Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 130 of 279
Found at i:41607710 original size:14 final size:15
Alignment explanation
Indices: 41607671--41607712 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41607661 TTTAAACATA
*
41607671 ATTATTATTAAATAT
1 ATTATAATTAAATAT
41607686 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
41607700 A-TATAATTTAATA
1 ATTATAATTAAATA
41607713 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:41607830 original size:14 final size:15
Alignment explanation
Indices: 41607781--41607832 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41607771 ATAAAATATA
41607781 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
41607796 TATTAAATATATTAT
1 AATTAAATATATTAT
41607811 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
41607824 AATTTAATA
1 AATTAAATA
41607833 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:41607929 original size:15 final size:16
Alignment explanation
Indices: 41607911--41607969 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
41607901 AATTATCATA
*
41607911 ATTATTATT-AAATAT
1 ATTATAATTAAAATAT
41607926 ATTATAATTAAAATAT
1 ATTATAATTAAAATAT
*
41607942 ATAATTTAA-TAAAAT-T
1 AT--TATAATTAAAATAT
41607958 ATTAATAATTAA
1 ATT-ATAATTAA
41607970 TATTCTTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
14 1 0.03
15 11 0.31
16 14 0.39
17 6 0.17
18 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTATAATTAAAATAT
Found at i:41607943 original size:18 final size:18
Alignment explanation
Indices: 41607922--41607969 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
41607912 TTATTATTAA
41607922 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
41607940 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
41607957 -TAT-TAATAATTAA
1 ATATATTATAATTAA
41607970 TATTCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:41607950 original size:14 final size:15
Alignment explanation
Indices: 41607911--41607952 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41607901 AATTATCATA
*
41607911 ATTATTATTAAATAT
1 ATTATAATTAAATAT
41607926 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
41607940 A-TATAATTTAATA
1 ATTATAATTAAATA
41607953 AAATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:41608016 original size:120 final size:120
Alignment explanation
Indices: 41607665--41607986 Score: 610
Period size: 120 Copynumber: 2.7 Consensus size: 120
41607655 ATCATATTTA
41607665 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
41607730 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
41607785 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
41607850 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* * *
41607905 ATCATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
41607970 TATTCTTATAT-AATTTA
66 TATTCTTATATGAATTTA
41607987 ATAAAACAAT
Statistics
Matches: 199, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
119 6 0.03
120 193 0.97
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:41609203 original size:20 final size:20
Alignment explanation
Indices: 41609180--41609218 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
41609170 CATTGAGATT
41609180 TCGAAACATCTTGCATCAGG
1 TCGAAACATCTTGCATCAGG
41609200 TCGAAACATCTTGCATCAG
1 TCGAAACATCTTGCATCAG
41609219 AACCAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (20 bp):
TCGAAACATCTTGCATCAGG
Found at i:41610550 original size:14 final size:14
Alignment explanation
Indices: 41610524--41610562 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
41610514 TCATAAACCT
*
41610524 TAAACCCTCAATCA
1 TAAACCCTAAATCA
* *
41610538 TATACCCTAAATCG
1 TAAACCCTAAATCA
41610552 TAAACCCTAAA
1 TAAACCCTAAA
41610563 CTATAATGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.31, G:0.03, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:41610767 original size:15 final size:15
Alignment explanation
Indices: 41610744--41610780 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
41610734 AGACCCCTAA
*
41610744 CCCTTAACCCATAAT
1 CCCTAAACCCATAAT
41610759 CCCTAAACCCATAAT
1 CCCTAAACCCATAAT
*
41610774 CCATAAA
1 CCCTAAA
41610781 ACTTAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.22
Consensus pattern (15 bp):
CCCTAAACCCATAAT
Found at i:41610767 original size:22 final size:21
Alignment explanation
Indices: 41610738--41610779 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
41610728 AATCATAGAC
*
41610738 CCCTAACCCTTAACCCATAAT
1 CCCTAACCCATAACCCATAAT
*
41610759 CCCTAAACCCATAATCCATAA
1 CCCT-AACCCATAACCCATAA
41610780 AACTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.21
Consensus pattern (21 bp):
CCCTAACCCATAACCCATAAT
Found at i:41610981 original size:14 final size:13
Alignment explanation
Indices: 41610964--41610993 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
41610954 GGTTTAGTAT
41610964 TTTAGGGGTTATAG
1 TTTAGGGGTTA-AG
41610978 TTTAGGGGTTAAG
1 TTTAGGGGTTAAG
41610991 TTT
1 TTT
41610994 TTTTAAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (13 bp):
TTTAGGGGTTAAG
Found at i:41611207 original size:42 final size:41
Alignment explanation
Indices: 41611082--41611220 Score: 199
Period size: 41 Copynumber: 3.4 Consensus size: 41
41611072 GTTATATGAC
* *
41611082 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCCCGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCTGT
*
41611123 TTTTAGCGGCGTTATACCAAAAGCGCCGCTAATGCTCCTGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCTGT
* * *
41611164 TTTTAGCGGCGCTTTTAACAAAAAACGCCGCTATTGCT-CTGT
1 TTTTAGCGGCG-TTTT-ACCAAAAGCGCCGCTAATGCTCCTGT
41611206 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
41611221 TGGTAAAACG
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
41 53 0.60
42 18 0.20
43 18 0.20
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.33
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCTGT
Found at i:41616169 original size:200 final size:200
Alignment explanation
Indices: 41615826--41616223 Score: 760
Period size: 200 Copynumber: 2.0 Consensus size: 200
41615816 CTTCTCTCCT
41615826 TACAACTTTCTCAATGGAGAATCATCATCCTTCAACTCTTTTATCTATGGATTCGAGTGCTCACG
1 TACAACTTTCTCAATGGAGAATCATCATCCTTCAACTCTTTTATCTATGGATTCGAGTGCTCACG
*
41615891 ACGAGTTCGATTTAGAAAAAAATCGGCAATCGGTTCTGTCCCGGCCACCGGATATCAATTTGCCG
66 ACGAGTTCGATTTAGAAAAAAATCGGCAATCGGTTCTGTCCCGGCCACCGGATATCAATTTGCCA
* * *
41615956 TTATCTGCTGAGCGTAGCCCTCCACCGCAGCAGCCATGGAACTCCGATCAGTGTGATATTCTTGA
131 TTATCTGCTGAGCGTAGCCCTCCACCACAGCAGCCATGGAACTCCGATCAGTGCGATATTCTAGA
41616021 TGTCG
196 TGTCG
41616026 TACAACTTTCTCAATGGAGAATCATCATCCTTCAACTCTTTTATCTATGGATTCGAGTGCTCACG
1 TACAACTTTCTCAATGGAGAATCATCATCCTTCAACTCTTTTATCTATGGATTCGAGTGCTCACG
41616091 ACGAGTTCGATTTAGAAAAAAATCGGCAATCGGTTCTGTCCCGGCCACCGGATATCAATTTGCCA
66 ACGAGTTCGATTTAGAAAAAAATCGGCAATCGGTTCTGTCCCGGCCACCGGATATCAATTTGCCA
41616156 TTATCTGCTGAGCGTAGCCCTCCACCACAGCAGCCATGGAACTCCGATCAGTGCGATATTCTAGA
131 TTATCTGCTGAGCGTAGCCCTCCACCACAGCAGCCATGGAACTCCGATCAGTGCGATATTCTAGA
41616221 TGT
196 TGT
41616224 TGGGCTGTGT
Statistics
Matches: 194, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 194 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (200 bp):
TACAACTTTCTCAATGGAGAATCATCATCCTTCAACTCTTTTATCTATGGATTCGAGTGCTCACG
ACGAGTTCGATTTAGAAAAAAATCGGCAATCGGTTCTGTCCCGGCCACCGGATATCAATTTGCCA
TTATCTGCTGAGCGTAGCCCTCCACCACAGCAGCCATGGAACTCCGATCAGTGCGATATTCTAGA
TGTCG
Found at i:41619002 original size:24 final size:24
Alignment explanation
Indices: 41618970--41619021 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
41618960 TTTTTTATTA
*
41618970 TTTTCATTTTC-CTCTGTTTTTTC
1 TTTTCATTTTCTCTCTGTTTTCTC
41618993 TTTTCTATTTTCTTCTCTGTTTTCTC
1 TTTTC-ATTTTC-TCTCTGTTTTCTC
41619019 TTT
1 TTT
41619022 ATTGGCCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 5 0.20
24 6 0.24
26 14 0.56
ACGTcount: A:0.04, C:0.21, G:0.04, T:0.71
Consensus pattern (24 bp):
TTTTCATTTTCTCTCTGTTTTCTC
Found at i:41625696 original size:2 final size:2
Alignment explanation
Indices: 41625689--41625715 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41625679 AAGCAAATCC
41625689 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
41625716 ATTGAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41627426 original size:22 final size:23
Alignment explanation
Indices: 41627379--41627427 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
41627369 TTGTACATTG
*
41627379 ATAT-TATAATGCTATTGCTATT
1 ATATATATAATGCTATTGATATT
*
41627401 -TATATATAATGTTATT-ATATT
1 ATATATATAATGCTATTGATATT
41627422 ATATAT
1 ATATAT
41627428 TCTATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (23 bp):
ATATATATAATGCTATTGATATT
Found at i:41630880 original size:19 final size:20
Alignment explanation
Indices: 41630856--41630893 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41630846 AAGGTCAAAT
41630856 AAAACTAAG-AATAAAGCAA
1 AAAACTAAGCAATAAAGCAA
*
41630875 AAAACTACGCAATAAAGCA
1 AAAACTAAGCAATAAAGCA
41630894 TTGACCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.63, C:0.16, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAACTAAGCAATAAAGCAA
Found at i:41630957 original size:95 final size:95
Alignment explanation
Indices: 41630794--41630983 Score: 326
Period size: 95 Copynumber: 2.0 Consensus size: 95
41630784 TAGAACCAGT
41630794 AAGCATTGACCATTAACACTTATCAGCTCTGTAATAAGACTTTTAAGAGCCAAAGGTCAAATAAA
1 AAGCATTGACCATTAACACTTATCAGCTCTGTAATAAGACTTTTAAGAGCCAAAGGTCAAATAAA
*
41630859 ACTAAGAATAAAGCAAAAAACTACGCAATA
66 ACTAAGAATAAAGCAAAAAACTACACAATA
* ** *
