Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 146 of 444
Found at i:39225580 original size:55 final size:54
Alignment explanation
Indices: 39225451--39225644 Score: 239
Period size: 54 Copynumber: 3.6 Consensus size: 54
39225441 TTGGTAAGAT
* *
39225451 AAGGATATCATGTAAGACCATGCCAAGCCATGACATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTTCTATAAGGC
* ** *
39225505 AAGGAAATAATGTAAGACCATGTCAAGACATGACATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTT-CTATAAGGC
* * * * *
39225560 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTTCTATAAGGC
* *
39225613 AAGGATACCACGTAAGACCATGTCAAGACATG
1 AAGGATACCATGTAAGACCATGCCAAGACATG
39225645 GCAATGGTAA
Statistics
Matches: 120, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
52 4 0.03
53 30 0.25
54 42 0.35
55 40 0.33
56 4 0.03
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTTCTATAAGGC
Found at i:39225656 original size:108 final size:109
Alignment explanation
Indices: 39225459--39225657 Score: 292
Period size: 108 Copynumber: 1.8 Consensus size: 109
39225449 ATAAGGATAT
* *
39225459 CATGTAAGACCATGCCAAGCCATGACATTGATAAGTTCTATAAGGCAAGGAAATAATGTAAGACC
1 CATGTAAGACCATGCCAAGCCATGACATTGATAAGTTCTATAAGGCAAGGAAACAACGTAAGACC
*
39225524 ATGTCAAGACATGACATTGATAAGTTACTATAAGGCAAAGGTCC
66 ATGTCAAGACATGACAATGATAAGTTACTATAAGGCAAAGGTCC
* * * * * *
39225568 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATACCACGTAAGACC
1 CATGTAAGACCATGCCAAGCCATGACATTGATAAGTTCTATAAGGCAAGGAAACAACGTAAGACC
* *
39225632 ATGTCAAGACATGGCAATGGTAAGTT
66 ATGTCAAGACATGACAATGATAAGTT
39225658 TAAAAAGGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
108 45 0.57
109 34 0.43
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (109 bp):
CATGTAAGACCATGCCAAGCCATGACATTGATAAGTTCTATAAGGCAAGGAAACAACGTAAGACC
ATGTCAAGACATGACAATGATAAGTTACTATAAGGCAAAGGTCC
Found at i:39229679 original size:28 final size:28
Alignment explanation
Indices: 39229647--39229761 Score: 101
Period size: 29 Copynumber: 4.0 Consensus size: 28
39229637 TACCTGTATC
*
39229647 TGGCCCACTAAGCCC-AATCATATTCATA
1 TGGCCCA-TAAGCCCAAATCACATTCATA
* *
39229675 TGGCCCATTAGACCCAAATCACCTGT-ATA
1 TGGCCCATAAG-CCCAAATCACAT-TCATA
* *
39229704 TGGCCCATTAGGCCCAAATCACATTGATA
1 TGGCCCA-TAAGCCCAAATCACATTCATA
* *
39229733 TGGCCCAGT-AGGCCAAGTCACATTCATA
1 TGGCCCA-TAAGCCCAAATCACATTCATA
39229761 T
1 T
39229762 TCATGCTCAC
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
27 3 0.04
28 27 0.38
29 38 0.54
30 3 0.04
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (28 bp):
TGGCCCATAAGCCCAAATCACATTCATA
Found at i:39229704 original size:29 final size:29
Alignment explanation
Indices: 39229662--39229761 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 29
39229652 CACTAAGCCC
* *
39229662 AATCATATTCATATGGCCCATTAGACCCA
1 AATCACATTGATATGGCCCATTAGACCCA
* *
39229691 AATCAC-CTGTATATGGCCCATTAGGCCCA
1 AATCACATTG-ATATGGCCCATTAGACCCA
* *
39229720 AATCACATTGATATGGCCCAGTAG-GCCA
1 AATCACATTGATATGGCCCATTAGACCCA
* *
39229748 AGTCACATTCATAT
1 AATCACATTGATAT
39229762 TCATGCTCAC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 16 0.27
29 42 0.70
30 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (29 bp):
AATCACATTGATATGGCCCATTAGACCCA
Found at i:39229999 original size:8 final size:8
Alignment explanation
Indices: 39229972--39230022 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
39229962 GTCGCCAAAC
39229972 TTTCGGCT
1 TTTCGGCT
* *
39229980 TTTCGACA
1 TTTCGGCT
*
39229988 TTTCGTCT
1 TTTCGGCT
39229996 TTTCGGCT
1 TTTCGGCT
*
39230004 TTTCAG-T
1 TTTCGGCT
39230011 ATTTCGGCT
1 -TTTCGGCT
39230020 TTT
1 TTT
39230023 GCAGATACAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
7 1 0.03
8 32 0.94
9 1 0.03
ACGTcount: A:0.08, C:0.22, G:0.18, T:0.53
Consensus pattern (8 bp):
TTTCGGCT
Found at i:39230014 original size:24 final size:24
Alignment explanation
Indices: 39229972--39230022 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
39229962 GTCGCCAAAC
*
39229972 TTTCGGCTTTTCGACATTTCGTCT
1 TTTCGGCTTTTCGACATTTCGGCT
*
39229996 TTTCGGCTTTTC-AGTATTTCGGCT
1 TTTCGGCTTTTCGA-CATTTCGGCT
39230020 TTT
1 TTT
39230023 GCAGATACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.08, C:0.22, G:0.18, T:0.53
Consensus pattern (24 bp):
TTTCGGCTTTTCGACATTTCGGCT
Found at i:39231151 original size:16 final size:16
Alignment explanation
Indices: 39231130--39231179 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
39231120 AGAAAATTTG
39231130 GGATTTCGGGATTTTT
1 GGATTTCGGGATTTTT
**
39231146 GGATTTTAGGATTTTT
1 GGATTTCGGGATTTTT
*
39231162 GGATTTCGAGATTTTT
1 GGATTTCGGGATTTTT
39231178 GG
1 GG
39231180 GCGTTACAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.16, C:0.04, G:0.30, T:0.50
Consensus pattern (16 bp):
GGATTTCGGGATTTTT
Found at i:39236482 original size:29 final size:29
Alignment explanation
Indices: 39236445--39236521 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
39236435 AACCATATTC
* * *
39236445 ATATCGCCCATTAGTCCCAAATCACCTGT
1 ATATGGCCCATTAGGCCCAAATCACATGT
*
39236474 ATATGGCCCATTAGGCCCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAATCACATGT
*
39236503 ATATGGCCCGTTAGGCCCA
1 ATATGGCCCATTAGGCCCA
39236522 GTCACATTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACATGT
Found at i:39237898 original size:16 final size:16
Alignment explanation
Indices: 39237877--39237926 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
39237867 AGAAAATTTG
39237877 GGATTTCGGGATTTTT
1 GGATTTCGGGATTTTT
**
39237893 GGATTTTAGGATTTTT
1 GGATTTCGGGATTTTT
*
39237909 GGATTTCGAGATTTTT
1 GGATTTCGGGATTTTT
39237925 GG
1 GG
39237927 GGCGTTACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.16, C:0.04, G:0.30, T:0.50
Consensus pattern (16 bp):
GGATTTCGGGATTTTT
Found at i:39238871 original size:250 final size:250
Alignment explanation
Indices: 39238424--39238928 Score: 875
Period size: 250 Copynumber: 2.0 Consensus size: 250
39238414 CTCTCCACTT
*
39238424 GTTTAAAACGAGCACTCAAAGTCTCATCCACTAATTGCTTACTCCTTATATGCTCGACCCATACC
1 GTTTAAAACGAGCACTCAAAGTCTCATCCACTAATTGCTTACTCCTTATATGCTCGACCCACACC
* *
39238489 GGCTTTACTTGAAGCTGAGCTAACAAGCTACCATTATCCAACAAACTTAAACGGGTGAGCATAGC
66 GGCTTTACTTGAAGCTCAGCTAACAAGCTACCATCATCCAACAAACTTAAACGGGTGAGCATAGC
* * *
39238554 TCTCAAGTCTATTTTAGCCCTATGACTCAACGCGTCGGCTACCACATTCGCTTTGCTAGGGTGGT
131 TCTCAAGTCTATCTTAGCCCTATGACTCAACGCGTCGGCTACCACATTCGCTTTGCCAGGATGGT
*
39238619 ATTCAATTGTACAATCATAATCATTCAATAATTCCACCCACCTACGTTGCCTAAG
196 ATTCAATCGTACAATCATAATCATTCAATAATTCCACCCACCTACGTTGCCTAAG
* * ** *
39238674 GTTTAAAACGAGCACTCAAAGTCTCATCCACTAATTGCTTACTCCTTATCTGTTCGATGCACACT
1 GTTTAAAACGAGCACTCAAAGTCTCATCCACTAATTGCTTACTCCTTATATGCTCGACCCACACC
*
39238739 GGCTTTACTTGAAGCTCAGCTAACAAGCTACCATCATCCAACAAACTTAAATGGGTGAGCATAGC
66 GGCTTTACTTGAAGCTCAGCTAACAAGCTACCATCATCCAACAAACTTAAACGGGTGAGCATAGC
* *
39238804 TCTCAAGTCTGTCTTAGCCCTATGACTCAATGCGTCGGCTACCACATTCGCTTTGCCAGGATGGT
131 TCTCAAGTCTATCTTAGCCCTATGACTCAACGCGTCGGCTACCACATTCGCTTTGCCAGGATGGT
39238869 ATTCAATCGTACAATCATAATCATTCAATAATTCCACCCACCTACGTTGCCTAAG
196 ATTCAATCGTACAATCATAATCATTCAATAATTCCACCCACCTACGTTGCCTAAG
39238924 GTTTA
1 GTTTA
39238929 GCTCCTTTTG
Statistics
Matches: 240, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
250 240 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (250 bp):
GTTTAAAACGAGCACTCAAAGTCTCATCCACTAATTGCTTACTCCTTATATGCTCGACCCACACC
GGCTTTACTTGAAGCTCAGCTAACAAGCTACCATCATCCAACAAACTTAAACGGGTGAGCATAGC
TCTCAAGTCTATCTTAGCCCTATGACTCAACGCGTCGGCTACCACATTCGCTTTGCCAGGATGGT
ATTCAATCGTACAATCATAATCATTCAATAATTCCACCCACCTACGTTGCCTAAG
Found at i:39241800 original size:46 final size:46
Alignment explanation
Indices: 39241744--39241911 Score: 209
Period size: 46 Copynumber: 3.6 Consensus size: 46
39241734 TGGTTGAGCA
39241744 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
39241790 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
39241835 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
39241883 CCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
39241912 TGTGACAGCC
Statistics
Matches: 104, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 57 0.55
47 30 0.29
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:39241900 original size:93 final size:93
Alignment explanation
Indices: 39241741--39241911 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
39241731 GGATGGTTGA
* *
39241741 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39241806 TGAGTCCGAGTTCATGAAATGTAACTAG
66 TGAGTCCGAGTTCATGAAATGTAACTAG
*
39241834 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39241899 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
39241912 TGTGACAGCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCATGAAATGTAACTAG
Found at i:39243698 original size:40 final size:40
Alignment explanation
Indices: 39243643--39243770 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 40
39243633 TGAATGATAC
* *
39243643 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* ** *
39243683 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGAT-ACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * * *
39243723 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
39243763 CC-GGCTAA
1 CCGGGCTAA
39243771 ATTCCGAAGA
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
