Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 15 of 211
Found at i:4973641 original size:29 final size:30
Alignment explanation
Indices: 4973609--4973665 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
4973599 CTCTCCCAAC
4973609 AAAAATTACAAAATAATTA-AAAAATTTTA
1 AAAAATTACAAAATAATTATAAAAATTTTA
* *
4973638 AAAAATTTCAAAATATTTATAAAAATTT
1 AAAAATTACAAAATAATTATAAAAATTT
4973666 CAAATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAAATTACAAAATAATTATAAAAATTTTA
Found at i:4973664 original size:20 final size:18
Alignment explanation
Indices: 4973629--4973674 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
4973619 AAATAATTAA
4973629 AAAATTTTAAAAAATTTC
1 AAAATTTTAAAAAATTTC
4973647 AAAATATTTATAAAAATTTC
1 AAAAT-TTTA-AAAAATTTC
4973667 -AAATTTTA
1 AAAATTTTA
4973675 TATATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.35
19 8 0.31
20 9 0.35
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTTTAAAAAATTTC
Found at i:4973678 original size:20 final size:20
Alignment explanation
Indices: 4973629--4973669 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
4973619 AAATAATTAA
4973629 AAAAT-TTTA-AAAAATTTC
1 AAAATATTTATAAAAATTTC
4973647 AAAATATTTATAAAAATTTC
1 AAAATATTTATAAAAATTTC
4973667 AAA
1 AAA
4973670 TTTTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 4 0.19
20 12 0.57
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATATTTATAAAAATTTC
Found at i:4980909 original size:15 final size:15
Alignment explanation
Indices: 4980889--4980929 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
4980879 TTTCTTTCGA
4980889 AAATAATAAAAAAGT
1 AAATAATAAAAAAGT
4980904 AAATAA-ACAAAAAGT
1 AAATAATA-AAAAAGT
4980919 AAATAAATAAA
1 AAAT-AATAAA
4980930 CTGAAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.04
15 17 0.74
16 4 0.17
17 1 0.04
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (15 bp):
AAATAATAAAAAAGT
Found at i:4981088 original size:21 final size:21
Alignment explanation
Indices: 4981064--4981131 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
4981054 TATCCTATTT
4981064 TTTTGTTATTATCTCCTACTA
1 TTTTGTTATTATCTCCTACTA
* * *
4981085 TTTTCTCTCTATAGGACTCCT--T-
1 TTTTGT-TAT-TA--TCTCCTACTA
4981107 TTTTGTTATTATCTCCTACTA
1 TTTTGTTATTATCTCCTACTA
4981128 TTTT
1 TTTT
4981132 CTCTCTATGG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
18 5 0.15
20 3 0.09
21 11 0.32
22 7 0.21
23 3 0.09
25 5 0.15
ACGTcount: A:0.16, C:0.21, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTTGTTATTATCTCCTACTA
Found at i:4981123 original size:43 final size:43
Alignment explanation
Indices: 4981062--4981158 Score: 176
Period size: 43 Copynumber: 2.3 Consensus size: 43
4981052 ATTATCCTAT
4981062 TTTTTTGTTATTATCTCCTACTATTTTCTCTCTATAGGACTCC
1 TTTTTTGTTATTATCTCCTACTATTTTCTCTCTATAGGACTCC
*
4981105 TTTTTTGTTATTATCTCCTACTATTTTCTCTCTATGGGACTCC
1 TTTTTTGTTATTATCTCCTACTATTTTCTCTCTATAGGACTCC
*
4981148 CTTTTTGTTAT
1 TTTTTTGTTAT
4981159 CTGGGCTATG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.14, C:0.22, G:0.08, T:0.56
Consensus pattern (43 bp):
TTTTTTGTTATTATCTCCTACTATTTTCTCTCTATAGGACTCC
Found at i:4981131 original size:22 final size:22
Alignment explanation
Indices: 4981063--4981131 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
4981053 TTATCCTATT
4981063 TTTTTGTTATTATCTCCTACTA
1 TTTTTGTTATTATCTCCTACTA
* *** *
4981085 TTTTCTCTCTA-TA-GGACTCCT-
1 TTTT-TGT-TATTATCTCCTACTA
4981106 TTTTTGTTATTATCTCCTACTA
1 TTTTTGTTATTATCTCCTACTA
4981128 TTTT
1 TTTT
4981132 CTCTCTATGG
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 2 0.06
20 4 0.12
21 8 0.25
22 12 0.38
23 4 0.12
24 2 0.06
ACGTcount: A:0.16, C:0.20, G:0.06, T:0.58
Consensus pattern (22 bp):
TTTTTGTTATTATCTCCTACTA
Found at i:4983194 original size:17 final size:17
Alignment explanation
Indices: 4983172--4983205 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4983162 TGGGAGTTTT
4983172 CCTTTTCTTTCTTTCCC
1 CCTTTTCTTTCTTTCCC
*
4983189 CCTTTTGTTTCTTTCCC
1 CCTTTTCTTTCTTTCCC
4983206 TTCTGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.38, G:0.03, T:0.59
Consensus pattern (17 bp):
CCTTTTCTTTCTTTCCC
Found at i:4984497 original size:22 final size:22
Alignment explanation
Indices: 4984472--4984515 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4984462 GGTTAATATA
*
4984472 ATTTTTTTTCA-TTAGTTTAACT
1 ATTTTTTTT-ATTTACTTTAACT
4984494 ATTTTTTTTATTTACTTTAACT
1 ATTTTTTTTATTTACTTTAACT
4984516 TTTATATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTTTTTTTATTTACTTTAACT
Found at i:4989959 original size:22 final size:22
Alignment explanation
Indices: 4989933--4989987 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
4989923 GTTCGGAATT
4989933 GATTCAACTAGTTTTTTAACTC
1 GATTCAACTAGTTTTTTAACTC
*
4989955 GATTCAACTAGTTTTTTGACTC
1 GATTCAACTAGTTTTTTAACTC
*
4989977 AATTCAACTAG
1 GATTCAACTAG
4989988 CTTGTACTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (22 bp):
GATTCAACTAGTTTTTTAACTC
Found at i:4990296 original size:8 final size:8
Alignment explanation
Indices: 4990283--4990308 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4990273 AAACTAAAGT
4990283 TTACCCAA
1 TTACCCAA
4990291 TTACCCAA
1 TTACCCAA
4990299 TTACCCAA
1 TTACCCAA
4990307 TT
1 TT
4990309 CAATAAAACT
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:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (8 bp):
TTACCCAA
Found at i:4990427 original size:9 final size:9
Alignment explanation
Indices: 4990415--4990473 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
4990405 AAAATAAAAA
4990415 AATTCGGGT
1 AATTCGGGT
4990424 AATTCGGGT
1 AATTCGGGT
*
4990433 ATTTTTC-GGT
1 A--ATTCGGGT
*
4990443 AATTCGGCT
1 AATTCGGGT
4990452 AATTCGGGT
1 AATTCGGGT
4990461 AATTCGGGT
1 AATTCGGGT
4990470 AATT
1 AATT
4990474 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
8 3 0.07
9 33 0.77
10 4 0.09
11 3 0.07
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (9 bp):
AATTCGGGT
Found at i:4995168 original size:3 final size:3
Alignment explanation
Indices: 4995160--4995194 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4995150 CATCAAATTT
4995160 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4995195 GAAACTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4996906 original size:21 final size:21
Alignment explanation
Indices: 4996867--4996906 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4996857 TTTAATAAAA
*
4996867 ATCAAAATTTAAATTTTTTTT
1 ATCAAAATTAAAATTTTTTTT
*
4996888 ATCAAAA-TAAAATTCTTTT
1 ATCAAAATTAAAATTTTTTT
4996907 CAATTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
ATCAAAATTAAAATTTTTTTT
Found at i:5002168 original size:19 final size:19
Alignment explanation
Indices: 5002140--5002176 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5002130 TATATTTCAT
*
5002140 TTTTTTTAATTTTATGAAC
1 TTTTTATAATTTTATGAAC
5002159 TTTTTATAATTTTATGAA
1 TTTTTATAATTTTATGAA
5002177 TTATGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTTATAATTTTATGAAC
Found at i:5004798 original size:14 final size:15
Alignment explanation
Indices: 5004774--5004808 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
5004764 TATATATATT
5004774 ACCATATAAATACTA
1 ACCATATAAATACTA
5004789 ACCATA-AAATACTA
1 ACCATATAAATACTA
5004803 ATCCAT
1 A-CCAT
5004809 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:5005700 original size:78 final size:82
Alignment explanation
Indices: 5005514--5005737 Score: 350
Period size: 78 Copynumber: 2.8 Consensus size: 82
5005504 CCCGATTCAT
* * * * * *
5005514 TTCACCGGCA-CAAAGCCTGCTAGACATAAAGTCGGAATTAATTCACCGGCATCAAGCCTGCTAG
1 TTCACCGGCATC-AAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAG
5005578 ACATAAAGTCTAAAATAA
65 ACATAAAGTCTAAAATAA
5005596 TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAG-
1 TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGA
5005660 CAT-AAGTCT-AAATAA
66 CATAAAGTCTAAAATAA
5005675 -TCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAG
1 TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAG
5005738 GCATTAAGCC
Statistics
Matches: 135, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
78 63 0.47
79 6 0.04
80 6 0.04
81 3 0.02
82 56 0.41
83 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (82 bp):
TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGA
CATAAAGTCTAAAATAA
Found at i:5005729 original size:119 final size:124
Alignment explanation
Indices: 5005475--5005752 Score: 372
Period size: 119 Copynumber: 2.3 Consensus size: 124
5005465 CTATATAAAA
* ** * * * *
5005475 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCG-ATTCATTTCACCGGCACAAAGCCTGCTAGAC
1 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATCAATCCACCGGCACAAAGCCTGCTAGAC
* * *
5005539 ATAAAGTCGGAATTAATTCACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
66 ATAAAGTCGGAAATAATTCACCGGCATCAAGCCTGCTAGACATAAAGCCTAAAATAATC
5005598 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAAT-AATCCACCGGCATC-AAGCCTGCTAG-
1 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATCAATCCACCGGCA-CAAAGCCTGCTAGA
* * * *
5005660 CAT-AAGTC-TAAATAA-TCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATC
65 CATAAAGTCGGAAATAATTCACCGGCATCAAGCCTGCTAGACATAAAGCCTAAAATAATC
5005717 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAA
1 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAA
5005753 ATCTCATATA
Statistics
Matches: 139, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
119 73 0.53
120 5 0.04
121 5 0.04
122 3 0.02
123 50 0.36
124 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (124 bp):
CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATCAATCCACCGGCACAAAGCCTGCTAGAC
ATAAAGTCGGAAATAATTCACCGGCATCAAGCCTGCTAGACATAAAGCCTAAAATAATC
Found at i:5005749 original size:41 final size:41
Alignment explanation
Indices: 5005475--5005752 Score: 334
Period size: 41 Copynumber: 6.9 Consensus size: 41
5005465 CTATATAAAA
* ** * * *
5005475 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCG-ATTCATTT
1 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAAT-AATT
* * * * *
5005516 CACCGGCA-CAAAGCCTGCTAGACATAAAGTCGGAATTAATT
1 CACCGGCATC-AAGCCTGCTAGGCATTAAGCCTGAAATAATT
* * * *
5005557 CACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
1 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATT
*
5005598 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATC
1 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATT
*
5005639 CACCGGCATCAAGCCTGCTA-GCA-TAAGTCT-AAATAA-T
1 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATT
*
5005676 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATC
1 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATT
5005717 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAA
1 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAA
