 8 0.25
31 20 0.62
32 4 0.12
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (30 bp):
AATTTTAATAAATTTATAATTTCTTTTCTA
Found at i:48332617 original size:86 final size:82
Alignment explanation
Indices: 48332405--48332617 Score: 230
Period size: 85 Copynumber: 2.5 Consensus size: 82
48332395 TAATAAGAGG
* * * * **
48332405 AGGGGCTTAATTGTTGTTTTGAAAAATTTTGAAGGTATTTTTGTTGCATTTTGAAAGTTCAAGTA
1 AGGGGCTTAATTCTTTTTTTGAAAAAGTTTG-AGGTGTTTTTAATGCATTTTGAAAGTTCAAGTA
48332470 CCAATTGAGTGAAAAAAA
65 CCAATTGAGTGAAAAAAA
* * * * *
48332488 AGGGGATTAGTTGCTTTTTTTGAAGAAGTTTGAGGGTGTTTTTTAATGCATTTTGAAATTTTAAG
1 AGGGGCTTAATT-CTTTTTTTGAAAAAGTTTGA-GGTG-TTTTTAATGCATTTTGAAAGTTCAAG
*
48332553 TGCTCAATTGAGTGCAAAAAAA
63 TAC-CAATTGAGTG-AAAAAAA
48332575 AGGGGGCTTAATTACTTTTTCTTGAAAAAGTTTGAGG-GTTTTT
1 A-GGGGCTTAATT-CTTTTT-TTGAAAAAGTTTGAGGTGTTTTT
48332618 TTACACATTT
Statistics
Matches: 107, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
83 11 0.10
84 18 0.17
85 24 0.22
86 15 0.14
87 9 0.08
88 17 0.16
89 13 0.12
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.40
Consensus pattern (82 bp):
AGGGGCTTAATTCTTTTTTTGAAAAAGTTTGAGGTGTTTTTAATGCATTTTGAAAGTTCAAGTAC
CAATTGAGTGAAAAAAA
Found at i:48337175 original size:14 final size:15
Alignment explanation
Indices: 48337158--48337198 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
48337148 GGTCATATTG
48337158 CAACAATCAGATT-T
1 CAACAATCAGATTAT
* *
48337172 CAACAATTATATTAT
1 CAACAATCAGATTAT
48337187 -AACAATCAGATT
1 CAACAATCAGATT
48337199 CCAATGATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (15 bp):
CAACAATCAGATTAT
Found at i:48337211 original size:28 final size:28
Alignment explanation
Indices: 48337150--48337212 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
48337140 AAATCAACGG
* *
48337150 TCATATTGCAACAATCAGATTTCAACAA
1 TCATATTACAACAATCAGATTCCAACAA
* * **
48337178 TTATATTATAACAATCAGATTCCAATGA
1 TCATATTACAACAATCAGATTCCAACAA
48337206 TCATATT
1 TCATATT
48337213 TTTGCATTAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.35
Consensus pattern (28 bp):
TCATATTACAACAATCAGATTCCAACAA
Found at i:48346856 original size:3 final size:3
Alignment explanation
Indices: 48346848--48346895 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
48346838 ATAAAAAGTA
48346848 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
48346896 CAAAAGAATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:48352815 original size:18 final size:18
Alignment explanation
Indices: 48352792--48352826 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48352782 ATCTGCTTCT
*
48352792 GCTGCTGCTGTTGTTGCC
1 GCTGCTGCTGCTGTTGCC
*
48352810 GCTGCTGTTGCTGTTGC
1 GCTGCTGCTGCTGTTGC
48352827 TGTGATTGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.34, T:0.40
Consensus pattern (18 bp):
GCTGCTGCTGCTGTTGCC
Found at i:48352926 original size:6 final size:6
Alignment explanation
Indices: 48352872--48352907 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
48352862 AGGAGTGGAA
48352872 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG
48352908 GTTGAATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TTAGGG
Found at i:48353117 original size:3 final size:3
Alignment explanation
Indices: 48353109--48353143 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
48353099 TAAGAGAAAT
* *
48353109 TGC TGC TGC TGC TGC TGC TGC TGC AGC CGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
48353144 AGGACTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.34, G:0.34, T:0.29
Consensus pattern (3 bp):
TGC
Found at i:48354670 original size:13 final size:13
Alignment explanation
Indices: 48354652--48354676 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48354642 TATAATACTA
48354652 ATTTTAAAAATAT
1 ATTTTAAAAATAT
48354665 ATTTTAAAAATA
1 ATTTTAAAAATA
48354677 AAGGTAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTTAAAAATAT
Found at i:48359954 original size:13 final size:13
Alignment explanation
Indices: 48359936--48359960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48359926 ACCGTTAATA
48359936 ATTTGATTCAATT
1 ATTTGATTCAATT
48359949 ATTTGATTCAAT
1 ATTTGATTCAAT
48359961 ATCTAATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
ATTTGATTCAATT
Found at i:48361687 original size:44 final size:44
Alignment explanation
Indices: 48361577--48361695 Score: 166
Period size: 44 Copynumber: 2.7 Consensus size: 44
48361567 TAAAAGAGAA
* * *
48361577 TACAATATATCACTGCAATTATACACTACACTTTAATTTGATAG
1 TACAATATATCACTGCAATTATACCCTACAATTTAATTTAATAG
*
48361621 TACAATATATCACTGCAGTTATACCCTACAATTTAATTTAATAG
1 TACAATATATCACTGCAATTATACCCTACAATTTAATTTAATAG
* ** *
48361665 TACAATATATCATTAAAATTATACCTTACAA
1 TACAATATATCACTGCAATTATACCCTACAA
48361696 AATATTGAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (44 bp):
TACAATATATCACTGCAATTATACCCTACAATTTAATTTAATAG
Found at i:48365757 original size:21 final size:22
Alignment explanation
Indices: 48365733--48365781 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
48365723 CCCATTGCTT
*
48365733 GTGGCTATACAA-TTGTTTGCA
1 GTGGCTATACAATTTATTTGCA
*
48365754 GTGGCTATATAATTTATTTGCA
1 GTGGCTATACAATTTATTTGCA
48365776 GTGGCT
1 GTGGCT
48365782 CCATCTGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.41
Consensus pattern (22 bp):
GTGGCTATACAATTTATTTGCA
