Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 116 of 290
Found at i:39550824 original size:54 final size:54
Alignment explanation
Indices: 39550574--39550824 Score: 249
Period size: 54 Copynumber: 4.6 Consensus size: 54
39550564 ATTATCATTT
** * * **
39550574 TACCCTCGATTTACAAAATTACTAAAATA-CCCTTAGTTTACAAAATTACCAAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCCCTGA-TTTGTAAAATTACCAAAA
** * **
39550628 TACCCTCGATCAGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTATTAAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAA
* *
39550682 TACCC-CTGGTTTGTAAAATTACCAAAATACCCCT-AGCTTGTAAAATTACCAAAA
1 TACCCTC-GATTTGTAAAATTACCAAAATACCCCTGA-TTTGTAAAATTACCAAAA
* * * *
39550736 TACCCT-TAGCTTGTAAAATTACCAAAATACCCCTGATTTGTGAAATTATCAAAA
1 TACCCTCGA-TTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAA
* * * *
39550790 TACTCTCGATTTGTAGAATTATCGAAATACCCCTG
1 TACCCTCGATTTGTAAAATTACCAAAATACCCCTG
39550825 TAGGGTAGAA
Statistics
Matches: 160, Mismatches: 30, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 153 0.96
55 6 0.04
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (54 bp):
TACCCTCGATTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAA
Found at i:39550832 original size:27 final size:27
Alignment explanation
Indices: 39550802--39551001 Score: 249
Period size: 27 Copynumber: 7.4 Consensus size: 27
39550792 CTCTCGATTT
*
39550802 GTAGAATTATCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
39550829 GTAGAATTACCGAAATACCCCTATAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
** *
39550856 GTAGAATTACTAAAATAACCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
39550883 GTAGAATTACCGAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
**
39550910 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* **
39550937 GTAGAATTACTGAAATACCATTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
39550964 GTAGAATTACCGAGATA-CCCTGGTGGG
1 GTAGAATTACCGAAATACCCCT-GTAGG
*
39550991 GTAAAATTACC
1 GTAGAATTACC
39551002 ATTTTTCCCC
Statistics
Matches: 148, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
26 2 0.01
27 146 0.99
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:39550837 original size:81 final size:80
Alignment explanation
Indices: 39550588--39550850 Score: 246
Period size: 81 Copynumber: 3.2 Consensus size: 80
39550578 CTCGATTTAC
* * ** **
39550588 AAAATTACTAAAATA-CCCTTAGTTTACAAAATTACCAAAATACCCTCGATCAGTAAAATTACCA
1 AAAATTACCAAAATACCCCTGA-TTTGTAAAATTACCAAAATA-CCTCGATTTGTAAAATTACCA
*
39550652 AAATACCCCTGGT-TTGT
64 AAATACCCCT-GTAGTGT
** * * * *
39550669 AAAATTATTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTAGCTTGTAAAATTACCAA
1 AAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACCTCGA-TTTGTAAAATTACCAA
39550734 AATA-CCCT-TAGCTTGT
65 AATACCCCTGTAG--TGT
* * * * *
39550750 AAAATTACCAAAATACCCCTGATTTGTGAAATTATCAAAATACTCTCGATTTGTAGAATTATCGA
1 AAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATAC-CTCGATTTGTAAAATTACCAA
*
39550815 AATACCCCTGTAGGGT
65 AATACCCCTGTAGTGT
* *
39550831 AGAATTACCGAAATACCCCT
1 AAAATTACCAAAATACCCCT
39550851 ATAAGGTAGA
Statistics
Matches: 149, Mismatches: 25, Indels: 16
0.78 0.13 0.08
Matches are distributed among these distances:
78 1 0.01
80 8 0.05
81 126 0.85
82 11 0.07
83 3 0.02
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (80 bp):
AAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACCTCGATTTGTAAAATTACCAAA
ATACCCCTGTAGTGT
Found at i:39551280 original size:24 final size:25
Alignment explanation
Indices: 39551204--39551273 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
39551194 AGGAAGTGCT
* * *
39551204 AAAAGGGCTATGCCCTAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
39551229 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
39551254 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
39551274 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:39551286 original size:24 final size:24
Alignment explanation
Indices: 39551203--39551286 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
39551193 GAGGAAGTGC
* *
39551203 TAAAAGGGCTATGCCCTAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
39551227 CGAAAAGGGCTTTGCCCCAGTTTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
*
39551252 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
39551276 TAAAAGAGGCT
1 TAAAAG-GGCT
39551287 AGGCCTCTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
23 5 0.09
24 8 0.15
25 40 0.75
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:39551542 original size:31 final size:31
Alignment explanation
Indices: 39551493--39551575 Score: 127
Period size: 31 Copynumber: 2.8 Consensus size: 31
39551483 CGCTTACAGT
39551493 AAAA-GCTTCGG-CCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
39551522 AAAAGGCTTCGGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
* *
39551553 AAAAGGTTTCTGCCCAGT-ATATG
1 AAAAGGCTTCGGCCCAGTGATATG
39551576 TCGAGACTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
29 4 0.08
30 12 0.24
31 34 0.68
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (31 bp):
AAAAGGCTTCGGCCCAGTGATATGATTTATG
Found at i:39559896 original size:23 final size:21
Alignment explanation
Indices: 39559870--39559918 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
39559860 TTATCTTATG
*
39559870 ATTTTATCACCACTGAATTTAAA
1 ATTTTATCA-CA-TGAATTCAAA
* *
39559893 ATTTTTTTACATGAATTCAAA
1 ATTTTATCACATGAATTCAAA
39559914 ATTTT
1 ATTTT
39559919 GTCCATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 14 0.61
22 2 0.09
23 7 0.30
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (21 bp):
ATTTTATCACATGAATTCAAA
Found at i:39560119 original size:25 final size:27
Alignment explanation
Indices: 39560087--39560143 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
39560077 GTATCTTGTA
*
39560087 TTTTTATA-AATCATTAAGTACACTT-
1 TTTTTATATAATCATAAAGTACACTTG
* *
39560112 TTTTTATATTATTATAAAGTACACTTG
1 TTTTTATATAATCATAAAGTACACTTG
39560139 TTTTT
1 TTTTT
39560144 CTTTAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 8 0.30
26 14 0.52
27 5 0.19
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (27 bp):
TTTTTATATAATCATAAAGTACACTTG
Found at i:39560808 original size:18 final size:19
Alignment explanation
Indices: 39560774--39560809 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39560764 AAAATAATCT
39560774 TTAATACTAAGTATATAAC
1 TTAATACTAAGTATATAAC
*
39560793 TTAATACTTA-TATATAA
1 TTAATACTAAGTATATAA
39560810 TCAAACTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (19 bp):
TTAATACTAAGTATATAAC
Found at i:39563656 original size:24 final size:24
Alignment explanation
Indices: 39563624--39563672 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
39563614 TATTAAAGTG
39563624 TAAGAAGAGGGAGATGTCGATACC
1 TAAGAAGAGGGAGATGTCGATACC
39563648 TAAGAAGAGGGAGATGTCGATACC
1 TAAGAAGAGGGAGATGTCGATACC
39563672 T
1 T
39563673 GAAAGAGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.33, T:0.18
Consensus pattern (24 bp):
TAAGAAGAGGGAGATGTCGATACC
Found at i:39563685 original size:24 final size:24
Alignment explanation
Indices: 39563624--39563685 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
39563614 TATTAAAGTG
*
39563624 TAAGAAGAGGGAGATGTCGATACC
1 TAAGAAGAGAGAGATGTCGATACC
*
39563648 TAAGAAGAGGGAGATGTCGATACC
1 TAAGAAGAGAGAGATGTCGATACC
*
39563672 TGA-AAGAGTAGAGA
1 TAAGAAGAG-AGAGA
39563686 AGAGAAGAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 5 0.14
24 30 0.86
ACGTcount: A:0.40, C:0.10, G:0.34, T:0.16
Consensus pattern (24 bp):
TAAGAAGAGAGAGATGTCGATACC
Found at i:39577055 original size:34 final size:34
Alignment explanation
Indices: 39577007--39577104 Score: 126
Period size: 34 Copynumber: 2.9 Consensus size: 34
39576997 TCTAATTTGT
*
39577007 TATGACATTTTGATATGATATATGTTTATGGAAA
1 TATGACATTATGATATGATATATGTTTATGGAAA
* *
39577041 TATGACATTATGATATGATATATGTTTCTGGTAA
1 TATGACATTATGATATGATATATGTTTATGGAAA
* * *
39577075 TATGACA-TACTGATCTGATATTTGTATATG
1 TATGACATTA-TGATATGATATATGTTTATG
39577105 TCTACATCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 2 0.04
34 54 0.96
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (34 bp):
TATGACATTATGATATGATATATGTTTATGGAAA
Found at i:39579264 original size:21 final size:21
Alignment explanation
Indices: 39579240--39579283 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
39579230 TTGCTTATTC
*
39579240 TAGTTCTAGGGAATAGAAAGG
1 TAGTTCTAGGGAATAAAAAGG
*
39579261 TAGTTTTAGGGAATAAAAAGG
1 TAGTTCTAGGGAATAAAAAGG
39579282 TA
1 TA
39579284 ATGTGGTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.27
Consensus pattern (21 bp):
TAGTTCTAGGGAATAAAAAGG
Found at i:39580964 original size:5 final size:5
Alignment explanation
Indices: 39580956--39581002 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
39580946 AGCATATAAT
*
39580956 ATATC ATATC -TAATC ATATC ATATC ATATATC ATATC ATTTC ATATC
1 ATATC ATATC AT-ATC ATATC ATATC --ATATC ATATC ATATC ATATC
39581003 GTTGCCCCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
4 1 0.03
5 29 0.81
6 1 0.03
7 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATC
Found at i:39580988 original size:17 final size:17
Alignment explanation
Indices: 39580956--39581001 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
39580946 AGCATATAAT
39580956 ATATCATATC-TA-ATC
1 ATATCATATCATATATC
39580971 ATATCATATCATATATC
1 ATATCATATCATATATC
*
39580988 ATATCATTTCATAT
1 ATATCATATCATAT
39581002 CGTTGCCCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 10 0.36
16 2 0.07
17 16 0.57