5005753 ATCTCATATA
Statistics
Matches: 212, Mismatches: 18, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
37 20 0.09
38 9 0.04
39 12 0.06
40 9 0.04
41 158 0.75
42 4 0.02
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (41 bp):
CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATT
Found at i:5005985 original size:64 final size:63
Alignment explanation
Indices: 5005867--5006047 Score: 262
Period size: 64 Copynumber: 2.9 Consensus size: 63
5005857 GCAAACAAAC
*
5005867 ATTCGAACCACATATGT-AT-AATTTACA-ACATTAAAATTCAGCTCAAAGAA-TTTGTAACCTA
1 ATTCGAACCACATATGTAATAAAATT-CATACATT-AAATTCAGCTC-AAGAACTTTGTAACCTA
5005928 T
63 T
5005929 ATTCGAACCACATATGTAAGTAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
1 ATTCGAACCACATATGTAA-TAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
* *
5005993 ATTTGAACCACATATGTATATAAAATTCATACATTAAATACAGCTCAAGAACTTT
1 ATTCGAACCACATATGTA-ATAAAATTCATACATTAAATTCAGCTCAAGAACTTT
5006048 AAATATATAT
Statistics
Matches: 110, Mismatches: 3, Indels: 10
0.89 0.02 0.08
Matches are distributed among these distances:
62 17 0.15
63 6 0.05
64 77 0.70
65 10 0.09
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (63 bp):
ATTCGAACCACATATGTAATAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
Found at i:5007959 original size:3 final size:3
Alignment explanation
Indices: 5007951--5008016 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
5007941 TTCTGTAATT
* * *
5007951 TTA TTA TTA TTA TT- TTA TCA TTT TTA TTA TT- TATA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
*
5007995 CTTA TCA -TA TTA TTA TTA TTA T
1 -TTA TTA TTA TTA TTA TTA TTA T
5008017 ATAGTAGCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
2 4 0.08
3 42 0.84
4 4 0.08
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5008380 original size:4 final size:4
Alignment explanation
Indices: 5008299--5008362 Score: 51
Period size: 4 Copynumber: 16.0 Consensus size: 4
5008289 TTTTATGTTC
* * * * *
5008299 ATTT ATGT ATTT ATTT ATGT -GTT CTTT -TTT ATAT ACTTT AGTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT A-TTT ATTT
5008347 ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT
5008363 GCTATGATTG
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
3 4 0.08
4 37 0.77
5 7 0.15
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:5008677 original size:109 final size:109
Alignment explanation
Indices: 5008481--5008951 Score: 753
Period size: 109 Copynumber: 4.3 Consensus size: 109
5008471 AATTTTTTCT
* * * * * * * *
5008481 AAATGAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTTCTGGATGTTGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCCGGGTGTCGATT
5008546 TTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
66 TTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
* *
5008590 AAATAAGGCAATGTTTTGCGTTTAGAAATTCGAGAAAACATGCCCTAAGGTGCCGGGTGTTGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCCGGGTGTCGATT
* * *
5008655 TTTTTCGTTCAATCAAATGGCTTAATATCCTTTTAAAAAATTTA
66 TTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
* * *
5008699 AAATAAGGTAATATTTTGCGTTTGGAAAATTCGAGAAAACATGTCCTAAGGTGCCGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGG-AAATTCGAGAAAACATGCCCTAAGGTGCCGGGTGTCGAT
*
5008764 TTTTCTCGTTCAACCAAATGGTTTAATATCCTTTTAAAAATTTTA
65 TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
*
5008809 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCCGGGTGTCGATT
* *
5008874 TTTCTCGTTCAATCAAATGGCTTAATATCCTTTTAAAAATTTCA
66 TTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
5008918 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG
5008952 GAACATGTCT
Statistics
Matches: 334, Mismatches: 27, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
109 233 0.70
110 101 0.30
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (109 bp):
AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCCGGGTGTCGATT
TTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
Found at i:5008885 original size:219 final size:218
Alignment explanation
Indices: 5008476--5008960 Score: 785
Period size: 219 Copynumber: 2.2 Consensus size: 218
5008466 AAGGAAATTT
* * * * * * *
5008476 TTTCTAAATGAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTTCTGGATGT
1 TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGTCCTAAGGTGCCGGATGT
*
5008541 TGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATAAGGCAATGTTT
66 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATAAGGCAATGTTT
* *
5008606 TGCGTTTAGAAATTCGAGAAAACATGCCCTAAGGTGCCGGGTGTTGATTTTTTTCGTTCAATCAA
131 TGCGTTTAGAAATTCGAGAAAACATGCCCTAAGGTGCCGGGTGTCGATTTTTCTCGTTCAATCAA
5008671 ATGGCTTAATATCCTTTTAAAAAA
196 ATGGCTTAATATCCTTTT-AAAAA
* *
5008695 TTT-AAAATAAGGTAATATTTTGCGTTTGGAAAATTCGAGAAAACATGTCCTAAGGTGCCGGGTG
1 TTTCAAAATAAGGCAATATTTTGCGTTTGG-AAATTCGAGAAAACATGTCCTAAGGTGCCGGATG
*
5008759 TCGATTTTTCTCGTTCAACCAAATGGTTTAATATCCTTTTAAAAATTTTAAAATAAGGCAATGTT
65 TCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATAAGGCAATGTT
* *
5008824 TTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAATCA
130 TTGCGTTTAGAAATTCGAGAAAACATGCCCTAAGGTGCCGGGTGTCGATTTTTCTCGTTCAATCA
5008889 AATGGCTTAATATCCTTTTAAAAA
195 AATGGCTTAATATCCTTTTAAAAA
* *
5008913 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACATGTC
1 TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGTC
5008961 TTAATGTGTT
Statistics
Matches: 246, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
217 8 0.03
218 38 0.15
219 200 0.81
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (218 bp):
TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGTCCTAAGGTGCCGGATGT
CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATAAGGCAATGTTT
TGCGTTTAGAAATTCGAGAAAACATGCCCTAAGGTGCCGGGTGTCGATTTTTCTCGTTCAATCAA
ATGGCTTAATATCCTTTTAAAAA
Found at i:5014752 original size:29 final size:29
Alignment explanation
Indices: 5014714--5014774 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
5014704 TGAGCTTGTG
*
5014714 TGGCTTACATGATCTGACACACGACTATA
1 TGGCTCACATGATCTGACACACGACTATA
* * * *
5014743 TGGCTCACATGTTCTGGCACACGGCTGTA
1 TGGCTCACATGATCTGACACACGACTATA
5014772 TGG
1 TGG
5014775 TGTTGACAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (29 bp):
TGGCTCACATGATCTGACACACGACTATA
Found at i:5018869 original size:288 final size:288
Alignment explanation
Indices: 5018353--5018969 Score: 1027
Period size: 288 Copynumber: 2.1 Consensus size: 288
5018343 TCCAAAAATA
* * *
5018353 AAGAAGTATGTCATTTTCATAGATGTTTTCGATAAATTATCACCCTATTATCAAAAGTTGTTCAT
1 AAGAAGTATGTCATTTTCATAGATGTTTTCGATAAACTATCACCATATTATCAAAAGTTATTCAT
* * * *
5018418 GATGATGAGAAAAGTAGTTTACAACTACTTCTTGAAAGAAACATGGAAGCTCTAAATGATGAAGA
66 AATGATGAGAAAAGTAGCTTACAACTACTTCCTGAAAGAAACATAGAAGCTCTAAATGATGAAGA
*
5018483 CCCTTTAACATCTGATACCTCAAATGTGGAAGGTGGTGAGCAAGAACCCCAAAAGAAATCCACAA
131 CCCTTCAACATCTGATACCTCAAATGTGGAAGGTGGTGAGCAAGAACCCCAAAAGAAATCCACAA
*
5018548 GGGAGAAGAGGCAACCACAATACTTGAAAGATTATGAGGTGCAAACCAACAATTGCTCAATTACT
196 GGGAGAAGAGGCAACCACAATACCTGAAAGATTATGAGGTGCAAACCAACAATTGCTCAATTACT
*
5018613 TTATACTTCTTTATTGGAGAAATGGATG
261 TCATACTTCTTTATTGGAGAAATGGATG
* *
5018641 AAGAAGTATGTCATTTTCATAGATGTTTTCAATAAACTATCATCATATTATCAAAAGTTATTCAT
1 AAGAAGTATGTCATTTTCATAGATGTTTTCGATAAACTATCACCATATTATCAAAAGTTATTCAT
*
5018706 AATGATGAGAAAAGTAGCTTACAACTACTTCCTGAAAGCAACATAGAAGCTCTAAATGATGAAGA
66 AATGATGAGAAAAGTAGCTTACAACTACTTCCTGAAAGAAACATAGAAGCTCTAAATGATGAAGA
* * * * *
5018771 TCCTTCAACATCTGATACCTTAGATGTGGAAGGTGGTGAGCAAGAACTCCAAAGGAAATCCACAA
131 CCCTTCAACATCTGATACCTCAAATGTGGAAGGTGGTGAGCAAGAACCCCAAAAGAAATCCACAA
* * *
5018836 GGGAGAAGAGGTAACCACAATACCTGAAAGATTATGTGGTGCAAACCAACAATTGTTCAATTACT
196 GGGAGAAGAGGCAACCACAATACCTGAAAGATTATGAGGTGCAAACCAACAATTGCTCAATTACT
5018901 TCATACTTCTTTATTGGAGAAATGGATG
261 TCATACTTCTTTATTGGAGAAATGGATG
* *
5018929 AAGGAGTATGTCATTTTCATAGATGTTTTCGATAAAGTATC
1 AAGAAGTATGTCATTTTCATAGATGTTTTCGATAAACTATC
5018970 TGTTGAGATT
Statistics
Matches: 305, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
288 305 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (288 bp):
AAGAAGTATGTCATTTTCATAGATGTTTTCGATAAACTATCACCATATTATCAAAAGTTATTCAT
AATGATGAGAAAAGTAGCTTACAACTACTTCCTGAAAGAAACATAGAAGCTCTAAATGATGAAGA
CCCTTCAACATCTGATACCTCAAATGTGGAAGGTGGTGAGCAAGAACCCCAAAAGAAATCCACAA
GGGAGAAGAGGCAACCACAATACCTGAAAGATTATGAGGTGCAAACCAACAATTGCTCAATTACT
TCATACTTCTTTATTGGAGAAATGGATG
Found at i:5027858 original size:18 final size:17
Alignment explanation
Indices: 5027836--5027882 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
5027826 TATAAAATTT
*
5027836 TAAAAATATATAATACA
1 TAAAAATATATAAAACA
5027853 TCAAAAATACTA-AAAACA
1 T-AAAAATA-TATAAAACA
*
5027871 TTAAAATATATA
1 TAAAAATATATA
5027883 TTTCTCAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 2 0.08
17 8 0.32
18 13 0.52
19 2 0.08
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAAATATATAAAACA
Found at i:5028024 original size:11 final size:11
Alignment explanation
Indices: 5027991--5028033 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
5027981 AAAATAACAA
5027991 CAAAATAGTAG
1 CAAAATAGTAG
*
5028002 CAACATTA-TAG
1 CAA-AATAGTAG
*
5028013 CAAAATGGTAG
1 CAAAATAGTAG
5028024 CAAAATAGTA
1 CAAAATAGTA
5028034 AAAAAAAAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.08
11 21 0.81
12 3 0.12
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:5028656 original size:17 final size:18
Alignment explanation
Indices: 5028634--5028668 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5028624 TTATATATTC
*
5028634 TTATAATTAAAT-TTTTG
1 TTATAAATAAATATTTTG
5028651 TTATAAATAAATATTTTG
1 TTATAAATAAATATTTTG
5028669 GGTACAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
TTATAAATAAATATTTTG
Found at i:5030695 original size:21 final size:22
Alignment explanation
Indices: 5030669--5030712 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
5030659 GGTTTTAACG
5030669 TTCAAGTTCATCCAT-AAAGGT
1 TTCAAGTTCATCCATAAAAGGT
5030690 TTCAAGTTCATCCATAAAAGGT
1 TTCAAGTTCATCCATAAAAGGT
5030712 T
1 T
5030713 AGCCATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (22 bp):
TTCAAGTTCATCCATAAAAGGT
Found at i:5050694 original size:10 final size:10
Alignment explanation
Indices: 5050657--5050699 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
5050647 ACTACAAATT
5050657 TATTTTAAAA
1 TATTTTAAAA
5050667 -ATTTTAAAAA
1 TATTTT-AAAA
5050677 GTATTTTTAAAA
1 -TA-TTTTAAAA
5050689 TATTTTAAAA
1 TATTTTAAAA
5050699 T
1 T
5050700 TAAAAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.17
10 13 0.45
11 2 0.07
12 5 0.17
13 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:5058418 original size:21 final size:22
Alignment explanation
Indices: 5058392--5058438 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
5058382 CTCTGCTCAA
*