Found at i:48366635 original size:23 final size:23
Alignment explanation
Indices: 48366566--48366638 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
48366556 GTATATTAAA
48366566 ATATAATTAAAATCATTTTGATT
1 ATATAATTAAAATCATTTTGATT
*** * * *
48366589 ATATAA-TATTTTTA-ATTGA-A
1 ATATAATTAAAATCATTTTGATT
48366609 ATATAATTAAAATCATTTTGATT
1 ATATAATTAAAATCATTTTGATT
48366632 ATATAAT
1 ATATAAT
48366639 ATTAATATAA
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 6 0.17
21 8 0.23
22 8 0.23
23 13 0.37
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (23 bp):
ATATAATTAAAATCATTTTGATT
Found at i:48369878 original size:18 final size:17
Alignment explanation
Indices: 48369850--48369884 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48369840 AATTATAAGA
*
48369850 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
48369867 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
48369885 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:48369995 original size:156 final size:156
Alignment explanation
Indices: 48369711--48369997 Score: 547
Period size: 156 Copynumber: 1.8 Consensus size: 156
48369701 NNNNNNNNNN
*
48369711 ATTTTAATTAAAATATATTTAATAAAAATTATGTTTAAATATGATTAAATTATTTATTACTGATA
1 ATTTTAATTAAAATATATTTAATAAAAATTATGTTTAAATATGATTAAAATATTTATTACTGATA
48369776 ATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAACAAATTTATGCTA
66 ATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAACAAATTTATGCTA
48369841 ATTATAAGAATTTTATTAAATTATAT
131 ATTATAAGAATTTTATTAAATTATAT
*
48369867 ATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAAATATTTATTACTGATA
1 ATTTTAATTAAAATATATTTAATAAAAATTATGTTTAAATATGATTAAAATATTTATTACTGATA
*
48369932 ATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAACAATTTTATGCTA
66 ATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAACAAATTTATGCTA
48369997 A
131 A
48369998 GGGTATTTTA
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
156 128 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (156 bp):
ATTTTAATTAAAATATATTTAATAAAAATTATGTTTAAATATGATTAAAATATTTATTACTGATA
ATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAACAAATTTATGCTA
ATTATAAGAATTTTATTAAATTATAT
Found at i:48370114 original size:44 final size:45
Alignment explanation
Indices: 48370049--48370139 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
48370039 ACCTCTATTC
* * *
48370049 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
48370093 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
48370138 CA
1 CA
48370140 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:48370141 original size:16 final size:16
Alignment explanation
Indices: 48370120--48370155 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
48370110 GATTAGCTAT
48370120 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
48370136 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
48370152 TACA
1 TACA
48370156 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:48372135 original size:15 final size:16
Alignment explanation
Indices: 48372117--48372158 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
48372107 CAACATCTAA
48372117 TTTTAAAATATTAT-T
1 TTTTAAAATATTATAT
*
48372132 TTTTAAAA-ATTTTCAT
1 TTTTAAAATATTAT-AT
48372148 TTTTAAAATAT
1 TTTTAAAATAT
48372159 ACTACATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 4 0.17
15 8 0.35
16 9 0.39
17 2 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAAATATTATAT
Found at i:48376747 original size:32 final size:32
Alignment explanation
Indices: 48376711--48376775 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
48376701 AAAGTGTTAA
48376711 AGGGGATCTTAGGTAGCCTAATCACCTATACT
1 AGGGGATCTTAGGTAGCCTAATCACCTATACT
48376743 AGGGGATCTTAGGTAGCCTAATCACCTATACT
1 AGGGGATCTTAGGTAGCCTAATCACCTATACT
48376775 A
1 A
48376776 AGTTCCATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (32 bp):
AGGGGATCTTAGGTAGCCTAATCACCTATACT
Found at i:48380589 original size:42 final size:42
Alignment explanation
Indices: 48380510--48380596 Score: 106
Period size: 42 Copynumber: 2.0 Consensus size: 42
48380500 CTTCGTTTTC
* * *
48380510 TCGATGCCATAGTCCTATTATGGTCTTGCACATAATCACA-AA
1 TCGATGCCATAGCCCAACTATGGTCTT-CACATAATCACATAA
48380552 TCGATGCCATAGCCCAACTATGGTCTT-ACATGGAATCACATAA
1 TCGATGCCATAGCCCAACTATGGTCTTCACAT--AATCACATAA
48380595 TC
1 TC
48380597 ACAGACCGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
40 4 0.10
42 31 0.79
43 4 0.10
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (42 bp):
TCGATGCCATAGCCCAACTATGGTCTTCACATAATCACATAA
Found at i:48380615 original size:50 final size:50
Alignment explanation
Indices: 48380538--48380897 Score: 352
Period size: 50 Copynumber: 7.3 Consensus size: 50
48380528 TATGGTCTTG
* * *
48380538 CACATAATCACAAATCGATGCCATAGCCCAACTATGGTCTTACATGGAAT
1 CACATAATCACATACCGATGCCATAGCCCAGCTATGGTCTTACATGGAAT
* * * * *
48380588 CACATAATCACAGACCGATGTCGTAGCCTAGCTATGGTCTTACATTGAAT
1 CACATAATCACATACCGATGCCATAGCCCAGCTATGGTCTTACATGGAAT
* * * * ***
48380638 CACGTAACCATATACCGATGCCATAGCCCAACTATGGTCTTACGCAGAAT
1 CACATAATCACATACCGATGCCATAGCCCAGCTATGGTCTTACATGGAAT
* * *
48380688 CACATAATCACATACCGATGCCATAACCCAGCTATGATATTACATGGAAT
1 CACATAATCACATACCGATGCCATAGCCCAGCTATGGTCTTACATGGAAT
* * * * ** * *
48380738 TAC---ACCATATAACGATTTCATAGCCCATCTATAGTCTTACATGGAAT
1 CACATAATCACATACCGATGCCATAGCCCAGCTATGGTCTTACATGGAAT