39 6 0.08
40 64 0.90
41 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:39245422 original size:19 final size:20
Alignment explanation
Indices: 39245385--39245422 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39245375 ATAATGTGGT
39245385 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
39245405 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
39245423 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:39250383 original size:37 final size:37
Alignment explanation
Indices: 39250333--39250423 Score: 164
Period size: 37 Copynumber: 2.4 Consensus size: 37
39250323 TTATTACGAA
39250333 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
39250370 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
39250407 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
39250424 TTTCCAAGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 47 0.90
38 5 0.10
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:39250518 original size:48 final size:48
Alignment explanation
Indices: 39250463--39250662 Score: 346
Period size: 48 Copynumber: 4.2 Consensus size: 48
39250453 TGTTACAACA
*
39250463 TTCACATTAGCCATTCGGCTTTACCACACATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
*
39250511 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
* *
39250559 TTCACATTAGCCCTTCGGCTTTACCACGTATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
* *
39250607 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATGT
1 TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
39250655 TTCACATT
1 TTCACATT
39250663 CATCACATCG
Statistics
Matches: 143, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 143 1.00
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.33
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACACATCACACATATAT
Found at i:39250762 original size:47 final size:47
Alignment explanation
Indices: 39250654--39250987 Score: 542
Period size: 47 Copynumber: 7.0 Consensus size: 47
39250644 CACACATATG
*
39250654 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATACAC
* * *
39250703 CTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
39250750 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATGTATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACA--TATATACAC
39250799 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATACAC
* * *
39250848 CTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACTC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
*
39250895 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACTC
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
39250942 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACA
39250988 TCTCCTACAT
Statistics
Matches: 270, Mismatches: 11, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
47 144 0.53
49 125 0.46
51 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (47 bp):
TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
Found at i:39251004 original size:145 final size:144
Alignment explanation
Indices: 39250654--39250985 Score: 630
Period size: 145 Copynumber: 2.3 Consensus size: 144
39250644 CACACATATG
*
39250654 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
39250719 TCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTAT
66 TCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTAT
39250784 CACATGTATATACAC
131 CACA-GTATATACAC
39250799 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
39250864 TCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTAT
66 TCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTAT
*
39250929 CACA-TATATACTC
131 CACAGTATATACAC
39250942 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
39250986 CATCTCCTAC
Statistics
Matches: 185, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
143 52 0.28
145 133 0.72
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (144 bp):
TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA
TCGGCCATTAGGCCTTATCACATATATACTCTTTCACATTCATCACATTGGCCATTAGGCCTTAT
CACAGTATATACAC
Found at i:39254909 original size:40 final size:39
Alignment explanation
Indices: 39254864--39255071 Score: 191
Period size: 40 Copynumber: 5.2 Consensus size: 39
39254854 CGGAATACAA
*
39254864 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** *
39254904 CCGGATAGAATGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
39254944 CCGAATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
39254984 CCGGATTTAGTCACTAGCATAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
* * * * *
39255024 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
39255064 CCGGATAT
1 CCGGATAT
39255072 CATTTAATTG
Statistics
Matches: 138, Mismatches: 29, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
39 1 0.01
40 137 0.99
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:39255012 original size:80 final size:80
Alignment explanation
Indices: 39254879--39255070 Score: 240
Period size: 80 Copynumber: 2.4 Consensus size: 80
39254869 TATAACCACA
* * *
39254879 TGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTTGCACAAATGCCTTCGGGTATTAGC
1 TGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATCACTAGCACAAATGCCTTCGGGTATTAAC
39254944 CCGAATTTAACAACT
66 CCGAATTTAACAACT
** * * * *
39254959 TGCACGAATGCCTTCGGGTCTTAGCCCGGATTTAGTCACTAGCATAATTGCCTTCGGGTCTTAAC
1 TGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATCACTAGCACAAATGCCTTCGGGTATTAAC
* *
39255024 CCGGATTTAACTACT
66 CCGAATTTAACAACT
* ** * *
39255039 AGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 TGCACGAATGCCTTCGGGTCTTAGCCCGGATA
39255071 TCATTTAATT
Statistics
Matches: 95, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
80 95 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (80 bp):
TGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATCACTAGCACAAATGCCTTCGGGTATTAAC
CCGAATTTAACAACT
Found at i:39257715 original size:40 final size:40
Alignment explanation
Indices: 39257588--39257717 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
39257578 ATGCTGGAAA
* *
39257588 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
39257628 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
39257668 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
*
39257708 TTGTATCCGG
1 TTATATCCGG
39257718 TTGTATATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:39261792 original size:29 final size:29
Alignment explanation
Indices: 39261751--39261827 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
39261741 AACCATATTC
*
39261751 ATATGGCCCATTAGGCCCAAATCACCTGT
1 ATATGGCCCATTAGGCCCAAATCACATGT
* *
39261780 ATATGGCCTATTAGGCCCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAATCACATGT
39261809 ATATGGCCCATTAGGCCCA
1 ATATGGCCCATTAGGCCCA
39261828 GTCACATTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACATGT
Found at i:39262084 original size:24 final size:24
Alignment explanation
Indices: 39262051--39262101 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
39262041 GTAGCCAAAC
* *
39262051 TTTCGGCTTTTCGACATTTTGGCT
1 TTTCGCCTTTTCGACATTTCGGCT
*
39262075 TTTCGCCTTTTCGGCATTTCGGCT
1 TTTCGCCTTTTCGACATTTCGGCT
39262099 TTT
1 TTT
39262102 GCCAATACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.06, C:0.24, G:0.20, T:0.51
Consensus pattern (24 bp):
TTTCGCCTTTTCGACATTTCGGCT
Found at i:39262086 original size:8 final size:8
Alignment explanation
Indices: 39262051--39262101 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
39262041 GTAGCCAAAC
39262051 TTTCGGCT
1 TTTCGGCT
*
39262059 TTTCGACAT
1 TTTCGGC-T
39262068 TTT-GGCT
1 TTTCGGCT
*
39262075 TTTCGCCT
1 TTTCGGCT
*
39262083 TTTCGGCA
1 TTTCGGCT
39262091 TTTCGGCT
1 TTTCGGCT
39262099 TTT
1 TTT
39262102 GCCAATACAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 4 0.11
8 27 0.77
9 4 0.11
ACGTcount: A:0.06, C:0.24, G:0.20, T:0.51
Consensus pattern (8 bp):
TTTCGGCT
Found at i:39264568 original size:16 final size:16
Alignment explanation
Indices: 39264547--39264579 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39264537 GAAAATTCAA
39264547 GATTTTGAGATTTTTG
1 GATTTTGAGATTTTTG
*
39264563 GATTTTGGGATTTTTG
1 GATTTTGAGATTTTTG
39264579 G
1 G
39264580 GGCGTTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.55
Consensus pattern (16 bp):
GATTTTGAGATTTTTG
Found at i:39266171 original size:15 final size:15
Alignment explanation
Indices: 39266148--39266178 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39266138 TCCAAAATTC
39266148 CAATACAAAACATAT
1 CAATACAAAACATAT
*
39266163 CAATCCAAAACATAT
1 CAATACAAAACATAT
39266178 C
1 C
39266179 TTTCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:39271273 original size:26 final size:26
Alignment explanation
Indices: 39271243--39271300 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
39271233 TGTTTCGAGC
39271243 TTGATTTTAGATGATTTTTATGTTTT
1 TTGATTTTAGATGATTTTTATGTTTT
39271269 TTGATTTTAGATGATTTTTATGTTTT
1 TTGATTTTAGATGATTTTTATGTTTT
39271295 TGTGAT
1 T-TGAT
39271301 CGGTGCTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 27 0.87
27 4 0.13
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (26 bp):
TTGATTTTAGATGATTTTTATGTTTT
Found at i:39272062 original size:28 final size:28
Alignment explanation
Indices: 39272038--39272112 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