5058392 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
5058413 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
5058435 ACTC
1 ACTC
5058439 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:5065958 original size:20 final size:19
Alignment explanation
Indices: 5065933--5065977 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
5065923 AAATATGTAA
5065933 ATTTAA-CCTTAAATCTTAT
1 ATTTAATCCTTAAAT-TTAT
*
5065952 ATATTAATGCTTAAATTTAT
1 AT-TTAATCCTTAAATTTAT
5065972 ATTTAA
1 ATTTAA
5065978 GGATTAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTTAATCCTTAAATTTAT
Found at i:5082507 original size:13 final size:13
Alignment explanation
Indices: 5082489--5082513 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5082479 CTAAATCATA
5082489 ATTTTAGTAAAAT
1 ATTTTAGTAAAAT
5082502 ATTTTAGTAAAA
1 ATTTTAGTAAAA
5082514 CCTTTTTGGT
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTTTAGTAAAAT
Found at i:5086063 original size:18 final size:19
Alignment explanation
Indices: 5086017--5086055 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5086007 TATAAATGGG
*
5086017 TAAACAATAAAGGCAAATAA
1 TAAA-AATAAAAGCAAATAA
5086037 TAAAAATAAAAGC-AATAA
1 TAAAAATAAAAGCAAATAA
5086055 T
1 T
5086056 GATAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.18
Consensus pattern (19 bp):
TAAAAATAAAAGCAAATAA
Found at i:5086431 original size:22 final size:24
Alignment explanation
Indices: 5086401--5086446 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
5086391 ATTCATTTTT
*
5086401 TAAACAAACAAAGAAAAA-GAAAA
1 TAAACAAACAAAAAAAAAGGAAAA
5086424 TAAA-AAACAAAAAAAAAGGAAAA
1 TAAACAAACAAAAAAAAAGGAAAA
5086447 CTGAGAGCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.80, C:0.07, G:0.09, T:0.04
Consensus pattern (24 bp):
TAAACAAACAAAAAAAAAGGAAAA
Found at i:5088485 original size:23 final size:26
Alignment explanation
Indices: 5088428--5088485 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
5088418 TCAATAAATT
*
5088428 AAAACATTATATTGAAAATAATGAAA
1 AAAACATTAGATTGAAAATAATGAAA
*
5088454 AAAATATTAGATT-AAAA-AATG-AA
1 AAAACATTAGATTGAAAATAATGAAA
5088477 AAAACATTA
1 AAAACATTA
5088486 TTTCATTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.34
24 4 0.14
25 4 0.14
26 11 0.38
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (26 bp):
AAAACATTAGATTGAAAATAATGAAA
Found at i:5091282 original size:22 final size:21
Alignment explanation
Indices: 5091252--5091310 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
5091242 ATACAATCGT
*
5091252 AGATTTGATATGTAATCTTAGG
1 AGATTTGATTTGTAATCTTA-G
*
5091274 AGATATGATTTTGTAAATCTTAG
1 AGATTTGA-TTTGT-AATCTTAG
5091297 AGATTTGATTTGTA
1 AGATTTGATTTGTA
5091311 GATACCATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.03
22 12 0.38
23 12 0.38
24 7 0.22
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.44
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:5096416 original size:22 final size:21
Alignment explanation
Indices: 5096391--5096449 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
5096381 ATACAATCGT
*
5096391 AGATTTGATATGTAATCTTAGG
1 AGATTTGATTTGTAATCTTA-G
*
5096413 AGATATGATTTTGTAAATCTTAG
1 AGATTTGA-TTTGT-AATCTTAG
5096436 AGATTTGATTTGTA
1 AGATTTGATTTGTA
5096450 GATACCATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.03
22 12 0.38
23 12 0.38
24 7 0.22
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.44
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:5100374 original size:16 final size:16
Alignment explanation
Indices: 5100355--5100387 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5100345 GAATGGTCTC
*
5100355 TGTTTCTTTTCTTCTT
1 TGTTTCTTTTATTCTT
5100371 TGTTTCTTTTATTCTT
1 TGTTTCTTTTATTCTT
5100387 T
1 T
5100388 TACTTTATTT
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:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTTATTCTT
Found at i:5103506 original size:24 final size:26
Alignment explanation
Indices: 5103456--5103509 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
5103446 TTAATAAATT
*
5103456 AAAACATTATATTGAAAATAATGAAA
1 AAAACATTAGATTGAAAATAATGAAA
* *
5103482 AAAATATTAGATT-AAAA-AATTAAA
1 AAAACATTAGATTGAAAATAATGAAA
5103506 AAAA
1 AAAA
5103510 AATTTCTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 10 0.40
25 4 0.16
26 11 0.44
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.26
Consensus pattern (26 bp):
AAAACATTAGATTGAAAATAATGAAA
Found at i:5107571 original size:33 final size:36
Alignment explanation
Indices: 5107504--5107574 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 36
5107494 TATAAATAAG
5107504 TTATAAAATATGTATGGGTATAGGTATATATATATATA
1 TTATAAAATATGTAT-GGTATA-GTATATATATATATA
*
5107542 TTATAAAA-ATGTAT-GTAT-GTATATTTATATATA
1 TTATAAAATATGTATGGTATAGTATATATATATATA
5107575 ATTAAATCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
33 14 0.44
35 4 0.12
37 6 0.19
38 8 0.25
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (36 bp):
TTATAAAATATGTATGGTATAGTATATATATATATA
Found at i:5107674 original size:460 final size:461
Alignment explanation
Indices: 5106796--5107720 Score: 1766
Period size: 460 Copynumber: 2.0 Consensus size: 461
5106786 TGAAACATTC
5106796 TTTTAAAATAATAATGAAAGCGTAAATAGATAAATAAAAAAATGAATAAAATTATAAGAACGTAA
1 TTTTAAAATAATAATGAAAGCGTAAATAGATAAATAAAAAAATGAATAAAATTATAAGAACGTAA
5106861 AAAGATATATGTATGTACATATATATATAAATTATAAGATATAATAAGAAATATATATAAGCATG
66 AAAGATATATGTATGTACATATATATATAAATTATAAGATATAATAAGAAATATATATAAGCATG
5106926 TATATATATATTTATGAAAATTAAAAAATATGTATATATATATATAGATATGCATAAAAATTATA
131 TATATATATATTTATGAAAATTAAAAAATATG-ATATATATATATAGATATGCATAAAAATTATA
5106991 AAATATAAAAAAAATATAAGAAGGTATATATATATGAATTATAAATAAGTTATAAAATATGTATG
195 AAATATAAAAAAAATATAAGAAGGTATATATATATGAATTATAAATAAGTTATAAAATATGTATG
5107056 GCTATAGGTATATATATATATATATATTATAAAAATGTATGTATGTATATTTATATATAATTAAA
260 GCTATAGG---ATATATATATATATATTATAAAAATGTATGTATGTATATTTATATATAATTAAA
5107121 TCCAAAATTAAAAAGGTATAAATGAGTAAATAATAATAATAATAATAAGATTAAAAGATATTAAA
322 TCCAAAATTAAAAAGGTATAAATGAGTAAATAATAATAATAATAATAAGATTAAAAGATATTAAA
5107186 CTTAGATAAGTAAATAAAATAATAACAATAATAATACAAAAATAATAGCATAATATAATAATATA
387 CTTAGATAAGTAAATAAAATAATAACAATAATAATACAAAAATAATAGCATAATATAATAATATA
5107251 ATAGTGAGGA
452 ATAGTGAGGA
5107261 TTTTAAAATAATAATGAAAGCGTAAATAGATAAATAAAAAAATGAATAAAATTATAAGAACGTAA
1 TTTTAAAATAATAATGAAAGCGTAAATAGATAAATAAAAAAATGAATAAAATTATAAGAACGTAA
5107326 AAAGATATATGTATGTACATATATATATATAAATTATAAGATATAATAAGAAATATATATAAGCA
66 AAAGATATATGTATGTAC--ATATATATATAAATTATAAGATATAATAAGAAATATATATAAGCA
5107391 TGTATATATATATTTATGAAAATTAAAAAATATG-TATATATATATAGATATGCATAAAAATTAT
129 TGTATATATATATTTATGAAAATTAAAAAATATGATATATATATATAGATATGCATAAAAATTAT
5107455 AAAATAT-AAAAAAATATAAGAAGGTATATATATATGAATTATAAATAAGTTATAAAATATGTAT
194 AAAATATAAAAAAAATATAAGAAGGTATATATATATGAATTATAAATAAGTTATAAAATATGTAT
*
5107519 GGGTATAGG-TATATATATATATATTATAAAAATGTATGTATGTATATTTATATATAATTAAATC
259 GGCTATAGGATATATATATATATATTATAAAAATGTATGTATGTATATTTATATATAATTAAATC
5107583 CAAAATTAAAAAGGTATAAATGAGTAAATAATAATAATAATAATAAGATTAAAAGATATTAAACT
324 CAAAATTAAAAAGGTATAAATGAGTAAATAATAATAATAATAATAAGATTAAAAGATATTAAACT
5107648 TAGATAAGTAAATAAAATAATAACAATAATAATACAAAAATAATAGCATAATATAATAATATAAT
389 TAGATAAGTAAATAAAATAATAACAATAATAATACAAAAATAATAGCATAATATAATAATATAAT
5107713 AGTGAGGA
454 AGTGAGGA
5107721 ATAAATAAAT
Statistics
Matches: 457, Mismatches: 1, Indels: 9
0.98 0.00 0.02
Matches are distributed among these distances:
460 193 0.42
464 65 0.14
465 120 0.26
467 79 0.17
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (461 bp):
TTTTAAAATAATAATGAAAGCGTAAATAGATAAATAAAAAAATGAATAAAATTATAAGAACGTAA
AAAGATATATGTATGTACATATATATATAAATTATAAGATATAATAAGAAATATATATAAGCATG
TATATATATATTTATGAAAATTAAAAAATATGATATATATATATAGATATGCATAAAAATTATAA
AATATAAAAAAAATATAAGAAGGTATATATATATGAATTATAAATAAGTTATAAAATATGTATGG
CTATAGGATATATATATATATATTATAAAAATGTATGTATGTATATTTATATATAATTAAATCCA
AAATTAAAAAGGTATAAATGAGTAAATAATAATAATAATAATAAGATTAAAAGATATTAAACTTA
GATAAGTAAATAAAATAATAACAATAATAATACAAAAATAATAGCATAATATAATAATATAATAG
TGAGGA
Found at i:5111389 original size:7 final size:7
Alignment explanation
Indices: 5111379--5111407 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5111369 TAACATTCAC
5111379 ATATTAT
1 ATATTAT
5111386 ATATTAT
1 ATATTAT
5111393 ATATTAT
1 ATATTAT
5111400 ATATTAT
1 ATATTAT
5111407 A
1 A
5111408 AAAGTAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATATTAT
Found at i:5112741 original size:20 final size:21
Alignment explanation
Indices: 5112713--5112765 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
5112703 CCTAAACCCT
*
5112713 AAACCCTAAACCATGAAT-CA
1 AAACACTAAACCATGAATACA
** *
5112733 AAACACTAAACTTTGAATACT
1 AAACACTAAACCATGAATACA
5112754 AAACACTAAACC
1 AAACACTAAACC
5112766 TTAAATCTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.51, C:0.26, G:0.04, T:0.19
Consensus pattern (21 bp):
AAACACTAAACCATGAATACA
Found at i:5112743 original size:7 final size:7
Alignment explanation
Indices: 5112700--5112724 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5112690 TTGAACCCCG
5112700 AACCCTA
1 AACCCTA
5112707 AACCCTA
1 AACCCTA
5112714 AACCCTA
1 AACCCTA
5112721 AACC
1 AACC
5112725 ATGAATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.12
Consensus pattern (7 bp):
AACCCTA
Found at i:5112778 original size:21 final size:21
Alignment explanation
Indices: 5112711--5112771 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
5112701 ACCCTAAACC
* * *
5112711 CTAAACCCTAAACCATGAAT-
1 CTAAACACTAAACCTTAAATA
* * *
5112731 CAAAACACTAAACTTTGAATA
1 CTAAACACTAAACCTTAAATA
5112752 CTAAACACTAAACCTTAAAT
1 CTAAACACTAAACCTTAAAT
5112772 CTTAAACCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.49, C:0.25, G:0.03, T:0.23
Consensus pattern (21 bp):
CTAAACACTAAACCTTAAATA
Found at i:5112803 original size:7 final size:7
Alignment explanation
Indices: 5112787--5112825 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
5112777 ACCTTTCATA
*
5112787 GTTTAGG
1 GTTTAAG
5112794 GTTTAAG
1 GTTTAAG
*
5112801 GTTCAA-
1 GTTTAAG
5112807 GTTTAAG
1 GTTTAAG
5112814 GTTTAAG
1 GTTTAAG
5112821 GTTTA
1 GTTTA
5112826 GGATTTGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.26, C:0.03, G:0.28, T:0.44
Consensus pattern (7 bp):
GTTTAAG
Found at i:5112811 original size:20 final size:21
Alignment explanation
Indices: 5112781--5112823 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
5112771 TCTTAAACCT
*
5112781 TTCATAGTTTAGGGTTTAAGG
1 TTCATAGTTTAAGGTTTAAGG
5112802 TTCA-AGTTTAAGGTTTAAGG
1 TTCATAGTTTAAGGTTTAAGG
5112822 TT
1 TT
5112824 TAGGATTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.44
Consensus pattern (21 bp):
TTCATAGTTTAAGGTTTAAGG
Found at i:5115969 original size:3 final size:3
Alignment explanation