41630889 AAGCATTGACCATTATCACTTATCAGCTCTGTTTTAAGACTTTTAAGAGCCGAAGGTCAAATAAA
1 AAGCATTGACCATTAACACTTATCAGCTCTGTAATAAGACTTTTAAGAGCCAAAGGTCAAATAAA
*
41630954 ACTAAGACTAAAGCAAAAAACTACACAATA
66 ACTAAGAATAAAGCAAAAAACTACACAATA
41630984 GCAACTCTAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 89 1.00
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (95 bp):
AAGCATTGACCATTAACACTTATCAGCTCTGTAATAAGACTTTTAAGAGCCAAAGGTCAAATAAA
ACTAAGAATAAAGCAAAAAACTACACAATA
Found at i:41631416 original size:160 final size:148
Alignment explanation
Indices: 41631010--41631463 Score: 509
Period size: 148 Copynumber: 3.0 Consensus size: 148
41631000 AGCCAAAGTT
* * *
41631010 TAATTCAACAAATAGCTAACAGTTCACCTAAATATTCAAGAAACAGTACGATTCAGCTTCGAACT
1 TAATTCATCAAATAGCTAACAGTTCACATAAAGATTCAA-AAACAGTACGATTCAGCTTCGAACT
* * * * *
41631075 AGGATCTAAAAACAAGCTAAAGT-TGTCCTCCCTACGTAAATCTTATAAAACTTAGCTCGTAAAC
65 AGAATCTAAAAACAAGCTAAA-TCTGTTCTTCCTACGTAAAGCTCATAAAACTTAGCTCGTAAAC
41631139 TTCAGATCTGTATTTTTTTG
129 TTCAGATCTGTATTTTTTTG
* *
41631159 TAATTCATCAAACAGCT-ACAGTTCACATAAGGATTCAAAAAACAGTACGATTCAGCTTCGAACT
1 TAATTCATCAAATAGCTAACAGTTCACATAAAGATTC-AAAAACAGTACGATTCAGCTTCGAACT
* * *
41631223 ATAATCTAAAACCAAGCTAAAGCTGTTCTTCCTACGCTAGTCATAGGCTCATAGCAAACTTAGCT
65 AGAATCTAAAAACAAGCTAAATCTGTTCTTCCTACG-TA---A-A-GCTCATA--AAACTTAGCT
* *
41631288 CGTAAACTTCAGTTTTGTATTTTTTTTTG
122 CGTAAACTTCAGATCTGTA--TTTTTTTG
* * * *
41631317 TAATTCATCAAATAGATAATAGTTCACGTAAAGATTCAAAAACCGGTATC-ATTCAAGCTTCGAA
1 TAATTCATCAAATAGCTAACAGTTCACATAAAGATTCAAAAA-CAGTA-CGATTC-AGCTTCGAA
* * * *** *
41631381 CTAGAATCTAAAAACAAGTTAAATCTGTTCTTCCTACGTAAATCTTAGCGATCTTAGCTCGTAAA
63 CTAGAATCTAAAAACAAGCTAAATCTGTTCTTCCTACGTAAAGCTCATAAAACTTAGCTCGTAAA
41631446 CTTCAGATCTGTATTTTT
128 CTTCAGATCTGTATTTTT
41631464 AAGCAAAACA
Statistics
Matches: 256, Mismatches: 33, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
148 70 0.27
149 19 0.07
150 5 0.02
152 26 0.10
153 1 0.00
154 8 0.03
155 1 0.00
156 28 0.11
158 28 0.11
159 26 0.10
160 44 0.17
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (148 bp):
TAATTCATCAAATAGCTAACAGTTCACATAAAGATTCAAAAACAGTACGATTCAGCTTCGAACTA
GAATCTAAAAACAAGCTAAATCTGTTCTTCCTACGTAAAGCTCATAAAACTTAGCTCGTAAACTT
CAGATCTGTATTTTTTTG
Found at i:41632418 original size:13 final size:13
Alignment explanation
Indices: 41632400--41632426 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41632390 AGAATAAAAT
41632400 AATTTTTTTATTA
1 AATTTTTTTATTA
41632413 AATTTTTTTATTA
1 AATTTTTTTATTA
41632426 A
1 A
41632427 TTTGTATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
AATTTTTTTATTA
Found at i:41632428 original size:12 final size:12
Alignment explanation
Indices: 41632399--41632429 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
41632389 AAGAATAAAA
41632399 TAATTTTTTTAT
1 TAATTTTTTTAT
41632411 TAAATTTTTTTAT
1 T-AATTTTTTTAT
41632424 TAATTT
1 TAATTT
41632430 GTATTACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TAATTTTTTTAT
Found at i:41637248 original size:21 final size:21
Alignment explanation
Indices: 41637222--41637262 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41637212 AGACGAGCAA
* *
41637222 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
41637243 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
41637263 TTGAGTAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:41641777 original size:12 final size:12
Alignment explanation
Indices: 41641752--41641788 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
41641742 TAATTATAAA
41641752 TTTTTAA-A-TT
1 TTTTTAATATTT
41641762 TTTTTAATATTT
1 TTTTTAATATTT
41641774 TTTTTAATAATTT
1 TTTTTAAT-ATTT
41641787 TT
1 TT
41641789 AATTTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 7 0.29
11 1 0.04
12 10 0.42
13 6 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTAATATTT
Found at i:41647885 original size:16 final size:15
Alignment explanation
Indices: 41647845--41647886 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
41647835 GCTTGAGTGT
41647845 CAAATCTG-AATGAC
1 CAAATCTGAAATGAC
* *
41647859 AAAACCTGAAATGACC
1 CAAATCTGAAATGA-C
41647875 CAAATCTGAAAT
1 CAAATCTGAAAT
41647887 TATCCGACCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 6 0.27
15 5 0.23
16 11 0.50
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (15 bp):
CAAATCTGAAATGAC
Found at i:41653021 original size:144 final size:146
Alignment explanation
Indices: 41652792--41653075 Score: 461
Period size: 144 Copynumber: 2.0 Consensus size: 146
41652782 AATATTAAAA
41652792 TTTGAAAAGTAAAGGGACTAATAGCTAAAATTAACCAAACATTTAAAGAACAAAAAATTCAGTGT
1 TTTGAAAAGTAAAGGGA-TAATAGCTAAAATTAACCAAACATTTAAAGAACAAAAAATTCAGTGT
41652857 GGCTGCTGGGATTCGAGCCCAGGTCTCCACGGCCACAACGTGGAATTCTTACCACTAAACTACAG
65 GGCTGCTGGGATTCGAGCCCAGGTCTCCACGGCCACAACGTGGAATTCTTACCACTAAACTACAG
41652922 CCACAACTTGTTAAAGT
130 CCACAACTTGTTAAAGT
* * **
41652939 TTTGAAAAGTAAAGCTG-TAATATCTAAAATTAACCAAAACATATT-AA-AA-AAAAAATT-TTT
1 TTTGAAAAGTAAAG-GGATAATAGCTAAAATTAACC-AAACAT-TTAAAGAACAAAAAATTCAGT
41652999 GTGGCTGCTGGGATTCGAGCCCAGGTCTCCACGGCCACAACGTGGAATTCTTACCACTAAACTAC
63 GTGGCTGCTGGGATTCGAGCCCAGGTCTCCACGGCCACAACGTGGAATTCTTACCACTAAACTAC
41653064 AGCCACAACTTG
128 AGCCACAACTTG
41653076 AGAACCTTAG
Statistics
Matches: 130, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
144 78 0.60
145 8 0.06
146 19 0.15
147 22 0.17
148 3 0.02
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.24
Consensus pattern (146 bp):
TTTGAAAAGTAAAGGGATAATAGCTAAAATTAACCAAACATTTAAAGAACAAAAAATTCAGTGTG
GCTGCTGGGATTCGAGCCCAGGTCTCCACGGCCACAACGTGGAATTCTTACCACTAAACTACAGC
CACAACTTGTTAAAGT
Found at i:41665247 original size:113 final size:109
Alignment explanation
Indices: 41665089--41665308 Score: 305
Period size: 113 Copynumber: 2.0 Consensus size: 109
41665079 TTTCTGGCCT
* * * *
41665089 TTTGTTTTGGTATTAAATCTAGCATTTGAGGGTTTAAGTTGTTACTTTTATGTTGTTTCTCGGAA
1 TTTGTTTTGGTATTAAATCTAGCATTTGAAGGTTTAAGGTGTTACTTTTATGCTGTTTCTCGAAA
* *
41665154 GAATTTCGGGTCATTCGAGATTGTTTAGTGTGTGTTTATGTGCC
66 GAATTTCAGGTCATTCGAGATTGTTTAGGGTGTGTTTATGTGCC
* *
41665198 TTTGTTTTGGTTTTGAAATGTAGCATTTGGATTAGGTTTAAGGTGTTACTTTTATGCTGTTTCTC
1 TTTGTTTTGGTATT-AAATCTAGCATTT-GA--AGGTTTAAGGTGTTACTTTTATGCTGTTTCTC
* * *
41665263 GAAAGAATTTCAGGTCATTCGAGTTTGTTTGGGGTGTGTTTTTGTG
62 GAAAGAATTTCAGGTCATTCGAGATTGTTTAGGGTGTGTTTATGTG
41665309 TTACAAAGTT
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
109 13 0.14
110 12 0.12
111 2 0.02
113 69 0.72
ACGTcount: A:0.18, C:0.08, G:0.26, T:0.48
Consensus pattern (109 bp):
TTTGTTTTGGTATTAAATCTAGCATTTGAAGGTTTAAGGTGTTACTTTTATGCTGTTTCTCGAAA
GAATTTCAGGTCATTCGAGATTGTTTAGGGTGTGTTTATGTGCC
Found at i:41665486 original size:156 final size:152
Alignment explanation
Indices: 41665195--41665528 Score: 429
Period size: 156 Copynumber: 2.2 Consensus size: 152
41665185 GTGTTTATGT
** * * *
41665195 GCCTTTGTTTTGGTTTTGAAATGTAGCATTTGGATTAGGTTTAAGGTGTTACTTTTATGCTGTTT
1 GCCTTTGTTTTGGTACTGAAATGTAGCACTTGAATTAGGTTTAAGGTGTTACTTTTATGCTCTTT
* * * **
41665260 CTCGAAAGAATTTCAGGTCATTCGAGTTTGTTTGGGGTGTGTTTTTGTGTTACAAAGTTCAAGTA
66 CTCGAAAGAATTTCAGGTCATTCGAGATTGTTTAGGGTGTGTTTATGCATTACAAAGTTCAAGTA
* *
41665325 TACTTAATTAT-GTTCATTTTCTG
131 CACTTAATTATAG-TCA-TATCTG
*
41665348 GCCTTCTGTTTTGGTACTGAAATGTAGCACTTGAATTAGGGTTTAAGTTGTTACTTTTACT-CTC
1 GCCTT-TGTTTTGGTACTGAAATGTAGCACTTGAATTA-GGTTTAAGGTGTTACTTTTA-TGCTC
* * *
41665412 TTTTTCGAAAGAATTTCAGGGTCATTTGAGATTGTTTAGTGTGTGTTTATGCATTACAAAGTTCA
63 TTTCTCGAAAGAATTTCA-GGTCATTCGAGATTGTTTAGGGTGTGTTTATGCATTACAAAGTTCA
41665477 AGTACACTTAATTATAGTCATATCTG
127 AGTACACTTAATTATAGTCATATCTG
*
41665503 GCCTTTTTATTTTGGTACTGAAATGT
1 GCC--TTTGTTTTGGTACTGAAATGT
41665529 GCATTTTGCT
Statistics
Matches: 157, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
153 5 0.03
154 28 0.18
155 46 0.29
156 75 0.48
157 3 0.02
ACGTcount: A:0.22, C:0.11, G:0.21, T:0.45
Consensus pattern (152 bp):
GCCTTTGTTTTGGTACTGAAATGTAGCACTTGAATTAGGTTTAAGGTGTTACTTTTATGCTCTTT
CTCGAAAGAATTTCAGGTCATTCGAGATTGTTTAGGGTGTGTTTATGCATTACAAAGTTCAAGTA
CACTTAATTATAGTCATATCTG
Found at i:41667901 original size:22 final size:22
Alignment explanation
Indices: 41667871--41667920 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
41667861 CATGCTGGTT
*
41667871 CTTTCTTTTCTC-TTGTTGATAG
1 CTTTTTTTTCTCATTGTTG-TAG
*
41667893 CTTTTTTTTTTCATTTGTTGTAG
1 CTTTTTTTTCTCA-TTGTTGTAG
41667916 CTTTT
1 CTTTT
41667921 GAAATATTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.42
23 8 0.33
24 6 0.25
ACGTcount: A:0.08, C:0.14, G:0.12, T:0.66
Consensus pattern (22 bp):
CTTTTTTTTCTCATTGTTGTAG
Found at i:41679395 original size:13 final size:14
Alignment explanation
Indices: 41679367--41679395 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41679357 AGTTATTGAG
41679367 ATAAGTTTTGATAT
1 ATAAGTTTTGATAT
41679381 ATAAGTTTT-ATAT
1 ATAAGTTTTGATAT
41679394 AT
1 AT
41679396 TGTTATTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (14 bp):
ATAAGTTTTGATAT
Found at i:41680971 original size:46 final size:46
Alignment explanation
Indices: 41680921--41681017 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
41680911 AATTGTGTTT
41680921 AATTTTAAACATAAAATTTATTTTTGAGTAGCTTAACTCATCAACA
1 AATTTTAAACATAAAATTTATTTTTGAGTAGCTTAACTCATCAACA
*
41680967 AATTTTAAACATAAAATTTCTTTTTGAGTAGCTTAACTCATCAACA
1 AATTTTAAACATAAAATTTATTTTTGAGTAGCTTAACTCATCAACA
41681013 AATTT
1 AATTT
41681018 AATTGTAATG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (46 bp):
AATTTTAAACATAAAATTTATTTTTGAGTAGCTTAACTCATCAACA
Found at i:41683609 original size:39 final size:39