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATCATATCATATATC
Found at i:39581254 original size:4 final size:4
Alignment explanation
Indices: 39581247--39581306 Score: 120
Period size: 4 Copynumber: 15.0 Consensus size: 4
39581237 TGATATCATT
39581247 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
39581295 CATA CATA CATA
1 CATA CATA CATA
39581307 TATCACAAGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:39587830 original size:26 final size:24
Alignment explanation
Indices: 39587801--39587861 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
39587791 TATTATTATT
39587801 ATTATTTTTACCATTTCATAATAACA
1 ATTATTTTTACCATTT-ATAA-AACA
** *
39587827 ATTAAAATTTATCATTTATAAAACA
1 ATT-ATTTTTACCATTTATAAAACA
39587852 ATGTATTTTT
1 AT-TATTTTT
39587862 CACAAACTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
25 10 0.36
26 8 0.29
27 10 0.36
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTATTTTTACCATTTATAAAACA
Found at i:39589216 original size:36 final size:36
Alignment explanation
Indices: 39589135--39589216 Score: 83
Period size: 36 Copynumber: 2.2 Consensus size: 36
39589125 TATTTTCCCT
* *
39589135 TTTTCTTTCTTTTTCTTCTTTTCTTTCCCCTGTTTCG
1 TTTTCTTT-TTGTTCTTCTTTCCTTTCCCCTGTTTCG
** * ***
39589172 AATGCTTTTTGTTCTTCTTTCCTTTCTTTTGTTTCG
1 TTTTCTTTTTGTTCTTCTTTCCTTTCCCCTGTTTCG
39589208 TTTTCTTTT
1 TTTTCTTTT
39589217 ATTTAGTTTA
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
36 29 0.85
37 5 0.15
ACGTcount: A:0.02, C:0.22, G:0.07, T:0.68
Consensus pattern (36 bp):
TTTTCTTTTTGTTCTTCTTTCCTTTCCCCTGTTTCG
Found at i:39603049 original size:56 final size:56
Alignment explanation
Indices: 39602958--39603178 Score: 318
Period size: 56 Copynumber: 3.9 Consensus size: 56
39602948 TCTTACATGT
* * * * * *
39602958 AATCACATATCGATTCCAACGTACTAGACGCGGTCTAACTTGTACACATATATTGG
1 AATCACATATCGATTCCAACGTATTAAACGTGGTCTTACTCGCACACATATATTGG
* *
39603014 AATCACATATCGATTCCAACATATTAAACGTGGTCTTACTCGCACACATATATCGG
1 AATCACATATCGATTCCAACGTATTAAACGTGGTCTTACTCGCACACATATATTGG
* * * *
39603070 AATCACATATTGATGCCAACGTATTAAACATGGTCTTACTCGCACATATATATTGG
1 AATCACATATCGATTCCAACGTATTAAACGTGGTCTTACTCGCACACATATATTGG
39603126 AATCACATATCG-TTGCCAACGTATTAAACGTGGTCTTACTCGCACACATATAT
1 AATCACATATCGATT-CCAACGTATTAAACGTGGTCTTACTCGCACACATATAT
39603179 CGATGCCATG
Statistics
Matches: 146, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
55 1 0.01
56 145 0.99
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (56 bp):
AATCACATATCGATTCCAACGTATTAAACGTGGTCTTACTCGCACACATATATTGG
Found at i:39607161 original size:49 final size:49
Alignment explanation
Indices: 39607100--39607198 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
39607090 TTCCAAAAAG
39607100 ATAATCTCTTGATCTCATTATGAAAAGGAATGTAAATCGAAAGGGTAAT
1 ATAATCTCTTGATCTCATTATGAAAAGGAATGTAAATCGAAAGGGTAAT
*
39607149 ATAATCTTTTGATCTCATTATGAAAAGGAATGTAAATCGAAAGGGTAAT
1 ATAATCTCTTGATCTCATTATGAAAAGGAATGTAAATCGAAAGGGTAAT
39607198 A
1 A
39607199 CTTGAAAAGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.31
Consensus pattern (49 bp):
ATAATCTCTTGATCTCATTATGAAAAGGAATGTAAATCGAAAGGGTAAT
Found at i:39608969 original size:96 final size:96
Alignment explanation
Indices: 39608803--39608985 Score: 267
Period size: 96 Copynumber: 1.9 Consensus size: 96
39608793 ATGATGCCGT
* * * *
39608803 TCACACAAGCTGACGAGTATCCGCAACAAATGTTGGAACTCAGTCATCGGTAGGACATTCAGGAC
1 TCACACAAGCTGACGAGCATCCGCAACAAATGTCGGAACTCAGCCATCGGTAAGACATTCAGGAC
* ** *
39608868 TAGCACCCTGAACATGGTAACCTGGGTCTGC
66 GAGCACCCAAAACAAGGTAACCTGGGTCTGC
* * *
39608899 TCACACAAGCTGATGAGCATCTGCAACAAATGTCGGAACTCAGCCATCGGTAAGACATTCAGTAC
1 TCACACAAGCTGACGAGCATCCGCAACAAATGTCGGAACTCAGCCATCGGTAAGACATTCAGGAC
39608964 GAGCACCCAAAACAAGGTAACC
66 GAGCACCCAAAACAAGGTAACC
39608986 CTAATGACAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 76 1.00
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.19
Consensus pattern (96 bp):
TCACACAAGCTGACGAGCATCCGCAACAAATGTCGGAACTCAGCCATCGGTAAGACATTCAGGAC
GAGCACCCAAAACAAGGTAACCTGGGTCTGC
Found at i:39610830 original size:104 final size:104
Alignment explanation
Indices: 39610646--39610853 Score: 389
Period size: 104 Copynumber: 2.0 Consensus size: 104
39610636 TATCACCCTT
*
39610646 ATGACAGTGTTTAGGTTGTGTTTAAATTATGAAATCAAATAAGGTGGTTAGTGGAGAGATTTAGT
1 ATGACAGTGTTTAGGTTGTGTTTAAACTATGAAATCAAATAAGGTGGTTAGTGGAGAGATTTAGT
* *
39610711 GGGAGTGTGGGTGGTTAATATTTGTTTAAAATAAAATAA
66 AGGAGTGTGGATGGTTAATATTTGTTTAAAATAAAATAA
39610750 ATGACAGTGTTTAGGTTGTGTTTAAACTATGAAATCAAATAAGGTGGTTAGTGGAGAGATTTAGT
1 ATGACAGTGTTTAGGTTGTGTTTAAACTATGAAATCAAATAAGGTGGTTAGTGGAGAGATTTAGT
39610815 AGGAGTGTGGATGGTTAATATTTGTTTAAAATAAAATAA
66 AGGAGTGTGGATGGTTAATATTTGTTTAAAATAAAATAA
39610854 TTAGTTTTCA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (104 bp):
ATGACAGTGTTTAGGTTGTGTTTAAACTATGAAATCAAATAAGGTGGTTAGTGGAGAGATTTAGT
AGGAGTGTGGATGGTTAATATTTGTTTAAAATAAAATAA
Found at i:39611369 original size:3 final size:3
Alignment explanation
Indices: 39611361--39611397 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
39611351 CATGGTTAAG
39611361 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
39611398 ATATCATGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:39626992 original size:5 final size:5
Alignment explanation
Indices: 39626982--39627009 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
39626972 TTGTGTGTTC
39626982 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
39627010 CACACTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:39627768 original size:54 final size:54
Alignment explanation
Indices: 39627675--39627787 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
39627665 GAGTATTTTG
* * *
39627675 ACTTTAATCCCTCTCTCGTATGTGATTTCTTGGCAATTTTTCAGCAGGCAGATGA
1 ACTTTAAT-CCTCTCTCATATGTGATTTCCTGGCAATTTTTCAGCAGGAAGATGA
* * * *
39627730 CACTTTAAT-CTCTCTCATGTGTGATTTCCTGTCCATTTTTTAGCAGGAAGATGA
1 -ACTTTAATCCTCTCTCATATGTGATTTCCTGGCAATTTTTCAGCAGGAAGATGA
39627784 ACTT
1 ACTT
39627788 GTTACTAGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
53 4 0.08
54 38 0.76
56 8 0.16
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (54 bp):
ACTTTAATCCTCTCTCATATGTGATTTCCTGGCAATTTTTCAGCAGGAAGATGA
Found at i:39629744 original size:33 final size:31
Alignment explanation
Indices: 39629677--39629735 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
39629667 AGAAAAAAGT
*
39629677 ATATTTTATAATATATATCGAAGGTATAAAA
1 ATATTTTATAAAATATATCGAAGGTATAAAA
* *
39629708 ATATTTTGTAAAATATATTGAAGGTATA
1 ATATTTTATAAAATATATCGAAGGTATA
39629736 TGCAAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.41
Consensus pattern (31 bp):
ATATTTTATAAAATATATCGAAGGTATAAAA
Found at i:39634304 original size:31 final size:31
Alignment explanation
Indices: 39634269--39634330 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
39634259 TACTAAAAAA
* *
39634269 ATTACTTTTTTGTTTCTCTCATCTACTTCTT
1 ATTACATTTTAGTTTCTCTCATCTACTTCTT
39634300 ATTACATTTTAGTTTCTCTCATCTACTTCTT
1 ATTACATTTTAGTTTCTCTCATCTACTTCTT
39634331 CTCTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.58
Consensus pattern (31 bp):
ATTACATTTTAGTTTCTCTCATCTACTTCTT
Found at i:39635137 original size:32 final size:32
Alignment explanation
Indices: 39635096--39635159 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
39635086 GAATTTGTTC
*
39635096 CATGTTACACAGCTGTTTGGTAGGTCGTGTAG
1 CATGTTACACAGCTGTTTGGTAGGCCGTGTAG
39635128 CATGTTACACAGCTGTTTGGTAGGCCGTGTAG
1 CATGTTACACAGCTGTTTGGTAGGCCGTGTAG
39635160 GGGTACTCGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (32 bp):
CATGTTACACAGCTGTTTGGTAGGCCGTGTAG
Found at i:39642390 original size:22 final size:21
Alignment explanation
Indices: 39642355--39642430 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
39642345 AAAGGATATC
* *
39642355 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
39642376 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
39642399 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
39642418 TGC-AATCATATCT
1 TACAAATCATATCT
39642431 AAGATTGCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:39642427 original size:18 final size:19
Alignment explanation
Indices: 39642391--39642445 Score: 103
Period size: 18 Copynumber: 2.9 Consensus size: 19
39642381 AATCATATCT
39642391 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
39642410 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
39642428 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
39642446 TGAAGATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:39642601 original size:21 final size:20
Alignment explanation
Indices: 39642564--39642602 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
39642554 TTGGACTTTG
**
39642564 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
39642584 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
39642603 TCAGGGCCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:39642672 original size:19 final size:19
Alignment explanation
Indices: 39642648--39642692 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
39642638 ACAACAATAT
39642648 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
* *
39642667 ATATCACATCTAAGATTTC
1 ATATCATATCTAAGATTGC
39642686 ATATCAT
1 ATATCAT
39642693 TAAAGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:39642849 original size:21 final size:20
Alignment explanation
Indices: 39642811--39642850 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
39642801 TTGGACTTTG
**
39642811 TTTTTTTTTTGGGTTTATTA
1 TTTTTTTTTTGGACTTATTA