Indices: 5115961--5116021 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
5115951 CATCTCTCTC
5115961 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
5116009 CTT CTT CTT CTT C
1 CTT CTT CTT CTT C
5116022 CCTCCCCTAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:5116728 original size:24 final size:25
Alignment explanation
Indices: 5116700--5116770 Score: 81
Period size: 28 Copynumber: 2.7 Consensus size: 25
5116690 ATAAATACCA
5116700 AAAAATTATTTTAAAAATAAA-AAAT
1 AAAAA-TATTTTAAAAATAAATAAAT
*
5116725 AAAAATATTTTAAAATTTAAAAATAAAT
1 AAAAATATTTTAAAA---ATAAATAAAT
*
5116753 AAAAGTATTTTAAAAATA
1 AAAAATATTTTAAAAATA
5116771 TTTTAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 10 0.26
25 7 0.18
27 4 0.10
28 18 0.46
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (25 bp):
AAAAATATTTTAAAAATAAATAAAT
Found at i:5121305 original size:21 final size:21
Alignment explanation
Indices: 5121279--5121334 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
5121269 AATAGCGGTG
*
5121279 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
5121300 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
5121321 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
5121335 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:5125629 original size:12 final size:12
Alignment explanation
Indices: 5125612--5125637 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5125602 TAAATAGTGC
5125612 ATGTATATATAT
1 ATGTATATATAT
5125624 ATGTATATATAT
1 ATGTATATATAT
5125636 AT
1 AT
5125638 ATTAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATGTATATATAT
Found at i:5125875 original size:21 final size:21
Alignment explanation
Indices: 5125851--5125894 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5125841 AATGCACGTG
5125851 TATATATATG-TATAATAATAA
1 TATATA-ATGTTATAATAATAA
5125872 TATATAATGTTATAATAATAA
1 TATATAATGTTATAATAATAA
5125893 TA
1 TA
5125895 GCAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
TATATAATGTTATAATAATAA
Found at i:5127772 original size:50 final size:51
Alignment explanation
Indices: 5127718--5128065 Score: 244
Period size: 50 Copynumber: 6.9 Consensus size: 51
5127708 CGGGGAAACC
* * *
5127718 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTC-AGGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTCTAGGGAAATA
* * * ** * * * **
5127768 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATC-AGGGAAACC
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTCTAGGGAAATA
* * *
5127818 AGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTG-CTAAGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTCTAGGGAAATA
* * * * ** * * * **
5127868 AGATCCGCCATTGTGGCTTCAATCTTTTTAATTGCAAC-ATC-AAGGAAACCC
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGC-ACTGTCTAGGGAAA-TA
**
5127919 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTG-CTAACGAAATA
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTCTAGGGAAATA
* * * ** * * * **
5127969 AGATCCGCCGTTGTTGCTTCAATCTTTTTAATTGCAATATC-AGGGAAACC
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTCTAGGGAAATA
* * *
5128019 AGATCTGCCGTCGTAGCTTCAATATGTTCCACTGCACTG-CTAAGGAA
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTCTAGGGAA
5128066 GTAAAATTAC
Statistics
Matches: 218, Mismatches: 72, Indels: 16
0.71 0.24 0.05
Matches are distributed among these distances:
49 2 0.01
50 178 0.82
51 38 0.17
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (51 bp):
AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTCTAGGGAAATA
Found at i:5127865 original size:100 final size:100
Alignment explanation
Indices: 5127684--5128069 Score: 603
Period size: 100 Copynumber: 3.9 Consensus size: 100
5127674 GGTCTGAAAT
* * * *
5127684 CTTCAATCTATTCAATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
5127749 CCGCACCG-TCAGGGAAGTAAGATCCGCCGTTGTGG
66 CTGCACTGCT-AAGGAAGTAAGATCCGCCGTTGTGG
*
5127784 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
*
5127849 CTGCACTGCTAAGGAAGTAAGATCCGCCATTGTGG
66 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
* *
5127884 CTTCAATCTTTTTAATTGCAACATCAAGGAAACCCAGATCCGCCGTCGTAGCTTCAATCTGTTCC
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAA-CCAGATCCGCCGTCGTAGCTTCAATCTGTTCC
* * *
5127949 ACTGCACTGCTAACGAAATAAGATCCGCCGTTGTTG
65 ACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
* *
5127985 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATATGTTCCA
1 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
5128050 CTGCACTGCTAAGGAAGTAA
66 CTGCACTGCTAAGGAAGTAA
5128070 AATTACTGGC
Statistics
Matches: 262, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
100 168 0.64
101 94 0.36
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (100 bp):
CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
Found at i:5128028 original size:201 final size:200
Alignment explanation
Indices: 5127684--5128069 Score: 630
Period size: 201 Copynumber: 1.9 Consensus size: 200
5127674 GGTCTGAAAT
** **
5127684 CTTCAATCTATTCAATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTCAATTGCAACATCAAGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
** *
5127749 CCGCACCGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGA
66 CCGCACCGTCAACGAAATAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGA
*
5127814 AACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCAT
131 AACCAGATCTGCCGTCGTAGCTTCAATATGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCAT
5127879 TGTGG
196 TGTGG
* *
5127884 CTTCAATCTTTTTAATTGCAACATCAAGGAAACCCAGATCCGCCGTCGTAGCTTCAATCTGTTCC
1 CTTCAATCTATTCAATTGCAACATCAAGGAAA-CCAGATCCGCCGTCGTAGCTTCAATCTGTTCC
* * *
5127949 ACTGCACTG-CTAACGAAATAAGATCCGCCGTTGTTGCTTCAATCTTTTTAATTGCAATATCAGG
65 ACCGCACCGTC-AACGAAATAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGG
5128013 GAAACCAGATCTGCCGTCGTAGCTTCAATATGTTCCACTGCACTGCTAAGGAAGTAA
129 GAAACCAGATCTGCCGTCGTAGCTTCAATATGTTCCACTGCACTGCTAAGGAAGTAA
5128070 AATTACTGGC
Statistics
Matches: 171, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
200 27 0.16
201 144 0.84
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (200 bp):
CTTCAATCTATTCAATTGCAACATCAAGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
CCGCACCGTCAACGAAATAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGA
AACCAGATCTGCCGTCGTAGCTTCAATATGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCAT
TGTGG
Found at i:5128153 original size:44 final size:44
Alignment explanation
Indices: 5128103--5128285 Score: 125
Period size: 44 Copynumber: 4.2 Consensus size: 44
5128093 ATTCAACTTC
** *
5128103 AGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTT
1 AGGGAGGTAAAATCCGCCATCTTCAATCTACTCCACTACTGCTT
* * * ** * * **
5128147 AGGGAGGCAATATCTGAAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGGTAAAATCCGCCATCTTCAATCTACTCCACTACTGCTT
* * ** *** * * **
5128191 AGGGAAGTAGAAT-TACTGGCTTCAATGTACTCCACTGCAACTT
1 AGGGAGGTAAAATCCGCCATCTTCAATCTACTCCACTACTGCTT
* *
5128234 CAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
1 -AGGGAGGTAAAATCCGCCATCTTCAATCTACTCCACTACTGCTT
5128279 AGGGAGG
1 AGGGAGG
5128286 CAAGATCTGA
Statistics
Matches: 97, Mismatches: 40, Indels: 4
0.69 0.28 0.03
Matches are distributed among these distances:
43 19 0.20
44 59 0.61
45 19 0.20
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (44 bp):
AGGGAGGTAAAATCCGCCATCTTCAATCTACTCCACTACTGCTT
Found at i:5128245 original size:132 final size:131
Alignment explanation
Indices: 5128062--5128304 Score: 432
Period size: 132 Copynumber: 1.8 Consensus size: 131
5128052 GCACTGCTAA
* * *
5128062 GGAAGTAAAATTACTGGCTTCAATGTACTTCATTCAACTTCAGGGAGGTAAAATCCGCCATCTTT
1 GGAAGTAAAATTACTGGCTTCAATGTACTCCATGCAACTTCAGGGAGGTAAAATCCGCCATCTTC
*
5128127 GATCTGCTCCACTACTGCTTAGGGAGGCAATATCTGAAATCTTCAATCTATTCCACTGCTGCCCA
66 GATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCA
5128192 G
131 G
*
5128193 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTT
1 GGAAGTAAAATTACTGGCTTCAATGTACTCCA-TGCAACTTCAGGGAGGTAAAATCCGCCATCTT
5128258 CGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAA
65 CGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAA
5128305 CCTGCTCCAC
Statistics
Matches: 106, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
131 30 0.28
132 76 0.72
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (131 bp):
GGAAGTAAAATTACTGGCTTCAATGTACTCCATGCAACTTCAGGGAGGTAAAATCCGCCATCTTC
GATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCA
G
Found at i:5128301 original size:44 final size:44
Alignment explanation
Indices: 5128128--5128315 Score: 123
Period size: 44 Copynumber: 4.3 Consensus size: 44
5128118 GCCATCTTTG
*
5128128 ATCTGCTCCACTACTGCTTAGGGAGGCAATATCTGAAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCA
** * ** * * *
5128172 ATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTG---GCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGGCAAG-A-T-CTGAAATCTTCA
* * * ** * * * ** *
5128215 ATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTTCG
1 ATCTGCTCCACTACTGCTT-AGGGAGGCAAGATCTGAAATCTTCA
5128260 ATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCA
*
5128304 ACCTGCTCCACT
1 ATCTGCTCCACT
5128316 GCCTCCGAGG
Statistics
Matches: 103, Mismatches: 33, Indels: 16
0.68 0.22 0.11
Matches are distributed among these distances:
42 2 0.02
43 20 0.19
44 58 0.56
45 20 0.19
46 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCA
Found at i:5129682 original size:46 final size:46
Alignment explanation
Indices: 5129611--5129702 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
5129601 AGCCTCTTCT
* * * *
5129611 TTTTTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTC
1 TTTTTTTTTTGACTCAAAGCACCCTTTGTAGGCTTTCACCCTGGTC
*
5129657 TTTTTTTTTTGACTCAAAGCACCCTTTGTAGGCTTTCACCTTGGTC
1 TTTTTTTTTTGACTCAAAGCACCCTTTGTAGGCTTTCACCCTGGTC
5129703 CCACCTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.13, C:0.24, G:0.16, T:0.47
Consensus pattern (46 bp):
TTTTTTTTTTGACTCAAAGCACCCTTTGTAGGCTTTCACCCTGGTC
Found at i:5129712 original size:46 final size:46
Alignment explanation
Indices: 5129616--5129712 Score: 104
Period size: 46 Copynumber: 2.1 Consensus size: 46
5129606 CTTCTTTTTT
* * * * *****
5129616 TTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTCTTTTT
1 TTTTTGACTCAAAGCACCCTTTGTAGGCTTTCACCCTGGTCCCACC
*
5129662 TTTTTGACTCAAAGCACCCTTTGTAGGCTTTCACCTTGGTCCCACC
1 TTTTTGACTCAAAGCACCCTTTGTAGGCTTTCACCCTGGTCCCACC
5129708 TTTTT
1 TTTTT
5129713 TAAGCAGAGT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.13, C:0.27, G:0.15, T:0.44
Consensus pattern (46 bp):
TTTTTGACTCAAAGCACCCTTTGTAGGCTTTCACCCTGGTCCCACC
Found at i:5133808 original size:12 final size:12
Alignment explanation
Indices: 5133791--5133816 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5133781 TAAATAGTGC
5133791 ATGTATATATAT