Alignment explanation
Indices: 41683555--41683658 Score: 190
Period size: 39 Copynumber: 2.7 Consensus size: 39
41683545 AGCTTCAGTT
41683555 CTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTCCGGG
1 CTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTCCGGG
*
41683594 CTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTTCGGG
1 CTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTCCGGG
*
41683633 CTGCCGTTTAGCACTTATGTGCTTCA
1 CTTCCGTTTAGCACTTATGTGCTTCA
41683659 ACTAGATTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.38
Consensus pattern (39 bp):
CTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTCCGGG
Found at i:41684599 original size:14 final size:14
Alignment explanation
Indices: 41684580--41684606 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41684570 TATCCATAAT
41684580 TTAAAAATACCTTG
1 TTAAAAATACCTTG
41684594 TTAAAAATACCTT
1 TTAAAAATACCTT
41684607 AAGACGTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (14 bp):
TTAAAAATACCTTG
Found at i:41686655 original size:31 final size:31
Alignment explanation
Indices: 41686587--41686655 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
41686577 TAGTTTTTAA
41686587 CAAGTCCCTTTACTCTTCACCAATTCAAAATT
1 CAAGTCCCTTTACTCTTCA-CAATTCAAAATT
* * *
41686619 -TAGTCCCTTTACTTTTCA-AATTTTAAAATT
1 CAAGTCCCTTTACTCTTCACAA-TTCAAAATT
41686649 CAAGTCC
1 CAAGTCC
41686656 AATTGTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
29 2 0.06
30 8 0.26
31 21 0.68
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.39
Consensus pattern (31 bp):
CAAGTCCCTTTACTCTTCACAATTCAAAATT
Found at i:41688311 original size:13 final size:13
Alignment explanation
Indices: 41688293--41688317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41688283 TAATGTTGTA
41688293 AATATTAGATTAT
1 AATATTAGATTAT
41688306 AATATTAGATTA
1 AATATTAGATTA
41688318 AATGCTTCTA
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):
AATATTAGATTAT
Found at i:41691435 original size:22 final size:22
Alignment explanation
Indices: 41691349--41691450 Score: 82
Period size: 22 Copynumber: 4.6 Consensus size: 22
41691339 AGAGTCTTAC
*
41691349 CAGAGTACGCCAC-CAGAGCTAGA
1 CAGAATACGCCACACAG-GCTA-A
* * *
41691372 CATATTACGCCACAAAGGCT-A
1 CAGAATACGCCACACAGGCTAA
*** * *
41691393 CAGAATACATTATACAAGCTAA
1 CAGAATACGCCACACAGGCTAA
41691415 CAGAATACGCCACACAGGCTAA
1 CAGAATACGCCACACAGGCTAA
*
41691437 AAGAATACGCCACA
1 CAGAATACGCCACA
41691451 AGAGCTAGAT
Statistics
Matches: 60, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
21 13 0.22
22 31 0.52
23 14 0.23
24 2 0.03
ACGTcount: A:0.42, C:0.27, G:0.17, T:0.14
Consensus pattern (22 bp):
CAGAATACGCCACACAGGCTAA
Found at i:41691457 original size:22 final size:23
Alignment explanation
Indices: 41691409--41691457 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
41691399 ACATTATACA
*
41691409 AGCTAACAGAATACGCCACACAG
1 AGCTAAAAGAATACGCCACACAG
41691432 -GCTAAAAGAATACGCCACA-AG
1 AGCTAAAAGAATACGCCACACAG
41691453 AGCTA
1 AGCTA
41691458 GATCAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.10
Consensus pattern (23 bp):
AGCTAAAAGAATACGCCACACAG
Found at i:41692545 original size:46 final size:46
Alignment explanation
Indices: 41692485--41692942 Score: 801
Period size: 46 Copynumber: 10.0 Consensus size: 46
41692475 TTTGACATGA
* * * * * *
41692485 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* *** *
41692531 TGCCATGGTATCTTTCAACAATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
41692577 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
41692623 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
41692669 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
41692715 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
41692761 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
41692807 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
41692853 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
41692899 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
41692943 AGAGCACACT
Statistics
Matches: 399, Mismatches: 12, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
45 4 0.01
46 395 0.99
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:41698645 original size:24 final size:24
Alignment explanation
Indices: 41698613--41698663 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
41698603 TAATATAAAG
41698613 ACAAATGTATAG-TAAATAAAATAT
1 ACAAATGTATAGATAAA-AAAATAT
* * *
41698637 ACAAGTGTATGGATAAAAATATAT
1 ACAAATGTATAGATAAAAAAATAT
41698661 ACA
1 ACA
41698664 TTTGTAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (24 bp):
ACAAATGTATAGATAAAAAAATAT
Found at i:41698958 original size:20 final size:21
Alignment explanation
Indices: 41698924--41698964 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
41698914 GCAGGGGAAG
41698924 GAAAGAAAGAAAAAGAGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
*
41698945 GAAAGAAA-AAAAAGGGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
41698965 TCAAAGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAAAGAGAAAA
Found at i:41698970 original size:21 final size:21
Alignment explanation
Indices: 41698925--41698971 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
41698915 CAGGGGAAGG
*
41698925 AAAGAAAGAAAAAGAGAAAAG
1 AAAGAAAGAAAAAGAGAAAAC
*
41698946 AAAGAAA-AAAAAGGGAAAATC
1 AAAGAAAGAAAAAGAGAAAA-C
41698967 AAAGA
1 AAAGA
41698972 TGTGAAGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (21 bp):
AAAGAAAGAAAAAGAGAAAAC
Found at i:41700849 original size:54 final size:54
Alignment explanation
Indices: 41700779--41700915 Score: 247
Period size: 54 Copynumber: 2.5 Consensus size: 54
41700769 ATTGTCGTTG
41700779 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATAAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATAAGTTTATATTA
* *
41700833 CAGGGGATTTAGCCTGGATTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATAAGTTTATATTA
*
41700887 CAGGGGATTTAGCCTGGACTAGTAATCCC
1 CAGGGGATTTAGCCTGGACTGGTAATCCC
41700916 ACTGTAAGGA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (54 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATAAGTTTATATTA
Found at i:41701021 original size:46 final size:46
Alignment explanation
Indices: 41700949--41701219 Score: 524
Period size: 46 Copynumber: 5.9 Consensus size: 46
41700939 AGTGTGCTCT
* *
41700949 CTGAGATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
41700995 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
41701041 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
41701087 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
41701133 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
41701179 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATG
41701220 AGTTTATATT
Statistics
Matches: 223, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 223 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:41701350 original size:46 final size:46
Alignment explanation
Indices: 41701298--41701433 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
41701288 GCTCTCTGAG
* * *
41701298 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
41701344 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
41701390 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
41701434 TCAAAGATAA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 1 0.01
46 79 0.99
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:41706801 original size:23 final size:23
Alignment explanation
Indices: 41706772--41706817 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
41706762 TAACTCTTTG
41706772 TTGTATTGATATCTCTCATTATT
1 TTGTATTGATATCTCTCATTATT
41706795 TTGTATTGATATCTCTCATTATT
1 TTGTATTGATATCTCTCATTATT
41706818 GATACTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.57
Consensus pattern (23 bp):
TTGTATTGATATCTCTCATTATT
Found at i:41716391 original size:21 final size:21
Alignment explanation
Indices: 41716365--41716405 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41716355 ATCTGCTCAA
* *
41716365 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
41716386 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
41716406 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:41722534 original size:22 final size:22
Alignment explanation
Indices: 41722509--41722550 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41722499 ATTATTCTTT
*
41722509 TTTTTTCACAATTTTGTTGTTG
1 TTTTCTCACAATTTTGTTGTTG
**
41722531 TTTTCTCACTGTTTTGTTGT
1 TTTTCTCACAATTTTGTTGT
41722551 CATTATGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (22 bp):
TTTTCTCACAATTTTGTTGTTG
Found at i:41722982 original size:23 final size:23
Alignment explanation
Indices: 41722945--41723004 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
41722935 ATATTTTTAA
41722945 ATTTATTTTCAAATAGTTTGGAAAT
1 ATTTATTTT--AATAGTTTGGAAAT
* * *
41722970 ATTTATTTTAATATTTTTGATAT
1 ATTTATTTTAATAGTTTGGAAAT
41722993 ATTATATTTTAA
1 ATT-TATTTTAA
41723005 AATTCTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.45
24 8 0.26
25 9 0.29
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (23 bp):
ATTTATTTTAATAGTTTGGAAAT
Found at i:41723000 original size:24 final size:23
Alignment explanation
Indices: 41722968--41723017 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
41722958 TAGTTTGGAA
*
41722968 ATATTTATTTTAATATT-TTTGAT
1 ATATTTATTTTAAAATTCTTT-AT
41722991 ATATTATATTTTAAAATTCTTTAT
1 ATATT-TATTTTAAAATTCTTTAT
41723015 ATA
1 ATA
41723018 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 16 0.67