* * *
48380785 CACATAATCACATACCGATGTCATAGCCTAGCTATGGTCTTACA-CGAAT
1 CACATAATCACATACCGATGCCATAGCCCAGCTATGGTCTTACATGGAAT
* * * * *
48380834 CGCACT-ATCACATATCGGTGCCATATCCCAGCTATGGTCTTACACGGAAT
1 CACA-TAATCACATACCGATGCCATAGCCCAGCTATGGTCTTACATGGAAT
**
48380884 CACATTGTCACATA
1 CACATAATCACATA
48380898 TCCACATATT
Statistics
Matches: 247, Mismatches: 57, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
47 36 0.15
49 41 0.17
50 170 0.69
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (50 bp):
CACATAATCACATACCGATGCCATAGCCCAGCTATGGTCTTACATGGAAT
Found at i:48383094 original size:46 final size:46
Alignment explanation
Indices: 48383027--48383119 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
48383017 ATTTGGACAC
48383027 TAAGACTACTTAACACGAACATCTATTTCAAAACTTTATTTTAACA
1 TAAGACTACTTAACACGAACATCTATTTCAAAACTTTATTTTAACA
48383073 TAAGACTACTTAACACGAACATCTATTTCAAAACTTTATTTTAACA
1 TAAGACTACTTAACACGAACATCTATTTCAAAACTTTATTTTAACA
48383119 T
1 T
48383120 GAATAGACAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.35
Consensus pattern (46 bp):
TAAGACTACTTAACACGAACATCTATTTCAAAACTTTATTTTAACA
Found at i:48392875 original size:7 final size:7
Alignment explanation
Indices: 48392863--48392887 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
48392853 AGTCGATTGA
48392863 TATTTAG
1 TATTTAG
48392870 TATTTAG
1 TATTTAG
48392877 TATTTAG
1 TATTTAG
48392884 TATT
1 TATT
48392888 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:48393565 original size:18 final size:18
Alignment explanation
Indices: 48393538--48393595 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
48393528 CAGGTGCGTT
*
48393538 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
48393556 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
48393574 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
48393592 TCCT
1 TCCT
48393596 TTTCAGAGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.24, C:0.29, G:0.07, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:48393875 original size:21 final size:21
Alignment explanation
Indices: 48393851--48393899 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
48393841 AGATGCCGTA
48393851 CCGGAAGAACCAA-AATCC-CCG
1 CCGGAAGAA-CAACAA-CCGCCG
*
48393872 CCGGAGGAACAACAACCGCCG
1 CCGGAAGAACAACAACCGCCG
48393893 CCGGAAG
1 CCGGAAG
48393900 CTAGAGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.35, C:0.37, G:0.27, T:0.02
Consensus pattern (21 bp):
CCGGAAGAACAACAACCGCCG
Found at i:48394082 original size:26 final size:25
Alignment explanation
Indices: 48394024--48394147 Score: 116
Period size: 25 Copynumber: 5.1 Consensus size: 25
48394014 TATTTTAAAG
* * *
48394024 TTTATTTCACGTAATAAAATAGAAG
1 TTTATTTGATGTAATAAAATAGAAA
48394049 TTTATTTGATGTAATAAAAATAGAAAA
1 TTTATTTGATGTAAT-AAAATAG-AAA
** * *
48394076 TTT-TTTGA-GT--T-ATTTTGATA
1 TTTATTTGATGTAATAAAATAGAAA
*
48394096 -TTATTTGATGTAATAAAATAGAAG
1 TTTATTTGATGTAATAAAATAGAAA
48394120 TTTATTTGATGTAATAAAATAGAAA
1 TTTATTTGATGTAATAAAATAGAAA
48394145 TTT
1 TTT
48394148 TTGAATATTT
Statistics
Matches: 78, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.03
20 7 0.09
21 5 0.06
23 2 0.03
24 4 0.05
25 41 0.53
26 12 0.15
27 5 0.06
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.44
Consensus pattern (25 bp):
TTTATTTGATGTAATAAAATAGAAA
Found at i:48394100 original size:71 final size:68
Alignment explanation
Indices: 48394002--48394165 Score: 215
Period size: 71 Copynumber: 2.4 Consensus size: 68
48393992 TTATTTGTAC
* *
48394002 AAATATTTTGAGTATTTTAAAGT-TTATTTCACGTAATAAAATAGAAGTTTATTTGATGTAATAA
1 AAAT-TTTTGAATATTTTGAA-TATTATTTCACGTAATAAAATAGAAGTTTATTTGATGTAAT-A
48394066 AAATAG
63 AAATAG
* * *
48394072 AAAATTTTTTGAGTTATTTTG-ATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATA
1 -AAA-TTTTTGA-ATATTTTGAATATTATTTCACGTAATAAAATAGAAGTTTATTTGATGTAATA
48394136 AAATAG
63 AAATAG
48394142 AAATTTTTGAATATTTTGAATATT
1 AAATTTTTGAATATTTTGAATATT
48394166 TTGAATATTT
Statistics
Matches: 84, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
67 7 0.08
68 12 0.14
69 3 0.04
70 8 0.10
71 47 0.56
72 7 0.08
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.45
Consensus pattern (68 bp):
AAATTTTTGAATATTTTGAATATTATTTCACGTAATAAAATAGAAGTTTATTTGATGTAATAAAA
TAG
Found at i:48394160 original size:9 final size:9
Alignment explanation
Indices: 48394146--48394178 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
48394136 AAATAGAAAT
48394146 TTTTGAATA
1 TTTTGAATA
48394155 TTTTGAATA
1 TTTTGAATA
48394164 TTTTGAATA
1 TTTTGAATA
48394173 TTTTGA
1 TTTTGA
48394179 GAATTCTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (9 bp):
TTTTGAATA
Found at i:48394235 original size:23 final size:23
Alignment explanation
Indices: 48394209--48394335 Score: 170
Period size: 23 Copynumber: 5.5 Consensus size: 23
48394199 AATGGAAAAG
48394209 AAAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAATTA
*
48394232 AAAACCCTAACCTAATTAAA-AA
1 AAAACCCTAACCTAATTAAATTA
48394254 GAAAACCCTAACCTAATTAAACCTT-
1 -AAAACCCTAACCTAATTAAA--TTA
48394279 -AAACCCTAACCTAATTAAATTA
1 AAAACCCTAACCTAATTAAATTA
* *
48394301 AAAACCCTAACTTAATTAAATTG
1 AAAACCCTAACCTAATTAAATTA
*
48394324 AAAACTCTAACC
1 AAAACCCTAACC
48394336 CTTAACATTC
Statistics
Matches: 92, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