39642831 TTTTTGTTTTTGGACTTATT
1 TTTTT-TTTTTGGACTTATT
39642851 TCAGGGCCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTTGGACTTATTA
Found at i:39643159 original size:44 final size:45
Alignment explanation
Indices: 39643043--39643316 Score: 259
Period size: 45 Copynumber: 6.1 Consensus size: 45
39643033 GGAAGGCGAT
* *
39643043 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAAAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAAAGACGCCAA
* * *
39643088 ATCTGTTATCTTCGATCTACTCCCCGTCTAATATAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAAAGACGCCAA
* * * * *
39643133 ATTTGCT-TCTTCAATCTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAAAGACGCCAA
* * *
39643177 ATCTGTTATCTCCGATTTGCTCCCCGTCTAATACAAAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAAAGACGCCAA
* * * * * * * *
39643222 ATCTGTCATCTTGGATCTGCT--TCGATGTAA-ACACATGAAGGTCAG
1 ATCTGTTATCTTCGATCTGCTCCCCG-TCTAATACA-AAG-ACGCCAA
* * *
39643267 ATCTGCTATGTCTTCAATCTGCTCCCCGTCTAATACAAAGATGCCAA
1 ATCTG-T-TATCTTCGATCTGCTCCCCGTCTAATACAAAGACGCCAA
39643314 ATC
1 ATC
39643317 ATCTTGGATC
Statistics
Matches: 183, Mismatches: 37, Indels: 16
0.78 0.16 0.07
Matches are distributed among these distances:
43 5 0.03
44 44 0.24
45 104 0.57
46 1 0.01
47 18 0.10
48 6 0.03
49 5 0.03
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAAAGACGCCAA
Found at i:39643176 original size:89 final size:89
Alignment explanation
Indices: 39643057--39643223 Score: 262
Period size: 89 Copynumber: 1.9 Consensus size: 89
39643047 GCTATCTTTG
* *
39643057 ATCTGCTCCCCGTCTAATACAAAGACGCCAAATCTGTTATCTTCGATCTACTCCCCGTCTAATAT
1 ATCTGCTCCCCGTCTAATACAAAGACGCCAAATCTGTTATCTCCGATCTACTCCCCGTCTAATAC
*
39643122 AGAGACGCCAAATTTGCTTCTTCA
66 AAAGACGCCAAATTTGCTTCTTCA
* * * *
39643146 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTCCGATTTGCTCCCCGTCTAATAC
1 ATCTGCTCCCCGTCTAATACAAAGACGCCAAATCTGTTATCTCCGATCTACTCCCCGTCTAATAC
*
39643211 AAAGATGCCAAAT
66 AAAGACGCCAAAT
39643224 CTGTCATCTT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 70 1.00
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.29
Consensus pattern (89 bp):
ATCTGCTCCCCGTCTAATACAAAGACGCCAAATCTGTTATCTCCGATCTACTCCCCGTCTAATAC
AAAGACGCCAAATTTGCTTCTTCA
Found at i:39643387 original size:78 final size:79
Alignment explanation
Indices: 39643256--39643429 Score: 273
Period size: 78 Copynumber: 2.2 Consensus size: 79
39643246 ATGTAAACAC
*
39643256 ATGAAGGT-CAGATCTGCTATGTCTTCAATCTGCTCCCCGTCTAATACAAAGATGCCAAATCATC
1 ATGAAGGTCCAGATCTGCTATGTCTTCAATATGCTCCCCGTCTAATACAAAGATGCCAAATCATC
*
39643320 TTGGATCTGCTTCA
66 TTGGATCTACTTCA
* * *
39643334 ATGAAGGTCCA-ATCTGTTATGTCTTCGATATGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGTCCAGATCTGCTATGTCTTCAATATGCTCCCCGTCTAATACAAAGATGCCAAATCATC
39643398 TTGGATCTACTTCA
66 TTGGATCTACTTCA
*
39643412 ATAAAGGT-CAGATCTGCT
1 ATGAAGGTCCAGATCTGCT
39643430 CTCAATAGAA
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
77 2 0.02
78 83 0.95
79 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (79 bp):
ATGAAGGTCCAGATCTGCTATGTCTTCAATATGCTCCCCGTCTAATACAAAGATGCCAAATCATC
TTGGATCTACTTCA
Found at i:39643605 original size:44 final size:44
Alignment explanation
Indices: 39643534--39644113 Score: 733
Period size: 44 Copynumber: 13.2 Consensus size: 44
39643524 CACGTGAAAA
* * * * *
39643534 CCAAATCTACTATGTCTTCAATTTGCTCTCTGACAATATAGAGATG
1 CCAAATCTGCTA--TCTTCGATCTGCTCTCTGACAATACAGAGACG
39643580 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACG
** * * * *
39643624 CCAAA--T-C-ATCTTAAATCCGCT-TCAG-CGTAA-ACACGTGAAAG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGAC--AATACA-GAG-ACG
* * * * *
39643665 CCAAATCTGCTATATCTTCAATTTTCTCTCTGAAAATACAGAGATG
1 CCAAATCTGC--TATCTTCGATCTGCTCTCTGACAATACAGAGACG
*
39643711 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACG
* *
39643755 CCAAATCTGCTATCTTCAATCTGCCCTCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACG
* *
39643799 CCAAATCTTCTATCTTCGATCTGCTCCCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACG
* * * *
39643843 CCAAATCTTCTATTTTCGATCTACCCTCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACG
*
39643887 CCAAATCTGCTATCTTCGATCTGCTCCCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACG
* * *
39643931 CCAATTCTGCTATCTTCGATGTGCCCTCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACG
*
39643975 CCAAATCTGCTATCTTCGATCTGCTCCCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACG
* * *
39644019 CCAATTCTGCTATCTTCGATGTGCCCTCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACG
*
39644063 CCAAATCTGCTATCTTCGATCTGCTCCCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACG
39644107 CCAAATC
1 CCAAATC
39644114 ATCTTAGATC
Statistics
Matches: 466, Mismatches: 55, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.00
39 6 0.01
40 15 0.03
41 8 0.02
42 1 0.00
43 1 0.00
44 391 0.84
46 23 0.05
47 14 0.03
48 6 0.01
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (44 bp):
CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACG
Found at i:39645096 original size:8 final size:8
Alignment explanation
Indices: 39645085--39645149 Score: 62
Period size: 8 Copynumber: 7.8 Consensus size: 8
39645075 CCATTTTTTA
39645085 TTTTTTC-
1 TTTTTTCT
39645092 TTTTTTCT
1 TTTTTTCT
39645100 TTTTTTCT
1 TTTTTTCT
39645108 TTTTATT-T
1 TTTT-TTCT
*
39645116 TTTTCTCTTT
1 TTTT-T-TCT
39645126 TTATTTTCT
1 TT-TTTTCT
39645135 TTTTTTCCT
1 TTTTTT-CT
39645144 TTTTTT
1 TTTTTT
39645150 TTGAAATAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
7 7 0.14
8 22 0.44
9 15 0.30
10 4 0.08
11 2 0.04
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTCT
Found at i:39645097 original size:14 final size:15
Alignment explanation
Indices: 39645079--39645132 Score: 76
Period size: 14 Copynumber: 3.7 Consensus size: 15
39645069 GCCTCTCCAT
39645079 TTTTTATTTTTTCT-
1 TTTTTATTTTTTCTC
*
39645093 TTTTTCTTTTTT-TC
1 TTTTTATTTTTTCTC
39645107 TTTTTATTTTTTTCTC
1 TTTTTA-TTTTTTCTC
39645123 TTTTTATTTT
1 TTTTTATTTT
39645133 CTTTTTTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 1 0.03
14 16 0.46
15 10 0.29
16 8 0.23
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTATTTTTTCTC
Found at i:39645103 original size:22 final size:21
Alignment explanation
Indices: 39645078--39645149 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 21
39645068 GGCCTCTCCA
39645078 TTTTTTATTTTTTCTTTTTTCT
1 TTTTTTATTTTTT-TTTTTTCT
*
39645100 TTTTTTCTTTTTATTTTTTTCT
1 TTTTTTATTTTT-TTTTTTTCT
* *
39645122 CTTTTTATTTTCTTTTTTTCCT
1 TTTTTTATTTT-TTTTTTTTCT
39645144 TTTTTT
1 TTTTTT
39645150 TTGAAATAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
22 41 0.95
23 2 0.05
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTTTATTTTTTTTTTTTCT
Found at i:39645137 original size:10 final size:9
Alignment explanation
Indices: 39645092--39645150 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
39645082 TTATTTTTTC
39645092 TTTTTTC-T
1 TTTTTTCTT
39645100 TTTTTTCTT
1 TTTTTTCTT
39645109 TTTATTT-TT
1 TTT-TTTCTT
*
39645118 TTCTCTT-TT
1 TT-TTTTCTT
*
39645127 TATTTTCTT
1 TTTTTTCTT
*
39645136 TTTTTCCTT
1 TTTTTTCTT
39645145 TTTTTT
1 TTTTTT
39645151 TGAAATAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
8 10 0.24
9 27 0.66
10 4 0.10
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:39645139 original size:7 final size:7
Alignment explanation
Indices: 39645078--39645139 Score: 65
Period size: 7 Copynumber: 8.9 Consensus size: 7
39645068 GGCCTCTCCA
*
39645078 TTTTTTA
1 TTTTTTC
39645085 TTTTTTC
1 TTTTTTC
39645092 TTTTTTC
1 TTTTTTC
39645099 TTTTTTTC
1 -TTTTTTC
39645107 TTTTTAT-
1 TTTTT-TC
39645114 TTTTTTC
1 TTTTTTC
*
39645121 TCTTTT-
1 TTTTTTC
*
39645127 TATTTTC
1 TTTTTTC
39645134 TTTTTT
1 TTTTTT
39645140 TCCTTTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
6 6 0.13
7 33 0.70
8 8 0.17
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:39645140 original size:14 final size:13
Alignment explanation
Indices: 39645078--39645140 Score: 72
Period size: 14 Copynumber: 4.5 Consensus size: 13
39645068 GGCCTCTCCA
39645078 TTTTTTATTTTTTC
1 TTTTTT-TTTTTTC
39645092 TTTTTTCTTTTTTTC
1 -TTTTT-TTTTTTTC
39645107 TTTTTATTTTTTTC
1 TTTTT-TTTTTTTC
* *
39645121 TCTTTTTATTTTC
1 TTTTTTTTTTTTC
39645134 TTTTTTT
1 TTTTTTT
39645141 CCTTTTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
13 13 0.30
14 17 0.40
15 12 0.28
16 1 0.02
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:39650735 original size:113 final size:113
Alignment explanation
Indices: 39650537--39650762 Score: 434
Period size: 113 Copynumber: 2.0 Consensus size: 113
39650527 TAAAATAAAA
39650537 AAGGTTGAAAAACTAAGATAGACGAAGAATAAAATAAGAACAAACCACAGAAAGTAAGAACGCAA
1 AAGGTTGAAAAACTAAGATAGACGAAGAATAAAATAAGAACAAACCACAGAAAGTAAGAACGCAA
39650602 GAGGGAGAGAAATTTGAGTGAATGCTCTCAAGAATTCTTATTGCTTCC
66 GAGGGAGAGAAATTTGAGTGAATGCTCTCAAGAATTCTTATTGCTTCC
* *
39650650 AAGGTTGAAAAACTAAGATAGACGAAGAATAAAATAAGAACAAACCACAGAGAGTAAGAACGTAA
1 AAGGTTGAAAAACTAAGATAGACGAAGAATAAAATAAGAACAAACCACAGAAAGTAAGAACGCAA
39650715 GAGGGAGAGAAATTTGAGTGAATGCTCTCAAGAATTCTTATTGCTTCC
66 GAGGGAGAGAAATTTGAGTGAATGCTCTCAAGAATTCTTATTGCTTCC
39650763 CAAAACTCCA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.20
Consensus pattern (113 bp):
AAGGTTGAAAAACTAAGATAGACGAAGAATAAAATAAGAACAAACCACAGAAAGTAAGAACGCAA
GAGGGAGAGAAATTTGAGTGAATGCTCTCAAGAATTCTTATTGCTTCC
Found at i:39650908 original size:22 final size:21
Alignment explanation
Indices: 39650873--39650948 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
39650863 AAAGGATATC
* *