25 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
ATATTTATTTTAAAATTCTTTAT
Found at i:41731874 original size:113 final size:113
Alignment explanation
Indices: 41731673--41731890 Score: 282
Period size: 113 Copynumber: 1.9 Consensus size: 113
41731663 TTTGAAGAAC
* * *
41731673 GAAAACGCGGGAGAGTTTTGAATTTTTTTGTTTTGTTTGATGGGTTTAAACCTTCATCTAATCCC
1 GAAAACGCGGGAGAGCTTTGAA--TTTTTGTTTTGTTTGATAGGTTCAAACCTTCATCTAATCCC
* * *
41731738 TTTGGTTTTTTAATATTTAAAATTTAGTTCCTCTATTTTTAATAAGGAGGAAA
64 TGTGATTTTTTAATATTTAAAATTCAG-TCCT-T-TTTTTAATAAGGAGGAAA
*
41731791 GAAAACGCGGGAGAGCTTTGAA-TTTT-TTTTGTTT-ATAGG-TCAAACTCTTCTTCTAATCCCT
1 GAAAACGCGGGAGAGCTTTGAATTTTTGTTTTGTTTGATAGGTTCAAAC-CTTCATCTAATCCCT
*
41731852 GTGATTTTTTAGTATTTAAAATTCAGTCCTTTTTTTAAT
65 GTGATTTTTTAATATTTAAAATTCAGTCCTTTTTTTAAT
41731891 CTCATGAATT
Statistics
Matches: 91, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
110 8 0.09
111 1 0.01
112 9 0.10
113 40 0.44
114 8 0.09
115 4 0.04
118 21 0.23
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (113 bp):
GAAAACGCGGGAGAGCTTTGAATTTTTGTTTTGTTTGATAGGTTCAAACCTTCATCTAATCCCTG
TGATTTTTTAATATTTAAAATTCAGTCCTTTTTTTAATAAGGAGGAAA
Found at i:41732963 original size:14 final size:14
Alignment explanation
Indices: 41732946--41732983 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
41732936 AATATAATTT
41732946 TAAAAATTAA-AATA
1 TAAAAATTAATAA-A
41732960 TAAAAA-TAATAAA
1 TAAAAATTAATAAA
41732973 TAAAAATTAAT
1 TAAAAATTAAT
41732984 TTAAAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAAAATTAATAAA
Found at i:41733432 original size:21 final size:21
Alignment explanation
Indices: 41733381--41733432 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
41733371 TATATATAAG
* *
41733381 AATAAAATAATAATTTCATAT
1 AATAAAACAGTAATTTCATAT
41733402 AATAAAACAGTAATTTCATAT
1 AATAAAACAGTAATTTCATAT
41733423 AATAAAACAG
1 AATAAAACAG
41733433 GATGGAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.31
Consensus pattern (21 bp):
AATAAAACAGTAATTTCATAT
Found at i:41737860 original size:16 final size:16
Alignment explanation
Indices: 41737834--41737909 Score: 89
Period size: 16 Copynumber: 4.8 Consensus size: 16
41737824 AAACAATACT
*
41737834 TAGAACTGTAATGGAA
1 TAGAGCTGTAATGGAA
* **
41737850 TAGGGCTGTAATTTAA
1 TAGAGCTGTAATGGAA
* *
41737866 TAGAGTTGTAATAGAA
1 TAGAGCTGTAATGGAA
41737882 TAGAGCTGTAATGGAA
1 TAGAGCTGTAATGGAA
*
41737898 TAGAACTGTAAT
1 TAGAGCTGTAAT
41737910 AAGTAATTCA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.30
Consensus pattern (16 bp):
TAGAGCTGTAATGGAA
Found at i:41737900 original size:32 final size:32
Alignment explanation
Indices: 41737834--41737910 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
41737824 AAACAATACT
* * **
41737834 TAGAACTGTAATGGAATAGGGCTGTAATTTAA
1 TAGAACTGTAATAGAATAGAGCTGTAATGGAA
**
41737866 TAGAGTTGTAATAGAATAGAGCTGTAATGGAA
1 TAGAACTGTAATAGAATAGAGCTGTAATGGAA
41737898 TAGAACTGTAATA
1 TAGAACTGTAATA
41737911 AGTAATTCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (32 bp):
TAGAACTGTAATAGAATAGAGCTGTAATGGAA
Found at i:41737948 original size:46 final size:44
Alignment explanation
Indices: 41737891--41737983 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
41737881 ATAGAGCTGT
*
41737891 AATGGAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAT-AGT-ATTCAACTGTTTGGTTGAAAGG
***
41737937 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAAAGG
1 AATGGAATAGAACTGTAATAGTATTCAACTGTTTGGTTGAAAGG
41737981 AAT
1 AAT
41737984 AATGATGTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 21 0.49
45 3 0.07
46 19 0.44
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.34
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCAACTGTTTGGTTGAAAGG
Found at i:41738178 original size:17 final size:17
Alignment explanation
Indices: 41738156--41738188 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41738146 AATTATTATT
41738156 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
41738173 AAATATAATTTAATAA
1 AAATATAATTTAATAA
41738189 CATTCATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:41738716 original size:18 final size:18
Alignment explanation
Indices: 41738693--41738727 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41738683 ACGTGGTAGT
*
41738693 CCAACTAGATTTTAAGTG
1 CCAACTAGATCTTAAGTG
41738711 CCAACTAGATCTTAAGT
1 CCAACTAGATCTTAAGT
41738728 ATATCTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (18 bp):
CCAACTAGATCTTAAGTG
Found at i:41738786 original size:40 final size:40
Alignment explanation
Indices: 41738735--41738979 Score: 382
Period size: 40 Copynumber: 6.1 Consensus size: 40
41738725 AGTATATCTG
* * *
41738735 TTAATACATACTTCATCCGGGTAAATTATACAATTTTCTG
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
*
41738775 TTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTA
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
* * *
41738815 TTAATACATACTTCATCCGGATAAATTATACAGTTTTCTG
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
*
41738855 TTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTA
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
*
41738895 TTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTA
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
* * *
41738935 TTAATATATACTTCATCCGGATAAATTATACAGTTTTCTA
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
41738975 TTAAT
1 TTAAT
41738980 GTGCTTGTGA
Statistics
Matches: 189, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 189 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (40 bp):
TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
Found at i:41738946 original size:120 final size:120
Alignment explanation
Indices: 41738731--41738979 Score: 444
Period size: 120 Copynumber: 2.1 Consensus size: 120
41738721 CTTAAGTATA
* *
41738731 TCTGTTAATACATACTTCATCCGGGTAAATTATACAATTTTCTGTTAATACATACTTTACCCGGG
1 TCTGTTAATACATACTTCACCCGGGTAAATTATACAATTTTCTATTAATACATACTTTACCCGGG
41738796 TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
66 TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
* *
41738851 TCTGTTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTATTAATACATACTTTACCCGGG
1 TCTGTTAATACATACTTCACCCGGGTAAATTATACAATTTTCTATTAATACATACTTTACCCGGG
*
41738916 TAAATTATACAGTTTTCTATTAATATATACTTCATCCGGATAAATTATACAGTTT
66 TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
*
41738971 TCTATTAAT
1 TCTGTTAAT
41738980 GTGCTTGTGA
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 123 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.41
Consensus pattern (120 bp):
TCTGTTAATACATACTTCACCCGGGTAAATTATACAATTTTCTATTAATACATACTTTACCCGGG
TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
Found at i:41745678 original size:25 final size:25
Alignment explanation
Indices: 41745644--41745693 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
41745634 GTTGTAGTCG
41745644 CCTAATAGTCAAGGTGTTTCAGTTT
1 CCTAATAGTCAAGGTGTTTCAGTTT
41745669 CCTAATAGTCAAGGTGTTTCAGTTT
1 CCTAATAGTCAAGGTGTTTCAGTTT
41745694 ACTTTCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (25 bp):
CCTAATAGTCAAGGTGTTTCAGTTT
Found at i:41749397 original size:18 final size:17
Alignment explanation
Indices: 41749362--41749394 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41749352 CTTTTTATTC
41749362 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
41749379 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
41749395 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:41749821 original size:15 final size:14
Alignment explanation
Indices: 41749803--41749833 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
41749793 TTAATTTATT
41749803 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
41749818 TAATAATAATCTAA
1 TAATAATAATCTAA
41749832 TA
1 TA
41749834 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:41749844 original size:21 final size:20
Alignment explanation
Indices: 41749820--41749888 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
41749810 AATGCTAATA
41749820 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
41749841 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
41749860 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
41749881 ATAATAAT
1 ATAATAAT
41749889 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:41757126 original size:31 final size:29
Alignment explanation
Indices: 41757080--41757139 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
41757070 TTTTTAATTT
41757080 AACTCGAACAATTTCACTTGATTCGACTC
1 AACTCGAACAATTTCACTTGATTCGACTC
* *
41757109 AACTCGACACAAATTTCATTTTATTCGACTC
1 AACTCGA-AC-AATTTCACTTGATTCGACTC
41757140 GATTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 7 0.26
30 2 0.07
31 18 0.67
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.33
Consensus pattern (29 bp):
AACTCGAACAATTTCACTTGATTCGACTC
Found at i:41763756 original size:3 final size:3
Alignment explanation
Indices: 41763748--41763795 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
41763738 ATCACATGTT
41763748 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41763796 GGATGTAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41763873 original size:73 final size:73
Alignment explanation
Indices: 41763796--41763980 Score: 361
Period size: 73 Copynumber: 2.5 Consensus size: 73
41763786 ATTATTATTA
41763796 GGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTA
1 GGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTA
41763861 TTTTAAGT
66 TTTTAAGT