21 2 0.02
22 1 0.01
23 89 0.97
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (23 bp):
AAAACCCTAACCTAATTAAATTA
Found at i:48394539 original size:115 final size:115
Alignment explanation
Indices: 48394340--48394557 Score: 350
Period size: 115 Copynumber: 1.9 Consensus size: 115
48394330 CTAACCCTTA
* *
48394340 ACATTCACATAATGTTAGATTTGGAAAAATGTTTTTTCCTGGTACTAACAATTAATAATTTTATA
1 ACATTCACATAATGTTAGATTTGGAAAAA-GTATTTTCCTGGTACTAACAAATAATAATTTTATA
* *
48394405 TAATTTGATAATTTTACTAACAATTAATACAATTTATCGGATAATAATTTT
65 CAAATTGATAATTTTACTAACAATTAATACAATTTATCGGATAATAATTTT
48394456 ACATTCACATAATGTTAGATTTGGAAAAA-TATTTTCACTGGTACTAACAAATAATAATTTTATA
1 ACATTCACATAATGTTAGATTTGGAAAAAGTATTTTC-CTGGTACTAACAAATAATAATTTTATA
*
48394520 CAAATTGA-AATTTTTACTAACCATTAATACAATTTATC
65 CAAATTGATAA-TTTTACTAACAATTAATACAATTTATC
48394558 AATTAATAAT
Statistics
Matches: 95, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
114 8 0.08
115 58 0.61
116 29 0.31
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (115 bp):
ACATTCACATAATGTTAGATTTGGAAAAAGTATTTTCCTGGTACTAACAAATAATAATTTTATAC
AAATTGATAATTTTACTAACAATTAATACAATTTATCGGATAATAATTTT
Found at i:48397807 original size:124 final size:124
Alignment explanation
Indices: 48397578--48397942 Score: 586
Period size: 124 Copynumber: 2.9 Consensus size: 124
48397568 CCCAAACATG
*
48397578 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTT-ACAAATTATTCTCAAATAGCATCCTG
* *
48397643 CAAAAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCATCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCATCCATGAC
* * *
48397703 CTATTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTTACAAATTATTCTCAAATAGCATCCTGT
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTATTCTCAAATAGCATCCTGC
* *
48397768 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTTAAAAAAATTTATTTCATCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCATCCATGAC
* * *
48397827 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTTTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTATTCTCAAATAGCATCCTGC
* **
48397892 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAACTCAAAATTATTTC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTC
48397943 TTGCTGGACC
Statistics
Matches: 220, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
124 174 0.79
125 46 0.21
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTATTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCATCCATGAC
Found at i:48398847 original size:22 final size:22
Alignment explanation
Indices: 48398821--48398873 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
48398811 CAATAATAGT
48398821 TTAGTACGTGAAACATGAGAGC
1 TTAGTACGTGAAACATGAGAGC
* **
48398843 TTAGTACGTTAGCCATGAGAGC
1 TTAGTACGTGAAACATGAGAGC
48398865 TTAGTACGT
1 TTAGTACGT
48398874 TAGCCATGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (22 bp):
TTAGTACGTGAAACATGAGAGC
Found at i:48398874 original size:22 final size:22
Alignment explanation
Indices: 48398834--48398897 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
48398824 GTACGTGAAA
48398834 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
48398856 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * *
48398878 CATGAGGGTTTAGTTCGTTA
1 CATGAGAGCTTAGTACGTTA
48398898 AACAATTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:48412466 original size:16 final size:17
Alignment explanation
Indices: 48412445--48412498 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
48412435 AAAAATTATC
*
48412445 TTTTCTA-TCTTTCCAT
1 TTTTCTACTCTTTCCAA
*
48412461 TTTTCTACCCTTT-CAA
1 TTTTCTACTCTTTCCAA
*
48412477 TTTTC-ATTCTTTCCAA
1 TTTTCTACTCTTTCCAA
48412493 TTTTCT
1 TTTTCT
48412499 TTCCACTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 5 0.16
16 22 0.71
17 4 0.13
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTCTACTCTTTCCAA
Found at i:48422732 original size:114 final size:114
Alignment explanation
Indices: 48422565--48422901 Score: 518
Period size: 114 Copynumber: 3.0 Consensus size: 114
48422555 AAAACAGGCT
**** *
48422565 TTTAGCGGCGTTTTCCAAAAAGCGCCGC--AAAAAACTAAGCCCAACGGCGCCGTTCTCAGAGCT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCAGAGCT
* *
48422628 TTCAAGGATTTAGCGGCGTTTTTAAGAAAGCGCGGCTAATGCTCAGGGC
66 TTCGAGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* *
48422677 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACTGCGCCGTTTTGTA-AGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTT-CAGAGC
48422741 TTTCGAGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
65 TTTCGAGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* *
48422791 TTTAGCGGCGTTTTTGGGAATGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCAGAGCT
* * *
48422856 CTCGGGGATTTAGCGGCGTTTGTAAGAAAGCGCCGCTAATGCTCAG
66 TTCGAGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAG
48422902 AGATTTAAAA
Statistics
Matches: 205, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
112 24 0.12
114 180 0.88
115 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCAGAGCT
TTCGAGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:48423191 original size:22 final size:21
Alignment explanation
Indices: 48423166--48423215 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
48423156 GTGCTATGCT
*
48423166 TTAGGTGTTAGGGGATTTAGGG