39650873 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
39650894 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
39650917 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
39650936 TGC-AATCATATCT
1 TACAAATCATATCT
39650949 AAGATTGCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:39650945 original size:18 final size:19
Alignment explanation
Indices: 39650909--39650963 Score: 103
Period size: 18 Copynumber: 2.9 Consensus size: 19
39650899 AATCATATCT
39650909 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
39650928 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
39650946 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
39650964 TGAAGATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:39651119 original size:21 final size:20
Alignment explanation
Indices: 39651082--39651120 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
39651072 TTGGACTTTG
**
39651082 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
39651102 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
39651121 TCAGGGCCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:39651190 original size:19 final size:19
Alignment explanation
Indices: 39651166--39651210 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
39651156 ACAACAATAT
39651166 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
* *
39651185 ATATCACATCTAAGATTTC
1 ATATCATATCTAAGATTGC
39651204 ATATCAT
1 ATATCAT
39651211 TAAAGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:39651355 original size:247 final size:246
Alignment explanation
Indices: 39650920--39651395 Score: 819
Period size: 247 Copynumber: 1.9 Consensus size: 246
39650910 CTAAGATTGC
* * *
39650920 ATATCATATCTAAGATTGCAATCATATCTAAGATTGCATATCATTGAAGATTATATTTCTATATG
1 ATATCATATCTAAGATTGCAATCACATCTAAGATTGCATATCATTAAAGATTATATTTCCATATG
39650985 AGTCAAGCTTGTAGATAGACCTTAAATCTTTTCAAGTAATGGGCCATTCCGATCGAGCCAAATTA
66 AGTCAAGCTTGTAGATAGACCTTAAATCTTTTCAAGTAATGGGCCATTCCGATCGAGCCAAATTA
* *
39651050 TATTTGTATTTATGGACAGAACTTGGACTTTGTTTTTTTTTGGGTTTATTATTTTTGTTTTTGGA
131 TATTTGTAATTATGGACAGAACTTGGACTTTGTTTTTTTTGGGGTTTATTATTTTTGTTTTTGGA
39651115 CTTATTTCAGGGCCCGGGCAAAATTGAGTGTCTAAAATTATACAACAATAT
196 CTTATTTCAGGGCCCGGGCAAAATTGAGTGTCTAAAATTATACAACAATAT
*
39651166 ATATCATATCTAAGATTGCATATCACATCTAAGATTTCATATCATTAAAGATTATATTTCCATAT
1 ATATCATATCTAAGATTGCA-ATCACATCTAAGATTGCATATCATTAAAGATTATATTTCCATAT
* *
39651231 GAGTCAAGCTTGTAGATGGACCTTAAATCTTTTCAAGTAATGGGCCATTCCGATCGGGCCAAATT
65 GAGTCAAGCTTGTAGATAGACCTTAAATCTTTTCAAGTAATGGGCCATTCCGATCGAGCCAAATT
* *
39651296 ATATTTGTAATTATGGACTGAACTT-GACTTTGTTTTTTTTGGGGGTTTATTGTTTTTGTTTTTG
130 ATATTTGTAATTATGGACAGAACTTGGACTTTGTTTTTTTT-GGGGTTTATTATTTTTGTTTTTG
* *
39651360 GACTTTTTTCTGGGCCCGGGCAAAATTGAGTGTCTA
194 GACTTATTTCAGGGCCCGGGCAAAATTGAGTGTCTA
39651396 CAGATGGTTT
Statistics
Matches: 216, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
246 35 0.16
247 181 0.84
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (246 bp):
ATATCATATCTAAGATTGCAATCACATCTAAGATTGCATATCATTAAAGATTATATTTCCATATG
AGTCAAGCTTGTAGATAGACCTTAAATCTTTTCAAGTAATGGGCCATTCCGATCGAGCCAAATTA
TATTTGTAATTATGGACAGAACTTGGACTTTGTTTTTTTTGGGGTTTATTATTTTTGTTTTTGGA
CTTATTTCAGGGCCCGGGCAAAATTGAGTGTCTAAAATTATACAACAATAT
Found at i:39652015 original size:18 final size:18
Alignment explanation
Indices: 39651992--39652033 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
39651982 AATTTGAAAT
* *
39651992 AAAACATGAACTTTTGGG
1 AAAACATGAAATTTTAGG
39652010 AAAACATGAAATTTTAGG
1 AAAACATGAAATTTTAGG
39652028 AAAACA
1 AAAACA
39652034 GTGGTCACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.24
Consensus pattern (18 bp):
AAAACATGAAATTTTAGG
Found at i:39652291 original size:85 final size:85
Alignment explanation
Indices: 39652148--39652312 Score: 303
Period size: 85 Copynumber: 1.9 Consensus size: 85
39652138 TGGGTATTTG
*
39652148 TGTAACACCCCTTACCCGTATCCGAGGCCGAGCTAAGGTACGAGGCGTTACCAGACAAACATACA
1 TGTAACACCCCTTACCCGTATCCAAGGCCGAGCTAAGGTACGAGGCGTTACCAGACAAACATACA
39652213 AACATTAAAATAAAACTAAA
66 AACATTAAAATAAAACTAAA
*
39652233 TGTAACACCCCTTACCCGTATCCAAGGTCGAGCTAAGGTACGAGGCGTTACCAGACAAACATACA
1 TGTAACACCCCTTACCCGTATCCAAGGCCGAGCTAAGGTACGAGGCGTTACCAGACAAACATACA
*
39652298 AACATTAAACTAAAA
66 AACATTAAAATAAAA
39652313 TACGAGCCAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 77 1.00
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.18
Consensus pattern (85 bp):
TGTAACACCCCTTACCCGTATCCAAGGCCGAGCTAAGGTACGAGGCGTTACCAGACAAACATACA
AACATTAAAATAAAACTAAA
Found at i:39657134 original size:18 final size:18
Alignment explanation
Indices: 39657101--39657150 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
39657091 TTAGTCATAT
*
39657101 TTTTCTAGTTTTTCTTTTC
1 TTTTCTA-TTTTTCTTCTC
39657120 TTTT-TATTGTTTCTTCTC
1 TTTTCTATT-TTTCTTCTC
39657138 TTTTCTATTTTTC
1 TTTTCTATTTTTC
39657151 AGGTTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.07
18 18 0.64
19 8 0.29
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.74
Consensus pattern (18 bp):
TTTTCTATTTTTCTTCTC
Found at i:39660456 original size:50 final size:49
Alignment explanation
Indices: 39660381--39660617 Score: 208
Period size: 50 Copynumber: 4.8 Consensus size: 49
39660371 TGAATACACG
* * * *
39660381 TGTGTAGTACTGAGTGTAGGCTACTACGTGTATCATACTGTTAAGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTGTTAA-TCACA
* * ** *
39660431 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCAATGACT-TCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TC-A-GACTGTTAATCACA
* * * *
39660482 TGTGTAGTATTAAGTGCAGGCTACTACGTGTATCAGA-TGATGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTG-TTA-ATCACA
* * * * * *
39660532 TGTGTAGTACTAAGTGTAGGCTACTACATGTACCAGATTGTTGATCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTGTTAATCACA
* * *
39660581 TGTGCAGTACTAAGTGCAGGCTACTATGCGTATCAGA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA
39660618 TAGCTTCGGC
Statistics
Matches: 150, Mismatches: 30, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
47 1 0.01
48 2 0.01
49 36 0.24
50 69 0.46
51 36 0.24
52 3 0.02
53 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTGTTAATCACA
Found at i:39666405 original size:40 final size:40
Alignment explanation
Indices: 39666338--39666594 Score: 272
Period size: 40 Copynumber: 6.5 Consensus size: 40
39666328 ACCCAAGTAT
*
39666338 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
39666377 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
39666417 CTTCGGGTCTTAGCCTGGATATAATC-AC-CAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTC-GCACAAATGC
* * * **
39666457 CTTCGGGACATAGCCCGGATACAGCAACTTACACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
39666497 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* ** * *
39666537 CTTCGGGACAAAGCCCGGATATAGAAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
39666577 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
39666595 TTATCATCCG
Statistics
Matches: 178, Mismatches: 32, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
38 1 0.01
39 15 0.08
40 158 0.89
41 4 0.02
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:39666471 original size:80 final size:79
Alignment explanation
Indices: 39666338--39666594 Score: 340
Period size: 80 Copynumber: 3.2 Consensus size: 79
39666328 ACCCAAGTAT
* * *
39666338 CTTCGGGAT-TTAGCCGGATATAA-CAACTC-GCACAAATGCCTTCGGGTCTTAGCCCGGATATA
1 CTTCGGG-TCTTAGCCGGATATAATC-AC-CAGCATAAATGCCTTCGGGACATAGCCCGGATATA
39666400 GCAACTCGCACAAATGC
63 GCAACTCGCACAAATGC
*
39666417 CTTCGGGTCTTAGCCTGGATATAATCACCAGCATAAATGCCTTCGGGACATAGCCCGGATACAGC
1 CTTCGGGTCTTAGCC-GGATATAATCACCAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
**
39666482 AACTTACACAAATGC
65 AACTCGCACAAATGC
* * *
39666497 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACAAAGCCCGGATATAGA
1 CTTCGGGTCTTAG-CCGGATATAATCACCAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
*
39666562 AACTCGCACGAATGC
65 AACTCGCACAAATGC
*
39666577 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAG-CCGG
39666595 TTATCATCCG
Statistics
Matches: 158, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
78 1 0.01
79 14 0.09
80 140 0.89
81 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (79 bp):
CTTCGGGTCTTAGCCGGATATAATCACCAGCATAAATGCCTTCGGGACATAGCCCGGATATAGCA
ACTCGCACAAATGC
Found at i:39672451 original size:46 final size:46
Alignment explanation
Indices: 39672375--39673458 Score: 1751
Period size: 46 Copynumber: 23.6 Consensus size: 46
39672365 CCATAGTGTC
* * ** * * * *
39672375 TTTCAACTATGGTCTTACTCATTTTTTGTCATGTTACCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
** * * * **
39672421 TTTCAACCATGGTCTTATTCTTTTCATGTCATGTTGCCATGGTAGC
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
** * * * * * *
39672467 TTTCAACCATGGTCTTATTCATTTTATGTCACGCTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
* ** * * * * *
39672513 TTTCTACCATGGTCTTATTCATTTC-TCGTCTTGCTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCAT-ATCATGTTGCCATGATATT
** * ** * *
39672559 TTTCAACCATGGTCTTATTC-TTTCATGTCACATTGTCATGGTATCT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATAT-T
39672605 TTT-AACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
* *