41763869 GGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTA
1 GGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTA
41763934 TTTTAAGT
66 TTTTAAGT
*
41763942 GGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 GGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTT
41763981 GTCAAGTTGT
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (73 bp):
GGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTTA
TTTTAAGT
Found at i:41768206 original size:3 final size:3
Alignment explanation
Indices: 41768198--41768259 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
41768188 ATCACATGTT
41768198 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41768246 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
41768260 TGGATGTAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41768377 original size:72 final size:72
Alignment explanation
Indices: 41768260--41768443 Score: 359
Period size: 72 Copynumber: 2.6 Consensus size: 72
41768250 TATTATTATT
41768260 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
41768325 TTTTAAG
66 TTTTAAG
41768332 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
41768397 TTTTAAG
66 TTTTAAG
*
41768404 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTT
41768444 GTCAAGTTGT
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 111 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.42
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:41769732 original size:7 final size:7
Alignment explanation
Indices: 41769720--41769756 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
41769710 TAGGACTCAA
41769720 AAATATC
1 AAATATC
41769727 AAATATC
1 AAATATC
41769734 AAATATC
1 AAATATC
41769741 AAATATC
1 AAATATC
41769748 AAATATC
1 AAATATC
41769755 AA
1 AA
41769757 GAACAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATATC
Found at i:41776266 original size:21 final size:21
Alignment explanation
Indices: 41776240--41776280 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41776230 ATCTGCTCAA
* *
41776240 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
41776261 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
41776281 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:41786059 original size:25 final size:25
Alignment explanation
Indices: 41786014--41786085 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 25
41786004 TCACTTCTCG
41786014 CTAAGCTTGCAGCTTTG-ACATCTTA
1 CTAAGCTTGCAGC-TTGCACATCTTA
* *
41786039 CTAAGCTTGCAGCTTGCACATTTTTG
1 CTAAGCTTGCAGCTTGCACA-TCTTA
* *
41786065 CTGAGCCTGCAGCTTGCACAT
1 CTAAGCTTGCAGCTTGCACAT
41786086 TGGAAAGCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.07
25 17 0.41
26 21 0.51
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.33
Consensus pattern (25 bp):
CTAAGCTTGCAGCTTGCACATCTTA
Found at i:41795875 original size:24 final size:24
Alignment explanation
Indices: 41795843--41795892 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
41795833 AGTAACGATG
41795843 TATGTGCATGAATATGGAACTAAT
1 TATGTGCATGAATATGGAACTAAT
41795867 TATGTGCATGAATATGGAACTAAT
1 TATGTGCATGAATATGGAACTAAT
41795891 TA
1 TA
41795893 CACAGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (24 bp):
TATGTGCATGAATATGGAACTAAT
Found at i:41796196 original size:15 final size:15
Alignment explanation
Indices: 41796176--41796253 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
41796166 TTTATGGAAA
41796176 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
41796191 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
41796205 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
41796221 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
41796235 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
41796251 ATC
1 ATC
41796254 GAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:41796213 original size:30 final size:30
Alignment explanation
Indices: 41796172--41796253 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
41796162 CATATTTATG
*
41796172 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
41796202 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
41796232 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
41796254 GAGATATTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:41800254 original size:15 final size:15
Alignment explanation
Indices: 41800236--41800284 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
41800226 AGCAGGATAA
41800236 TATCAAAGATATGGG
1 TATCAAAGATATGGG
* *
41800251 TATCAAATAT-TGGA
1 TATCAAAGATATGGG
*
41800265 AAGTCAAAGATATGGG
1 TA-TCAAAGATATGGG
41800281 TATC
1 TATC
41800285 GAGATATTGG
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 4 0.15
15 18 0.69
16 4 0.15
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (15 bp):
TATCAAAGATATGGG
Found at i:41822573 original size:9 final size:9
Alignment explanation
Indices: 41822559--41822592 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
41822549 TTAAATAATT
41822559 ATTTTAAAA
1 ATTTTAAAA
41822568 ATTTTAAAA
1 ATTTTAAAA
*
41822577 A-TTAAAAA
1 ATTTTAAAA
41822585 ATTTTAAA
1 ATTTTAAA
41822593 TATTAAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:41822586 original size:17 final size:17
Alignment explanation
Indices: 41822564--41822599 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
41822554 TAATTATTTT
41822564 AAAAATTTTAAAAATTA
1 AAAAATTTTAAAAATTA
*
41822581 AAAAATTTTAAATATTA
1 AAAAATTTTAAAAATTA
41822598 AA
1 AA
41822600 TTGGTGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAATTTTAAAAATTA
Found at i:41823791 original size:100 final size:101
Alignment explanation
Indices: 41823617--41823821 Score: 349
Period size: 100 Copynumber: 2.0 Consensus size: 101
41823607 GTTAGGTAGA
* * *
41823617 ATTTTGCTTTTAATTTGATGAATTTATTTTACTCTGAGTGAGCTAGCGGTTGTATTTGTGATGAT
1 ATTTTGCGTTTAATTTAATGAATTTATTTTACTCGGAGTGAGCTAGCGGTTGTATTTGTGATGAT
* *
41823682 ATATTGTTAATTGATTAGAGATTAGTATTTGTTATG
66 ATAGTGTTAATTGATTACAGATTAGTATTTGTTATG
*
41823718 ATTTTGCGTTTAATTTAATGAATTTA-TTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGAT
1 ATTTTGCGTTTAATTTAATGAATTTATTTTACTCGGAGTGAGCTAGCGGTTGTATTTGTGATGAT
41823782 ATAGTGTTAATTGATTACAGATTAGTATTTGTTATG
66 ATAGTGTTAATTGATTACAGATTAGTATTTGTTATG
41823818 ATTT
1 ATTT
41823822 AGTATTGATG
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
100 74 0.76
101 24 0.24
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.49
Consensus pattern (101 bp):
ATTTTGCGTTTAATTTAATGAATTTATTTTACTCGGAGTGAGCTAGCGGTTGTATTTGTGATGAT
ATAGTGTTAATTGATTACAGATTAGTATTTGTTATG
Found at i:41831871 original size:23 final size:23
Alignment explanation
Indices: 41831845--41831901 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
41831835 AGGTGATTAT
41831845 ATATAAAATTATAATAAATTAAA
1 ATATAAAATTATAATAAATTAAA
*
41831868 ATATATAAATT-TATTAAATTAAA
1 ATATA-AAATTATAATAAATTAAA
41831891 ATA-AATAATTA
1 ATATAA-AATTA
41831902 AATTTACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.03
22 5 0.17
23 19 0.63
24 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATAAAATTATAATAAATTAAA
Found at i:41832865 original size:19 final size:19
Alignment explanation
Indices: 41832833--41832900 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 19
41832823 TTGAGTTAAT
41832833 TTTTTTAGATAATTATGTTTA
1 TTTTTTA-A-AATTATGTTTA
* *
41832854 TTTTTTAAAATTAAGAGTTA
1 TTTTTTAAAATTATG-TTTA
**
41832874 TTTTTTTAATTTTATGTATTA
1 -TTTTTTAAAATTATGT-TTA
41832895 TTTTTT
1 TTTTTT
41832901 CATTTAATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
19 6 0.16
20 10 0.26
21 22 0.58
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (19 bp):
TTTTTTAAAATTATGTTTA
Found at i:41832912 original size:19 final size:20
Alignment explanation
Indices: 41832875--41832912 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41832865 TAAGAGTTAT
*
41832875 TTTTTTAATTTTATGTATTA
1 TTTTTTAATTTAATGTATTA
*
41832895 TTTTTTCATTTAAT-TATT
1 TTTTTTAATTTAATGTATT
41832913 TTCACATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTTTTAATTTAATGTATTA
Found at i:41836840 original size:21 final size:21
Alignment explanation
Indices: 41836816--41836863 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
41836806 CCAAGAAGCT
41836816 CTTGGTTCATCAAATGAAAAC
1 CTTGGTTCATCAAATGAAAAC
**
41836837 CTTGAATCATCAAATGAAAAC
1 CTTGGTTCATCAAATGAAAAC
41836858 CTTGGT
1 CTTGGT
41836864 GGAGCTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (21 bp):
CTTGGTTCATCAAATGAAAAC
Found at i:41837678 original size:25 final size:24
Alignment explanation
Indices: 41837647--41837705 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 24
41837637 TATATGGAAA
41837647 AAAAAATTAAATTTATTAAACTATT
1 AAAAAATTAAATTTATTAAA-TATT
* * *
41837672 AATAAATTTACATTTATTAAATTTT
1 AA-AAAATTAAATTTATTAAATATT
41837697 AAAAAATTA
1 AAAAAATTA
41837706 TAAAATAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 6 0.21
25 7 0.24
26 16 0.55
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (24 bp):
AAAAAATTAAATTTATTAAATATT
Found at i:41837802 original size:99 final size:100
Alignment explanation
Indices: 41837688--41837884 Score: 351
Period size: 100 Copynumber: 2.0 Consensus size: 100
41837678 TTTACATTTA
* *
41837688 TTAAATTTTAAAAAATTATAAAATAGTCACTAAATTATCTGAAA-ATTTTATTTAAGTCATTGGG
1 TTAAATTTTAAAAAATTACAAAATAATCACTAAATTATCTGAAAGATTTTATTTAAGTCATTGGG
*
41837752 TTATTAAGTTTTTATTTAAGCAACGGTTCATATGG
66 TTATCAAGTTTTTATTTAAGCAACGGTTCATATGG
*
41837787 TTAAATTTTAAAAAATTACAAAATAATCACTAAATTATCTGAAAGATTTTATTTAATTCATTGGG
1 TTAAATTTTAAAAAATTACAAAATAATCACTAAATTATCTGAAAGATTTTATTTAAGTCATTGGG