1 ATGTATATATAT
5133803 ATGTATATATAT
1 ATGTATATATAT
5133815 AT
1 AT
5133817 TAAAAATGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATGTATATATAT
Found at i:5134052 original size:18 final size:18
Alignment explanation
Indices: 5134029--5134066 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
5134019 AATGCACGTG
5134029 TATATATATG-TATAATAA
1 TATATA-ATGTTATAATAA
5134047 TATATAATGTTATAATAA
1 TATATAATGTTATAATAA
5134065 TA
1 TA
5134067 ATAGCAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
TATATAATGTTATAATAA
Found at i:5141515 original size:13 final size:13
Alignment explanation
Indices: 5141497--5141527 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5141487 GGTAGGCAAA
*
5141497 TTTTTTTTTGCGG
1 TTTTTTTTTGCGC
5141510 TTTTTTTTTGCGC
1 TTTTTTTTTGCGC
5141523 TTTTT
1 TTTTT
5141528 GCTGTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.16, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTGCGC
Found at i:5148762 original size:22 final size:22
Alignment explanation
Indices: 5148720--5148764 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5148710 CTCATATTTA
* *
5148720 TAATTTTTATTTCATGTTGTTT
1 TAATTTTTATTTAATGATGTTT
5148742 TAATTTTT-TTTAATGAATGTTT
1 TAATTTTTATTTAATG-ATGTTT
5148764 T
1 T
5148765 TAACGTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (22 bp):
TAATTTTTATTTAATGATGTTT
Found at i:5153153 original size:3 final size:3
Alignment explanation
Indices: 5153145--5153200 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
5153135 CCACTCATTT
*
5153145 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5153193 TAA TAA TA
1 TAA TAA TA
5153201 CTTACCTTAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5155578 original size:8 final size:8
Alignment explanation
Indices: 5155548--5155580 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
5155538 TATGTATGCG
5155548 TATATATT
1 TATATATT
5155556 TATAT-TT
1 TATATATT
5155563 TATAATATT
1 TAT-ATATT
5155572 TATATATT
1 TATATATT
5155580 T
1 T
5155581 TCCATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 5 0.22
8 13 0.57
9 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATATATT
Found at i:5158687 original size:9 final size:9
Alignment explanation
Indices: 5158675--5158699 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5158665 AGGTTAGGAA
5158675 GCTATTCGG
1 GCTATTCGG
5158684 GCTATTCGG
1 GCTATTCGG
5158693 GCTATTC
1 GCTATTC
5158700 AGGAATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.24, G:0.28, T:0.36
Consensus pattern (9 bp):
GCTATTCGG
Found at i:5162065 original size:53 final size:51
Alignment explanation
Indices: 5161976--5162081 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 51
5161966 TTTTATTTAT
* * *
5161976 TATATTTTTTACTCTTACTTTCAACTTGTTGAAAAGGTTATACAAAGTTATCA
1 TATAATTTCTACTCTTACTTTCAACTTGTTGAAAAGG-T-TACAAAGTCATCA
*
5162029 TATAATTTCTACTCTTACTTTCTACTTGTTGAAAAGGTTACAAAGTCATCA
1 TATAATTTCTACTCTTACTTTCAACTTGTTGAAAAGGTTACAAAGTCATCA
5162080 TA
1 TA
5162082 CATTTCCTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
51 14 0.29
52 1 0.02
53 34 0.69
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (51 bp):
TATAATTTCTACTCTTACTTTCAACTTGTTGAAAAGGTTACAAAGTCATCA
Found at i:5167029 original size:28 final size:28
Alignment explanation
Indices: 5166989--5167044 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
5166979 ATTACACACA
5166989 GCCCTGTCTAAACATTGTAATAAGTGAC
1 GCCCTGTCTAAACATTGTAATAAGTGAC
*
5167017 GCCCTGTCTAAACATTGTGATAAGTGAC
1 GCCCTGTCTAAACATTGTAATAAGTGAC
5167045 TTCTACTCCA
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:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (28 bp):
GCCCTGTCTAAACATTGTAATAAGTGAC
Found at i:5168515 original size:33 final size:33
Alignment explanation
Indices: 5168495--5168562 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
5168485 TTAAAGGTAT
* *
5168495 ATGTTTTAATTAAATAATAAAAAATATATAAAA
1 ATGTTTTAATTAAATAATAAAAAATAAAGAAAA
* *
5168528 ATGTTTTAATTAAATAATAAAAAATATATAAAA
1 ATGTTTTAATTAAATAATAAAAAATAAAGAAAA
5168561 AT
1 AT
5168563 AAAAAATACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (33 bp):
ATGTTTTAATTAAATAATAAAAAATAAAGAAAA
Found at i:5169071 original size:20 final size:20
Alignment explanation
Indices: 5169040--5169079 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5169030 TTAAGATATT
5169040 ATTTTAATAAAATAT-TTAA
1 ATTTTAATAAAATATATTAA
5169059 ATTTTATATAAAATATATTAA
1 ATTTTA-ATAAAATATATTAA
5169080 TCATATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTTAATAAAATATATTAA
Found at i:5173460 original size:70 final size:69
Alignment explanation
Indices: 5173331--5173692 Score: 303
Period size: 69 Copynumber: 5.2 Consensus size: 69
5173321 AATTTGTGAA
* * * * * * *
5173331 CCTTAATGTGACAACTAGAAACTTTTAACTCTCACTAATTGTTTGAAGGTTGCGGTGTTAAACCT
1 CCTTAATATGACAACTGGGAGCTTTTAACTCTCGCTAACTGTTTG-AGGGTGCGGTGTTAAACCT
5173396 ACGAG
65 ACGAG
* * * * * * * *
5173401 TCTTTATATGACAGCTGGGAGCTTTTAACTTTCACTAACTGTTTGGGGGCTGCGATGTTAAACTT
1 CCTTAATATGACAACTGGGAGCTTTTAACTCTCGCTAACTGTTTGAGGG-TGCGGTGTTAAACCT
*
5173466 GCGAG
65 ACGAG
* * ** * * * * * *
5173471 CCGGAATAATATGATAGTTGGGAGCTTTTAACTCTCGGTAATTGTTTGAGAGTGTGGTGTCAAAT
1 CC---TTAATATGACAACTGGGAGCTTTTAACTCTCGCTAACTGTTTGAGGGTGCGGTGTTAAAC
5173536 CTACGAG
63 CTACGAG
* * * **
5173543 CTTTAATATGACAACTAGGAGCTTTTAACTCTCGCTAACTGTTTGCGGGTGTAGTGTTAAACCTA
1 CCTTAATATGACAACTGGGAGCTTTTAACTCTCGCTAACTGTTTGAGGGTGCGGTGTTAAACCTA
* *
5173608 TGAA
66 CGAG
* * * **
5173612 CCTTAATATGACAATTGGGAGTTTTTAACTCTCGCTAACTGCTTG-GGAGCTTTGGTGTTAAACC
1 CCTTAATATGACAACTGGGAGCTTTTAACTCTCGCTAACTGTTTGAGG-G-TGCGGTGTTAAACC
*
5173676 TGCGAG
64 TACGAG
5173682 CCTTAATATGA
1 CCTTAATATGA
5173693 TACGAATGTT
Statistics
Matches: 230, Mismatches: 56, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
68 2 0.01
69 96 0.42
70 80 0.35
72 15 0.07
73 37 0.16
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (69 bp):
CCTTAATATGACAACTGGGAGCTTTTAACTCTCGCTAACTGTTTGAGGGTGCGGTGTTAAACCTA
CGAG
Found at i:5182478 original size:16 final size:17
Alignment explanation
Indices: 5182459--5182514 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 17
5182449 TAGGTGAAAT
*
5182459 TTTATATAAATAT-ATA
1 TTTATAAAAATATGATA
5182475 TTTATAAAAATATGATA
1 TTTATAAAAATATGATA
**
5182492 TAAATAACAAATAGTGAT-
1 TTTATAA-AAATA-TGATA
5182510 TTTAT
1 TTTAT
5182515 TGAAAGATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 12 0.38
17 8 0.25
18 8 0.25
19 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (17 bp):
TTTATAAAAATATGATA
Found at i:5185874 original size:17 final size:18
Alignment explanation
Indices: 5185854--5185888 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5185844 AAAATTTTTA
5185854 TAAAT-TTAAATATGACC
1 TAAATATTAAATATGACC
*
5185871 TAAATATTAAATGTGACC
1 TAAATATTAAATATGACC
5185889 ACTTACCTAT
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:0.11, G:0.09, T:0.34
Consensus pattern (18 bp):
TAAATATTAAATATGACC
Found at i:5189889 original size:28 final size:28
Alignment explanation
Indices: 5189836--5189896 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
5189826 ATCAAACATG
* * *
5189836 AATGATATAAATAGTCTTTAAATTTTTA
1 AATGATATAAATAGTATATAAATTTTAA
*
5189864 AATGATATAAATA-TATATATATTTTTAA
1 AATGATATAAATAGTATATA-AATTTTAA
5189892 AATGA
1 AATGA
5189897 ACAAAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.44
Consensus pattern (28 bp):
AATGATATAAATAGTATATAAATTTTAA
Found at i:5191115 original size:20 final size:20
Alignment explanation
Indices: 5191070--5191115 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
5191060 TTGTAAAAGT
*
5191070 TAAATTAAAAACAAAAATATC
1 TAAA-TAAAAACAAAAATAGC
* *
5191091 AAAATAAAAATAAAAATAGC
1 TAAATAAAAACAAAAATAGC
5191111 TAAAT
1 TAAAT
5191116 TAATAGAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.22
Consensus pattern (20 bp):
TAAATAAAAACAAAAATAGC
Found at i:5192783 original size:126 final size:126
Alignment explanation
Indices: 5192558--5192786 Score: 345
Period size: 126 Copynumber: 1.8 Consensus size: 126
5192548 ACAAAAGTCG
* * *
5192558 GCATAGTGTTGGATAAAACTGATTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCTTT
1 GCATAATGTTGGATAAAACTGAATCTTATTTAAGCGTTGCCTTAGGCATGCATATCCAAACCTTT
* * *
5192623 ATACAAAGAGTTGGCCAAAGCGTATGTTAACAAGTCTATCCTAACACTTAGGAAAGTGTCA
66 ATACAAAGAGTTGGCCAAAGCATACGTCAACAAGTCTATCCTAACACTTAGGAAAGTGTCA
* *
5192684 GCATAATGTTGGA-CAAACTCGAATCTTATTTAAGTGTTGCCTTAGGCATGCATATCTCAAACC-
1 GCATAATGTTGGATAAAACT-GAATCTTATTTAAGCGTTGCCTTAGGCATGCATATC-CAAACCT
*
5192747 TTATACAAAGAGTTGGCCAAAGCATACGTCGACAAGTCTA
64 TTATACAAAGAGTTGGCCAAAGCATACGTCAACAAGTCTA
5192787 GTTATTAGCT
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
125 5 0.05
126 82 0.89
127 5 0.05
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (126 bp):
GCATAATGTTGGATAAAACTGAATCTTATTTAAGCGTTGCCTTAGGCATGCATATCCAAACCTTT
ATACAAAGAGTTGGCCAAAGCATACGTCAACAAGTCTATCCTAACACTTAGGAAAGTGTCA
Found at i:5193620 original size:34 final size:34
Alignment explanation
Indices: 5193576--5193643 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
5193566 GCACAGTTGA
* *
5193576 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTAT-AGTG
*
5193611 ACAGT-TTGGGCCTTAGCCCATCTCAGTATAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTATAGTG
5193644 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 4 0.13
34 21 0.70
35 5 0.17
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATCTCAGTATAGTG
Found at i:5196775 original size:19 final size:18
Alignment explanation
Indices: 5196752--5197236 Score: 125
Period size: 18 Copynumber: 26.0 Consensus size: 18
5196742 ACAACCCCTT
5196752 TTTTTTGAAAACACGAAA
1 TTTTTTGAAAACACGAAA
* *
5196770 TTTTTTTAAAACGC-AAGA
1 TTTTTTGAAAACACGAA-A
* *
5196788 ATTTTAG-AAACACGAAA
1 TTTTTTGAAAACACGAAA
*
5196805 TTTTTCTTTAAAAAAACACGAAA
1 --TTT-TTT--GAAAACACGAAA
*
5196828 -ATTTTG-AAACACGAGAA
1 TTTTTTGAAAACACGA-AA
* *
5196845 TTTTTTCAAAACACGAATTT
1 TTTTTTGAAAACACGAA--A
5196865 TCTTTTTG-AAACACGAAA
1 T-TTTTTGAAAACACGAAA
*
5196883 -ATTTTGAAAACAC-AAA
1 TTTTTTGAAAACACGAAA
*
5196899 GTTTTATTTTGAAAACACAAAAGA
1 ---TT-TTTTGAAAACAC-GAA-A
* *
5196923 TTTGATAAATT-ACGAAACATGAGATT
1 TTT--T---TTGA--AAACACGA-A-A
5196949 TTTTTTG-AAACACGGAAA
1 TTTTTTGAAAACAC-GAAA
* *
5196967 -TTTATG-AAACACGGTCAA
1 TTTTTTGAAAACAC-G-AAA
5196985 -TTTTTGAAAACACGAAA
1 TTTTTTGAAAACACGAAA
* ** **
5197002 ATTTTTGAAAGACGGGATTT
1 TTTTTTGAAA-ACACGA-AA
5197022 TTTTTTGAAAACACGAAA
1 TTTTTTGAAAACACGAAA
* *
5197040 ATTTAT-AAAACACGGAAA
1 TTTTTTGAAAACAC-GAAA
* *
5197058 TTTTTTCTAAAAACAAGAAA
1 -TTTTT-TGAAAACACGAAA
* *
5197078 ATTTTCGAAAA-ACGAGAA
1 TTTTTTGAAAACACGA-AA
5197096 -TTTTTGAAAACACAGGAAA
1 TTTTTTGAAAACAC--GAAA
*
5197115 -TTTTTGAAAACATGAAA
1 TTTTTTGAAAACACGAAA
** *
5197132 TTTTTTG-TTACACTAGAA