1 TTAGGGGTTA-GGGATTTAGGG
*
48423188 TTAGGGGTTAGGGATTTGGGG
1 TTAGGGGTTAGGGATTTAGGG
48423209 TTTAGGG
1 -TTAGGG
48423216 TTTCAACAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (21 bp):
TTAGGGGTTAGGGATTTAGGG
Found at i:48423192 original size:15 final size:14
Alignment explanation
Indices: 48423165--48423217 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
48423155 AGTGCTATGC
48423165 TTTAGGTGTTAGGGG
1 TTTAGG-GTTAGGGG
48423180 ATTTAGGGTTAGGGG
1 -TTTAGGGTTAGGGG
*
48423195 -TTAGGGATTTGGGG
1 TTTAGGG-TTAGGGG
48423209 TTTAGGGTT
1 TTTAGGGTT
48423218 TCAACAGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 6 0.18
14 8 0.24
15 14 0.41
16 6 0.18
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.40
Consensus pattern (14 bp):
TTTAGGGTTAGGGG
Found at i:48423758 original size:43 final size:43
Alignment explanation
Indices: 48423697--48423852 Score: 231
Period size: 43 Copynumber: 3.6 Consensus size: 43
48423687 ACGTAAAATT
*
48423697 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGTAGAAGTGCCGC
1 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
* *
48423740 TAAAGGTCTTGTTCTTTAGCGGTGTTTGTGGTGGAAGCGCCGC
1 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
** * * *
48423783 TAAAGGTCACGATCTTTAACGACGTTTGTGGTAGAAGCGCCGC
1 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
*
48423826 TAAATGTCTTGTTCTTTAGCGGCGTTT
1 TAAAGGTCTTGTTCTTTAGCGGCGTTT
48423853 ATTTTTAAAA
Statistics
Matches: 97, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 97 1.00
ACGTcount: A:0.18, C:0.17, G:0.30, T:0.35
Consensus pattern (43 bp):
TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
Found at i:48423946 original size:22 final size:22
Alignment explanation
Indices: 48423916--48423957 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
48423906 CAGCGCTTCC
* *
48423916 AAAAGCGCCGCTAAAGGCCTAA
1 AAAAACGCCGCTAAAAGCCTAA
48423938 AAAAACGCCGCTAAAAGCCT
1 AAAAACGCCGCTAAAAGCCT
48423958 GTTTTGGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.29, G:0.19, T:0.10
Consensus pattern (22 bp):
AAAAACGCCGCTAAAAGCCTAA
Found at i:48435036 original size:16 final size:16
Alignment explanation
Indices: 48435015--48435048 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48435005 TATTTGAATG
* *
48435015 ATTTTATTGATTTATA
1 ATTTTATTAATTAATA
48435031 ATTTTATTAATTAATA
1 ATTTTATTAATTAATA
48435047 AT
1 AT
48435049 ATATTATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
ATTTTATTAATTAATA
Found at i:48439576 original size:74 final size:70
Alignment explanation
Indices: 48439474--48439617 Score: 211
Period size: 74 Copynumber: 2.0 Consensus size: 70
48439464 TTAATTTGTG
*
48439474 TTTTTGAATTGTTTATTATTTATTTTATAATATTTT-AATTGTTTTATAATATTTGTTTATTCAA
1 TTTTTCAATTGTTTATTATTTATTTTATAATATTTTAAATT-TTTTATAATA-TT-TTTATTCAA
48439538 ACATGTTTT
63 ACAT-TTTT
48439547 TTTTTCAATTTGTTTATTA-TTATTTTTATAATATTTTAAATTTTTTATAATATTTTTATTCAAA
1 TTTTTCAA-TTGTTTATTATTTA-TTTTATAATATTTTAAATTTTTTATAATATTTTTATTCAAA
48439611 CATTTTT
64 CATTTTT
48439618 AAAATATATA
Statistics
Matches: 67, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
71 4 0.06
72 13 0.19
73 12 0.18
74 34 0.51
75 4 0.06
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.64
Consensus pattern (70 bp):
TTTTTCAATTGTTTATTATTTATTTTATAATATTTTAAATTTTTTATAATATTTTTATTCAAACA
TTTTT
Found at i:48439583 original size:11 final size:11
Alignment explanation
Indices: 48439567--48439605 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
48439557 TGTTTATTAT
48439567 TATTTTTATAA
1 TATTTTTATAA
48439578 TA-TTTTA-AA
1 TATTTTTATAA
48439587 T-TTTTTATAA
1 TATTTTTATAA
48439597 TATTTTTAT
1 TATTTTTAT
48439606 TCAAACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.32
10 8 0.32
11 9 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTTTATAA
Found at i:48439602 original size:10 final size:10
Alignment explanation
Indices: 48439570--48439602 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
48439560 TTATTATTAT
48439570 TTTTATAATA
1 TTTTATAATA
*
48439580 TTTTA-AATT
1 TTTTATAATA
48439589 TTTTATAATA
1 TTTTATAATA
48439599 TTTT
1 TTTT
48439603 TATTCAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTATAATA
Found at i:48439824 original size:13 final size:13
Alignment explanation
Indices: 48439806--48439831 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48439796 ATATTATAAA
48439806 ACATTTAAAATAT
1 ACATTTAAAATAT
48439819 ACATTTAAAATAT
1 ACATTTAAAATAT
48439832 TATAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATTTAAAATAT
Found at i:48439897 original size:95 final size:92
Alignment explanation
Indices: 48439771--48439955 Score: 316
Period size: 95 Copynumber: 2.0 Consensus size: 92
48439761 TTTTAAATAT
*
48439771 AATTTAAAAAAATTTTGAATAAAAAATATTATAAAACATTTAAAATATACATTTAAAATATTATA
1 AATTTAAAAAAAGTTTGAATAAAAAATATTATAAAACATTTAAAATATACATTTAAAATATTATA
*
48439836 AAACAAATAATAAACAATTAAAAAACC
66 AAACAAATAATAAACAAATAAAAAACC
48439863 AATTTAAAAAAAACGTTTGAATAAATAAATATTATAAAACATTTAAAATATACATTTAAAATATT
1 AATTT-AAAAAAA-GTTTGAATAAA-AAATATTATAAAACATTTAAAATATACATTTAAAATATT
*
48439928 ATAATACAAATAATAAACAAATAAAAAA
63 ATAAAACAAATAATAAACAAATAAAAAA
48439956 ATGTGTTGGA
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
92 5 0.06
93 7 0.08
94 10 0.11
95 65 0.75
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (92 bp):