41837852 TTATCAAGTTTTTATTTAAGCAACGGTTCATAT
66 TTATCAAGTTTTTATTTAAGCAACGGTTCATAT
41837885 AGTGGGCCAA
Statistics
Matches: 93, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
99 42 0.45
100 51 0.55
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (100 bp):
TTAAATTTTAAAAAATTACAAAATAATCACTAAATTATCTGAAAGATTTTATTTAAGTCATTGGG
TTATCAAGTTTTTATTTAAGCAACGGTTCATATGG
Found at i:41838616 original size:24 final size:25
Alignment explanation
Indices: 41838570--41838616 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
41838560 TACAATGGCT
*
41838570 AATTTTTAAAAGTAAAGATTAATGA
1 AATTTTTAAAAGTAAAGACTAATGA
* *
41838595 AATTTTTAACAG-AATGACTAAT
1 AATTTTTAAAAGTAAAGACTAAT
41838617 TTGTTTCTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (25 bp):
AATTTTTAAAAGTAAAGACTAATGA
Found at i:41841634 original size:20 final size:19
Alignment explanation
Indices: 41841576--41841636 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
41841566 ATAATTCTAA
*
41841576 AAAATTATA-AAAAATCTT
1 AAAATTATATAAAAATATT
* * *
41841594 AAAAATAAATATAAATGATT
1 AAAATTATATAAAAAT-ATT
41841614 AAAATTATATTAAAAATATT
1 AAAATTATA-TAAAAATATT
41841634 AAA
1 AAA
41841637 TCAAAAGCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
18 7 0.21
19 5 0.15
20 15 0.45
21 6 0.18
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATTATATAAAAATATT
Found at i:41844695 original size:10 final size:10
Alignment explanation
Indices: 41844680--41844704 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41844670 ATTTTTTTAT
41844680 TTTATAATAA
1 TTTATAATAA
41844690 TTTATAATAA
1 TTTATAATAA
41844700 TTTAT
1 TTTAT
41844705 TTAATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTATAATAA
Found at i:41853596 original size:33 final size:33
Alignment explanation
Indices: 41853554--41853619 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
41853544 TTAGATGGTA
41853554 GCTTACACTAATACACATAACGATAAATTATTT
1 GCTTACACTAATACACATAACGATAAATTATTT
*
41853587 GCTTACACTAATACGCATAACGATAAATTATTT
1 GCTTACACTAATACACATAACGATAAATTATTT
41853620 ATGTTTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (33 bp):
GCTTACACTAATACACATAACGATAAATTATTT
Found at i:41858728 original size:15 final size:16
Alignment explanation
Indices: 41858694--41858731 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41858684 AAAATTTAAT
*
41858694 TAATTAATTTAAACAA
1 TAATAAATTTAAACAA
*
41858710 TAATAAATTTATA-AA
1 TAATAAATTTAAACAA
41858725 TAATAAA
1 TAATAAA
41858732 AGAATCAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAAATTTAAACAA
Found at i:41858885 original size:12 final size:12
Alignment explanation
Indices: 41858868--41858892 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41858858 ATTTTACTCT
41858868 TTCAACTAAAAA
1 TTCAACTAAAAA
41858880 TTCAACTAAAAA
1 TTCAACTAAAAA
41858892 T
1 T
41858893 ACATGTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (12 bp):
TTCAACTAAAAA
Found at i:41863535 original size:13 final size:13
Alignment explanation
Indices: 41863517--41863541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41863507 AGTATCGAAT
41863517 TTTTTAATTAATG
1 TTTTTAATTAATG
41863530 TTTTTAATTAAT
1 TTTTTAATTAAT
41863542 AAACATCATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:41864442 original size:16 final size:17
Alignment explanation
Indices: 41864411--41864446 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
41864401 TAGGATTTCT
*
41864411 AAATTGAAAAAGAAAAA
1 AAATTGAAAAAAAAAAA
41864428 AAATT-AAAAAAAAAAA
1 AAATTGAAAAAAAAAAA
41864444 AAA
1 AAA
41864447 GCTTTGTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (17 bp):
AAATTGAAAAAAAAAAA
Found at i:41871703 original size:44 final size:44
Alignment explanation
Indices: 41871654--41871880 Score: 160
Period size: 44 Copynumber: 5.2 Consensus size: 44
41871644 AGTTACAGAT
*
41871654 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
* * * ** * * * * *
41871698 CTTGCC-TCTTTCGGTTGTGATG-G-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCTAC-ATTGACA-GCGAAGCAGATCGAAGACACAA-AC
*
41871742 CTTGCCTTTCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
* * * ** * * * * *
41871786 CTTGCC-TCTTTCGGTTGTGATG-G-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCTAC-ATTGACA-GCGAAGCAGATCGAAGACACAA-AC
41871830 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
41871874 CTTGCCT
1 CTTGCCT
41871881 CTTTCGGTTG
Statistics
Matches: 129, Mismatches: 42, Indels: 24
0.66 0.22 0.12
Matches are distributed among these distances:
43 37 0.29
44 55 0.43
45 37 0.29
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (44 bp):
CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
Found at i:41871922 original size:44 final size:44
Alignment explanation
Indices: 41871698--41871924 Score: 167
Period size: 44 Copynumber: 5.2 Consensus size: 44
41871688 AGACACAAAC
*
41871698 CTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTTTCGGTTGTGATCGAGCTGGTTGAAGACAAAAGAT
* ** * * * * * *
41871742 CTTGCCT-TTCTAC-ATTGACAGCGAAGCAGATCGAAGACACAA-AC
1 CTTGCCTCTT-T-CGGTTGTGATCG-AGCTGGTTGAAGACAAAAGAT
*
41871786 CTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTTTCGGTTGTGATCGAGCTGGTTGAAGACAAAAGAT
* * * ** * * * * * *
41871830 CTTGCCTTCCTAC-ATTGACAGCGAAGCAGATCGAAGACACAA-AC
1 CTTGCC-TCTTTCGGTTGTGATCG-AGCTGGTTGAAGACAAAAGAT
*
41871874 CTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTTTCGGTTGTGATCGAGCTGGTTGAAGACAAAAGAT
41871918 CTTGCCT
1 CTTGCCT
41871925 TCCTACATTA
Statistics
Matches: 129, Mismatches: 44, Indels: 20
0.67 0.23 0.10
Matches are distributed among these distances:
43 35 0.27
44 59 0.46
45 35 0.27
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (44 bp):
CTTGCCTCTTTCGGTTGTGATCGAGCTGGTTGAAGACAAAAGAT
Found at i:41872081 original size:86 final size:88
Alignment explanation
Indices: 41871650--41872077 Score: 591
Period size: 88 Copynumber: 4.9 Consensus size: 88
41871640 ATGAAGTTAC
*
41871650 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
41871715 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
*
41871738 AGATCTTGCCTTTCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
41871803 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
41871826 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
*
41871891 TGATAGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * ** *
41871914 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCGTCCATCGATT
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGGTT
* * * **
41871977 G-CAGTGGAGCTAGTTAAAGA-AGC
65 GTGA-TGGAGCTGGTTGAAGACAAA
* * * * **
41872000 AGATCTTGCCTTCCTGCATTAACAGCAAAGCAGATC-AA-AAACAAAGCCTTGCCTCCATCGGTT
1 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGGTT
*
41872063 G-CATTGGAGCTGGTT
65 GTGA-TGGAGCTGGTT
41872078 AAAGGTTACA
Statistics
Matches: 316, Mismatches: 21, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
85 3 0.01
86 75 0.24
87 28 0.09
88 210 0.66
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (88 bp):
AGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:41872326 original size:43 final size:44
Alignment explanation
Indices: 41872226--41872331 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
41872216 GATCTTGTCC
* * *
41872226 CCCTGAAGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCT
1 CCCTGAAGTTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
* * **
41872270 CCCCG-AGATTACAGCGGAGCAGATCGAAGACA-CTATCCTATCT
1 CCCTGAAG-TTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
41872313 CCCTGAAGTTACAGTGGAG
1 CCCTGAAGTTACAGTGGAG
41872332 TGGGTTAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
43 24 0.47
44 27 0.53
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (44 bp):
CCCTGAAGTTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
Found at i:41873963 original size:3 final size:3
Alignment explanation
Indices: 41873955--41873993 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
41873945 GATTTAGTCC
41873955 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41873994 CAAACCTTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41874262 original size:88 final size:88
Alignment explanation
Indices: 41873994--41874271 Score: 457
Period size: 88 Copynumber: 3.1 Consensus size: 88
41873984 TTATTATTAT
41873994 CAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATT
1 CAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATT
41874059 AACAGCGAAGCAGATCGAAGACA
66 AACAGCGAAGCAGATCGAAGACA
* * * *
41874082 CAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGAAAAAAAGATCTTGCCTTCCTGCAT
1 CAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAG-ACAAAAGATCTTGCCTTCCTACAT
* * * *
41874147 TGACAGCGAAGCAGGTCGAAAAGA
65 TAACAGCGAAGCAGATCGAAGACA
* *
41874171 CAAATCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGGAGACAAAAGATCTTGCCTTCCTACATT
1 CAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATT
41874236 AACAGCGAAGCAGATCGAAGACA
66 AACAGCGAAGCAGATCGAAGACA
41874259 CAAACCTTGCCTC
1 CAAACCTTGCCTC
41874272 ATCGATTGCA
Statistics
Matches: 170, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
88 92 0.54
89 78 0.46
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (88 bp):
CAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATT
AACAGCGAAGCAGATCGAAGACA
Found at i:41874811 original size:44 final size:43
Alignment explanation
Indices: 41874758--41875175 Score: 235
Period size: 44 Copynumber: 9.8 Consensus size: 43
41874748 AAAGCCAGAG
*
41874758 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGGATAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAA-GATAGTA