1 TTTTTTGAAAACACGA-AA
5197150 --TTTTGAAAACACGAAGA
1 TTTTTTGAAAACACGAA-A
* *
5197167 -TTTTTG-AAACATGAGGA
1 TTTTTTGAAAACACGA-AA
*
5197184 -TTTTTGAAAACACGAAG
1 TTTTTTGAAAACACGAAA
* *
5197201 CTTTTTG-AAACATGAGAA
1 TTTTTTGAAAACACGA-AA
* *
5197219 TTTTTTGAGAACATGAAA
1 TTTTTTGAAAACACGAAA
5197237 ACATGAAAAT
Statistics
Matches: 347, Mismatches: 64, Indels: 112
0.66 0.12 0.21
Matches are distributed among these distances:
16 22 0.06
17 85 0.24
18 92 0.27
19 61 0.18
20 32 0.09
21 27 0.08
22 1 0.00
23 12 0.03
24 3 0.01
25 3 0.01
26 9 0.03
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (18 bp):
TTTTTTGAAAACACGAAA
Found at i:5196860 original size:35 final size:35
Alignment explanation
Indices: 5196754--5196861 Score: 103
Period size: 35 Copynumber: 2.9 Consensus size: 35
5196744 AACCCCTTTT
* *
5196754 TTTTGAAAACACGAAATTTTTTTAAAACGC-AAGAA
1 TTTTG-AAACACGAAATTTTTTAAAAACACGAAGAA
5196789 TTTTAGAAACACGAAATTTTTCTTTAAAAAAACACGAA-AA
1 TTTT-GAAACACGAAA--TTT-TTT--AAAAACACGAAGAA
*
5196829 TTTTGAAACACGAGAATTTTTTCAAAACACGAA
1 TTTTGAAACACGA-AATTTTTTAAAAACACGAA
5196862 TTTTCTTTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
35 24 0.39
36 1 0.02
37 6 0.10
38 6 0.10
39 9 0.15
40 14 0.23
41 2 0.03
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
TTTTGAAACACGAAATTTTTTAAAAACACGAAGAA
Found at i:5196903 original size:16 final size:16
Alignment explanation
Indices: 5196818--5196848 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5196808 TTCTTTAAAA
5196818 AAACACGAAAATTTTG
1 AAACACGAAAATTTTG
*
5196834 AAACACGAGAATTTT
1 AAACACGAAAATTTT
5196849 TTCAAAACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (16 bp):
AAACACGAAAATTTTG
Found at i:5196909 original size:37 final size:37
Alignment explanation
Indices: 5196828--5196920 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 37
5196818 AAACACGAAA
* *
5196828 ATTTTGAAACACGAGAATTTTTTCAAAACACGAATTTTC
1 ATTTTGAAACACGA-AA-ATTTTCAAAACACAAATTTTC
* *
5196867 TTTTTGAAACACGAAAATTTTGAAAACACAAAGTTTT-
1 ATTTTGAAACACGAAAATTTTCAAAACACAAA-TTTTC
5196904 ATTTTGAAAACAC-AAAA
1 ATTTTG-AAACACGAAAA
5196921 GATTTGATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
37 22 0.47
38 12 0.26
39 13 0.28
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (37 bp):
ATTTTGAAACACGAAAATTTTCAAAACACAAATTTTC
Found at i:5196976 original size:17 final size:17
Alignment explanation
Indices: 5196950--5197231 Score: 101
Period size: 17 Copynumber: 15.6 Consensus size: 17
5196940 CATGAGATTT
5196950 TTTTTGAAACACGGAAA
1 TTTTTGAAACACGGAAA
* *
5196967 TTTATGAAACACGGTCAA
1 TTTTTGAAACACGG-AAA
*
5196985 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGGAAA
* **
5197003 TTTTTGAAAGACGGGATTTT
1 TTTTTGAAACAC-GGA--AA
*
5197023 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGGAAA
* *
5197041 TTTATAAAACACGGAAA
1 TTTTTGAAACACGGAAA
* * *
5197058 TTTTTTCTAAAAACAAGAAAA
1 --TTTT-T-GAAACACGGAAA
* *
5197079 TTTTCGAAAAAC-GAGAA
1 TTTTTGAAACACGGA-AA
5197096 TTTTTGAAAACACAGGAAA
1 TTTTTG-AAACAC-GGAAA
*
5197115 TTTTTGAAA-ACATGAAA
1 TTTTTGAAACAC-GGAAA
** *
5197132 TTTTTTGTTACAC-TAGAA
1 -TTTTTGAAACACGGA-AA
5197150 -TTTTGAAAACAC-GAAGA
1 TTTTTG-AAACACGGAA-A
* *
5197167 TTTTTGAAACA-TGAGGA
1 TTTTTGAAACACGGA-AA
*
5197184 TTTTTGAAAACAC-GAAGC
1 TTTTTG-AAACACGGAA-A
* *
5197202 TTTTTGAAACATGAGAAT
1 TTTTTGAAACACG-GAAA
5197220 TTTTTGAGAACA
1 TTTTTGA-AACA
5197232 TGAAAACATG
Statistics
Matches: 199, Mismatches: 38, Indels: 54
0.68 0.13 0.19
Matches are distributed among these distances:
16 7 0.04
17 72 0.36
18 63 0.32
19 31 0.16
20 11 0.06
21 15 0.08
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (17 bp):
TTTTTGAAACACGGAAA
Found at i:5197036 original size:38 final size:38
Alignment explanation
Indices: 5196947--5197123 Score: 141
Period size: 38 Copynumber: 4.8 Consensus size: 38
5196937 AAACATGAGA
* *
5196947 TTTTTTTTG-AAACACGGAAATTTATGAAACAC-GG-T
1 TTTTTTTTGAAAACACGAAAATTTTTGAAACACGGGAT
*** *
5196982 CAATTTTTGAAAACACGAAAATTTTTGAAAGACGGGAT
1 TTTTTTTTGAAAACACGAAAATTTTTGAAACACGGGAT
* * * *
5197020 TTTTTTTTGAAAACACGAAAATTTATAAAACACGGAAA
1 TTTTTTTTGAAAACACGAAAATTTTTGAAACACGGGAT
* * * * * *
5197058 TTTTTTCTAAAAACAAGAAAATTTTCGAAAAACGAGA-
1 TTTTTTTTGAAAACACGAAAATTTTTGAAACACGGGAT
* *
5197095 --ATTTTTGAAAACACAGGAAATTTTTGAAA
1 TTTTTTTTGAAAACAC-GAAAATTTTTGAAA
5197124 ACATGAAATT
Statistics
Matches: 109, Mismatches: 29, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
35 16 0.15
36 32 0.29
37 2 0.02
38 59 0.54
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (38 bp):
TTTTTTTTGAAAACACGAAAATTTTTGAAACACGGGAT
Found at i:5197077 original size:20 final size:20
Alignment explanation
Indices: 5197054--5197137 Score: 65
Period size: 19 Copynumber: 4.5 Consensus size: 20
5197044 ATAAAACACG
*
5197054 GAAATTTTTTCTAAAAACAA
1 GAAATTTTTTCGAAAAACAA
* *
5197074 GAAA-ATTTTCGAAAAACGA
1 GAAATTTTTTCGAAAAACAA
*
5197093 G-AA-TTTTT-GAAAACACAG
1 GAAATTTTTTCGAAAA-ACAA
*
5197111 GAAA-TTTTT-G-AAAACAT
1 GAAATTTTTTCGAAAAACAA
5197128 GAAATTTTTT
1 GAAATTTTTT
5197138 GTTACACTAG
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
17 12 0.22
18 17 0.31
19 21 0.39
20 4 0.07
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (20 bp):
GAAATTTTTTCGAAAAACAA
Found at i:5197134 original size:36 final size:35
Alignment explanation
Indices: 5196950--5197212 Score: 125
Period size: 35 Copynumber: 7.3 Consensus size: 35
5196940 CATGAGATTT
* *
5196950 TTTTTGAAACAC-GGAAATTTATG-AAACACGGTCAA
1 TTTTTGAAACACAGGAAATTTTTGAAAACAC-G-AAA
* ** **
5196985 TTTTTGAAA-ACACGAAAATTTTTGAAAGACGGGATTTT
1 TTTTTGAAACACA-GGAAATTTTTGAAA-ACACGA--AA
* *
5197023 TTTTTGAAA-ACACGAAAATTTAT-AAAACACGGAAA
1 TTTTTGAAACACA-GGAAATTTTTGAAAACAC-GAAA
* * * *
5197058 TTTTTTCTAAAAACAAGAAAATTTTCGAAAA-ACGAGAA
1 -TTTTT-GAAACAC-AGGAAATTTTTGAAAACACGA-AA
*
5197096 TTTTTGAAAACACAGGAAATTTTTGAAAACATGAAA
1 TTTTTG-AAACACAGGAAATTTTTGAAAACACGAAA
**
5197132 TTTTTTGTTACACTA-G-AA-TTTTGAAAACACGAAGA
1 -TTTTTGAAACAC-AGGAAATTTTTGAAAACACGAA-A
* *
5197167 TTTTTGAAACATGAGG--ATTTTTGAAAACACGAAGC
1 TTTTTGAAACA-CAGGAAATTTTTGAAAACACGAA-A
5197202 TTTTTGAAACA
1 TTTTTGAAACA
5197213 TGAGAATTTT
Statistics
Matches: 180, Mismatches: 27, Indels: 42
0.72 0.11 0.17
Matches are distributed among these distances:
34 27 0.15
35 40 0.22
36 37 0.21
37 33 0.18
38 38 0.21
39 5 0.03
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (35 bp):
TTTTTGAAACACAGGAAATTTTTGAAAACACGAAA
Found at i:5197152 original size:35 final size:34
Alignment explanation
Indices: 5197068--5197223 Score: 131
Period size: 35 Copynumber: 4.5 Consensus size: 34
5197058 TTTTTTCTAA
* * *
5197068 AAACAAGAAAATTTTCGAAAA-ACGAGAATTTTTG
1 AAACATGAGAATTTTTGAAAACACGA-AATTTTTG
* *
5197102 AAAACA-CAGGAAATTTTTGAAAACATGAAATTTTTTG
1 -AAACATGA-G-AATTTTTGAAAACACGAAA-TTTTTG
**
5197139 TTACACT-AGAA-TTTTGAAAACACGAAGATTTTTG
1 AAACA-TGAGAATTTTTGAAAACACGAA-ATTTTTG
* *
5197173 AAACATGAGGATTTTTGAAAACACGAAGCTTTTTG
1 AAACATGAGAATTTTTGAAAACACGAA-ATTTTTG
5197208 AAACATGAGAATTTTT
1 AAACATGAGAATTTTT
5197224 TGAGAACATG
Statistics
Matches: 100, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
33 1 0.01
34 27 0.27
35 45 0.45
36 17 0.17
37 10 0.10
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (34 bp):
AAACATGAGAATTTTTGAAAACACGAAATTTTTG
Found at i:5197357 original size:48 final size:48
Alignment explanation
Indices: 5197304--5197422 Score: 195
Period size: 48 Copynumber: 2.5 Consensus size: 48
5197294 GTCAAGAGAG
5197304 TTTTTTGAAACACG-GAATTTTTTTTGAAAAAAAGAAACACAAATATAT
1 TTTTTTGAAACACGAGAA-TTTTTTTGAAAAAAAGAAACACAAATATAT
* *
5197352 TTTTTTGAAACACGAGAAATTTTTTGAAAAAAAGAAACACGAATATAT
1 TTTTTTGAAACACGAGAATTTTTTTGAAAAAAAGAAACACAAATATAT
*
5197400 TTTTTTGAAACACGAGAAATTTT
1 TTTTTTGAAACACGAGAATTTTT
5197423 ATTATTATTA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
48 65 0.96
49 3 0.04
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (48 bp):
TTTTTTGAAACACGAGAATTTTTTTGAAAAAAAGAAACACAAATATAT
Found at i:5197473 original size:18 final size:17
Alignment explanation
Indices: 5197432--5197480 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
5197422 TATTATTATT
5197432 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGAGAA
*
5197449 ATTTTGAAGACATGA-AA
1 ATTTTGAA-ACACGAGAA
5197466 ATTTTTGAAACACGA
1 A-TTTTGAAACACGA
5197481 TTTTTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (17 bp):
ATTTTGAAACACGAGAA
Found at i:5197607 original size:19 final size:20
Alignment explanation
Indices: 5197585--5197627 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5197575 ATATTTAATC
5197585 AGGA-TTCTAATAAAACACG
1 AGGATTTCTAATAAAACACG
* *
5197604 AGGATTTTTATTAAAACACG
1 AGGATTTCTAATAAAACACG
5197624 AGGA
1 AGGA
5197628 ATTTTGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.26
Consensus pattern (20 bp):
AGGATTTCTAATAAAACACG
Found at i:5198316 original size:7 final size:7
Alignment explanation
Indices: 5198306--5198384 Score: 52
Period size: 6 Copynumber: 12.3 Consensus size: 7
5198296 TTTCTTCTAT
5198306 TTTCTTC
1 TTTCTTC
5198313 TTTCTTC
1 TTTCTTC
5198320 TTTCTT-
1 TTTCTTC
5198326 TTT-TTC
1 TTTCTTC
5198332 -TT-TT-
1 TTTCTTC
*
5198336 TTTCCTC
1 TTTCTTC
5198343 ATTTCTT-
1 -TTTCTTC
5198350 TTTCTTTCC
1 TTTC-TT-C
5198359 TTT-TTC
1 TTTCTTC
5198365 TTT-TTC
1 TTTCTTC
5198371 TTTC-T-
1 TTTCTTC
5198376 TTTCTTC
1 TTTCTTC
5198383 TT
1 TT
5198385 CCTTTCAAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
5 12 0.20
6 20 0.34
7 19 0.32
8 5 0.08
9 3 0.05
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTCTTC
Found at i:5198449 original size:7 final size:7
Alignment explanation
Indices: 5198437--5198464 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
5198427 AGTGCCGGCG
5198437 CTTCTCC
1 CTTCTCC
5198444 CTTCTCC
1 CTTCTCC
5198451 CTTCTCC
1 CTTCTCC
5198458 CTTCTCC
1 CTTCTCC
5198465 TCCTCTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (7 bp):
CTTCTCC
Found at i:5198493 original size:14 final size:16
Alignment explanation
Indices: 5198470--5198515 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
5198460 TCTCCTCCTC
5198470 TCTCTTCTTTCTCTCT
1 TCTCTTCTTTCTCTCT
5198486 T-T-TTCTTT-T-TCT
1 TCTCTTCTTTCTCTCT
*
5198498 TCTCTTCTTCCTCTCT
1 TCTCTTCTTTCTCTCT
5198514 TC
1 TC
5198516 CTTACTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
12 4 0.16
13 2 0.08
14 11 0.44
15 2 0.08
16 6 0.24
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (16 bp):
TCTCTTCTTTCTCTCT
Found at i:5199138 original size:29 final size:29
Alignment explanation
Indices: 5199075--5199139 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
5199065 GTGCAAAGTT
*
5199075 TTTAGGGCAAAAATGTGATTTTAGGAAAA
1 TTTAGGGCAAAAATGTAATTTTAGGAAAA
* *
5199104 TATAGGG-ACAAAATGTAATTTCTA-GAAAG
1 TTTAGGGCA-AAAATGTAATTT-TAGGAAAA
5199133 TTTAGGG
1 TTTAGGG