39272028 AATATGGAAA
*
39272038 TTAGTGTGCGAAATATTGAGAATGGCAC
1 TTAGTGTGCAAAATATTGAGAATGGCAC
* * *
39272066 TTAGGGTGCCAGATATTGAGAATGGCAC
1 TTAGTGTGCAAAATATTGAGAATGGCAC
39272094 TTAGTGTGCAAAATATTGA
1 TTAGTGTGCAAAATATTGA
39272113 ATGATTCAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (28 bp):
TTAGTGTGCAAAATATTGAGAATGGCAC
Found at i:39277367 original size:39 final size:39
Alignment explanation
Indices: 39277313--39277475 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
39277303 ATGTGATGAA
39277313 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
39277352 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
** *
39277391 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
39277430 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
39277470 TGTGCG
1 TGTGCG
39277476 GGTTACCATA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:39277491 original size:40 final size:39
Alignment explanation
Indices: 39277313--39277505 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
39277303 ATGTGATGAA
* *
39277313 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* *
39277352 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
39277391 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
39277430 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* ** * *
39277470 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGG
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGG
39277506 TGTTTTGAAC
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:39285414 original size:39 final size:39
Alignment explanation
Indices: 39285361--39285522 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
39285351 TGTGTATGAA
39285361 TGTGCG-ATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
39285399 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
** *
39285438 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
39285477 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
39285517 TGTGCG
1 TGTGCG
39285523 GGTTACCATA
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
38 6 0.05
39 92 0.80
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:39285538 original size:40 final size:39
Alignment explanation
Indices: 39285361--39285552 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
39285351 TGTGTATGAA
*
39285361 TGTGCGA-TTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* *
39285399 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
39285438 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
39285477 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* ** * *
39285517 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGG
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGG
39285553 TGTTTTGAAC
Statistics
Matches: 138, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
38 7 0.05
39 91 0.66
40 40 0.29
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:39288317 original size:40 final size:40
Alignment explanation
Indices: 39288253--39288331 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
39288243 TATACGTACC
* *
39288253 ACTTGGTGTGTAGGGTTGGATGGGTTGATTCTATCCCCAT
1 ACTTGGTGTGTAGGGTAGGATGGGTCGATTCTATCCCCAT
*
39288293 ACTTGGTGTGTAGGGCTAGG-TGGGTCGATTTTATCCCCA
1 ACTTGGTGTGTAGGG-TAGGATGGGTCGATTCTATCCCCA
39288332 CATGGTGTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 32 0.91
41 3 0.09
ACGTcount: A:0.15, C:0.16, G:0.33, T:0.35
Consensus pattern (40 bp):
ACTTGGTGTGTAGGGTAGGATGGGTCGATTCTATCCCCAT
Found at i:39291243 original size:48 final size:48
Alignment explanation
Indices: 39291172--39291273 Score: 177
Period size: 48 Copynumber: 2.1 Consensus size: 48
39291162 TTTCGAATGA
* * *
39291172 TATGAGTAAAGTTCTGACATGAAATAATCTGAACTCGAGATGAACTAT
1 TATGAATAAAGTTCAGACATGAAATAATCTGAACTCGAGATAAACTAT
39291220 TATGAATAAAGTTCAGACATGAAATAATCTGAACTCGAGATAAACTAT
1 TATGAATAAAGTTCAGACATGAAATAATCTGAACTCGAGATAAACTAT
39291268 TATGAA
1 TATGAA
39291274 GTTATACTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (48 bp):
TATGAATAAAGTTCAGACATGAAATAATCTGAACTCGAGATAAACTAT
Found at i:39298997 original size:14 final size:14
Alignment explanation
Indices: 39298980--39299010 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39298970 CTGTTATTTA
*
39298980 TTATTTTTATGTTT
1 TTATTTTTATCTTT
39298994 TTATTTTTATCTTT
1 TTATTTTTATCTTT
39299008 TTA
1 TTA
39299011 AAACTACTTT
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:0.16, C:0.03, G:0.03, T:0.77
Consensus pattern (14 bp):
TTATTTTTATCTTT
Found at i:39309501 original size:22 final size:22
Alignment explanation
Indices: 39309473--39309515 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
39309463 CACTAAGTCA
* *
39309473 ATAGGATGGCTCAACGTCGTAG
1 ATAGGATGGCTAAAAGTCGTAG
39309495 ATAGGATGGCTAAAAGTCGTA
1 ATAGGATGGCTAAAAGTCGTA
39309516 AATATTGCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (22 bp):
ATAGGATGGCTAAAAGTCGTAG
Found at i:39310160 original size:9 final size:9
Alignment explanation
Indices: 39310146--39310178 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
39310136 GGGCCCATAG
39310146 GCCCATCGA
1 GCCCATCGA
39310155 GCCCATCGA
1 GCCCATCGA
39310164 GCCCATCGA
1 GCCCATCGA
39310173 GGCCCA
1 -GCCCA
39310179 GAATAGCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.21, C:0.45, G:0.24, T:0.09
Consensus pattern (9 bp):
GCCCATCGA
Found at i:39318832 original size:16 final size:16
Alignment explanation
Indices: 39318811--39318844 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
39318801 TAAGGGAGAG
39318811 TTCAATCATGGTACTT
1 TTCAATCATGGTACTT
39318827 TTCAATCATGGTACTT
1 TTCAATCATGGTACTT
39318843 TT
1 TT
39318845 AGTATACTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.47
Consensus pattern (16 bp):
TTCAATCATGGTACTT
Found at i:39319775 original size:21 final size:21
Alignment explanation
Indices: 39319742--39319784 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
39319732 TTATTGTTCA
*
39319742 TTTTTCTCCCTTTTCTTATTG
1 TTTTTCTCCCTTTACTTATTG
** *
39319763 TTTTTCTTTCTTTACTTTTTG
1 TTTTTCTCCCTTTACTTATTG
39319784 T
1 T
39319785 GGTATCATAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.19, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTTCTCCCTTTACTTATTG
Found at i:39320355 original size:29 final size:28
Alignment explanation
Indices: 39320297--39320393 Score: 158
Period size: 29 Copynumber: 3.4 Consensus size: 28
39320287 TATTTGGGCC
*
39320297 TGTGGGCCACACGAACTGTGTCAGGCTA
1 TGTGGGCCACACGAAGTGTGTCAGGCTA
39320325 TGTGGGCCACACGAATGTGTGTCAGGCTA
1 TGTGGGCCACACGAA-GTGTGTCAGGCTA
*
39320354 TGTGGGCCACACGAACGTGTGTCAGGCCA
1 TGTGGGCCACACGAA-GTGTGTCAGGCTA
39320383 TGTGGGCCACA
1 TGTGGGCCACA
39320394 TGGGCTTTTG
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
28 15 0.23
29 50 0.77
ACGTcount: A:0.21, C:0.25, G:0.34, T:0.21
Consensus pattern (28 bp):
TGTGGGCCACACGAAGTGTGTCAGGCTA
Found at i:39321762 original size:21 final size:21
Alignment explanation
Indices: 39321737--39321784 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
39321727 ACAAAATTAA
39321737 AATTGGG-TTAAAAAATAATTT
1 AATTGGGATT-AAAAATAATTT
*
39321758 AATTGGGATTAAAATTAATTT
1 AATTGGGATTAAAAATAATTT
39321779 AATTGG
1 AATTGG
39321785 AAAATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.40
Consensus pattern (21 bp):
AATTGGGATTAAAAATAATTT
Found at i:39321795 original size:18 final size:20
Alignment explanation
Indices: 39321737--39321800 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
39321727 ACAAAATTAA
* *
39321737 AATTGGGTTAAAAAATAATTT
1 AATTGGGAT-AAAATTAATTT
39321758 AATTGGGATTAAAATTAATTT
1 AATTGGGA-TAAAATTAATTT
*
39321779 AATT-GGA-AAATTTAATTT
1 AATTGGGATAAAATTAATTT
39321797 AATT
1 AATT
39321801 TAGTATAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
18 14 0.36
20 3 0.08
21 21 0.54
22 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (20 bp):
AATTGGGATAAAATTAATTT
Found at i:39322331 original size:26 final size:26
Alignment explanation
Indices: 39322295--39322344 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
39322285 TCCAAACATT
39322295 TTTTTGGTTGTATATCGTGGTTATTG
1 TTTTTGGTTGTATATCGTGGTTATTG
*
39322321 TTTTTGGTTGTATATTGTGGTTAT
1 TTTTTGGTTGTATATCGTGGTTAT
39322345 CCTTGGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.12, C:0.02, G:0.26, T:0.60
Consensus pattern (26 bp):
TTTTTGGTTGTATATCGTGGTTATTG
Found at i:39324440 original size:16 final size:16
Alignment explanation
Indices: 39324421--39324496 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 16
39324411 TCGTGTCCAT
39324421 AAAAATTCAAACTTAA
1 AAAAATTCAAACTTAA
* *
39324437 AAAAGTTTC-AACCT-A
1 AAAA-ATTCAAACTTAA
*
39324452 AAAAATTCAAAGTTGAA
1 AAAAATTCAAACTT-AA
* *
39324469 AAAAA-TAAAAATCTAA
1 AAAAATTCAAACT-TAA
39324485 AAAAATTCAAAC
1 AAAAATTCAAAC
39324497 ACGAGAACGT
Statistics
Matches: 45, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
14 3 0.07
15 8 0.18
16 20 0.44
17 14 0.31
ACGTcount: A:0.62, C:0.12, G:0.04, T:0.22
Consensus pattern (16 bp):
AAAAATTCAAACTTAA
Found at i:39325899 original size:10 final size:10
Alignment explanation
Indices: 39325884--39325992 Score: 53
Period size: 10 Copynumber: 10.8 Consensus size: 10
39325874 GACTGAACCA
39325884 AAAAATTATT
1 AAAAATTATT
39325894 AAAAATTA-T
1 AAAAATTATT
*
39325903 AAAAAATATT
1 AAAAATTATT