* * * * * *
41874802 ATCCTATCTCCTTGAGATTACAATGGAGCGGAT-TA-A-AG-G
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAGATAGTA
* * * *
41874841 ATCTTATCTCTCTGA-AGTTACAGTAGAGAAGATC-ACATCAG--
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAGAT-AGTA
* * * *
41874882 GTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTCA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATC-AAGATA-GT-A
*
41874927 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTA
1 -ATCTTATCTCCCTGAGATTACAGTGGAGCAGATC-AAGATAGTA
* * * * * *
41874972 ATCCTATCTCCTTGAGATTACAATGGAGCGGAT-TA-A-AG-G
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAGATAGTA
* * * *
41875011 ATCTTATCTCTCTGA-AGTTACAGTAGAGAAGATC-ACATCAG--
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAGAT-AGTA
* * * *
41875052 GTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTCA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATC-AAGATA-GT-A
* * * **
41875097 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAG-A
1 -ATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TCAAGATAGTA
*
41875141 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATC
1 -ATCTTATCTCCCTGAGATTACAGTGGAGCAGATC
41875176 NNNNNNNNNN
Statistics
Matches: 286, Mismatches: 59, Indels: 59
0.71 0.15 0.15
Matches are distributed among these distances:
38 2 0.01
39 50 0.17
40 6 0.02
41 56 0.20
42 7 0.02
43 6 0.02
44 89 0.31
45 1 0.00
46 67 0.23
47 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAGATAGTA
Found at i:41874944 original size:170 final size:170
Alignment explanation
Indices: 41874756--41875130 Score: 732
Period size: 170 Copynumber: 2.2 Consensus size: 170
41874746 CTAAAGCCAG
*
41874756 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
41874821 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
41874886 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
131 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
41874926 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
41874991 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
41875056 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
131 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
*
41875096 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGAT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGAT
41875131 TGAAGCCAGA
Statistics
Matches: 203, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 203 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (170 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
Found at i:41874950 original size:46 final size:44
Alignment explanation
Indices: 41874878--41875175 Score: 206
Period size: 46 Copynumber: 6.9 Consensus size: 44
41874868 GAAGATCACA
* *
41874878 TCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATT
1 TCAGATCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-T
* *
41874924 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-
1 TCAGATCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAT
* * * * * *
41874967 T-AGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG--
1 TCAG--ATCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAT
* * *
41875010 ---GATCTTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--ACA-
1 TCAGATCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGAT
* *
41875048 TCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATT
1 TCAGATCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-T
* * * ** **
41875094 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCC
1 TCAGATCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAT
** * *
41875138 AGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATC
1 TCAGATCTTATCTCCCTGAGATTACAGTGGAACAGATC
41875176 NNNNNNNNNN
Statistics
Matches: 200, Mismatches: 37, Indels: 32
0.74 0.14 0.12
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 23 0.12
40 1 0.00
41 28 0.14
42 3 0.01
43 2 0.01
44 67 0.34
45 1 0.00
46 73 0.37
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (44 bp):
TCAGATCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAT
Found at i:41882485 original size:13 final size:13
Alignment explanation
Indices: 41882467--41882491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41882457 ATATTGTTTT
41882467 TTCAGTGTTTTAA
1 TTCAGTGTTTTAA
41882480 TTCAGTGTTTTA
1 TTCAGTGTTTTA
41882492 GTTGGATTTT
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:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (13 bp):
TTCAGTGTTTTAA
Found at i:41891071 original size:139 final size:138
Alignment explanation
Indices: 41890821--41891149 Score: 622
Period size: 139 Copynumber: 2.4 Consensus size: 138
41890811 TTCCACATTT
* *
41890821 TAACAAATTGATACCTATATAAGCAAAGATCAAAACTTTAGCATAATTGATAACAGCCATGAAAT
1 TAACAAATTGATACCTACATAAGCAAAGATCAAAACTTTAACATAATTGATAACAGCCATGAAAT
*
41890886 CAATGTAACTCTCAAAACATTAACAAAATGCACTCAATCAGTGCCAATTTTCTACATTTTTTAAC
66 CAATGTAACTCTCAAAACATTAACAAAATGCACTCAATCAGTGCCAATTTTCTACA-TTTGTAAC
41890951 AGTGTAAGG
130 AGTGTAAGG
41890960 TAACAAATTGATACCTACATAAGCAAAGATCAAAACTTTAACATAATTGATAACAGCCATGAAAT
1 TAACAAATTGATACCTACATAAGCAAAGATCAAAACTTTAACATAATTGATAACAGCCATGAAAT
41891025 CAATGTAACTCTCAAAACATTAACAAAATGCACTCAATCAGTGCCAATTTTCTACATTTGTAACA
66 CAATGTAACTCTCAAAACATTAACAAAATGCACTCAATCAGTGCCAATTTTCTACATTTGTAACA
41891090 GTGTAAGG
131 GTGTAAGG
41891098 TAACAAATTGATACCTACATAAGCAAAGATCAAAACTTTAACATAATTGATA
1 TAACAAATTGATACCTACATAAGCAAAGATCAAAACTTTAACATAATTGATA
41891150 CCACTAACTA
Statistics
Matches: 187, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
138 68 0.36
139 119 0.64
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (138 bp):
TAACAAATTGATACCTACATAAGCAAAGATCAAAACTTTAACATAATTGATAACAGCCATGAAAT
CAATGTAACTCTCAAAACATTAACAAAATGCACTCAATCAGTGCCAATTTTCTACATTTGTAACA
GTGTAAGG
Found at i:41895856 original size:21 final size:19
Alignment explanation
Indices: 41895831--41895888 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
41895821 AAAAAAATTA
*
41895831 AATTTTTTATAACTTCTTTAT
1 AATTTTTTATAA-TT-TATAT
*
41895852 AATTTTTAATAATTTATAT
1 AATTTTTTATAATTTATAT
41895871 AATATTTTT-TAAATTTAT
1 AAT-TTTTTAT-AATTTAT
41895889 GTGACATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 8 0.25
20 13 0.41
21 11 0.34
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTTTATAATTTATAT
Found at i:41901944 original size:22 final size:22
Alignment explanation
Indices: 41901921--41901964 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
41901911 ATGAACTCTT
41901921 AAACTCTTAAAGTGATTCAATTA
1 AAACT-TTAAAGTGATTCAATTA
*
41901944 AAAGTTTAAAGTGATTCAATT
1 AAACTTTAAAGTGATTCAATT
41901965 GAAGAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (22 bp):
AAACTTTAAAGTGATTCAATTA
Found at i:41904668 original size:62 final size:60
Alignment explanation
Indices: 41904596--41904800 Score: 241
Period size: 62 Copynumber: 3.3 Consensus size: 60
41904586 GCATACATTC
41904596 TTTGCCTTCAATTCAATAAATTCAACCAAAGAAGAGGGAACTTTAGGTCATATTACCCAACA
1 TTTGCCTTCAATTCAATAAATTCAACCAAA-AAGAGGGAACTTTAGGTCA-ATTACCCAACA
* * *
41904658 TTTGCCTTCAATTTACCCAAAAAATTCAACCAAAAA-AGAGGAACCTTAGGTCAATTTACCTAAC
1 TTTGCCTTCAA-TT---CAATAAATTCAACCAAAAAGAG-GGAACTTTAGGTCAA-TTACCCAAC
41904722 A
60 A
* * * *
41904723 TTTGCCTTCAATTCCATAAATTCAAGCAGAAAAGAGGGATCTTTAGGTCAATTAACCCAATA
1 TTTGCCTTCAATTCAATAAATTCAACCA-AAAAGAGGGAACTTTAGGTCAATT-ACCCAACA
*
41904785 TTTGCTTTCAATTCAA
1 TTTGCCTTCAATTCAA
41904801 AACCCAACAT
Statistics
Matches: 122, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
61 14 0.11
62 48 0.39
63 4 0.03
64 5 0.04
65 35 0.29
66 16 0.13
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (60 bp):
TTTGCCTTCAATTCAATAAATTCAACCAAAAAGAGGGAACTTTAGGTCAATTACCCAACA
Found at i:41906304 original size:48 final size:48
Alignment explanation
Indices: 41906252--41906347 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
41906242 TGTTTCATGC
41906252 TATAATATCGCTATAGTATTTAATCTCACCACCACCACTGTTTTTACA
1 TATAATATCGCTATAGTATTTAATCTCACCACCACCACTGTTTTTACA
* *
41906300 TATAATATCGCTATAGTATTTAATCTCACTACCACCGCTGTTTTTACA
1 TATAATATCGCTATAGTATTTAATCTCACCACCACCACTGTTTTTACA
41906348 CTAACCAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (48 bp):
TATAATATCGCTATAGTATTTAATCTCACCACCACCACTGTTTTTACA
Found at i:41910748 original size:62 final size:62
Alignment explanation
Indices: 41910651--41910778 Score: 238
Period size: 62 Copynumber: 2.1 Consensus size: 62
41910641 ACCTTTAGCT
*
41910651 TTGTTCCAAGCAACCCTAACCCTAAACTCTATATCTAAATGAAGTGTTTGGATATGAAAAAG
1 TTGTTCCAAGCAACCCTAACCCTAAACCCTATATCTAAATGAAGTGTTTGGATATGAAAAAG
*
41910713 TTGTTCCAAGGAACCCTAACCCTAAACCCTATATCTAAATGAAGTGTTTGGATATGAAAAAG
1 TTGTTCCAAGCAACCCTAACCCTAAACCCTATATCTAAATGAAGTGTTTGGATATGAAAAAG
41910775 TTGT
1 TTGT
41910779 GGAAAGGGGG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (62 bp):
TTGTTCCAAGCAACCCTAACCCTAAACCCTATATCTAAATGAAGTGTTTGGATATGAAAAAG
Found at i:41913274 original size:33 final size:33
Alignment explanation
Indices: 41913232--41913298 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
41913222 ATCTATGAGA
*
41913232 ACTATATACATCATAATTTGCCCCTCTTAATGT
1 ACTATATACATCATAATTTGCCCCTCTAAATGT
41913265 ACTATATACATCATAATTTGCCCCTCTAAATGT
1 ACTATATACATCATAATTTGCCCCTCTAAATGT
41913298 A
1 A
41913299 GGTAAATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (33 bp):
ACTATATACATCATAATTTGCCCCTCTAAATGT
Found at i:41924075 original size:6 final size:6
Alignment explanation