39672650 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39672696 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39672742 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39672788 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39672834 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39672880 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39672926 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39672972 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39673018 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39673064 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39673110 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39673156 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39673202 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39673248 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39673294 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39673340 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
* *
39673386 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
39673432 TTTCAACCATGGTCTTACACATTTCAT
1 TTTCAACCATGGTCTTACACATTTCAT
39673459 TTCAGAGAGC
Statistics
Matches: 997, Mismatches: 36, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
45 36 0.04
46 961 0.96
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (46 bp):
TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATT
Found at i:39688159 original size:20 final size:20
Alignment explanation
Indices: 39688129--39688173 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
39688119 CTGTTTTATT
39688129 ATGGG-CCAACTGTATTAAA
1 ATGGGCCCAACTGTATTAAA
* *
39688148 ATGGGCCCAACTGTGTTAAT
1 ATGGGCCCAACTGTATTAAA
39688168 ATGGGC
1 ATGGGC
39688174 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTGTATTAAA
Found at i:39688234 original size:28 final size:27
Alignment explanation
Indices: 39688202--39688302 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 27
39688192 ACTTGTAATA
39688202 GGGCTACGGCCCAGATTGATACTGATAT
1 GGGCTA-GGCCCAGATTGATACTGATAT
* *
39688230 GGGCTAGGCCCAGTATACTCTGTTACTG-TAAG
1 GGGCTAGGCCCAG---A-T-TGATACTGAT-AT
* *
39688262 GGGCTATGGCCCAGATTAATATTGATAT
1 GGGCTA-GGCCCAGATTGATACTGATAT
39688290 GGGCTAAGGCCCA
1 GGGCT-AGGCCCA
39688303 TTTAACACTA
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
27 7 0.12
28 23 0.40
29 3 0.05
30 2 0.03
31 2 0.03
32 14 0.24
33 7 0.12
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (27 bp):
GGGCTAGGCCCAGATTGATACTGATAT
Found at i:39688266 original size:60 final size:60
Alignment explanation
Indices: 39688166--39688302 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 60
39688156 AACTGTGTTA
* *
39688166 ATATGGGCAAGGCCCAATATATCTTGACTTGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAGGCCCAATATATCTTGACTTGTAATAGGGCTACGGCCCAGATTAATACTG
* * * * *
39688226 ATATGGGCTAGGCCCAGTATACTCTGTTAC-TGTAA-GGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAATATA-TCT-TGACTTGTAATAGGGCTACGGCCCAGATTAATACTG
39688286 ATATGGGCTAAGGCCCA
1 ATATGGGCT-AGGCCCA
39688303 TTTAACACTA
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
60 49 0.73
61 15 0.22
62 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (60 bp):
ATATGGGCTAGGCCCAATATATCTTGACTTGTAATAGGGCTACGGCCCAGATTAATACTG
Found at i:39692743 original size:14 final size:14
Alignment explanation
Indices: 39692724--39692754 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
39692714 ATGATAACCG
39692724 TTTGTTTTCTATTA
1 TTTGTTTTCTATTA
39692738 TTTGTTTTCTATTA
1 TTTGTTTTCTATTA
39692752 TTT
1 TTT
39692755 TACTAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.74
Consensus pattern (14 bp):
TTTGTTTTCTATTA
Found at i:39698022 original size:37 final size:37
Alignment explanation
Indices: 39697981--39698052 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
39697971 ATGAAACATG
*
39697981 CCAAATGCTCATAAGAGCTAATCCAACCAATAACACA
1 CCAAACGCTCATAAGAGCTAATCCAACCAATAACACA
* *
39698018 CCAAACGCTCATGAGAGCTAATCCAACCGATAACA
1 CCAAACGCTCATAAGAGCTAATCCAACCAATAACA
39698053 TGCTTCGGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.43, C:0.31, G:0.11, T:0.15
Consensus pattern (37 bp):
CCAAACGCTCATAAGAGCTAATCCAACCAATAACACA
Found at i:39699232 original size:12 final size:13
Alignment explanation
Indices: 39699215--39699243 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39699205 CTTTTAATTT
39699215 CTTTAA-TTTTAA
1 CTTTAATTTTTAA
39699227 CTTTAATTTTTAA
1 CTTTAATTTTTAA
39699240 CTTT
1 CTTT
39699244 TACTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTTAATTTTTAA
Found at i:39702526 original size:66 final size:66
Alignment explanation
Indices: 39702420--39702557 Score: 240
Period size: 66 Copynumber: 2.1 Consensus size: 66
39702410 TTTTTTATAA
* *
39702420 TTCATATTATTTCCTTATTCAATTTCCCTCAAAAGTTTAATATAACCATCAAACTTTCATCATTT
1 TTCATATTATTTCCTTATTCAATTTCCCTCAAAACTTTAATATAACCATCAAACTTTAATCATTT
39702485 T
66 T
*
39702486 TTCATATTATTTCCTTATTCAATTTCCCTCAAAACTTTAATATAACCATTAAACTTTAATCATTT
1 TTCATATTATTTCCTTATTCAATTTCCCTCAAAACTTTAATATAACCATCAAACTTTAATCATTT
39702551 T
66 T
*
39702552 TCCATA
1 TTCATA
39702558 ATTTTGAATT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.33, C:0.21, G:0.01, T:0.46
Consensus pattern (66 bp):
TTCATATTATTTCCTTATTCAATTTCCCTCAAAACTTTAATATAACCATCAAACTTTAATCATTT
T
Found at i:39702847 original size:5 final size:5
Alignment explanation
Indices: 39702837--39702876 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
39702827 AATTTCTCCT
39702837 TTTTC TTTTC TTTTC --TTC TTTT- TTTTC TATTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC TTTTC TT
39702877 CTCTGTAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
3 3 0.10
4 4 0.13
5 19 0.61
6 5 0.16
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:39702869 original size:18 final size:18
Alignment explanation
Indices: 39702837--39702871 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39702827 AATTTCTCCT
39702837 TTTTCTTTTCTTTTCTTC
1 TTTTCTTTTCTTTTCTTC
39702855 TTTT-TTTTCTATTTCTT
1 TTTTCTTTTCT-TTTCTT
39702872 TTCTTCTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTCTTTTCTTC
Found at i:39702869 original size:23 final size:22
Alignment explanation
Indices: 39702836--39702878 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
39702826 TAATTTCTCC
39702836 TTTTTCTTTTCTTTTCTTCTTT
1 TTTTTCTTTTCTTTTCTTCTTT
39702858 TTTTTCTATTTCTTTTCTTCT
1 TTTTTCT-TTTCTTTTCTTCT
39702879 CTGTAACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCTTTTCTTTTCTTCTTT
Found at i:39703310 original size:20 final size:21
Alignment explanation
Indices: 39703264--39703311 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
39703254 TCCTTTCTTA
*
39703264 CTAATTACTTCTAATTAAAAAT
1 CTAATT-CTCCTAATTAAAAAT
*
39703286 -AAATTCTCCTAATT-AAAAT
1 CTAATTCTCCTAATTAAAAAT
39703305 CTAATTC
1 CTAATTC
39703312 AACTTGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 5 0.23
20 13 0.59
21 4 0.18
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.40
Consensus pattern (21 bp):
CTAATTCTCCTAATTAAAAAT
Found at i:39703800 original size:20 final size:20
Alignment explanation
Indices: 39703775--39703814 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39703765 ATCGTACAGA
39703775 GTCAACCAATCCATACCAAG
1 GTCAACCAATCCATACCAAG
39703795 GTCAACCAATCCATACCAAG
1 GTCAACCAATCCATACCAAG
39703815 AATCTCATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.35, G:0.10, T:0.15
Consensus pattern (20 bp):
GTCAACCAATCCATACCAAG
Found at i:39707005 original size:41 final size:41
Alignment explanation
Indices: 39706942--39707074 Score: 185
Period size: 41 Copynumber: 3.2 Consensus size: 41
39706932 CCAAATACAT
* * *
39706942 CCTTTTCATTTGTTATCCTTTTCGGATAACATCCTTTTAAA
1 CCTTTTCATTTGATATCATTTTCGGATAACATCCTTTTCAA
* *
39706983 CCTTTTCATTTGATGTCATTTTCGGATAACATCATTTTCAA
1 CCTTTTCATTTGATATCATTTTCGGATAACATCCTTTTCAA
* * **
39707024 TCTTTTTATTTGATATCATTTTTAGATAACATCCTTTTCAA
1 CCTTTTCATTTGATATCATTTTCGGATAACATCCTTTTCAA
39707065 CCTTTTCATT
1 CCTTTTCATT
39707075 GATTCAAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 79 1.00
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (41 bp):
CCTTTTCATTTGATATCATTTTCGGATAACATCCTTTTCAA
Found at i:39707162 original size:20 final size:20
Alignment explanation
Indices: 39707137--39707175 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39707127 CCTTTTAGAG
39707137 TGTATTTCAATCACGGTCCA
1 TGTATTTCAATCACGGTCCA
*
39707157 TGTATTTCAATCATGGTCC
1 TGTATTTCAATCACGGTCC
39707176 TTTCTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATTTCAATCACGGTCCA
Found at i:39709182 original size:59 final size:59
Alignment explanation
Indices: 39709090--39709208 Score: 211
Period size: 59 Copynumber: 2.0 Consensus size: 59
39709080 TAAAGCTCAA
* *
39709090 TGAGTGCACATGCATACAACACAAATATACACACCAAACATGTTAGGATTTAAACATAG
1 TGAGTACACATGCATACAACACAAATATACACACCAAACATGTTAGGATATAAACATAG
*
39709149 TGAGTACACATGCATACAACACAAATATACACACCAAACATTTTAGGATATAAACATAG
1 TGAGTACACATGCATACAACACAAATATACACACCAAACATGTTAGGATATAAACATAG
39709208 T
1 T
39709209 TTAAAAATTC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (59 bp):
TGAGTACACATGCATACAACACAAATATACACACCAAACATGTTAGGATATAAACATAG
Found at i:39709229 original size:59 final size:58
Alignment explanation
Indices: 39709102--39709231 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 58
39709092 AGTGCACATG
* * * *
39709102 CATACAACACAAATATACACACCAAACATGTTAGGATTTAAACATAGTGAGTACACATG
1 CATACAACACAAATATACACACCAAACATGTTAGGATATAAACATAGT-AGTAAAAATA
* *
39709161 CATACAACACAAATATACACACCAAACATTTTAGGATATAAACATAGT-TTAAAAATTCA
1 CATACAACACAAATATACACACCAAACATGTTAGGATATAAACATAGTAGTAAAAA-T-A
*
39709220 CATATAACACAA
1 CATACAACACAA
39709232 TTTTCATACT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
57 4 0.06
58 1 0.02
59 57 0.92