AATTTAAAAAAAGTTTGAATAAAAAATATTATAAAACATTTAAAATATACATTTAAAATATTATA
AAACAAATAATAAACAAATAAAAAACC
Found at i:48439917 original size:13 final size:13
Alignment explanation
Indices: 48439901--48439926 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48439891 ATATTATAAA
48439901 ACATTTAAAATAT
1 ACATTTAAAATAT
48439914 ACATTTAAAATAT
1 ACATTTAAAATAT
48439927 TATAATACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATTTAAAATAT
Found at i:48440589 original size:22 final size:22
Alignment explanation
Indices: 48440564--48440608 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
48440554 AAAATTTAAA
48440564 AAAGAAAATATAAAAATATTTT
1 AAAGAAAATATAAAAATATTTT
* * * *
48440586 AAAGATATTATGAATATATTTT
1 AAAGAAAATATAAAAATATTTT
48440608 A
1 A
48440609 TAATTTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (22 bp):
AAAGAAAATATAAAAATATTTT
Found at i:48441262 original size:43 final size:43
Alignment explanation
Indices: 48441211--48441480 Score: 233
Period size: 43 Copynumber: 6.3 Consensus size: 43
48441201 TTTTAGAAAT
*
48441211 AAACGCCGCTAAAGACCATGACTTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
* * *
48441254 AAATGCCGCTAAAGGCCATGACCTTTAGCGGCGCTTCT-CCAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
* * * * *
48441296 CAAACGCCGCTAAAGACCATGGCCTTTAGCGACGCTTTTACGAG
1 -AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
* * * ** *
48441340 AAACGCCGCTATAGATCAGGATATTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
* * * * * * *
48441383 AAACGCTGCTATAG-CTAAAGACCTTTAGCAGCGCTTTTACCAC
1 AAACGCCGCTAAAGAC-CATGACCTTTAGCGGCGCTTTTCCCAA
* * * * *
48441426 AAACGCCGCTATAGAACA-AACCTTTAGCGACGCTTCTT-GCAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTT-TTCCCAA
*
48441468 AAACGCCACTAAA
1 AAACGCCGCTAAA
48441481 AACATAACAT
Statistics
Matches: 183, Mismatches: 39, Indels: 11
0.79 0.17 0.05
Matches are distributed among these distances:
42 31 0.17
43 150 0.82
44 2 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAA
Found at i:48441309 original size:86 final size:85
Alignment explanation
Indices: 48441211--48441480 Score: 265
Period size: 86 Copynumber: 3.2 Consensus size: 85
48441201 TTTTAGAAAT
* * * * **
48441211 AAACGCCGCTAAAGACCATGACTTTTAGCGGCGCTTTTCCCAAAAATGCCGCTAAAGGCCATGAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCAAAAACGCCGCTATAGAACA-GAC
48441276 CTTTAGCGGCGCTTCTCCAAC
65 CTTTAGCGGCGCTTCTCCAAC
* * * * * *
48441297 AAACGCCGCTAAAGACCATGGCCTTTAGCGACGCTTTTACGAGAAACGCCGCTATAGATCAGGAT
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCAAAAACGCCGCTATAGAACA-GAC
* * *
48441362 ATTTAGCGGCGCTTTTCCCAC
65 CTTTAGCGGCGCTTCTCCAAC
* * * * * * *
48441383 AAACGCTGCTATAG-CTAAAGACCTTTAGCAGCGCTTTTACCACAAACGCCGCTATAGAACAAAC
1 AAACGCCGCTAAAGAC-CATGACCTTTAGCGGCGCTTTTACCAAAAACGCCGCTATAGAACAGAC
* *
48441447 CTTTAGCGACGCTTCTTGCAA-
65 CTTTAGCGGCGCTTC-TCCAAC
*
48441468 AAACGCCACTAAA
1 AAACGCCGCTAAA
48441481 AACATAACAT
Statistics
Matches: 147, Mismatches: 35, Indels: 5
0.79 0.19 0.03
Matches are distributed among these distances:
85 24 0.16
86 123 0.84
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (85 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCAAAAACGCCGCTATAGAACAGACC
TTTAGCGGCGCTTCTCCAAC
Found at i:48441406 original size:129 final size:128
Alignment explanation
Indices: 48441211--48441460 Score: 308
Period size: 129 Copynumber: 1.9 Consensus size: 128
48441201 TTTTAGAAAT
* * * *
48441211 AAACGCCGCTAAAGACCATGACTTTTAGCGGCGCTTTTCCCAAAAATGCCGCTAAAGGCCATGAC
1 AAACGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGGCAAAGAC
* * **
48441276 CTTTAGCGGCGCTTCT-CCAACAAACGCCGCTAAAGACCATGGCCTTTAGCGACGCTTTTACGAG
66 CTTTAGCAGCGCTTCTACC-ACAAACGCCGCTAAAGAACA-AACCTTTAGCGACGCTTTTACGAG
* * * * *
48441340 AAACGCCGCTATAGATCAGGA-TATTTAGCGGCGCTTTTCCCACAAACGCTGCTATA-GCTAAAG
1 AAACGCCGCTAAAGACCAGGACT-TTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGGC-AAAG
* *
48441403 ACCTTTAGCAGCGCTTTTACCACAAACGCCGCTATAGAACAAACCTTTAGCGACGCTT
64 ACCTTTAGCAGCGCTTCTACCACAAACGCCGCTAAAGAACAAACCTTTAGCGACGCTT
48441461 CTTGCAAAAA
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
128 18 0.17
129 83 0.81
130 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (128 bp):
AAACGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGGCAAAGAC
CTTTAGCAGCGCTTCTACCACAAACGCCGCTAAAGAACAAACCTTTAGCGACGCTTTTACGAG
Found at i:48447284 original size:21 final size:22
Alignment explanation
Indices: 48447251--48447291 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
48447241 TCTGAAATCC
48447251 TAAACCCCTAACCCCTAAACTT
1 TAAACCCCTAACCCCTAAACTT
* *
48447273 TAAATCCC-AACCCTTAAAC
1 TAAACCCCTAACCCCTAAAC
48447292 AATAAACCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAACCCCTAACCCCTAAACTT
Found at i:48447662 original size:15 final size:15
Alignment explanation
Indices: 48447627--48447667 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
48447617 NNNNNNNNTT
48447627 AATC-TAAACCT-TA
1 AATCTTAAACCTCTA
48447640 AATCTTAAACCTCTA
1 AATCTTAAACCTCTA
* *
48447655 ACTCTTAACCCTC
1 AATCTTAAACCTC
48447668 AACCCCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 4 0.17
14 7 0.29
15 13 0.54
ACGTcount: A:0.37, C:0.32, G:0.00, T:0.32
Consensus pattern (15 bp):
AATCTTAAACCTCTA
Found at i:48447676 original size:21 final size:21