* **
39325913 AAAATTTGAAA
1 AAAAATT-ATT
39325924 AAAAATATATT
1 AAAAAT-TATT
*
39325935 TAAAA-TATAT
1 AAAAATTAT-T
*
39325945 AAAAGTT-TT
1 AAAAATTATT
*
39325954 AAAATAATATT
1 AAAA-ATTATT
* *
39325965 TAATATTATT
1 AAAAATTATT
* * *
39325975 TAAAATCATA
1 AAAAATTATT
39325985 AAAAATTA
1 AAAAATTA
39325993 AATAACAGAA
Statistics
Matches: 71, Mismatches: 21, Indels: 14
0.67 0.20 0.13
Matches are distributed among these distances:
9 16 0.23
10 38 0.54
11 16 0.23
12 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.37
Consensus pattern (10 bp):
AAAAATTATT
Found at i:39325912 original size:19 final size:20
Alignment explanation
Indices: 39325883--39325931 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
39325873 TGACTGAACC
*
39325883 AAAAAATTATTAAAAATT-A
1 AAAAAAATATTAAAAATTGA
* *
39325902 TAAAAAATATTAAAATTTGA
1 AAAAAAATATTAAAAATTGA
39325922 AAAAAAATAT
1 AAAAAAATAT
39325932 ATTTAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAAAATATTAAAAATTGA
Found at i:39334285 original size:40 final size:41
Alignment explanation
Indices: 39334241--39334318 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
39334231 ACCGGCATTT
** *
39334241 AGCCTGCTAGGTTTTAAACCTGAATTCA-TCACCGGCACGA
1 AGCCTGCTAGACTTTAAACCTGAACTCATTCACCGGCACGA
**
39334281 AGCCTGCTAGACTTTAAGTCTGAACTCATTCACCGGCA
1 AGCCTGCTAGACTTTAAACCTGAACTCATTCACCGGCA
39334319 TTTCGCTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
40 23 0.72
41 9 0.28
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACTTTAAACCTGAACTCATTCACCGGCACGA
Found at i:39334360 original size:42 final size:43
Alignment explanation
Indices: 39334309--39334389 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
39334299 TCTGAACTCA
* * * *
39334309 TTCACCGGCATT-TCGCTTGCTAAGCCTGAAGCCCGATATCAT
1 TTCACCGGCATTATAGCCTACTAAGCCCGAAGCCCGATATCAT
*
39334351 TTCACCGGCATTATAGCCTACTAGGCCCGAAGCCCGATA
1 TTCACCGGCATTATAGCCTACTAAGCCCGAAGCCCGATA
39334390 ATATTATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
42 12 0.36
43 21 0.64
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (43 bp):
TTCACCGGCATTATAGCCTACTAAGCCCGAAGCCCGATATCAT
Found at i:39348769 original size:40 final size:40
Alignment explanation
Indices: 39348642--39348771 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
39348632 ATGCTGGAAA
* *
39348642 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
39348682 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
39348722 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
39348762 TTATATCCGG
1 TTATATCCGG
39348772 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:39356734 original size:40 final size:40
Alignment explanation
Indices: 39356607--39356736 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
39356597 ATGCTGGAAA
* *
39356607 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
39356647 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
39356687 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
39356727 TTATATCCGG
1 TTATATCCGG
39356737 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:39362306 original size:40 final size:40
Alignment explanation
Indices: 39362179--39362308 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
39362169 ATGCTGGAAA
* *
39362179 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
39362219 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
39362259 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
39362299 TTATATCCGG
1 TTATATCCGG
39362309 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:39370256 original size:40 final size:40
Alignment explanation
Indices: 39370129--39370258 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
39370119 ATGCTGGAAA
* *
39370129 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
39370169 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
39370209 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
39370249 TTATATCCGG
1 TTATATCCGG
39370259 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:39374249 original size:27 final size:27
Alignment explanation
Indices: 39374219--39374271 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
39374209 GGGGCAAAAT
* *
39374219 GGTAATTCTACCTTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
39374246 GGTAATTTTACCCTACAGGGGTATTT
1 GGTAATTCTACCCTACAGGGGTATTT
39374272 TAGTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:39374430 original size:27 final size:27
Alignment explanation
Indices: 39374235--39374417 Score: 233
Period size: 27 Copynumber: 6.8 Consensus size: 27
39374225 TCTACCTTAT
* * **
39374235 AGGGGTATTTCGGTAATTTTACCCTA-C
1 AGGGGTATTTTGGTAATTTT-GCAAACC
*
39374262 AGGGGTATTTTAGTAATTTTGCAAACC
1 AGGGGTATTTTGGTAATTTTGCAAACC
* *
39374289 ATGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTGCAAACC
39374316 AGGGGTATTTTGGTAATTTTGCAAACC
1 AGGGGTATTTTGGTAATTTTGCAAACC
*
39374343 AGGGATATTTTGGTAATTTTGCAAACC
1 AGGGGTATTTTGGTAATTTTGCAAACC
* * * *
39374370 AGGGGTATTTTAGTAGTTTTACAACCC
1 AGGGGTATTTTGGTAATTTTGCAAACC
*
39374397 AGGGGTATTTTGGAAATTTTG
1 AGGGGTATTTTGGTAATTTTG
39374418 TAAATCGAGG
Statistics
Matches: 135, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 2 0.01
27 133 0.99
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.38
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTGCAAACC
Found at i:39374438 original size:81 final size:81
Alignment explanation
Indices: 39374274--39374441 Score: 230
Period size: 81 Copynumber: 2.1 Consensus size: 81
39374264 GGGTATTTTA
* * *
39374274 GTAATTTTGCAAACCATGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGCA
1 GTAATTTTGCAAACCAGGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTGCA
***
39374339 AACCAGGGATATTTTG
66 AACCAGGGATAAAATG
* * *
39374355 GTAATTTTGCAAACCAGGGGTATTTTAGTAGTTTTACAACCCAGGGGTATTTTGGAAATTTTGTA
1 GTAATTTTGCAAACCAGGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTGCA
*
39374420 AATCGAGGG-TAAAATG
66 AA-CCAGGGATAAAATG
39374436 GTAATT
1 GTAATT
39374442 CTGTAAACTG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
81 71 0.93
82 5 0.07
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (81 bp):
GTAATTTTGCAAACCAGGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGAAATTTTGCA
AACCAGGGATAAAATG
Found at i:39374441 original size:27 final size:27
Alignment explanation
Indices: 39374411--39374559 Score: 210
Period size: 27 Copynumber: 5.5 Consensus size: 27
39374401 GTATTTTGGA
* *
39374411 AATTTTGTAAATCGAGGGTAAAATGGT
1 AATTCTGTAAATCGAGGGTAAAACGGT
*
39374438 AATTCTGTAAA-CTGAGGGTAAAATGGT
1 AATTCTGTAAATC-GAGGGTAAAACGGT
*
39374465 AATTCTATAAATCGAGGGTAAAACGGT
1 AATTCTGTAAATCGAGGGTAAAACGGT
* ** *
39374492 AATTTTAAAAATCGAGGGTAAAACGAT
1 AATTCTGTAAATCGAGGGTAAAACGGT
39374519 AATTCTGTAAATCGAGGGTAAAACGGT
1 AATTCTGTAAATCGAGGGTAAAACGGT
39374546 AATTCTGTAAATCG
1 AATTCTGTAAATCG
39374560 GGAGTAGTTT
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
26 1 0.01
27 108 0.98
28 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (27 bp):
AATTCTGTAAATCGAGGGTAAAACGGT
Found at i:39374484 original size:81 final size:80
Alignment explanation
Indices: 39374398--39374590 Score: 226
Period size: 81 Copynumber: 2.4 Consensus size: 80
39374388 TTACAACCCA
* * ** * * *
39374398 GGGGTATTTTGGAAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTAAA-CTGAGGGTAAAAT
1 GGGGTAATTTGGTAATTTTAAAAATCGAGGGTAAAACGATAATTCTGTAAATC-GAGGGTAAAAC
39374462 GGTAATTCTATAAATC
65 GGTAATTCTATAAATC
***
39374478 GAGGGTAAAACGGTAATTTTAAAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAAC
1 G-GGGTAATTTGGTAATTTTAAAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAAC
*
39374543 GGTAATTCTGTAAATC
65 GGTAATTCTATAAATC
* * *
39374559 GGGAGTAGTTTGGTAATTTTACAAGTCGAGGG
1 GGG-GTAATTTGGTAATTTTAAAAATCGAGGG
39374591 CATTTCAGTA
Statistics
Matches: 93, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
80 3 0.03
81 89 0.96
82 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (80 bp):
GGGGTAATTTGGTAATTTTAAAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACG
GTAATTCTATAAATC
Found at i:39374588 original size:54 final size:52
Alignment explanation
Indices: 39374418--39374590 Score: 179
Period size: 54 Copynumber: 3.2 Consensus size: 52
39374408 GGAAATTTTG
*
39374418 TAAATCGAGGGTAAAATGGTAATTCTGTAAA-CTGAGGGTAAAATGGTAATTCT
1 TAAATCGAGGGTAAAACGGTAATTCTGTAAATC-GAGGGTAAAATGGTAATT-T
* ** * *
39374471 ATAAATCGAGGGTAAAACGGTAATTTTAAAAATCGAGGGTAAAACGATAATTCT
1 -TAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATT-T
***
39374525 GTAAATCGAGGGTAAAACGGTAATTCTGTAAATCG-GGAGTAGTTTGGTAATTT
1 -TAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGG-GTAAAATGGTAATTT
39374578 TACAAGTCGAGGG
1 TA-AA-TCGAGGG
39374591 CATTTCAGTA
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
52 2 0.02
53 5 0.05
54 92 0.92
55 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (52 bp):
TAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTT
Found at i:39378124 original size:46 final size:45
Alignment explanation
Indices: 39378074--39378202 Score: 177
Period size: 46 Copynumber: 2.8 Consensus size: 45
39378064 TGTTTGGGCA
*
39378074 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAA-C
* *
39378120 TCCGAACTCGTTGAGTTGAGTCCGAGCTCACTCATGGATGCAAAC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAC
* * * *
39378165 ACCTGAGCTTGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39378203 GCGGGTTACA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 2 0.03
46 71 0.97
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAC
Found at i:39381586 original size:13 final size:13
Alignment explanation
Indices: 39381568--39381596 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
39381558 GTGAAGATTA
39381568 CTTTGCTTATGTG
1 CTTTGCTTATGTG
39381581 CTTTGCTTATGTG
1 CTTTGCTTATGTG
39381594 CTT
1 CTT
39381597 GATTCTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.21, T:0.55
Consensus pattern (13 bp):
CTTTGCTTATGTG
Found at i:39396564 original size:28 final size:28
Alignment explanation
Indices: 39396532--39396601 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
39396522 AATGAGATTG
*
39396532 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
39396560 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
39396588 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39396602 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:39404177 original size:44 final size:46
Alignment explanation
Indices: 39404124--39404231 Score: 141
Period size: 47 Copynumber: 2.3 Consensus size: 46
39404114 TGCACACTTT
* *
39404124 TCACAATTGGTCATTCGGCCTTATCAC-TAT-TCACTTACACATAT-A
1 TCAC-ATTGGCCATTCGGCCTTATCACATATAACACTTACACAT-TCA
*
39404169 TCACATTGGCCATTCGGCCTTATCACATATACACACTTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATA-ACACTTACACATTCA
39404216 TCACATTGGCCATTCG
1 TCACATTGGCCATTCG
39404232 ATCTTAAGCT
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
44 21 0.38
45 7 0.12
46 1 0.02
47 27 0.48
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (46 bp):
TCACATTGGCCATTCGGCCTTATCACATATAACACTTACACATTCA
Found at i:39406827 original size:22 final size:20
Alignment explanation
Indices: 39406787--39406827 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
39406777 AGTCCTATTA
*
39406787 ACTAAATTCACATGCAATTG
1 ACTAAATTCACATGAAATTG
39406807 ACTAAATTCAAACATGAAATT
1 ACTAAATTC--ACATGAAATT
39406828 TTCACACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (20 bp):
ACTAAATTCACATGAAATTG
Found at i:39408475 original size:2 final size:2
Alignment explanation
Indices: 39408463--39408493 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
39408453 AGTATAGTTG
39408463 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
39408494 GCATATTCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39408563 original size:2 final size:2
Alignment explanation
Indices: 39408556--39408589 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39408546 CACATTTGGC
39408556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39408590 AATGTATGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39409176 original size:28 final size:28
Alignment explanation
Indices: 39409144--39409213 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
39409134 AATGAGATTG
*
39409144 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
39409172 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
39409200 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39409214 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:39422408 original size:8 final size:8
Alignment explanation
Indices: 39422395--39422420 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39422385 TTTTAATGAT
39422395 ATTTTAAA
1 ATTTTAAA
39422403 ATTTTAAA
1 ATTTTAAA
39422411 ATTTTAAA
1 ATTTTAAA
39422419 AT
1 AT
39422421 AAAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTTTAAA
Found at i:39425898 original size:25 final size:25
Alignment explanation
Indices: 39425865--39425917 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
39425855 TTAACATATT
**
39425865 AATTCATTTTGTTATATCATTTAAA
1 AATTCATTTTAATATATCATTTAAA
*
39425890 AATTTATTTTAATATATCATTTAAA
1 AATTCATTTTAATATATCATTTAAA
39425915 AAT
1 AAT
39425918 AAAATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (25 bp):
AATTCATTTTAATATATCATTTAAA
Found at i:39427056 original size:20 final size:20
Alignment explanation
Indices: 39427017--39427057 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
39427007 TTTTTTAAAT
39427017 AATTAAGCTTATTTTCTTTA
1 AATTAAGCTTATTTTCTTTA
39427037 AATTAAGCGTTATTTT-TTTA
1 AATTAAGC-TTATTTTCTTTA
39427057 A
1 A
39427058 CTTCATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (20 bp):
AATTAAGCTTATTTTCTTTA
Found at i:39432912 original size:40 final size:40
Alignment explanation
Indices: 39432857--39433012 Score: 280
Period size: 40 Copynumber: 4.0 Consensus size: 40
39432847 TGGAAAAAAA
39432857 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
39432897 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
39432937 TATAACCGGG-TAAGT-CCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* *
39432975 TATAACCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT
39433013 GTTACATCCG
Statistics
Matches: 112, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
38 33 0.29
39 10 0.09
40 69 0.62
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.28
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Found at i:39432988 original size:78 final size:80
Alignment explanation
Indices: 39432857--39433012 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 80
39432847 TGGAAAAAAA
39432857 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGC
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGC
39432922 ATTCGTGCGGGTTAT
66 ATTCGTGCGGGTTAT
39432937 TATAACCGGG-TAAGT-CCGAAGGCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGC
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGC
* *
39433000 ATTTGTGCTGGTT
66 ATTCGTGCGGGTT
39433013 GTTACATCCG
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
78 59 0.80
79 5 0.07
80 10 0.14
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.28
Consensus pattern (80 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGC
ATTCGTGCGGGTTAT
Found at i:39434740 original size:21 final size:21
Alignment explanation
Indices: 39434699--39434740 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39434689 GATGTTTTGA
*
39434699 CATGTTTTGAGCTTGTTTAAT
1 CATGTTTTGAGCTTGTATAAT
39434720 CATGTTTTGAG-TTGGTATAAT
1 CATGTTTTGAGCTT-GTATAAT
39434741 TAATGGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (21 bp):
CATGTTTTGAGCTTGTATAAT
Found at i:39435471 original size:55 final size:55
Alignment explanation
Indices: 39435393--39435503 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
39435383 TTACGAGTTT
* *
39435393 TAGCTTATTAATAGGTCTTAGTTACTCTAGGTCTCATACAATAGAAATATTTAGA
1 TAGCTTATAAATAGGTCTTAGTTACTATAGGTCTCATACAATAGAAATATTTAGA
39435448 TAGCTTATAAATAGGTCTTAGTTACTATAGGTCTCATACAATAGAAATATTTAGA
1 TAGCTTATAAATAGGTCTTAGTTACTATAGGTCTCATACAATAGAAATATTTAGA
39435503 T
1 T
39435504 TGAGATAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (55 bp):
TAGCTTATAAATAGGTCTTAGTTACTATAGGTCTCATACAATAGAAATATTTAGA
Found at i:39436967 original size:42 final size:41
Alignment explanation
Indices: 39436921--39437042 Score: 120
Period size: 43 Copynumber: 2.9 Consensus size: 41
39436911 TCAGGGTTAC
* *
39436921 TGAGATTGCGTGTAAGACCATATATGGGACATGGCATCGATA
1 TGAGATT-CATGTAAGACCATATCTGGGACATGGCATCGATA
* * *
39436963 TGAGACTTCTTGTAAGACCATAGCTGGG-CTATTGACATCGATA
1 TGAGA-TTCATGTAAGACCATATCTGGGAC-A-TGGCATCGATA
* * *
39437006 CGAGATTACATGTAAGACCATATCTAGGATATGGCAT
1 TGAGATT-CATGTAAGACCATATCTGGGACATGGCAT
39437043 TGGTACGATA
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
41 1 0.02
42 30 0.46
43 34 0.52
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (41 bp):
TGAGATTCATGTAAGACCATATCTGGGACATGGCATCGATA
Found at i:39437196 original size:25 final size:25
Alignment explanation
Indices: 39437167--39437214 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
39437157 TAGTACAGGT
39437167 ATGTACATAAAGTTTATAAGCATCG
1 ATGTACATAAAGTTTATAAGCATCG
39437192 ATGTACATAAAGTTTATAAGCAT
1 ATGTACATAAAGTTTATAAGCAT
39437215 TGACTTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (25 bp):
ATGTACATAAAGTTTATAAGCATCG
Found at i:39440281 original size:46 final size:46
Alignment explanation
Indices: 39440231--39440403 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
39440221 TGGTTGAGCA
39440231 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * * *
39440277 TCCGAATTCGTTGAGTTGAGTCCAAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
39440322 CATCCGAACTCGTAGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
39440370 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
39440404 GGGGCGGGTT
Statistics
Matches: 101, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 58 0.57
47 26 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:39440365 original size:93 final size:93
Alignment explanation
Indices: 39440228--39440398 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
39440218 GGATGGTTGA
* * * *
39440228 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAATTCGTTGAGT
1 GCATCCGAACTCGTAGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39440293 TGAGTCCAAGTTCGTGAAATGTAACTAG
66 TGAGTCCAAGTTCGTGAAATGTAACTAG
*
39440321 GCATCCGAACTCGTAGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTAGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
39440386 TGAGTCCGAGTTC