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.23
Consensus pattern (58 bp):
CATACAACACAAATATACACACCAAACATGTTAGGATATAAACATAGTAGTAAAAATA
Found at i:39714630 original size:33 final size:31
Alignment explanation
Indices: 39714586--39714651 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
39714576 TCTTGGCAGG
*
39714586 TATATATAACA-AAAC-CTAAGCATAATATAT
1 TATATATAAAACAAACGCTAAGCATAA-ATAT
*
39714616 ATATATATAAAACAAACGCTATGCATAAATAT
1 -TATATATAAAACAAACGCTAAGCATAAATAT
39714648 TATA
1 TATA
39714652 AATTGAACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 14 0.45
32 8 0.26
33 9 0.29
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (31 bp):
TATATATAAAACAAACGCTAAGCATAAATAT
Found at i:39718189 original size:37 final size:37
Alignment explanation
Indices: 39718144--39718224 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
39718134 AATTTGAGCA
39718144 AATTTTGCAAAAGGTGATGAAAATTTAAATCTATTTG
1 AATTTTGCAAAAGGTGATGAAAATTTAAATCTATTTG
*
39718181 AATTTTGCAAAAGGTGATGAAATTTTAAATCTATTTG
1 AATTTTGCAAAAGGTGATGAAAATTTAAATCTATTTG
39718218 AATTTTG
1 AATTTTG
39718225 AAAGAGGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (37 bp):
AATTTTGCAAAAGGTGATGAAAATTTAAATCTATTTG
Found at i:39718670 original size:40 final size:40
Alignment explanation
Indices: 39718626--39718707 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
39718616 ATTGGATAGA
*
39718626 TTATAGATTTAATTTATTTTTAAAAACTAGATAAATACTT
1 TTATAGATTTAATTTATTCTTAAAAACTAGATAAATACTT
39718666 TTATAGATTTAATTTATTCTTAAAAACTAGATAAATACTT
1 TTATAGATTTAATTTATTCTTAAAAACTAGATAAATACTT
39718706 TT
1 TT
39718708 TTTCATAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (40 bp):
TTATAGATTTAATTTATTCTTAAAAACTAGATAAATACTT
Found at i:39719243 original size:12 final size:13
Alignment explanation
Indices: 39719221--39719250 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
39719211 CTAGCTTCGG
39719221 TTTTCAATTTTAA
1 TTTTCAATTTTAA
39719234 TTTT-AATTTTAA
1 TTTTCAATTTTAA
39719246 TTTTC
1 TTTTC
39719251 CTTTGTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTCAATTTTAA
Found at i:39725622 original size:16 final size:16
Alignment explanation
Indices: 39725601--39725632 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39725591 AGATTAGGTT
39725601 GACAATGCATCAATGC
1 GACAATGCATCAATGC
39725617 GACAATGCATCAATGC
1 GACAATGCATCAATGC
39725633 CCTGACCTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (16 bp):
GACAATGCATCAATGC
Found at i:39728374 original size:34 final size:34
Alignment explanation
Indices: 39728320--39728395 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 34
39728310 TAAAGTATCA
* *
39728320 TCATCA-TATTAACTAGGTCCTTTCATCAATTTC
1 TCATCATTATCAACCAGGTCCTTTCATCAATTTC
*
39728353 TCATCATTATCAACCAGGTCCTTTCATCAGTTTC
1 TCATCATTATCAACCAGGTCCTTTCATCAATTTC
39728387 TCATCATTA
1 TCATCATTA
39728396 ACTTGAACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 6 0.15
34 33 0.85
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.41
Consensus pattern (34 bp):
TCATCATTATCAACCAGGTCCTTTCATCAATTTC
Found at i:39743471 original size:220 final size:220
Alignment explanation
Indices: 39743089--39743986 Score: 1332
Period size: 220 Copynumber: 4.1 Consensus size: 220
39743079 GTAACAGGCT
*
39743089 AAGACATAGCAGATCTAACCTTCGGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATC
1 AAGACATAGCAGATCTAACATTCGGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATC
*
39743154 CTTGCGTTTACAAGGAGCAGATTGAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGC
66 CTTGCGTTTACAAGGAGCAGATCGAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGC
* * * *
39743219 AGATCTAAGATGATTTGGCATCTCTGTATTGTCAAAGAACAAATCGAAGAAATAGATTTGGCATC
131 AGATATAATATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATC
39743284 TCCATATTCGACGGAGAGCAAATCG
196 TCCATATTCGACGGAGAGCAAATCG
*
39743309 AAGACATAGCAGATCTAACATTCGGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGTATC
1 AAGACATAGCAGATCTAACATTCGGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATC
* * *
39743374 CTTGCATTTACAAGGAGCAGATCGAAGACATAGCAGATTTGGATTTCACGTGTTTACGCTGAAGT
66 CTTGCGTTTACAAGGAGCAGATCGAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGC
* **
39743439 AGATATAATATGATTTGGCATCTCTGTATTGTCAGAGAACAAATTGAAGAAACTTATTTGGCATC
131 AGATATAATATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATC
*
39743504 TCCATATTCGACGGATAGCAAATCG
196 TCCATATTCGACGGAGAGCAAATCG
* **
39743529 AAGACATAGTAGATCTAACCA-TCGGATGTTTTCACATTAAAGTAGATCCAAGATGATTTGGCAT
1 AAGACATAGCAGATCTAA-CATTCGGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCAT
* * **
39743593 CCTTACTTTTACAAGGAGCAGATCGAAGACATAATAGATTTGGCTTTCACGTGTTTACGCTGAAG
65 CCTTGCGTTTACAAGGAGCAGATCGAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAG
39743658 CAGATATAATATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGAAACAGATTTGGCAT
130 CAGATATAATATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGAAACAGATTTGGCAT
* *
39743723 CTCTATATTCGACGGAGAGCAAATAG
195 CTCCATATTCGACGGAGAGCAAATCG
*
39743749 AAGACATAGCAGATCTAACCTTCGGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATC
1 AAGACATAGCAGATCTAACATTCGGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATC
* * * * *
39743814 ATTGCGGTTACAAGGAGCAGATCGAAAACATAGTAGATTTGGCTTTCACGTGTGTACGCTGAAGC
66 CTTGCGTTTACAAGGAGCAGATCGAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGC
* * * * ** *
39743879 AGATCTAAGATAGCAGATTTGGCGTCCCTGTATTGTCAGAGAGTAGATCGAAGATAACAGATTTG
131 AGATAT-A-ATA--TGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGA-AACAGATTTG
* * * * * *
39743944 ACGTCTCTATATT-GTCAGAGAGCAGATCG
191 GCATCTCCATATTCGACGGAGAGCAAATCG
* *
39743973 AAGATATAGTAGAT
1 AAGACATAGCAGAT
39743987 TTGGCTTTCA
Statistics
Matches: 615, Mismatches: 56, Indels: 10
0.90 0.08 0.01
Matches are distributed among these distances:
219 1 0.00
220 529 0.86
221 3 0.00
222 3 0.00
224 58 0.09
225 21 0.03
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (220 bp):
AAGACATAGCAGATCTAACATTCGGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATC
CTTGCGTTTACAAGGAGCAGATCGAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGC
AGATATAATATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATC
TCCATATTCGACGGAGAGCAAATCG
Found at i:39743933 original size:44 final size:44
Alignment explanation
Indices: 39743876--39744070 Score: 189
Period size: 44 Copynumber: 4.4 Consensus size: 44
39743866 TGTACGCTGA
*
39743876 AGCAGATCTAAGATAGCAGATTTGGCGTCCCTGTATTGTCAGAG
1 AGCAGATCGAAGATAGCAGATTTGGCGTCCCTGTATTGTCAGAG
* * * * *
39743920 AGTAGATCGAAGATAACAGATTTGACGTCTCTATATTGTCAGAG
1 AGCAGATCGAAGATAGCAGATTTGGCGTCCCTGTATTGTCAGAG
* * * *
39743964 AGCAGATCGAAGATATAGTAGATTTGGCTTTCACGTGT-TTACG-CTGA-
1 AGCAGATCGAAG--ATAGCAGATTTGGC-GTC-CCTGTATT--GTCAGAG
* *
39744011 AGTAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAG
1 AGCAGATCGAAGATAGCAGATTTGGCGTCCCTGTATTGTCAGAG
* *
39744055 AGCAAATCGAATATAG
1 AGCAGATCGAAGATAG
39744071 TCTGTATTGT
Statistics
Matches: 118, Mismatches: 24, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
42 1 0.01
43 6 0.05
44 66 0.56
45 13 0.11
46 11 0.09
47 15 0.13
48 5 0.04
49 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (44 bp):
AGCAGATCGAAGATAGCAGATTTGGCGTCCCTGTATTGTCAGAG
Found at i:39751489 original size:37 final size:37
Alignment explanation
Indices: 39751448--39751548 Score: 139
Period size: 37 Copynumber: 2.7 Consensus size: 37
39751438 AGCTTGTAAA
39751448 AGCTAATCCACCCGATAACACGCCAGATGCTCATAAG
1 AGCTAATCCACCCGATAACACGCCAGATGCTCATAAG
* * * *
39751485 AGCTAATCCACCTGCTAACAAGCTAGATGCTCATAAG
1 AGCTAATCCACCCGATAACACGCCAGATGCTCATAAG
* * *
39751522 AGCTAGTCCAACCGAAAACACGCCAGA
1 AGCTAATCCACCCGATAACACGCCAGA
39751549 ACAGGGAGTA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.37, C:0.31, G:0.17, T:0.16
Consensus pattern (37 bp):
AGCTAATCCACCCGATAACACGCCAGATGCTCATAAG
Found at i:39759884 original size:8 final size:8
Alignment explanation
Indices: 39759866--39759895 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
39759856 ATGCTAATTA
39759866 TGTGTATTT
1 TGTG-ATTT
39759875 TGTGATTT
1 TGTGATTT
39759883 TGTGATTT
1 TGTGATTT
39759891 TGTGA
1 TGTGA
39759896 ATTAAGGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (8 bp):
TGTGATTT
Found at i:39760265 original size:29 final size:30
Alignment explanation
Indices: 39760212--39760269 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
39760202 CAGAAGTTTT
*
39760212 GGCACTAAGTGTGCGATTTAAACTAGCTTG
1 GGCACTAAGTGTGCAATTTAAACTAGCTTG
39760242 GGCACTAAGTGTGCAATTT-AACTAGCTT
1 GGCACTAAGTGTGCAATTTAAACTAGCTT
39760270 CAGCTATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (30 bp):
GGCACTAAGTGTGCAATTTAAACTAGCTTG
Found at i:39761668 original size:15 final size:16
Alignment explanation
Indices: 39761642--39761672 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
39761632 AGCAAATTTT
39761642 TTTAATAATAAATGAA
1 TTTAATAATAAATGAA
39761658 TTTAA-AATAAATGAA
1 TTTAATAATAAATGAA
39761673 GAAAAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TTTAATAATAAATGAA
Found at i:39768236 original size:34 final size:34
Alignment explanation
Indices: 39768197--39768265 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
39768187 ATATAGTAAG
39768197 ATTGCATGGTGTGCCATTGTCTATAGTGTCAGAC
1 ATTGCATGGTGTGCCATTGTCTATAGTGTCAGAC
39768231 ATTGCATGGTGTGCCATTGTCTATAGTGTCAGAC
1 ATTGCATGGTGTGCCATTGTCTATAGTGTCAGAC
39768265 A
1 A
39768266 GATATCCGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (34 bp):
ATTGCATGGTGTGCCATTGTCTATAGTGTCAGAC