Alignment explanation
Indices: 48447647--48447686 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
48447637 TTAAATCTTA
* *
48447647 AACCTCTAACTCTTAACCCTC
1 AACCCCTAACCCTTAACCCTC
48447668 AACCCCTAACCCTTAACCC
1 AACCCCTAACCCTTAACCC
48447687 CTAAACTTTA
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:0.30, C:0.47, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCCCTAACCCTTAACCCTC
Found at i:48447677 original size:14 final size:14
Alignment explanation
Indices: 48447660--48447690 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
48447650 CTCTAACTCT
48447660 TAACCCTCAACCCC
1 TAACCCTCAACCCC
*
48447674 TAACCCTTAACCCC
1 TAACCCTCAACCCC
48447688 TAA
1 TAA
48447691 ACTTTAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.19
Consensus pattern (14 bp):
TAACCCTCAACCCC
Found at i:48447727 original size:21 final size:20
Alignment explanation
Indices: 48447673--48447756 Score: 73
Period size: 21 Copynumber: 4.1 Consensus size: 20
48447663 CCCTCAACCC
*
48447673 CTAACCCTTAACCCCTAAACT
1 CTAACCCTTAAACCCTAAA-T
* * *
48447694 TTAAACCC--CAACCCTTAAT
1 CT-AACCCTTAAACCCTAAAT
*
48447713 CTATACCCTTAAACCATAAAT
1 CTA-ACCCTTAAACCCTAAAT
48447734 CGTAACCCTTAAACCCTAAAT
1 C-TAACCCTTAAACCCTAAAT
48447755 CT
1 CT
48447757 TAAAGCATAA
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
18 1 0.02
19 6 0.12
20 8 0.16
21 27 0.55
22 7 0.14
ACGTcount: A:0.37, C:0.36, G:0.01, T:0.26
Consensus pattern (20 bp):
CTAACCCTTAAACCCTAAAT
Found at i:48447810 original size:22 final size:24
Alignment explanation
Indices: 48447775--48447835 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 24
48447765 AAACTGTAAA
* *
48447775 CCATAACCCCTAAACTCA-TAA-T
1 CCATAAACCTTAAACTCAGTAACT
*
48447797 CCATAAACCTTAAAAT-AGTAACT
1 CCATAAACCTTAAACTCAGTAACT
48447820 CC-TAAACCTTAAACTC
1 CCATAAACCTTAAACTC
48447836 TAAATCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 28 0.88
23 3 0.09
ACGTcount: A:0.43, C:0.31, G:0.02, T:0.25
Consensus pattern (24 bp):
CCATAAACCTTAAACTCAGTAACT
Found at i:48448238 original size:41 final size:41
Alignment explanation
Indices: 48448181--48448454 Score: 392
Period size: 41 Copynumber: 6.7 Consensus size: 41
48448171 ATGTTTTTGT
*
48448181 GGCGCTT-TCTCAAAAACGCCGCTAAAAACCAGAGCATTAGC
1 GGCGCTTCTC-CAAAAACGCCGCTAAAGACCAGAGCATTAGC
48448222 GGCGCTTCTCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
1 GGCGCTTCTCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
48448263 GGCGCTTCTCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
1 GGCGCTTCTCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
48448304 GGCGCTT-TCCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
1 GGCGCTTCT-CCAAAAACGCCGCTAAAGACCAGAGCATTAGC
* * * *
48448345 GTCGCTTCCCCAAAAATGCCGCTAAAGACCAAAGCATTAGC
1 GGCGCTTCTCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
* * * *
48448386 GGTGCTTTTCTAAAAACGCCGCTAAA-ACCCTGAGCATTAGC
1 GGCGCTTCTCCAAAAACGCCGCTAAAGA-CCAGAGCATTAGC
* *
48448427 GGCGCTTTTCTAAAAAACGCCGCTAAAG
1 GGCGCTTCTC-CAAAAACGCCGCTAAAG
48448455 CCCCGAATGG
Statistics
Matches: 212, Mismatches: 15, Indels: 10
0.89 0.06 0.04
Matches are distributed among these distances:
40 2 0.01
41 193 0.91
42 17 0.08
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.18
Consensus pattern (41 bp):
GGCGCTTCTCCAAAAACGCCGCTAAAGACCAGAGCATTAGC
Found at i:48455161 original size:104 final size:104
Alignment explanation
Indices: 48454981--48455228 Score: 309
Period size: 104 Copynumber: 2.4 Consensus size: 104
48454971 CCTGTATGCA
* * * *
48454981 TGCCCGTGTGGCTCACACGGCCTAACACACGCCCGTGTCGTCTGCTTGTGTGGTTAAAAATCGTA
1 TGCCCGTGTGGCTCACACGGCCTGACACACGCCCGTGTCATCTGCTCGTGTGGGTAAAAATCGTA
48455046 AACAATGAGTCACACGACCTAGACACATGCTCGTGTCCT
66 AACAATGAGTCACACGACCTAGACACATGCTCGTGTCCT
* * ** *
48455085 TGCCCGTGTGGCTCACACGGCCTGACACTCGCCTGTGTCATCTAGC-CGTGTGGGTCTAAATTGT
1 TGCCCGTGTGGCTCACACGGCCTGACACACGCCCGTGTCATCT-GCTCGTGTGGGTAAAAATCGT
* * * * *
48455149 AAACACTGAGTCACACGGCTTGGACACATGTTCGTGTCCT
65 AAACAATGAGTCACACGACCTAGACACATGCTCGTGTCCT
* * * *
48455189 TGCCCATGTGACTCACACAGCCTGGGCACACGCCCGTGTC
1 TGCCCGTGTGGCTCACACGGCCT-GACACACGCCCGTGTC
48455229 CCTGGCCTGT
Statistics
Matches: 122, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
104 107 0.88
105 15 0.12
ACGTcount: A:0.20, C:0.31, G:0.25, T:0.24
Consensus pattern (104 bp):
TGCCCGTGTGGCTCACACGGCCTGACACACGCCCGTGTCATCTGCTCGTGTGGGTAAAAATCGTA
AACAATGAGTCACACGACCTAGACACATGCTCGTGTCCT
Found at i:48456411 original size:18 final size:18
Alignment explanation
Indices: 48456388--48456440 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
48456378 GCAATATATG
48456388 TAAAAATA-ATTTAAAATA
1 TAAAAATATA-TTAAAATA
*
48456406 TAAAAATTTATTAAAATA
1 TAAAAATATATTAAAATA
**
48456424 TATTAATATATGTAAAA
1 TAAAAATATAT-TAAAA
48456441 ACAACTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 23 0.79
19 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TAAAAATATATTAAAATA
Found at i:48456537 original size:14 final size:15
Alignment explanation
Indices: 48456515--48456591 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
48456505 CAATCAAACA
48456515 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
48456529 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
48456544 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