66 TGAGTCCAAGTTC
39440399 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTAGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCAAGTTCGTGAAATGTAACTAG
Found at i:39446004 original size:42 final size:41
Alignment explanation
Indices: 39445946--39446061 Score: 153
Period size: 42 Copynumber: 2.8 Consensus size: 41
39445936 TAGGGTTATT
* *
39445946 GAGATTACGTGTAAGACCATATCTGGAATATGGCATCGATA
1 GAGATTACATGTAAGACCATATCTGGGATATGGCATCGATA
* * *
39445987 TGAGACTT-CATGTAAGACTATAGCTGGGCTATTGGCATCGATA
1 -GAGA-TTACATGTAAGACCATATCTGGGATA-TGGCATCGATA
39446030 GAGATTACATGTAAGACCATATCTGGGATATG
1 GAGATTACATGTAAGACCATATCTGGGATATG
39446062 TCATTTGTAC
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
41 4 0.06
42 46 0.73
43 13 0.21
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (41 bp):
GAGATTACATGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:39470455 original size:34 final size:34
Alignment explanation
Indices: 39470374--39470456 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
39470364 CTGATATGTT
** * *
39470374 AATGGGCTTCGGCCCAGACTACTACTGTTACTGA
1 AATGGGCTAAGGCCCAGACTACTACTATTACTAA
* * *
39470408 AACGGGCTCAGGCCCAGACTGCTACTATTACTAA
1 AATGGGCTAAGGCCCAGACTACTACTATTACTAA
39470442 AATGGGCTAAGGCCC
1 AATGGGCTAAGGCCC
39470457 TAACTGTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.22
Consensus pattern (34 bp):
AATGGGCTAAGGCCCAGACTACTACTATTACTAA
Found at i:39476200 original size:29 final size:29
Alignment explanation
Indices: 39476161--39476240 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
39476151 CTTAATAATC
* * *
39476161 AACCACGCACAGTTAGTGCCATGTATTTTA
1 AACC-CGCACACTTAGTGCCATGCATTTCA
*
39476191 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
39476220 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
39476241 TCTCTCAACC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 41 0.93
30 3 0.07
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:39484031 original size:29 final size:29
Alignment explanation
Indices: 39483992--39484071 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
39483982 CTTAATAATC
*
39483992 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
39484022 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
39484051 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
39484072 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:39485759 original size:24 final size:24
Alignment explanation
Indices: 39485727--39485871 Score: 272
Period size: 24 Copynumber: 6.0 Consensus size: 24
39485717 GGGTAGAAAG
39485727 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
*
39485751 TTTATTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
39485775 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
39485799 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
39485823 TTTACTATGGCACTGTGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
*
39485847 TTTACTATGGCACTATGTGTGCGA
1 TTTACTATGGCACTGTGTGTGCGA
39485871 T
1 T
39485872 CATAATAAGC
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 118 1.00
ACGTcount: A:0.17, C:0.16, G:0.28, T:0.39
Consensus pattern (24 bp):
TTTACTATGGCACTGTGTGTGCGA
Found at i:39485884 original size:72 final size:72
Alignment explanation
Indices: 39485736--39485892 Score: 244
Period size: 72 Copynumber: 2.2 Consensus size: 72
39485726 GTTTACTATG
* * *
39485736 GCACTGTGTGTGCGATTTATTATGGCACTGTGTGTGCGATTTACTATGGCACTGTGTGTGCGATT
1 GCACTGTGTGTGCGATTTACTATGGCACTGTGTGTGCGATTTACTATGGCACTATGTGTGCGATA
* *
39485801 TACTATG
66 TAATATA
39485808 GCACTGTGTGTGCGATTTACTATGGCACTGTGTGTGCGATTTACTATGGCACTATGTGTGCGATC
1 GCACTGTGTGTGCGATTTACTATGGCACTGTGTGTGCGATTTACTATGGCACTATGTGTGCGAT-
39485873 ATAATA-A
65 ATAATATA
*
39485880 GCACTATGTGTGC
1 GCACTGTGTGTGC
39485893 CACATTCGGT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 74 0.95
73 4 0.05
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (72 bp):
GCACTGTGTGTGCGATTTACTATGGCACTGTGTGTGCGATTTACTATGGCACTATGTGTGCGATA
TAATATA
Found at i:39488194 original size:40 final size:40
Alignment explanation
Indices: 39488149--39488315 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
39488139 CGGAATATAA
*
39488149 CCGGATTTAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
39488189 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
39488229 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * ** *
39488269 CCGGATATAATTTCCAGCATAGTTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
39488308 CCGGATAT
1 CCGGATAT
39488316 CATTCAATTT
Statistics
Matches: 103, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 14 0.14
40 89 0.86
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:39491097 original size:35 final size:35
Alignment explanation
Indices: 39491048--39491152 Score: 201
Period size: 35 Copynumber: 3.0 Consensus size: 35
39491038 GCTCGAGAGA
39491048 ATGCTTCCTGATTATGTGCCCTAATTGGGTACCCT
1 ATGCTTCCTGATTATGTGCCCTAATTGGGTACCCT
*
39491083 ATGCTTCCTAATTATGTGCCCTAATTGGGTACCCT
1 ATGCTTCCTGATTATGTGCCCTAATTGGGTACCCT
39491118 ATGCTTCCTGATTATGTGCCCTAATTGGGTACCCT
1 ATGCTTCCTGATTATGTGCCCTAATTGGGTACCCT
39491153 TGAATATGAG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (35 bp):
ATGCTTCCTGATTATGTGCCCTAATTGGGTACCCT
Found at i:39494628 original size:9 final size:10
Alignment explanation
Indices: 39494614--39494653 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
39494604 GGGCCCAACA
39494614 GCCCA-TTAG
1 GCCCATTTAG
39494623 GCCCATTTA-
1 GCCCATTTAG
39494632 GCCCATTTAG
1 GCCCATTTAG
*
39494642 ACCCATTT-G
1 GCCCATTTAG
39494651 GCC
1 GCC
39494654 AATTCTTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 17 0.63
10 10 0.37
ACGTcount: A:0.20, C:0.35, G:0.17, T:0.28
Consensus pattern (10 bp):
GCCCATTTAG
Found at i:39494646 original size:19 final size:18
Alignment explanation
Indices: 39494613--39494649 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
39494603 TGGGCCCAAC
*
39494613 AGCCCATTAGGCCCATTT
1 AGCCCATTAGACCCATTT
39494631 AGCCCATTTAGACCCATTT
1 AGCCCA-TTAGACCCATTT
39494650 GGCCAATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.30
Consensus pattern (18 bp):
AGCCCATTAGACCCATTT
Found at i:39494781 original size:16 final size:16
Alignment explanation
Indices: 39494762--39494794 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39494752 CAACTTTCTA
39494762 CTTTTTGGCATTTCGG
1 CTTTTTGGCATTTCGG
39494778 CTTTTTGGCATTTCGG
1 CTTTTTGGCATTTCGG
39494794 C
1 C
39494795 ATTTCGGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.21, G:0.24, T:0.48
Consensus pattern (16 bp):
CTTTTTGGCATTTCGG
Found at i:39494797 original size:8 final size:8
Alignment explanation
Indices: 39494768--39494802 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
39494758 TCTACTTTTT
39494768 GGCATTTC
1 GGCATTTC
* *
39494776 GGCTTTTT
1 GGCATTTC
39494784 GGCATTTC
1 GGCATTTC
39494792 GGCATTTC
1 GGCATTTC
39494800 GGC
1 GGC
39494803 TTTTGCCGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.09, C:0.23, G:0.29, T:0.40
Consensus pattern (8 bp):
GGCATTTC
Found at i:39497613 original size:42 final size:41
Alignment explanation
Indices: 39497546--39497692 Score: 145
Period size: 42 Copynumber: 3.5 Consensus size: 41
39497536 TGTGGTATCG
* ** * *
39497546 TGTAAGACCACGTCTGCCACGTTGGCATCGATTTGAATTACG
1 TGTAAGACCACATCTGGGACATTGGCATCGATTTG-ATTACA
** *
39497588 TGTAAGACCATGTCTGGGACATTGGCATC-ATATATGATTTCA
1 TGTAAGACCACATCTGGGACATTGGCATCGAT-T-TGATTACA
*
39497630 TGTAAGACC-CTATCTGGGACAGTGGCATCGATATTTGATTACA
1 TGTAAGACCAC-ATCTGGGACATTGGCATCG--ATTTGATTACA
39497673 TGTAAGACCACATCTGGGAC
1 TGTAAGACCACATCTGGGAC
39497693 GTAGGCATTT
Statistics
Matches: 88, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
41 2 0.02
42 55 0.62
43 27 0.31
44 2 0.02
45 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (41 bp):
TGTAAGACCACATCTGGGACATTGGCATCGATTTGATTACA
Found at i:39497681 original size:43 final size:43
Alignment explanation
Indices: 39497568--39497700 Score: 150
Period size: 42 Copynumber: 3.1 Consensus size: 43
39497558 TCTGCCACGT
* * * *
39497568 TGGCATCG--ATTTGAATTACGTGTAAGACCATGTCTGGGACAT
1 TGGCATCGATATTTG-ATTACATGTAAGACCCTATCTGGGACAG
* *
39497610 TGGCATC-ATATATGATTTCATGTAAGACCCTATCTGGGACAG
1 TGGCATCGATATTTGATTACATGTAAGACCCTATCTGGGACAG
39497652 TGGCATCGATATTTGATTACATGTAAGACCAC-ATCTGGGAC-G
1 TGGCATCGATATTTGATTACATGTAAGACC-CTATCTGGGACAG
39497694 TAGGCAT
1 T-GGCAT
39497701 TTTACGAGCT
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
42 39 0.50
43 38 0.49
44 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (43 bp):
TGGCATCGATATTTGATTACATGTAAGACCCTATCTGGGACAG
Found at i:39504353 original size:43 final size:42
Alignment explanation
Indices: 39504197--39504354 Score: 176
Period size: 42 Copynumber: 3.7 Consensus size: 42
39504187 ATATATGTTA
* *
39504197 TCGTGTAAGACCACGTCTGGCACGTTGGCATCG-ATTTGATT
1 TCGTGTAAGACCATGTCTGGGACGTTGGCATCGTATTTGATT
* *
39504238 TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
1 T-CGTGTAAGACCATGTCTGGGACGTTGGCATCGTATTTGATT
* * ** *
39504281 TCGTATAAGACCCTGTCTAAGATAG-TGGCATCGATATTTGATT
1 TCGTGTAAGACCATGTCTGGGA-CGTTGGCATCG-TATTTGATT
* *
39504324 TCATGTAAGACCATGTTTGGGACGTTGGCAT
1 TCGTGTAAGACCATGTCTGGGACGTTGGCAT
39504355 TTTACGAGCT
Statistics
Matches: 94, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.01