Found at i:39768259 original size:17 final size:17
Alignment explanation
Indices: 39768205--39768259 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
39768195 AGATTGCATG
39768205 GTGTGCCATTGTCTATA
1 GTGTGCCATTGTCTATA
* *
39768222 GTGTCAGACATTG-C-ATG
1 GTGT--GCCATTGTCTATA
39768239 GTGTGCCATTGTCTATA
1 GTGTGCCATTGTCTATA
39768256 GTGT
1 GTGT
39768260 CAGACAGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 6 0.20
16 1 0.03
17 16 0.53
18 1 0.03
19 6 0.20
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.38
Consensus pattern (17 bp):
GTGTGCCATTGTCTATA
Found at i:39770325 original size:30 final size:29
Alignment explanation
Indices: 39770289--39770346 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
39770279 CAGAAGTTTT
39770289 GGCACTAAGTGTGCGATTTAAACTAGCTTA
1 GGCACTAAGTGTGCGATTT-AACTAGCTTA
39770319 GGCACTAAGTGTGCGATTTAACTAGCTT
1 GGCACTAAGTGTGCGATTTAACTAGCTT
39770347 CGGCTATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (29 bp):
GGCACTAAGTGTGCGATTTAACTAGCTTA
Found at i:39773873 original size:13 final size:13
Alignment explanation
Indices: 39773849--39773883 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
39773839 ATTTTTTTAT
39773849 TATATA-ATTGTG
1 TATATATATTGTG
*
39773861 TGTATATATTGTG
1 TATATATATTGTG
39773874 TATATATATT
1 TATATATATT
39773884 ATATGCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (13 bp):
TATATATATTGTG
Found at i:39774028 original size:3 final size:3
Alignment explanation
Indices: 39774020--39774098 Score: 140
Period size: 3 Copynumber: 26.3 Consensus size: 3
39774010 GTTGAAATTG
39774020 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
39774068 TTA TTA TTA TTA TTA TTA TTG TTA TTG TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
39774099 GGTTATATAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39774103 original size:12 final size:12
Alignment explanation
Indices: 39774029--39774109 Score: 63
Period size: 12 Copynumber: 6.7 Consensus size: 12
39774019 GTTATTATTA
**
39774029 TTATTATTATTA
1 TTATTATTATGG
**
39774041 TTATTATTATTA
1 TTATTATTATGG
**
39774053 TTATTATTATTA
1 TTATTATTATGG
**
39774065 TTATTATTATTA
1 TTATTATTATGG
*
39774077 TTATTATTATTG
1 TTATTATTATGG
*
39774089 TTATTGTTATGG
1 TTATTATTATGG
39774101 TTATATATT
1 TTAT-TATT
39774110 CAATTTTACG
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
12 61 0.95
13 3 0.05
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (12 bp):
TTATTATTATGG
Found at i:39779243 original size:44 final size:44
Alignment explanation
Indices: 39779179--39779264 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
39779169 AAACTGGTGT
* *
39779179 TTGGTTAGTGTGGTTGGTTATCGGTCTCACATACTAACATCATA
1 TTGGTTAGTGTGGTTAGTTATCAGTCTCACATACTAACATCATA
*
39779223 TTGGTTAGTGTGGTTAGTTATTAGTCTCACATACTAACATCA
1 TTGGTTAGTGTGGTTAGTTATCAGTCTCACATACTAACATCA
39779265 CAAATTCACT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (44 bp):
TTGGTTAGTGTGGTTAGTTATCAGTCTCACATACTAACATCATA
Found at i:39779652 original size:16 final size:16
Alignment explanation
Indices: 39779633--39779664 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39779623 ATTTTAAGTA
39779633 ACTTTAATTTTTTTTT
1 ACTTTAATTTTTTTTT
*
39779649 ACTTTACTTTTTTTTT
1 ACTTTAATTTTTTTTT
39779665 TTTGTTGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (16 bp):
ACTTTAATTTTTTTTT
Found at i:39779791 original size:41 final size:40
Alignment explanation
Indices: 39779745--39779848 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 40
39779735 TTCTAATTTG
* *
39779745 TTTTAATTTTTTTATTTTAATATAATTATTTTTTA-TTATAT
1 TTTTAATTTTTTTATTTTAATATAATTA--TTTTAGTCACAT
*
39779786 TTTTAATTTATGTATTATTTT-A-AGAATTATTTTAGTCACAT
1 TTTTAATTT-T-T-TTATTTTAATATAATTATTTTAGTCACAT
*
39779827 TTTT-ATTTTTTTGTTTTAATAT
1 TTTTAATTTTTTTATTTTAATAT
39779849 TTGTTTTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
37 6 0.12
38 2 0.04
39 2 0.04
40 9 0.17
41 17 0.33
42 7 0.13
43 2 0.04
44 7 0.13
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (40 bp):
TTTTAATTTTTTTATTTTAATATAATTATTTTAGTCACAT
Found at i:39789240 original size:18 final size:19
Alignment explanation
Indices: 39789205--39789255 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
39789195 TGAAATTATA
* *
39789205 ATAAAATAATATATAATAT
1 ATAAAATAATATAAAATAG
*
39789224 ATAAATTAA-ATAAAATAG
1 ATAAAATAATATAAAATAG
39789242 AT-AAA-AATATAAAA
1 ATAAAATAATATAAAA
39789256 GATATATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 2 0.07
17 8 0.30
18 9 0.33
19 8 0.30
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAAAATAATATAAAATAG
Found at i:39789250 original size:28 final size:29
Alignment explanation
Indices: 39789197--39789266 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
39789187 AAAAGTAATG
*
39789197 AAATTATAATAAAATAATATATAATATAT
1 AAATTATAATAAAATAATATAAAATATAT
*
39789226 AAATTA-AATAAAATAGATA-AAAATATAA
1 AAATTATAATAAAATA-ATATAAAATATAT
39789254 AAGATATATAATA
1 AA-AT-TATAATA
39789267 CATAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 18 0.51
29 11 0.31
30 2 0.06
31 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (29 bp):
AAATTATAATAAAATAATATAAAATATAT
Found at i:39791705 original size:73 final size:73
Alignment explanation
Indices: 39791618--39791803 Score: 363
Period size: 73 Copynumber: 2.5 Consensus size: 73
39791608 ACAACTTGAC
39791618 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
39791683 CACTAACA
66 CACTAACA
39791691 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
39791756 CACTAACA
66 CACTAACA
*
39791764 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
39791804 AATAATAATA
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 112 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:39791812 original size:3 final size:3
Alignment explanation
Indices: 39791804--39791829 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39791794 ATTACATCCA
39791804 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
39791830 AACATGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39796134 original size:73 final size:73
Alignment explanation
Indices: 39796047--39796378 Score: 637
Period size: 73 Copynumber: 4.5 Consensus size: 73
39796037 ACAACTTGAC
39796047 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
39796112 CACTAACA
66 CACTAACA
*
39796120 AACTTAGTTGGAATACAACTAAGTTTTATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
39796185 CACTAACA
66 CACTAACA
39796193 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
39796258 CACTAACA
66 CACTAACA
39796266 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
39796331 CACTAACA
66 CACTAACA
* *
39796339 AACTTAGTTGGAATACAACTAAGTTACATTATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
39796379 AATAATAATA
Statistics
Matches: 255, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 255 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:39799212 original size:17 final size:17
Alignment explanation
Indices: 39799190--39799224 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
39799180 TGAATATTAT
39799190 TAAAAAACCTTATAATC
1 TAAAAAACCTTATAATC
39799207 TAAAAAACCTTATAATC
1 TAAAAAACCTTATAATC
39799224 T
1 T
39799225 CATATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAACCTTATAATC
Found at i:39802781 original size:18 final size:17
Alignment explanation
Indices: 39802753--39802787 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39802743 ATTATTAAGA
*
39802753 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39802770 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39802788 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:39802808 original size:120 final size:120
Alignment explanation
Indices: 39802662--39803164 Score: 979
Period size: 120 Copynumber: 4.2 Consensus size: 120
39802652 TTTTCAAGTT
*
39802662 ATATATTTAATAATTATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
39802727 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
*
39802782 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
39802847 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
39802902 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
39802967 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
39803022 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
39803087 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
39803142 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
39803165 TAAATATGAT
Statistics
Matches: 378, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 378 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
Found at i:39803021 original size:18 final size:17
Alignment explanation
Indices: 39802993--39803027 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39802983 ATTATTAAGA
*
39802993 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39803010 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39803028 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:39803141 original size:18 final size:17
Alignment explanation
Indices: 39803113--39803147 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39803103 ATTATTAAGA
*
39803113 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39803130 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39803148 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:39811221 original size:34 final size:34
Alignment explanation
Indices: 39811156--39811221 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
39811146 TTTTGGGACT
* ***
39811156 AAATTTTTAATTTTTCCCAAAGGTGTGAATGGTG