48456564 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
48456578 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
48456592 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:48456556 original size:20 final size:20
Alignment explanation
Indices: 48456531--48456570 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
48456521 AATATTTTCC
*
48456531 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
48456551 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
48456571 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:48456576 original size:34 final size:35
Alignment explanation
Indices: 48456519--48456585 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
48456509 CAAACACCAG
*
48456519 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
48456554 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
48456586 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:48458805 original size:27 final size:28
Alignment explanation
Indices: 48458748--48458805 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
48458738 TAGTCGGCAG
* *
48458748 AAAAAAGTTCAAGTACTAATTTAAGACA
1 AAAAAAATTCAAGCACTAATTTAAGACA
* *
48458776 AAAAAAATTTAAGCACTAATTTGAGA-A
1 AAAAAAATTCAAGCACTAATTTAAGACA
48458803 AAA
1 AAA
48458806 TAGACAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.57, C:0.09, G:0.10, T:0.24
Consensus pattern (28 bp):
AAAAAAATTCAAGCACTAATTTAAGACA
Found at i:48464043 original size:24 final size:24
Alignment explanation
Indices: 48464011--48464060 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
48464001 TTAAAAGTAG
48464011 ATCTCTACCTCATTTATACTTTTT
1 ATCTCTACCTCATTTATACTTTTT
48464035 ATCTCTACCTCATTTATACTTTTT
1 ATCTCTACCTCATTTATACTTTTT
48464059 AT
1 AT
48464061 ACCTATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (24 bp):
ATCTCTACCTCATTTATACTTTTT
Found at i:48467340 original size:25 final size:25
Alignment explanation
Indices: 48467311--48467360 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
48467301 AACAATTTGA
*
48467311 GAACAATCGGGGGTCCTTTTGAAAC
1 GAACAATCCGGGGTCCTTTTGAAAC
48467336 GAACAATCCGGGGTCCTTTTGAAAC
1 GAACAATCCGGGGTCCTTTTGAAAC
48467361 AAAATGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (25 bp):
GAACAATCCGGGGTCCTTTTGAAAC
Found at i:48470833 original size:50 final size:51
Alignment explanation
Indices: 48470740--48470886 Score: 147
Period size: 50 Copynumber: 2.8 Consensus size: 51
48470730 ATATCCTAGA
* * *
48470740 TCGGTGCCCATGCCATGTCCCAGACATAGTCTT--ATGGGAGACCTCTC-ATC
1 TCGGTGCCAATGCCATGTCCCAGACATGGTATTACAT-GG-GACCTCTCAATC
*
48470790 TCGGTGCCAACGCCATGTCCCAGACATGGTATTACATGGGACCTCTCATAATC
1 TCGGTGCCAATGCCATGTCCCAGACATGGTATTACATGGGACCTCTC--AATC
** *
48470843 TCAATAATGCCAATGCCATGTCCCAGACATGGTTTTACATGGGA
1 TC---GGTGCCAATGCCATGTCCCAGACATGGTATTACATGGGA
48470887 TCTCATTCCC
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
50 37 0.46
51 2 0.02
52 2 0.02
53 5 0.06
56 35 0.43
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (51 bp):
TCGGTGCCAATGCCATGTCCCAGACATGGTATTACATGGGACCTCTCAATC
Found at i:48476470 original size:9 final size:9
Alignment explanation
Indices: 48476453--48476483 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
48476443 TCGAGTTGAT
48476453 TCGAATAAC
1 TCGAATAAC
*
48476462 TCGATTAAC
1 TCGAATAAC
48476471 TCGAATAAC
1 TCGAATAAC
48476480 TCGA
1 TCGA
48476484 TTTGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:48482853 original size:7 final size:7
Alignment explanation
Indices: 48482841--48482866 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
48482831 AAAATATTTT
48482841 AAAAATA
1 AAAAATA
48482848 AAAAATA
1 AAAAATA
48482855 AAAAATA
1 AAAAATA
48482862 AAAAA
1 AAAAA
48482867 AATATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:48482886 original size:45 final size:44
Alignment explanation
Indices: 48482835--48482920 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
48482825 AAACACAAAA
*
48482835 TATTTTAAAAATAAAAAATAAAAAATAAAAAAAATATTTTTAAAG
1 TATTTTAAAAATAAAAAAT-AAAAATAAAAAAAATATATTTAAAG
* *
48482880 TATTTTAAAATTAAAAAATAAAAATAAAAAATATATATTTA
1 TATTTTAAAAATAAAAAATAAAAATAAAAAAAATATATTTA
48482921 TTATATTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 20 0.53
45 18 0.47
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (44 bp):
TATTTTAAAAATAAAAAATAAAAATAAAAAAAATATATTTAAAG
Found at i:48485638 original size:50 final size:50
Alignment explanation
Indices: 48485579--48485681 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
48485569 CCAAGCTAAG
48485579 GCTTGAACTTGGGACCTCTCAAACATTTCCTAGAACACTTAACCACAAAA
1 GCTTGAACTTGGGACCTCTCAAACATTTCCTAGAACACTTAACCACAAAA
48485629 GCTTGAACTTGGGACCTCTCAAACATTTCCTAGAACACTTAACCACAAAA
1 GCTTGAACTTGGGACCTCTCAAACATTTCCTAGAACACTTAACCACAAAA
48485679 GCT
1 GCT
48485682 GATATATATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (50 bp):
GCTTGAACTTGGGACCTCTCAAACATTTCCTAGAACACTTAACCACAAAA
Found at i:48487490 original size:25 final size:25
Alignment explanation
Indices: 48487456--48487505 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
48487446 TCATGAAGTC
48487456 CGCGAGATGGTACATAAATATATAA
1 CGCGAGATGGTACATAAATATATAA
48487481 CGCGAGATGGTACATAAATATATAA
1 CGCGAGATGGTACATAAATATATAA
48487506 ATTCACATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (25 bp):
CGCGAGATGGTACATAAATATATAA
Done.