5199140 GCCTGACTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 1 0.03
29 27 0.90
30 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.31
Consensus pattern (29 bp):
TTTAGGGCAAAAATGTAATTTTAGGAAAA
Found at i:5199882 original size:78 final size:75
Alignment explanation
Indices: 5199672--5200151 Score: 548
Period size: 78 Copynumber: 6.3 Consensus size: 75
5199662 TAATAATTTT
* * * * * *
5199672 TTTTTTTG-AAAACATAAATTGAAAATACCACAGCGTGACCTGAGGCTTAACTCACCTCTCGCAT
1 TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAA
5199736 TATGAGTTGA
66 TATGAGTTGA
* *
5199746 --TTTTTGAAAAACGAAAAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTC
1 TTTTTTTGAAAAAC-AGAAATT-AAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTC
*
5199809 GTAATATGAGTTGA
62 GCAATATGAGTTGA
* * * *
5199823 TTTTTTTTGAAAAACAGAAATTTAAAATACCTTAGCGTGCGACCTGAGGCCCAACTCACCTCTCG
1 -TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCG
5199888 CAATATGAGTTGA
63 CAATATGAGTTGA
* *
5199901 --TTTTTGAAAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCTCTCGTA
1 TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCG-TGACCCGAGGCTCAACTCACCTCTCGCA
* *
5199963 TTGTGAGTTGA
65 ATATGAGTTGA
* * *
5199974 --TTTTTGAAAAAAAGAAAATTTAAAAGAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCT
1 TTTTTTTGAAAAACAG-AAA-TT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT
5200037 CGCAATATGAGTTGA
61 CGCAATATGAGTTGA
* *
5200052 TTTTTTTGAAAAACAGTAACTTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTA
1 TTTTTTTGAAAAACAG-AAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCA
*
5200117 TTATGAGTTGA
65 ATATGAGTTGA
*
5200128 --TTTTTGAAAAACAAAAATTAAAAA
1 TTTTTTTGAAAAACAGAAATTAAAAA
5200152 ATATAATTCT
Statistics
Matches: 349, Mismatches: 38, Indels: 39
0.82 0.09 0.09
Matches are distributed among these distances:
72 6 0.02
73 60 0.17
74 23 0.07
75 44 0.13
76 50 0.14
77 39 0.11
78 91 0.26
79 9 0.03
80 27 0.08
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (75 bp):
TTTTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGA
Found at i:5199972 original size:228 final size:227
Alignment explanation
Indices: 5199674--5200151 Score: 680
Period size: 228 Copynumber: 2.1 Consensus size: 227
5199664 ATAATTTTTT
* * *
5199674 TTTTTG-AAAACATAAATTGAAAATACCACAGCGTGACCTGAGGCTTAACTCACCTCTCGCATTA
1 TTTTTGAAAAACAAAAATTGAAAATACCACAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTA
* * *
5199738 TGAGTTGATTTTTG-AAAAACGAAAAATT-GAA-AAATACCTCGGCATGTGACCCGAGGCTCAAC
66 TGAGTTGATTTTTGAAAAAAAGAAAAATTAAAAGAAATACCTCGGC--GTGACCCGAGACTCAAC
* * *
5199800 TCACCTCTCGTAATATGAGTTGATTTTTTTTGAAAAACAG-AAATTTAAAATACCTTAGCGTGCG
129 TCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGTAAATTAAAAATACCTCAGCGT--G
*
5199864 ACCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGA
191 ACCCGAGGCCCAACTCACCTCTCGCAATATGAGTTGA
* * *
5199901 TTTTTGAAAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCTCTCGTATT
1 TTTTTGAAAAACAAAAATTGAAAATACCACAGCG-TGACCCGAGGCTCAACTCACCTCTCGCATT
* *
5199965 GTGAGTTGATTTTTGAAAAAAAGAAAATTTAAAAGAAATACCTCGGCGTGACCCGAGACTCAACT
65 ATGAGTTGATTTTTGAAAAAAAGAAAAATTAAAAGAAATACCTCGGCGTGACCCGAGACTCAACT
*
5200030 CACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGTAACTTAAAAATACCTCAGCGTGACCC
130 CACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGTAAATTAAAAATACCTCAGCGTGACCC
* * *
5200095 GAGGCTCAACTCACCTCTCGTATTATGAGTTGA
195 GAGGCCCAACTCACCTCTCGCAATATGAGTTGA
*
5200128 TTTTTGAAAAACAAAAATTAAAAA
1 TTTTTGAAAAACAAAAATTGAAAA
5200152 ATATAATTCT
Statistics
Matches: 225, Mismatches: 20, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
227 63 0.28
228 80 0.36
229 68 0.30
230 2 0.01
231 12 0.05
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (227 bp):
TTTTTGAAAAACAAAAATTGAAAATACCACAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTA
TGAGTTGATTTTTGAAAAAAAGAAAAATTAAAAGAAATACCTCGGCGTGACCCGAGACTCAACTC
ACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGTAAATTAAAAATACCTCAGCGTGACCCG
AGGCCCAACTCACCTCTCGCAATATGAGTTGA
Found at i:5200029 original size:151 final size:150
Alignment explanation
Indices: 5199693--5200152 Score: 603
Period size: 154 Copynumber: 3.0 Consensus size: 150
5199683 ACATAAATTG
* * *
5199693 AAAATACCACAGCGTGACCTGAGGCTTAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAC
1 AAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
* *
5199758 GAAAAATTGAAAAATACCTC-GGCATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTG
66 -AGAAATTG-AAAATACCTCAGG-A--TGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTG
5199822 ATTTTTTTTGAAAAACAG-AAATTT---
126 A---TTTTTGAAAAACAGAAAATTTAAA
* *
5199846 AAAATACCTTAGCGTGCGACCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGT--GACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
*
5199911 ACAGAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGTATTGTGAGTTGATT
64 ACAGAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATT
*
5199976 TTTGAAAAAAAGAAAATTTAAA
129 TTTGAAAAACAGAAAATTTAAA
* * *
5199998 AGAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
1 A-AAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAA
* *
5200063 AACAGTAACTTAAAAATACCTCAGCG-TGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTG
63 AACAG-AAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTG
5200127 ATTTTTGAAAAACA-AAAA-TTAAA
126 ATTTTTGAAAAACAGAAAATTTAAA
5200150 AAA
1 AAA
5200153 TATAATTCTT
Statistics
Matches: 277, Mismatches: 18, Indels: 26
0.86 0.06 0.08
Matches are distributed among these distances:
148 13 0.05
149 6 0.02
151 74 0.27
152 7 0.03
153 54 0.19
154 75 0.27
155 48 0.17
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (150 bp):
AAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
AGAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTT
TGAAAAACAGAAAATTTAAA
Found at i:5201024 original size:1 final size:1
Alignment explanation
Indices: 5201004--5201108 Score: 66
Period size: 1 Copynumber: 105.0 Consensus size: 1
5200994 TTCATCTTGA
* * * * * * * * * * *
5201004 TTTTCTTTTTCTTTTCTTTTTTCTTTTTTTGTTTTTGTTTTTGTTTTTTTTTGTTCTTTTTGTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
5201069 TTTTTGTTCTTTTATTTTTTTATTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5201109 AGGCATAATA
Statistics
Matches: 72, Mismatches: 32, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.85
Consensus pattern (1 bp):
T
Found at i:5201039 original size:9 final size:9
Alignment explanation
Indices: 5201020--5201108 Score: 74
Period size: 9 Copynumber: 9.6 Consensus size: 9
5201010 TTTTCTTTTC
*
5201020 TTTTTTCTT
1 TTTTTTGTT
*
5201029 TTTTTGTTTT
1 TTTTT-TGTT
5201039 TGTTTTTGTTT
1 T-TTTTTG-TT
5201050 TTTTTTGTT
1 TTTTTTGTT
*
5201059 CTTTTTGTT
1 TTTTTTGTT
*
5201068 CTTTTTGTT
1 TTTTTTGTT
5201077 CTTTTATT-TT
1 -TTTT-TTGTT
*
5201087 TTTATT-TT
1 TTTTTTGTT
5201095 TTTTTTGTT
1 TTTTTTGTT
5201104 TTTTT
1 TTTTT
5201109 AGGCATAATA
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
8 9 0.13
9 34 0.50
10 16 0.24
11 9 0.13
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.85
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:5212267 original size:17 final size:17
Alignment explanation
Indices: 5212242--5212280 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
5212232 CAAATTTTCT
*
5212242 TTTTG-AAACACGAAAA
1 TTTTGAAAACACAAAAA
5212258 TTTTGAAAACACAAAAA
1 TTTTGAAAACACAAAAA
*
5212275 ATTTGA
1 TTTTGA
5212281 TAAATTACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (17 bp):
TTTTGAAAACACAAAAA
Found at i:5212344 original size:18 final size:17
Alignment explanation
Indices: 5212302--5212488 Score: 81
Period size: 17 Copynumber: 10.3 Consensus size: 17
5212292 ACATGAGATT
5212302 TTTTTGAAACACGGAAA
1 TTTTTGAAACACGGAAA
* *
5212319 TTTATGAAACACGGTCAA
1 TTTTTGAAACACGG-AAA
**
5212337 TTTTTGAAAACACAAAAA
1 TTTTTG-AAACACGGAAA
* ***
5212355 TTTTTGAAAGACGGGTTTTT
1 TTTTTGAAACAC-GG--AAA
*
5212375 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGGAAA
* *
5212393 TTTATAAAACACGGAAA
1 TTTTTGAAACACGGAAA
* *
5212410 TTTTTTCTGAAAACAAGAAAA
1 --TTTT-TG-AAACACGGAAA
* *
5212431 TTTTCGAAAAAC-GAGAA
1 TTTTTGAAACACGGA-AA
*
5212448 TTTTTGAAAACACAAGAAA
1 TTTTTG-AAACAC-GGAAA
*
5212467 TTTTTGAAA-ACATGAAA
1 TTTTTGAAACAC-GGAAA
5212484 TTTTT
1 TTTTT
5212489 TGTTAAACTA
Statistics
Matches: 125, Mismatches: 31, Indels: 28
0.68 0.17 0.15
Matches are distributed among these distances:
16 1 0.01
17 51 0.41
18 28 0.22
19 21 0.17
20 10 0.08
21 14 0.11
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGGAAA
Found at i:5212393 original size:38 final size:38
Alignment explanation
Indices: 5212300--5212489 Score: 137
Period size: 38 Copynumber: 5.1 Consensus size: 38
5212290 AAACATGAGA
* * *
5212300 TTTTTTTG-AAACACGGAAATTTATGAAACACGGTCAA-
1 TTTTTTTGAAAACACGAAAATTTTTGAAACACGG-AAAT
* * ***
5212337 --TTTTTGAAAACACAAAAATTTTTGAAAGACGGGTTT
1 TTTTTTTGAAAACACGAAAATTTTTGAAACACGGAAAT
* *
5212373 TTTTTTTGAAAACACGAAAATTTATAAAACACGGAAAT
1 TTTTTTTGAAAACACGAAAATTTTTGAAACACGGAAAT
* * * *
5212411 TTTTTCTGAAAACAAGAAAATTTTCGAAAAAC-GAGAA-
1 TTTTTTTGAAAACACGAAAATTTTTGAAACACGGA-AAT
* *
5212448 --TTTTTGAAAACACAAGAAATTTTTGAAA-ACATGAAAT
1 TTTTTTTGAAAACACGA-AAATTTTTGAAACAC-GGAAAT
5212485 TTTTT
1 TTTTT
5212490 GTTAAACTAG
Statistics
Matches: 118, Mismatches: 24, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
35 20 0.17
36 34 0.29
37 4 0.03
38 57 0.48
39 3 0.03
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (38 bp):
TTTTTTTGAAAACACGAAAATTTTTGAAACACGGAAAT
Found at i:5212415 original size:74 final size:75
Alignment explanation
Indices: 5212300--5212439 Score: 189
Period size: 74 Copynumber: 1.9 Consensus size: 75
5212290 AAACATGAGA
* * * *
5212300 TTTTTTTGAAACACGGAAATTTATGAAACACGGTCAA-TTTT-TGAAAACACA-AAAATTTTTGA
1 TTTTTTTGAAACACGAAAATTTATAAAACACGGTAAATTTTTCTGAAAACA-AGAAAATTTTCGA
5212362 AAGACGGGTTT
65 AAGACGGGTTT
5212373 TTTTTTTGAAAACACGAAAATTTATAAAACACGG-AAATTTTTTCTGAAAACAAGAAAATTTTCG
1 TTTTTTTG-AAACACGAAAATTTATAAAACACGGTAAA-TTTTTCTGAAAACAAGAAAATTTTCG
5212437 AAA
64 AAA
5212440 AACGAGAATT
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
73 10 0.17
74 23 0.40
75 5 0.09
76 20 0.34
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (75 bp):
TTTTTTTGAAACACGAAAATTTATAAAACACGGTAAATTTTTCTGAAAACAAGAAAATTTTCGAA
AGACGGGTTT
Found at i:5212441 original size:19 final size:19
Alignment explanation
Indices: 5212419--5212527 Score: 72
Period size: 19 Copynumber: 6.1 Consensus size: 19
5212409 ATTTTTTCTG
*
5212419 AAAACAAGAAAATTTTCGA
1 AAAACAAGAAAATTTTTGA
*
5212438 AAAAC--GAGAATTTTTGA
1 AAAACAAGAAAATTTTTGA
5212455 AAACACAAG-AAATTTTTG-
1 AAA-ACAAGAAAATTTTTGA
* * *
5212473 AAAACATGAAATTTTTTGT
1 AAAACAAGAAAATTTTTGA
* *
5212492 TAAACTAG--AA-TTTTG-
1 AAAACAAGAAAATTTTTGA
* *