42 55 0.59
43 38 0.40
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (42 bp):
TCGTGTAAGACCATGTCTGGGACGTTGGCATCGTATTTGATT
Found at i:39508052 original size:42 final size:42
Alignment explanation
Indices: 39507898--39508053 Score: 145
Period size: 42 Copynumber: 3.7 Consensus size: 42
39507888 TGTGTTTTTG
* * *
39507898 TGTAAGACCACATCTAGGACGTTGGCAT-TAACTTATGATTTACG
1 TGTAAGACCACGTCTAGGACGTTGGCATCGAA-TT-TGA-TTACA
* * * ** * *
39507942 TGTAAGACCATGTCTGGGACATCAGCATCGTATTTGATTTCA
1 TGTAAGACCACGTCTAGGACGTTGGCATCGAATTTGATTACA
**
39507984 TGTAAGACCTTGTCTAGGACAG-TGGCATCGAATTTGATTACA
1 TGTAAGACCACGTCTAGGAC-GTTGGCATCGAATTTGATTACA
*
39508026 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTAGGACGTTGGCAT
39508054 TGTACGATTC
Statistics
Matches: 89, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
41 1 0.01
42 60 0.67
43 3 0.03
44 24 0.27
45 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (42 bp):
TGTAAGACCACGTCTAGGACGTTGGCATCGAATTTGATTACA
Found at i:39518768 original size:43 final size:42
Alignment explanation
Indices: 39518647--39518804 Score: 194
Period size: 43 Copynumber: 3.7 Consensus size: 42
39518637 ATGTGTTTTT
*
39518647 GTGTAAGACCACGTCTGGGACGTTGGCATCA-ACTTATGATTTAC
1 GTGTAAGACCATGTCTGGGACGTTGGCATCATA-TT-TGATTT-C
* * *
39518691 GTGTAAGACCATGTCTAGGACATCGGCATCATATTTGATTTC
1 GTGTAAGACCATGTCTGGGACGTTGGCATCATATTTGATTTC
* *
39518733 GTGTAAGACCCTGTCTGGGACAG-TGGCATCGATATTTGATTAC
1 GTGTAAGACCATGTCTGGGAC-GTTGGCATC-ATATTTGATTTC
*
39518776 ATGTAAGACCATGTCTGGGACGTTGGCAT
1 GTGTAAGACCATGTCTGGGACGTTGGCAT
39518805 TGTATGATTC
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
42 27 0.27
43 42 0.42
44 29 0.29
45 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGGACGTTGGCATCATATTTGATTTC
Found at i:39519026 original size:14 final size:15
Alignment explanation
Indices: 39519007--39519041 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
39518997 TATGAGCAAA
39519007 TGAATTGGAATTAT-
1 TGAATTGGAATTATG
39519021 TGAATTGGAATTATG
1 TGAATTGGAATTATG
39519036 TGAATT
1 TGAATT
39519042 TTAAATGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (15 bp):
TGAATTGGAATTATG
Found at i:39521502 original size:21 final size:21
Alignment explanation
Indices: 39521476--39521587 Score: 179
Period size: 21 Copynumber: 5.3 Consensus size: 21
39521466 GTACATCGTT
*
39521476 AACAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCATAAGAGCTG
39521497 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* *
39521518 AACAAAAGCTCATAAGAGCTT
1 AACAGAAGCTCATAAGAGCTG
* *
39521539 AACAGAAACTCATAAGAGCTT
1 AACAGAAGCTCATAAGAGCTG
39521560 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
39521581 AACAGAA
1 AACAGAA
39521588 AGTAAAGCAC
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 84 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:39525873 original size:7 final size:7
Alignment explanation
Indices: 39525861--39525893 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
39525851 CTCTTCTCTT
39525861 CTTTTAA
1 CTTTTAA
39525868 CTTTTAA
1 CTTTTAA
39525875 CTTTTAA
1 CTTTTAA
*
39525882 CTTTGAA
1 CTTTTAA
39525889 CTTTT
1 CTTTT
39525894 TGTTCCCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.03, T:0.58
Consensus pattern (7 bp):
CTTTTAA
Found at i:39530302 original size:2 final size:2
Alignment explanation
Indices: 39530295--39530356 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
39530285 CAGCTTAAAG
*
39530295 GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
39530337 GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA
39530357 ACCTTCTGAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39530497 original size:18 final size:19
Alignment explanation
Indices: 39530474--39530522 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
39530464 AAGTTTTATG
*
39530474 ATTTTTAGTATAT-TTTTA
1 ATTTTTAATATATATTTTA
39530492 ATTTTTAATATATATTTTATA
1 ATTTTTAATATATA-TTT-TA
39530513 ATTTTTAATA
1 ATTTTTAATA
39530523 ATAATTGACG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 12 0.44
20 3 0.11
21 12 0.44
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTTAATATATATTTTA
Found at i:39530516 original size:21 final size:20
Alignment explanation
Indices: 39530482--39530522 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
39530472 TGATTTTTAG
39530482 TATATTTTTAATTTTTAATA
1 TATATTTTTAATTTTTAATA
39530502 TATATTTTATAATTTTTAATA
1 TATATTTT-TAATTTTTAATA
39530523 ATAATTGACG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATTTTTAATTTTTAATA
Found at i:39534569 original size:21 final size:22
Alignment explanation
Indices: 39534543--39534584 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39534533 GCATGTCTGA
39534543 TTAATA-ATAATTAAAATCAAC
1 TTAATACATAATTAAAATCAAC
* *
39534564 TTAATACCTGATTAAAATCAA
1 TTAATACATAATTAAAATCAA
39534585 AATAAATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.33
Consensus pattern (22 bp):
TTAATACATAATTAAAATCAAC
Found at i:39539832 original size:28 final size:28
Alignment explanation
Indices: 39539792--39539847 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
39539782 GGCTGTGTCC
*
39539792 TAGCCTGTGTCTGACCCCGTGTAACTCT
1 TAGCCCGTGTCTGACCCCGTGTAACTCT
39539820 TAGCCCGTGTCTGACCCCGTGTAACTCT
1 TAGCCCGTGTCTGACCCCGTGTAACTCT
39539848 CTGACTTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.14, C:0.34, G:0.21, T:0.30
Consensus pattern (28 bp):
TAGCCCGTGTCTGACCCCGTGTAACTCT
Found at i:39543597 original size:20 final size:19
Alignment explanation
Indices: 39543563--39543608 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
39543553 GTCATTGTTG
39543563 AGTTTG-TGAAGTTTTTGA
1 AGTTTGATGAAGTTTTTGA
*
39543581 AGTTTGATGATAGTTTTTTA
1 AGTTTGATGA-AGTTTTTGA
*
39543601 AGCTTGAT
1 AGTTTGAT
39543609 AGCTAAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.25
19 3 0.12
20 15 0.62
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.50
Consensus pattern (19 bp):
AGTTTGATGAAGTTTTTGA
Found at i:39547114 original size:17 final size:17
Alignment explanation
Indices: 39547092--39547125 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
39547082 ATTTAAATTA
39547092 TTTAGATTCATGAATGG
1 TTTAGATTCATGAATGG
39547109 TTTAGATTCATGAATGG
1 TTTAGATTCATGAATGG
39547126 AAATTGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (17 bp):
TTTAGATTCATGAATGG
Found at i:39556097 original size:55 final size:55
Alignment explanation
Indices: 39556033--39556370 Score: 351
Period size: 55 Copynumber: 6.1 Consensus size: 55
39556023 ATATTCTTAA
* ** *
39556033 ATGTGGAAAGTCTGCCAAGACAATCTTATGTGGAAGTCTATAAGGACTATCTGAT
1 ATGTGGAAAGTCTGCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
* *
39556088 ATGTGGAAAGT-TAGCTAGGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
1 ATGTGGAAAGTCT-GCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
* ** * * ** **
39556143 ATG-GACAAAGTCCACCATGACTATCTTATGTGAAAGTCTATGAGGACTGCCTGAT
1 ATGTG-GAAAGTCTGCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
** * * * *
39556198 ATGTGGAAAGTCTATCAGGACTATCTTATATAGAAG-CCTGTAAGGACTATCTGAT
1 ATGTGGAAAGTCTGCCAAGACTATCTTATGTGGAAGTCC-GTGAGGACTATCTGAT
*
39556253 ATG-GGAAAAGTCTGCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGGT
1 ATGTGG-AAAGTCTGCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
* * * * * *
39556308 ATGGGGAAATTCCGTCAAGACTATCTTATGTGGAAGTCCGTTAGGACTATCTTAT
1 ATGTGGAAAGTCTGCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
*
39556363 ATGGGGAA
1 ATGTGGAA
39556371 GTCCACCAGG
Statistics
Matches: 234, Mismatches: 41, Indels: 16
0.80 0.14 0.05
Matches are distributed among these distances:
54 5 0.02
55 224 0.96
56 5 0.02
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (55 bp):
ATGTGGAAAGTCTGCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGAT
Found at i:39556108 original size:29 final size:28
Alignment explanation
Indices: 39556059--39556373 Score: 124
Period size: 26 Copynumber: 11.4 Consensus size: 28
39556049 AAGACAATCT
*
39556059 TATGTGGAAGTCTA-TAAGGACTATCTGA
1 TATGTGGAAGTC-AGTGAGGACTATCTGA
*
39556087 TATGTGGAAAGTTAGCT-AGGACTATCT--
1 TATGTGG-AAGTCAG-TGAGGACTATCTGA
*
39556114 TATGTGGAAGTCCGTGAGGACTATCTGA
1 TATGTGGAAGTCAGTGAGGACTATCTGA
* ** *
39556142 TATG-GACAAAGTCCA-CCATGACTATCT--
1 TATGTG--GAAGT-CAGTGAGGACTATCTGA
* **
39556169 TATGTGAAAGTCTA-TGAGGACTGCCTGA
1 TATGTGGAAGTC-AGTGAGGACTATCTGA
*
39556197 TATGTGGAAAGTCTA-TCAGGACTATCT--
1 TATGTGG-AAGTC-AGTGAGGACTATCTGA
* * * * *
39556224 TATATAGAAGCCTGTAAGGACTATCTGA
1 TATGTGGAAGTCAGTGAGGACTATCTGA
* ** *
39556252 TATG-GGAAAAGTCTGCCAAGACTATCT--
1 TATGTGG--AAGTCAGTGAGGACTATCTGA
* *
39556279 TATGTGGAAGTCCGTGAGGACTATCTGG
1 TATGTGGAAGTCAGTGAGGACTATCTGA
* * * * *
39556307 TATGGGGAAATTCCGTCAAGACTATCT--
1 TATGTGG-AAGTCAGTGAGGACTATCTGA
* * *
39556334 TATGTGGAAGTCCGTTAGGACTATCTTA
1 TATGTGGAAGTCAGTGAGGACTATCTGA
*
39556362 TATGGGGAAGTC
1 TATGTGGAAGTC
39556374 CACCAGGACT
Statistics
Matches: 221, Mismatches: 41, Indels: 50
0.71 0.13 0.16
Matches are distributed among these distances:
25 2 0.01
26 74 0.33
27 28 0.13
28 41 0.19
29 74 0.33
30 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (28 bp):
TATGTGGAAGTCAGTGAGGACTATCTGA
Found at i:39556197 original size:110 final size:109
Alignment explanation
Indices: 39556047--39556386 Score: 391