Indices: 41924058--41924095 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
41924048 ACCCTTCTTC
*
41924058 TCCCCTT TCCCCT TCCCCT TCCCTT TCCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
41924096 GGTTTGCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
TCCCCT
Found at i:41924095 original size:18 final size:18
Alignment explanation
Indices: 41924060--41924095 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
41924050 CCTTCTTCTC
41924060 CCCTTTCCCCTTCCCCTT
1 CCCTTTCCCCTTCCCCTT
41924078 CCCTTTCCCCTTCCCCTT
1 CCCTTTCCCCTTCCCCTT
41924096 GGTTTGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (18 bp):
CCCTTTCCCCTTCCCCTT
Found at i:41927253 original size:59 final size:58
Alignment explanation
Indices: 41927180--41927378 Score: 195
Period size: 59 Copynumber: 3.3 Consensus size: 58
41927170 AATACTAAGA
*
41927180 ATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTAAAATTAT
1 ATTTTA-TATATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTAAAATTAT
* ** * * * * * * *
41927239 ATTTTATAGTATTATATA-TTATGATTTTAGTAAATTCATATAAGAA-TATTTAATACTAAGA
1 ATTTTATA-TATTATATATTTTTG-TTAAATTATATTTA-ATAATAATTATTTAA-AATTA-T
* *
41927300 ATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTAT
1 ATTTTA-TATATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTAAAATTAT
41927359 ATTTTATAATATTATATATT
1 ATTTTAT-ATATTATATATT
41927379 ATAATTTTAG
Statistics
Matches: 107, Mismatches: 24, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
58 7 0.07
59 47 0.44
60 18 0.17
61 29 0.27
62 6 0.06
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (58 bp):
ATTTTATATATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTAAAATTAT
Found at i:41927314 original size:61 final size:59
Alignment explanation
Indices: 41927158--41927328 Score: 159
Period size: 59 Copynumber: 2.8 Consensus size: 59
41927148 TGATACAATC
* * * *
41927158 ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTA
1 ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATA-TTATGTTAAAGTAAATTCA
* * * * * **
41927218 ATAATAATTATTTAA-AATTA-TATTTTA-TAGTATTATATATTATGATTTTAGTAAATTCA
1 ATAAGAA-TATTTAATACTAAGAATTTTATTA-AATTATATATTATG-TTAAAGTAAATTCA
*
41927277 TATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAA
1 -ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATA-TTATGTTAAA
41927329 TTATATTTAA
Statistics
Matches: 84, Mismatches: 19, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
58 6 0.07
59 30 0.36
60 18 0.21
61 24 0.29
62 6 0.07
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (59 bp):
ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTATGTTAAAGTAAATTCA
Found at i:41927322 original size:18 final size:17
Alignment explanation
Indices: 41927300--41927434 Score: 95
Period size: 18 Copynumber: 8.0 Consensus size: 17
41927290 AATACTAAGA
41927300 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
41927317 ATTTTTGTTAAA-T-TAT
1 A-TTTTATTAAATTATAT
* *
41927333 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
* *
41927347 ATTTTAAATTATATTTTAT
1 ATTTT--ATTAAATTATAT
* *
41927366 AATATTA-TATATTATA-
1 -ATTTTATTAAATTATAT
*
41927382 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
41927400 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
41927417 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
41927435 TTAATAATAA
Statistics
Matches: 92, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
13 2 0.02
14 6 0.07
15 9 0.10
16 9 0.10
17 20 0.22
18 41 0.45
19 1 0.01
20 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:41927330 original size:120 final size:120
Alignment explanation
Indices: 41927158--41927400 Score: 459
Period size: 120 Copynumber: 2.0 Consensus size: 120
41927148 TGATACAATC
41927158 ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAAT
1 ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAAT
* *
41927223 AATTATTTAAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCAT
66 AATTATTTAAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCAT
41927278 ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAAT
1 ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAAT
*
41927343 AATTATTTTAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCAT
66 AATTATTTAAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCAT
41927398 ATA
1 ATA
41927401 TTTTATTAAA
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (120 bp):
ATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAAT
AATTATTTAAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCAT
Found at i:41927353 original size:26 final size:25
Alignment explanation
Indices: 41927315--41927373 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
41927305 ATTAAATTAT
*
41927315 ATATTTTTGTTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
41927341 ATAATTATTTTAAATTATATTTTATA
1 AT-ATTATTTTAAATTATATTTAATA
41927367 ATATTAT
1 ATATTAT
41927374 ATATTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 20 0.67
27 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATATTATTTTAAATTATATTTAATA
Found at i:41927372 original size:15 final size:15
Alignment explanation
Indices: 41927328--41927383 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
41927318 TTTTTGTTAA
*
41927328 ATTATATTTAATAAT
1 ATTATATTTTATAAT
*
41927343 AAT-TA-TTT-TAA-
1 ATTATATTTTATAAT
41927354 ATTATATTTTATAAT
1 ATTATATTTTATAAT
*
41927369 ATTATATATTATAAT
1 ATTATATTTTATAAT
41927384 TTTAGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.06
12 5 0.15
13 5 0.15
14 5 0.15
15 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATATTTTATAAT
Found at i:41927401 original size:41 final size:40
Alignment explanation
Indices: 41927179--41927419 Score: 121
Period size: 41 Copynumber: 6.0 Consensus size: 40
41927169 TAATACTAAG
* *
41927179 AATTTTATTAAATTATATATTTTTGTTAA-ATTATAT-TTAAT
1 AATTTTAGTAAATTATATA-TTTT-ATAATATTATATATT-AT
* * * *
41927220 AATAATTATTTAAAAT-TATATTTTATAGTATTATATATTAT
1 AAT-TTTA-GTAAATTATATATTTTATAATATTATATATTAT
* * * *
41927261 GATTTTAGTAAATTCATATA----AGAATATT-TAATACTAAG
1 AATTTTAGTAAATT-ATATATTTTATAATATTAT-ATA-TTAT
* *
41927299 AATTTTATTAAATTATATATTTTTGTTAA-ATTATAT-TTAAT
1 AATTTTAGTAAATTATATA-TTTT-ATAATATTATATATT-AT
**
41927340 AATAATTATTTTAAA-T-TATATTTTATAATATTATATATTAT
1 AAT--TT-TAGTAAATTATATATTTTATAATATTATATATTAT
41927381 AATTTTAGTAAATTCATATATTTTATTAA-ATTATATATT
1 AATTTTAGTAAATT-ATATATTTTA-TAATATTATATATT
41927420 TTTATTAAAT
Statistics
Matches: 153, Mismatches: 22, Indels: 50
0.68 0.10 0.22
Matches are distributed among these distances:
36 1 0.01
37 14 0.09
38 19 0.12
39 8 0.05
40 9 0.06
41 61 0.40
42 23 0.15
43 12 0.08
44 6 0.04
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (40 bp):
AATTTTAGTAAATTATATATTTTATAATATTATATATTAT
Found at i:41927624 original size:21 final size:21
Alignment explanation
Indices: 41927598--41927652 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
41927588 ACCGCTGTTT
*
41927598 CTAATCTCACTGCTACAGTATC
1 CTAATCTCACCGCTACAGTA-C
41927620 C-AATCTCACCGCTACAGTAC
1 CTAATCTCACCGCTACAGTAC
41927640 CTAATCTCACCGC
1 CTAATCTCACCGC
41927653 CACCGCTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.90
22 1 0.03
ACGTcount: A:0.27, C:0.38, G:0.09, T:0.25
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAC
Found at i:41928330 original size:275 final size:274
Alignment explanation
Indices: 41927831--41928333 Score: 699
Period size: 275 Copynumber: 1.8 Consensus size: 274
41927821 GGCACACATG
* *
41927831 GCCCATATACCTCCAAAAGGCCTTTTACCACTTAAGTGTTGCTATCCTTTTATATAGTCCAGGTC
1 GCCCATATACCCCCAAAAGGCCTTTTACCACTTAAGTGTTGCTACCCTTTTATATAGTCCAGGTC
* * *
41927896 TCTCTTATGCTTTGATGATGTAGATTTCTCTAAGGTATTACATCCACCCCCCTTAGGGACTCAAT
66 TCTCTCATGCTTTGACGATGAAGATTTCTCTAAGGTATTACATCCACCCCCCTTAGGGACTCAAT
* * * *
41927961 GTCCTCATTGAGGTTTGTCCCACCATCACTCAAGAAGCACAACAAGTGACTCTGATATCAATAAA
131 GTCCTCACTGAGGTTTGCCCCACCATCACTCAAGAAGCACAACAAATAACTCTGATATCAATAAA
* * *
41928026 TTTCATAGCCAACACCTAACCCGGTAAGATATTGTTTGCTTTAAGCGCACATGACCCTTATAGCT
196 TGTCATAGCCAACACCCAACCCAGTAAGATATTGTTTGCTTTAAGCGCACATGACCCTTATAGCT
41928091 TTATTCTTGGGAGT
261 TTATTCTTGGGAGT
*
41928105 GCCCATATACCCCCAAGAGGCCTTTTACCACTTAAGTGTTGCTACCCTTTTATATAG-CCTAGGT
1 GCCCATATACCCCCAAAAGGCCTTTTACCACTTAAGTGTTGCTACCCTTTTATATAGTCC-AGGT
* * * *
41928169 CTCTCTCGTGCTTTGCCGATGAAGGATTTGC-CTAGGGTATTACATTCACCCCCCTTAGGGAC-C
65 CTCTCTCATGCTTTGACGATGAA-GATTT-CTCTAAGGTATTACATCCACCCCCCTTAGGGACTC
* * ** * **
41928232 TAATGTCTTCGCTGAGGTTTGCCCCACCATTGCTCAAGAGGCATGACAAATAACTCTGATA-CTA
128 -AATGTCCTCACTGAGGTTTGCCCCACCATCACTCAAGAAGCACAACAAATAACTCTGATATC-A
* *
41928296 ATAAATGTCATAGCCAATACCCAACCTAGTAAGATATT
191 ATAAATGTCATAGCCAACACCCAACCCAGTAAGATATT
41928334 ATCCGCTTTG
Statistics
Matches: 198, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
273 2 0.01
274 78 0.39
275 117 0.59
276 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (274 bp):
GCCCATATACCCCCAAAAGGCCTTTTACCACTTAAGTGTTGCTACCCTTTTATATAGTCCAGGTC
TCTCTCATGCTTTGACGATGAAGATTTCTCTAAGGTATTACATCCACCCCCCTTAGGGACTCAAT
GTCCTCACTGAGGTTTGCCCCACCATCACTCAAGAAGCACAACAAATAACTCTGATATCAATAAA
TGTCATAGCCAACACCCAACCCAGTAAGATATTGTTTGCTTTAAGCGCACATGACCCTTATAGCT
TTATTCTTGGGAGT
Found at i:41929555 original size:18 final size:18
Alignment explanation
Indices: 41929532--41929566 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41929522 CAAGATAGTT
41929532 GAATTGCTTCTTTAAGAA
1 GAATTGCTTCTTTAAGAA
41929550 GAATTGCTTCTTTAAGA
1 GAATTGCTTCTTTAAGA
41929567 TGCATCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (18 bp):
GAATTGCTTCTTTAAGAA
Done.