5212507 AAAACACGAAGATTTTTGA
1 AAAACAAGAAAATTTTTGA
5212526 AA
1 AA
5212528 CATGAGGATT
Statistics
Matches: 68, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
15 5 0.07
16 5 0.07
17 19 0.28
18 18 0.26
19 20 0.29
20 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (19 bp):
AAAACAAGAAAATTTTTGA
Found at i:5212452 original size:74 final size:73
Alignment explanation
Indices: 5212296--5212489 Score: 184
Period size: 74 Copynumber: 2.6 Consensus size: 73
5212286 TACGAAACAT
* * *
5212296 GAGATTTTTTTG-AAACACGGAAATTTATGAAACACGGTCAA--TTTTTGAAAACACAAAAATTT
1 GAGATTTTTTTGAAAACACGAAAATTTATAAAACACGG-AAATTTTTTTGAAAACACAAAAATTT
* *
5212358 TTGAAAGAC
65 TCGAAAAAC
* *
5212367 GGGTTTTTTTTTTGAAAACACGAAAATTTATAAAACACGGAAATTTTTTCTGAAAACA-AGAAAA
1 GAG--ATTTTTTTGAAAACACGAAAATTTATAAAACACGGAAATTTTTT-TGAAAACACA-AAAA
5212431 TTTTCGAAAAAC
62 TTTTCGAAAAAC
* * * *
5212443 GAGA-ATTTTTGAAAACACAAGAAATTTTTGAAAACA-TGAAATTTTTT
1 GAGATTTTTTTGAAAACACGA-AAATTTAT-AAAACACGGAAATTTTTT
5212490 GTTAAACTAG
Statistics
Matches: 101, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
71 2 0.02
73 24 0.24
74 40 0.40
75 11 0.11
76 24 0.24
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (73 bp):
GAGATTTTTTTGAAAACACGAAAATTTATAAAACACGGAAATTTTTTTGAAAACACAAAAATTTT
CGAAAAAC
Found at i:5212476 original size:36 final size:36
Alignment explanation
Indices: 5212302--5212476 Score: 114
Period size: 36 Copynumber: 4.8 Consensus size: 36
5212292 ACATGAGATT
* * *
5212302 TTTTTG-AAACAC-GGAAATTTATGAAACACGGTCAA
1 TTTTTGAAAACACAAGAAATTTTTGAAAAACGGT-AA
* **
5212337 TTTTTGAAAACACAA-AAATTTTTGAAAGACGGGTTTTT
1 TTTTTGAAAACACAAGAAATTTTTGAAAAAC-GG--TAA
* * *
5212375 TTTTTGAAAACACGA-AAATTTAT-AAAACACGGAAA
1 TTTTTGAAAACACAAGAAATTTTTGAAAA-ACGGTAA
*
5212410 TTTTTTCTG-AAA-ACAAGAAAATTTTCGAAAAACGAG-AA
1 --TTTT-TGAAAACACAAG-AAATTTTTGAAAAACG-GTAA
5212448 TTTTTGAAAACACAAGAAATTTTTGAAAA
1 TTTTTGAAAACACAAGAAATTTTTGAAAA
5212477 CATGAAATTT
Statistics
Matches: 110, Mismatches: 15, Indels: 29
0.71 0.10 0.19
Matches are distributed among these distances:
35 8 0.07
36 41 0.37
37 19 0.17
38 36 0.33
39 6 0.05
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (36 bp):
TTTTTGAAAACACAAGAAATTTTTGAAAAACGGTAA
Found at i:5212489 original size:18 final size:17
Alignment explanation
Indices: 5212375--5212588 Score: 109
Period size: 18 Copynumber: 12.0 Consensus size: 17
5212365 ACGGGTTTTT
*
5212375 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACATG-AAA
* *
5212393 TTTAT-AAAACACGGAAA
1 TTTTTGAAAACA-TGAAA
*
5212410 TTTTTTCTGAAAACAAGAAAA
1 --TTTT-TGAAAACATG-AAA
* *
5212431 TTTTCGAAAA-ACGAGAA
1 TTTTTGAAAACATGA-AA
*
5212448 TTTTTGAAAACACAAGAAA
1 TTTTTG-AAA-ACATGAAA
5212467 TTTTTGAAAACATGAAA
1 TTTTTGAAAACATGAAA
*
5212484 TTTTTTGTTAAAC-T-AGAA
1 -TTTTTG-AAAACATGA-AA
*
5212502 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACATGAA-A
*
5212519 TTTTTG-AAACATGAGGA
1 TTTTTGAAAACATGA-AA
* *
5212536 TTTTTGAAAACACGAAGC
1 TTTTTGAAAACATGAA-A
5212554 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACATGA-AA
*
5212571 TTTTTTGAGAACATGAAA
1 -TTTTTGAAAACATGAAA
5212589 ACATGAAAAT
Statistics
Matches: 153, Mismatches: 20, Indels: 46
0.70 0.09 0.21
Matches are distributed among these distances:
15 4 0.03
16 7 0.05
17 49 0.32
18 52 0.34
19 27 0.18
20 5 0.03
21 9 0.06
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.32
Consensus pattern (17 bp):
TTTTTGAAAACATGAAA
Found at i:5212504 original size:35 final size:34
Alignment explanation
Indices: 5212375--5212575 Score: 142
Period size: 35 Copynumber: 5.6 Consensus size: 34
5212365 ACGGGTTTTT
* * *
5212375 TTTTTGAAAACACGAAAATTTAT-AAAACACGGAAA
1 TTTTTG-AAACATGAGAATTTTTGAAAACAC-GAAA
* * *
5212410 TTTTTTCTGAAAACAAGAAAATTTTCGAAAA-ACGAGAA
1 --TTTT-TG-AAACATGAGAATTTTTGAAAACACGA-AA
** *
5212448 TTTTTGAAAACACAAGAAATTTTTGAAAACATGAAA
1 TTTTTG-AAACATGAG-AATTTTTGAAAACACGAAA
5212484 TTTTTTGTTAAAC-T-AGAA-TTTTGAAAACACGAAGA
1 -TTTTTG--AAACATGAGAATTTTTGAAAACACGAA-A
* *
5212519 TTTTTGAAACATGAGGATTTTTGAAAACACGAAGC
1 TTTTTGAAACATGAGAATTTTTGAAAACACGAA-A
5212554 TTTTTGAAACATGAGAATTTTT
1 TTTTTGAAACATGAGAATTTTT
5212576 TGAGAACATG
Statistics
Matches: 139, Mismatches: 14, Indels: 24
0.79 0.08 0.14
Matches are distributed among these distances:
32 4 0.03
33 1 0.01
34 23 0.17
35 49 0.35
36 19 0.14
37 15 0.11
38 24 0.17
39 4 0.03
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (34 bp):
TTTTTGAAACATGAGAATTTTTGAAAACACGAAA
Found at i:5212736 original size:48 final size:47
Alignment explanation
Indices: 5212656--5212775 Score: 186
Period size: 48 Copynumber: 2.5 Consensus size: 47
5212646 TTCAAGAGAG
* *
5212656 TTTTTTGAAACACGGAATTTTTTTTTGGAAAAAAGAAACACGAATATAT
1 TTTTTTGAAACACGGAA--ATTTTTTGAAAAAAAGAAACACGAATATAT
5212705 TTTTTTGAAACACAGGAAATTTTTTGAAAAAAAGAAACACGAATATAT
1 TTTTTTGAAACAC-GGAAATTTTTTGAAAAAAAGAAACACGAATATAT
5212753 TTTTTTGAAACACGGGAAATTTT
1 TTTTTTGAAACAC-GGAAATTTT
5212776 ATTATTATTA
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
48 50 0.75
49 13 0.19
50 4 0.06
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (47 bp):
TTTTTTGAAACACGGAAATTTTTTGAAAAAAAGAAACACGAATATAT
Found at i:5212826 original size:18 final size:17
Alignment explanation
Indices: 5212785--5212831 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
5212775 TATTATTATT
5212785 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGAGAA
*
5212802 ATTTTGAAGACATGA-AA
1 ATTTTGAA-ACACGAGAA
5212819 ATTTTTGAAACAC
1 A-TTTTGAAACAC
5212832 AATTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.30
Consensus pattern (17 bp):
ATTTTGAAACACGAGAA
Found at i:5212961 original size:19 final size:20
Alignment explanation
Indices: 5212942--5212980 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5212932 TTAATCGGGA
5212942 TTCTAATAAAACACGAGGAT
1 TTCTAATAAAACACGAGGAT
* *
5212962 TTTTATTAAAACACGAGGA
1 TTCTAATAAAACACGAGGA
5212981 ATTTTGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (20 bp):
TTCTAATAAAACACGAGGAT
Found at i:5213664 original size:7 final size:7
Alignment explanation
Indices: 5213654--5213730 Score: 58
Period size: 7 Copynumber: 11.3 Consensus size: 7
5213644 TTTCTTCTAT
5213654 TTTCTTC
1 TTTCTTC
5213661 TTTCTTC
1 TTTCTTC
5213668 TTTCTTC
1 TTTCTTC
*
5213675 TTTTCTTT
1 -TTTCTTC
*
5213683 TTTCCTCC
1 TTT-CTTC
5213691 TTT-TT-
1 TTTCTTC
5213696 TTTCTTTCC
1 TTTC-TT-C
5213705 TTT-TTC
1 TTTCTTC
5213711 TTT-TTC
1 TTTCTTC
5213717 TTTC-T-
1 TTTCTTC
5213722 TTTCTTC
1 TTTCTTC
5213729 TT
1 TT
5213731 CCTTTCAAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
5 7 0.12
6 13 0.23
7 23 0.40
8 11 0.19
9 3 0.05
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTCTTC
Found at i:5213672 original size:11 final size:11
Alignment explanation
Indices: 5213658--5213736 Score: 55
Period size: 11 Copynumber: 7.6 Consensus size: 11
5213648 TTCTATTTTC
5213658 TTCTTTCTTCT
1 TTCTTTCTTCT
5213669 TTC-TTC-T-T
1 TTCTTTCTTCT
* *
5213677 TTCTTTTTTCC
1 TTCTTTCTTCT
*
5213688 TCCTTT-TT-T
1 TTCTTTCTTCT
5213697 TTCTTTCCTT-T
1 TTCTTT-CTTCT
5213708 TTCTTT-TTCT
1 TTCTTTCTTCT
5213718 TTCTTTTCTTCT
1 TTC-TTTCTTCT
*
5213730 TCCTTTC
1 TTCTTTC
5213737 AAACCCTAGC
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
8 4 0.07
9 10 0.19
10 10 0.19
11 24 0.44
12 6 0.11
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TTCTTTCTTCT
Found at i:5213675 original size:17 final size:17
Alignment explanation
Indices: 5213644--5213736 Score: 65
Period size: 17 Copynumber: 5.6 Consensus size: 17
5213634 CTGTTATTTT
5213644 TTTCTTCTATT-TTCTTC
1 TTTCTTCT-TTCTTCTTC
5213661 TTTCTTCTTTCTTC-T-
1 TTTCTTCTTTCTTCTTC
* *
5213676 TTTCTTTTTTCCTCCTT-
1 TTTCTTCTTT-CTTCTTC
* *
5213693 TTTTTTCTTTCCTTTTTC
1 TTTCTTCTTT-CTTCTTC
5213711 TTT-TTCTTTCTT-TTC
1 TTTCTTCTTTCTTCTTC
5213726 -TTCTTCCTTTC
1 TTTCTT-CTTTC
5213737 AAACCCTAGC
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
14 2 0.03
15 14 0.22
16 14 0.22
17 31 0.48
18 3 0.05
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCTTCTTTCTTCTTC
Found at i:5213686 original size:29 final size:31
Alignment explanation
Indices: 5213648--5213736 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 31
5213638 TATTTTTTTC
*
5213648 TTCTATTTTCTTCTTTCTTCTTTC-TT-CTT
1 TTCTTTTTTCTTCTTTCTTCTTTCTTTCCTT
*
5213677 TTCTTTTTTCCTCCTTT-TT-TTTCTTTCCTT
1 TTCTTTTTT-CTTCTTTCTTCTTTCTTTCCTT
*
5213707 TT-TCTTTTTCTTTCTTTTCTTCTTCCTTTC
1 TTCT-TTTTTC-TTC-TTTCTTCTTTCTTTC
5213737 AAACCCTAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
28 4 0.08
29 14 0.29
30 18 0.38
31 3 0.06
32 2 0.04
33 7 0.15
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (31 bp):
TTCTTTTTTCTTCTTTCTTCTTTCTTTCCTT
Found at i:5213701 original size:39 final size:42
Alignment explanation
Indices: 5213653--5213735 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 42
5213643 TTTTCTTCTA
5213653 TTTTCTTCTTT-CTTCTTTC-TTCT-TTTCTTTT-TTCCTCCT
1 TTTTCTTCTTTCCTT-TTTCTTTCTCTTTCTTTTCTTCCTCCT
* * *
5213692 TTTTTTTCTTTCCTTTTTCTTTTTCTTTCTTTTCTTCTTCCT
1 TTTTCTTCTTTCCTTTTTCTTTCTCTTTCTTTTCTTCCTCCT
5213734 TT
1 TT
5213736 CAAACCCTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
39 14 0.38
40 6 0.16
41 8 0.22
42 9 0.24
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (42 bp):
TTTTCTTCTTTCCTTTTTCTTTCTCTTTCTTTTCTTCCTCCT
Found at i:5213718 original size:42 final size:42
Alignment explanation
Indices: 5213653--5213735 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
5213643 TTTTCTTCTA
5213653 TTTTCTTCTTTCTTCTTTCTTCTTTTCTTTT-TTCCTCCTTTT
1 TTTTCTTCTTTCTTCTTTCTTC-TTTCTTTTCTTCCTCCTTTT
*
5213695 TTTTCTTTCCTTT-TTCTTT-TTCTTTCTTTTCTTCTTCCTTT
1 TTTTC-TT-CTTTCTTCTTTCTTCTTTCTTTTCTTCCTCCTTT
5213736 CAAACCCTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
41 8 0.22
42 17 0.46
43 8 0.22
44 4 0.11
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (42 bp):
TTTTCTTCTTTCTTCTTTCTTCTTTCTTTTCTTCCTCCTTTT
Found at i:5214478 original size:29 final size:30
Alignment explanation
Indices: 5214418--5214583 Score: 78
Period size: 29 Copynumber: 5.6 Consensus size: 30
5214408 CAAAGTTTTT
* *
5214418 GGGGCAAAAATGTGATTTTAGGAAAATATA
1 GGGGCCAAAATGTAATTTTAGGAAAATATA
* *
5214448 -GGGCCAAAATGTAATTTCTA-GAAAGTTTA
1 GGGGCCAAAATGTAATTT-TAGGAAAATATA
* * *
5214477 GGGGCC-AACTATAA-TTTA-CAAAATATTA
1 GGGGCCAAAATGTAATTTTAGGAAAATA-TA
* * * * *
5214505 GGGGTCAAGATGTAAATTTAGAAAAAGT-TG
1 GGGGCCAAAATGTAATTTTAGGAAAA-TATA
* ** * *
5214535 GGGGTCAAAAAATAATTTT-TGAAAAGT-TT
1 GGGGCCAAAATGTAATTTTAGGAAAA-TATA
5214564 GGAGGCCAAAATGTAATTTT
1 GG-GGCCAAAATGTAATTTT
5214584 TATTTTTTGT
Statistics
Matches: 103, Mismatches: 25, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
27 6 0.06
28 9 0.09
29 42 0.41
30 41 0.40
31 4 0.04
32 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (30 bp):
GGGGCCAAAATGTAATTTTAGGAAAATATA
Done.