1 AAATTTTTAATTTTTACCAAAGGTCAAAATGGTG
*
39811190 AAATTTTTAATTTTTATCAAAGGTCAAAATGG
1 AAATTTTTAATTTTTACCAAAGGTCAAAATGG
39811222 CCATTTCACA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.41
Consensus pattern (34 bp):
AAATTTTTAATTTTTACCAAAGGTCAAAATGGTG
Found at i:39814036 original size:21 final size:21
Alignment explanation
Indices: 39813996--39814034 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39813986 GTTAAAAATA
39813996 ATTATCATTTTCATCATTTAG
1 ATTATCATTTTCATCATTTAG
39814017 ATTATCATTTTCAT-ATTT
1 ATTATCATTTTCATCATTT
39814035 TAATCCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.28, C:0.13, G:0.03, T:0.56
Consensus pattern (21 bp):
ATTATCATTTTCATCATTTAG
Found at i:39820523 original size:37 final size:39
Alignment explanation
Indices: 39820471--39820633 Score: 213
Period size: 39 Copynumber: 4.2 Consensus size: 39
39820461 TTCAGTGATG
*
39820471 TATATCCAGACTTAGGGTCCGCAGGCTATGTGCTGGAA-
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* *
39820509 T-TATCCGAACTTAGGGTCCGTAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
** * *
39820547 TATATCCGGACCAAGGATCCACAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* * *
39820586 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
*
39820625 TATGTCCGG
1 TATATCCGG
39820634 GCTAAAGTCC
Statistics
Matches: 106, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
37 33 0.31
38 2 0.02
39 71 0.67
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:39820651 original size:39 final size:39
Alignment explanation
Indices: 39820471--39820671 Score: 148
Period size: 39 Copynumber: 5.2 Consensus size: 39
39820461 TTCAGTGATG
* * * *
39820471 TATATCCAGACTTAGGGT-CCGCAGGCTATGTGCTGGAA-
1 TATATCCGGAC-TAAGGTCCCGTAGGCTACGTGCTGGAAT
* * *
39820509 T-TATCCGAACTTAGGGT-CCGTAGGCTATGTGCTGGAAT
1 TATATCCGGAC-TAAGGTCCCGTAGGCTACGTGCTGGAAT
* *
39820547 TATATCCGGACCAAGGATCCAC--AGGCTATGTGCTGGAAT
1 TATATCCGGACTAAGG-TCC-CGTAGGCTACGTGCTGGAAT
* *
39820586 TATATCCGGACTTAAGGT-CCGCAGGCTACGTGCTGGAAA
1 TATATCCGGAC-TAAGGTCCCGTAGGCTACGTGCTGGAAT
* * * * * *
39820625 TATGTCCGGGCTAAAGTCCCGTAGGCTTCGAGCTGGTAT
1 TATATCCGGACTAAGGTCCCGTAGGCTACGTGCTGGAAT
39820664 TATA-CCGG
1 TATATCCGG
39820672 GTTTGTGCTG
Statistics
Matches: 136, Mismatches: 18, Indels: 18
0.79 0.10 0.10
Matches are distributed among these distances:
37 34 0.25
38 15 0.11
39 81 0.60
40 5 0.04
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGACTAAGGTCCCGTAGGCTACGTGCTGGAAT
Found at i:39835044 original size:24 final size:25
Alignment explanation
Indices: 39834994--39835045 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
39834984 AAATAATTTC
*
39834994 TAAAATTAAATAGAATACTTAAGAA
1 TAAAATTAAATAGAATAATTAAGAA
* *
39835019 TAAAATTAAATA-TATAATTAATAA
1 TAAAATTAAATAGAATAATTAAGAA
39835043 TAA
1 TAA
39835046 GTTTCAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (25 bp):
TAAAATTAAATAGAATAATTAAGAA
Found at i:39838456 original size:15 final size:16
Alignment explanation
Indices: 39838428--39838458 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
39838418 AAATAAAATG
39838428 TTGTTTTGGTTTGGTT
1 TTGTTTTGGTTTGGTT
39838444 TTGTTTT-GTTTGGTT
1 TTGTTTTGGTTTGGTT
39838459 GCGCAGCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (16 bp):
TTGTTTTGGTTTGGTT
Found at i:39847360 original size:30 final size:30
Alignment explanation
Indices: 39847326--39847422 Score: 74
Period size: 30 Copynumber: 3.2 Consensus size: 30
39847316 TTTATTTTGA
39847326 TCTTTGACTTGAAAATTAAATCCATTTTAT
1 TCTTTGACTTGAAAATTAAATCCATTTTAT
* * *** *
39847356 TCTTTAAATTTGGATTCTTTTCAAT--ATTTTGA-
1 TCTTT-GACTT-GA--AAATTAAATCCATTTT-AT
39847388 TCTTTGACTTGAAAATTAAATCCATTTTAT
1 TCTTTGACTTGAAAATTAAATCCATTTTAT
39847418 TCTTT
1 TCTTT
39847423 AAATTTGGAT
Statistics
Matches: 47, Mismatches: 12, Indels: 16
0.63 0.16 0.21
Matches are distributed among these distances:
28 5 0.11
29 1 0.02
30 17 0.36
31 6 0.13
32 12 0.26
33 1 0.02
34 5 0.11
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (30 bp):
TCTTTGACTTGAAAATTAAATCCATTTTAT
Found at i:39847391 original size:62 final size:62
Alignment explanation
Indices: 39847318--39847438 Score: 242
Period size: 62 Copynumber: 2.0 Consensus size: 62
39847308 TATTTTTATT
39847318 TATTTTGATCTTTGACTTGAAAATTAAATCCATTTTATTCTTTAAATTTGGATTCTTTTCAA
1 TATTTTGATCTTTGACTTGAAAATTAAATCCATTTTATTCTTTAAATTTGGATTCTTTTCAA
39847380 TATTTTGATCTTTGACTTGAAAATTAAATCCATTTTATTCTTTAAATTTGGATTCTTTT
1 TATTTTGATCTTTGACTTGAAAATTAAATCCATTTTATTCTTTAAATTTGGATTCTTTT
39847439 AAAATTTGAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (62 bp):
TATTTTGATCTTTGACTTGAAAATTAAATCCATTTTATTCTTTAAATTTGGATTCTTTTCAA
Found at i:39853574 original size:17 final size:17
Alignment explanation
Indices: 39853552--39853608 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
39853542 TATAGAGACA
39853552 TCTTTCATCAATATGTG
1 TCTTTCATCAATATGTG
* ***
39853569 TCTTTC-TGAATAATACA
1 TCTTTCATCAAT-ATGTG
*
39853586 TCTTTCATCAATAGGTG
1 TCTTTCATCAATATGTG
39853603 TCTTTC
1 TCTTTC
39853609 TGAATAATAA
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
16 4 0.14
17 21 0.72
18 4 0.14
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.46
Consensus pattern (17 bp):
TCTTTCATCAATATGTG
Found at i:39853587 original size:34 final size:34
Alignment explanation
Indices: 39853549--39853617 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
39853539 CTTTATAGAG
*
39853549 ACATCTTTCATCAATATGTGTCTTTCTGAATAAT
1 ACATCTTTCATCAATAGGTGTCTTTCTGAATAAT
39853583 ACATCTTTCATCAATAGGTGTCTTTCTGAATAAT
1 ACATCTTTCATCAATAGGTGTCTTTCTGAATAAT
39853617 A
1 A
39853618 ATGTCTTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (34 bp):
ACATCTTTCATCAATAGGTGTCTTTCTGAATAAT
Found at i:39856642 original size:16 final size:17
Alignment explanation
Indices: 39856589--39856642 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 17
39856579 ATTAATATAT
* *
39856589 TATAATTATATAATTTA
1 TATAATTATTTACTTTA
* *
39856606 -AT-ATAATTTACTTTT
1 TATAATTATTTACTTTA
39856621 TATAATTATTTAC-TTA
1 TATAATTATTTACTTTA
39856637 TATAAT
1 TATAAT
39856643 AAGTAAATTC
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 9 0.31
16 12 0.41
17 8 0.28
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (17 bp):
TATAATTATTTACTTTA
Found at i:39856841 original size:19 final size:20
Alignment explanation
Indices: 39856807--39856844 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
39856797 AGTCCTTTCA
39856807 CTAAATTAACCTTAATTAAG
1 CTAAATTAACCTTAATTAAG
*
39856827 CTAAATTTA-CTTAATTAA
1 CTAAATTAACCTTAATTAA
39856845 AATCTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
CTAAATTAACCTTAATTAAG
Found at i:39864925 original size:160 final size:160
Alignment explanation
Indices: 39864661--39864983 Score: 637
Period size: 160 Copynumber: 2.0 Consensus size: 160
39864651 TTTGGTTTAA
39864661 TTGATGAATGGTTGAGATTTTAATTATGAGTGGGCTAGGAATTAATAAGATGCCATAATAAAGGT
1 TTGATGAATGGTTGAGATTTTAATTATGAGTGGGCTAGGAATTAATAAGATGCCATAATAAAGGT
39864726 AAGATGGGAACGGTTGGTTGTGGATTGGTGCAAAGTGAACACTGATGGGGCTATACAAAGTGATG
66 AAGATGGGAACGGTTGGTTGTGGATTGGTGCAAAGTGAACACTGATGGGGCTATACAAAGTGATG
39864791 ATGACATGGTTGTGACAGGTGGTGATACTC
131 ATGACATGGTTGTGACAGGTGGTGATACTC
39864821 TTGATGAATGGTTGAGATTTTAATTATGAGTGGGCTAGGAATTAATAAGATGCCATAATAAAGGT
1 TTGATGAATGGTTGAGATTTTAATTATGAGTGGGCTAGGAATTAATAAGATGCCATAATAAAGGT
*
39864886 AAGATGGGAACGGTTGGTTGTTGATTGGTGCAAAGTGAACACTGATGGGGCTATACAAAGTGATG
66 AAGATGGGAACGGTTGGTTGTGGATTGGTGCAAAGTGAACACTGATGGGGCTATACAAAGTGATG
39864951 ATGACATGGTTGTGACAGGTGGTGATACTC
131 ATGACATGGTTGTGACAGGTGGTGATACTC
39864981 TTG
1 TTG
39864984 TTGGACGACA
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 162 1.00
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (160 bp):
TTGATGAATGGTTGAGATTTTAATTATGAGTGGGCTAGGAATTAATAAGATGCCATAATAAAGGT
AAGATGGGAACGGTTGGTTGTGGATTGGTGCAAAGTGAACACTGATGGGGCTATACAAAGTGATG
ATGACATGGTTGTGACAGGTGGTGATACTC
Found at i:39869895 original size:13 final size:13
Alignment explanation
Indices: 39869877--39869901 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39869867 CACTACTAGA
39869877 CTAATAATTATTC
1 CTAATAATTATTC
39869890 CTAATAATTATT
1 CTAATAATTATT
39869902 TACAAACCCG
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:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
CTAATAATTATTC
Found at i:39871028 original size:15 final size:15
Alignment explanation
Indices: 39871003--39871044 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
39870993 ATTAATGTCT
39871003 ATTGAGTATTAACTCA
1 ATTG-GTATTAACTCA
*
39871019 ATTGGTATTAACTCG
1 ATTGGTATTAACTCA
39871034 ATTGGTATTAA
1 ATTGGTATTAA
39871045 TATTATTGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (15 bp):
ATTGGTATTAACTCA
Found at i:39871601 original size:17 final size:18
Alignment explanation
Indices: 39871579--39871616 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
39871569 TTGGTTGTTA
39871579 AAATTTG-TAATTAGTTT
1 AAATTTGATAATTAGTTT
**
39871596 AAATTTGATCTTTAGTTT
1 AAATTTGATAATTAGTTT
39871614 AAA
1 AAA
39871617 ATCTAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50
Consensus pattern (18 bp):
AAATTTGATAATTAGTTT
Found at i:39879701 original size:14 final size:16
Alignment explanation
Indices: 39879667--39879709 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
39879657 CGTGTTTCAA
*
39879667 ATAAGTAAAAATATAT
1 ATAAATAAAAATATAT
39879683 ATAAATAAAAA-ATTAT
1 ATAAATAAAAATA-TAT
*
39879699 AAAAATAAAAA
1 ATAAATAAAAA
39879710 AAAATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
ATAAATAAAAATATAT
Done.