Period size: 110 Copynumber: 3.1 Consensus size: 109
39556037 GGAAAGTCTG
* * *
39556047 CCAAGACAATCTTATGTGGAAGTCTATAAGGACTATCTGATATGTGGAAAGTTAGCTAGGACTAT
1 CCAAGACTATCTTATGTGGAAGTCTATGAGGACTATCTGATATGTGGAAAGTTACCTAGGACTAT
*
39556112 CTTATGTGGAAGTCCGTGAGGACTATCTGATATGGACAAAGTCCA
66 CTTATGTGGAAGTCCGTAAGGACTATCTGATATGGA-AAAGTCCA
* * ** *
39556157 CCATGACTATCTTATGTGAAAGTCTATGAGGACTGCCTGATATGTGGAAAGTCTATC-AGGACTA
1 CCAAGACTATCTTATGTGGAAGTCTATGAGGACTATCTGATATGTGGAAAGT-TACCTAGGACTA
* * **
39556221 TCTTATATAGAAG-CCTGTAAGGACTATCTGATATGGGAAAAGTCTG
65 TCTTATGTGGAAGTCC-GTAAGGACTATCTGATAT-GGAAAAGTCCA
** * * *
39556267 CCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGGTATGGGGAAA-TT-CCGTCAAGACT
1 CCAAGACTATCTTATGTGGAAGTCTATGAGGACTATCTGATATGTGGAAAGTTACC-T-AGGACT
* * **
39556330 ATCTTATGTGGAAGTCCGTTAGGACTATCTTATATGGGGAAGTCCA
64 ATCTTATGTGGAAGTCCGTAAGGACTATCTGATATGGAAAAGTCCA
*
39556376 CCAGGACTATC
1 CCAAGACTATC
39556387 ATTTTGAGGA
Statistics
Matches: 192, Mismatches: 31, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
107 1 0.01
108 1 0.01
109 20 0.10
110 162 0.84
111 8 0.04
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (109 bp):
CCAAGACTATCTTATGTGGAAGTCTATGAGGACTATCTGATATGTGGAAAGTTACCTAGGACTAT
CTTATGTGGAAGTCCGTAAGGACTATCTGATATGGAAAAGTCCA
Found at i:39556305 original size:165 final size:165
Alignment explanation
Indices: 39556033--39556345 Score: 432
Period size: 165 Copynumber: 1.9 Consensus size: 165
39556023 ATATTCTTAA
* * * *
39556033 ATGTGGAAAGTCTGCCAAGACAATCTTATGTGGAAGTCTATAAGGACTATCTGATATGTGGAAAG
1 ATGTGGAAAGTCTACCAAGACAATCTTATATAGAAGCCTATAAGGACTATCTGATATGTGGAAAG
* * *
39556098 TTAGCTAGGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGATATGGACAAAGTCCACCATGA
66 TTAGCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGATATGGACAAAGTCCACCAAGA
39556163 CTATCTTATGTGAAAGTCTATGAGGACTGCCTGAT
131 CTATCTTATGTGAAAGTCTATGAGGACTGCCTGAT
* * * *
39556198 ATGTGGAAAGTCTATCAGGACTATCTTATATAGAAGCCTGTAAGGACTATCTGATATG-GGAAAA
1 ATGTGGAAAGTCTACCAAGACAATCTTATATAGAAGCCTATAAGGACTATCTGATATGTGG-AAA
* ** * **
39556262 GTCT-GCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGGTATGGGGAAATTCCGTCAA
65 GT-TAGCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGATATGGACAAAGTCCACCAA
*
39556326 GACTATCTTATGTGGAAGTC
129 GACTATCTTATGTGAAAGTC
39556346 CGTTAGGACT
Statistics
Matches: 128, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
164 2 0.02
165 125 0.98
166 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (165 bp):
ATGTGGAAAGTCTACCAAGACAATCTTATATAGAAGCCTATAAGGACTATCTGATATGTGGAAAG
TTAGCCAAGACTATCTTATGTGGAAGTCCGTGAGGACTATCTGATATGGACAAAGTCCACCAAGA
CTATCTTATGTGAAAGTCTATGAGGACTGCCTGAT
Found at i:39556381 original size:28 final size:27
Alignment explanation
Indices: 39556271--39556386 Score: 110
Period size: 28 Copynumber: 4.3 Consensus size: 27
39556261 AGTCTGCCAA
* *
39556271 GACTATC-TTATGTGGAAGTCCGTGAG
1 GACTATCTTTATGGGGAAGTCCGTCAG
* * *
39556297 GACTATCTGGTATGGGGAAATTCCGTCAA
1 GACTATCT-TTATGGGG-AAGTCCGTCAG
* *
39556326 GACTATC-TTATGTGGAAGTCCGTTAG
1 GACTATCTTTATGGGGAAGTCCGTCAG
**
39556352 GACTATCTTATATGGGGAAGTCCACCAG
1 GACTATCTT-TATGGGGAAGTCCGTCAG
39556380 GACTATC
1 GACTATC
39556387 ATTTTGAGGA
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
26 22 0.31
27 7 0.10
28 27 0.38
29 15 0.21
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (27 bp):
GACTATCTTTATGGGGAAGTCCGTCAG
Found at i:39557504 original size:14 final size:15
Alignment explanation
Indices: 39557479--39557512 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39557469 GTGGAACTCG
39557479 TTTTGAGAAATATGC
1 TTTTGAGAAATATGC
*
39557494 TTTTG-GAAATATGT
1 TTTTGAGAAATATGC
39557508 TTTTG
1 TTTTG
39557513 TATATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (15 bp):
TTTTGAGAAATATGC
Found at i:39557560 original size:18 final size:18
Alignment explanation
Indices: 39557537--39557572 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39557527 TTTGTATAAG
39557537 TTAGGACACATTAAACAT
1 TTAGGACACATTAAACAT
39557555 TTAGGACACATTAAACAT
1 TTAGGACACATTAAACAT
39557573 AATACAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (18 bp):
TTAGGACACATTAAACAT
Found at i:39557763 original size:30 final size:31
Alignment explanation
Indices: 39557727--39557784 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
39557717 TAATTTCTAT
39557727 CCATGCCACT-GGAAAATTGTAGTTTTCCAC
1 CCATGCCACTAGGAAAATTGTAGTTTTCCAC
** *
39557757 CCATGCCACTAGGGTAATTGTGGTTTTC
1 CCATGCCACTAGGAAAATTGTAGTTTTC
39557785 GACCTGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (31 bp):
CCATGCCACTAGGAAAATTGTAGTTTTCCAC
Found at i:39562356 original size:45 final size:46
Alignment explanation
Indices: 39562292--39562466 Score: 225
Period size: 45 Copynumber: 3.8 Consensus size: 46
39562282 TGTAACCCGC
*
39562292 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
39562337 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
* * *
39562387 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
39562430 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39562467 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 37 0.33
46 29 0.26
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:39562458 original size:93 final size:92
Alignment explanation
Indices: 39562300--39562470 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 92
39562290 GCCCATAAGT
*
39562300 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
39562365 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
*
39562392 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39562457 CGAGTTCGGATGCC
65 CGAGTTCGGATGCC
39562471 CAAATATCCC
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 27 0.36
93 49 0.64
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:39562485 original size:46 final size:45
Alignment explanation
Indices: 39562297--39562472 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 45
39562287 CCCGCCCATA
* * * * * *
39562297 AGTGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCAT-A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGCCCATACATCC
*
39562342 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-C
* * * * *
39562390 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCC
39562435 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA
39562473 AATATCCCAG
Statistics
Matches: 108, Mismatches: 16, Indels: 15
0.78 0.12 0.11
Matches are distributed among these distances:
44 8 0.07
45 31 0.29
46 32 0.30
47 32 0.30
48 1 0.01
49 4 0.04
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCC
Found at i:39564892 original size:30 final size:30
Alignment explanation
Indices: 39564848--39564936 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
39564838 CAAAGATAAC
39564848 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
39564877 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
39564907 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
39564937 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:39564896 original size:15 final size:15
Alignment explanation
Indices: 39564848--39564927 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
39564838 CAAAGATAAC
*
39564848 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
39564862 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
39564877 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
39564892 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
39564907 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
39564922 AAGAAA
1 AAGAAA
39564928 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:39564936 original size:15 final size:15
Alignment explanation
Indices: 39564859--39564936 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
39564849 AGAAAACCGA
39564859 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
39564874 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
39564888 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
39564903 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
39564919 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
39564934 ATA
1 ATA
39564937 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:39567957 original size:93 final size:93
Alignment explanation
Indices: 39567845--39568016 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
39567835 CCCCATAAGT
***
39567845 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39567910 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
39567938 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39568003 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
39568017 CAAATATCCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:39568012 original size:46 final size:46
Alignment explanation
Indices: 39567837--39568012 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
39567827 ATGTAACCCC
* ***
39567837 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
39567883 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
39567933 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39567976 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39568013 TGCCCAAATA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.58
47 29 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Done.