Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 16 of 132
Found at i:4501175 original size:76 final size:76
Alignment explanation
Indices: 4501044--4501808 Score: 1248
Period size: 76 Copynumber: 10.0 Consensus size: 76
4501034 ATCAGACCGC
*
4501044 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC-AGTTCTTTATCTCTGA
1 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAG-TCTTTATCTCTGA
4501108 AATTGAAGTAAG
65 AATTGAAGTAAG
* *
4501120 AGCAACG-TCATTTCTTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGA
1 AGCAA-GATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGA
*
4501184 AAATGAAGTAAG
65 AATTGAAGTAAG
* * * *
4501196 AGCAAGATCGTTT-CTCATCCTCTTGAAATTGAAGTAAAGCTGGATAACAGGTCTTTATCTCTGA
1 AGCAAGATCTTTTCCT-ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGA
*
4501260 AAATGAAGTAAG
65 AATTGAAGTAAG
* *
4501272 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGACAACACGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
*
4501337 AATGAAGTAAG
66 ATTGAAGTAAG
* * *
4501348 AGCAAGATCATTTCCTATTCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTTTGAA
1 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
4501413 ATTGAAGTAAG
66 ATTGAAGTAAG
* *
4501424 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
*
4501489 AATGAAGTAAG
66 ATTGAAGTAAG
* * *
4501500 AGCAAGATCATTTCCTATCCTCTTGAAATTAAAGTAGAGTTGGATAACAAGTCTTTATCTTTGAA
1 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
4501565 ATTGAAGTAAG
66 ATTGAAGTAAG
*
4501576 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCATTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
4501641 ATTGAAGTAAG
66 ATTGAAGTAAG
4501652 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
4501717 ATTGAAGTAAG
66 ATTGAAGTAAG
* *
4501728 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTG
1 AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTA--TCTCTG
4501793 AAATTGAAGTAAG
64 AAATTGAAGTAAG
4501806 AGC
1 AGC
4501809 TAGACGAAGC
Statistics
Matches: 645, Mismatches: 37, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
75 2 0.00
76 616 0.96
77 5 0.01
78 22 0.03
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (76 bp):
AGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
ATTGAAGTAAG
Found at i:4502185 original size:10 final size:11
Alignment explanation
Indices: 4502170--4502198 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4502160 TACTTTGAAA
4502170 TTAAATTT-AT
1 TTAAATTTAAT
4502180 TTAAATTTAAT
1 TTAAATTTAAT
4502191 TTAAATTT
1 TTAAATTT
4502199 GATATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:4502191 original size:15 final size:17
Alignment explanation
Indices: 4502155--4502193 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
4502145 AACCGTTTTA
4502155 AAATTTACTTTGAAATT
1 AAATTTACTTTGAAATT
4502172 AAATTTA-TTT-AAATT
1 AAATTTACTTTGAAATT
*
4502187 TAATTTA
1 AAATTTA
4502194 AATTTGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.52
16 3 0.14
17 7 0.33
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTACTTTGAAATT
Found at i:4503197 original size:59 final size:58
Alignment explanation
Indices: 4502980--4503322 Score: 376
Period size: 59 Copynumber: 5.9 Consensus size: 58
4502970 AAAACTTAAA
* * *
4502980 AAAATTACA-TTTTAACCTCGATTTCACCAAAAATTACTATTTTACCCCTGAACTTTCC
1 AAAATTCCATTTTTAACC-CGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
* * * * *
4503038 AAAATTCCATTTTTGACCCTAATTTTA-CTAAAATTACCATTTTACCCCCGAACTTTTC
1 AAAATTCCATTTTTAACCC-GATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
* * *
4503096 AAAATTCCA-TTTTAACCCCAATTTCACCTAAAATTACTATTTTACCCCCGAACTTTCC
1 AAAATTCCATTTTTAA-CCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
* * *
4503154 AAAATTCCATTTTTAATCCCGATTTCACCAAAAATTACCATTTTATCCTCAAACTTTCC
1 AAAATTCCATTTTTAA-CCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
* * *
4503213 AAAATTTCATTTTTAACCTCGATTTCACCAAAAATTACCGTTTTACCCCCGAACCATT-C
1 AAAATTCCATTTTTAACC-CGATTTCACCAAAAATTACCATTTTACCCCCGAA-CTTTCC
* * *
4503272 AAAATCCCATTTTTAATCCTGAATTTTC-CC-AAAATTA-CATTTTGCCCCCGA
1 AAAATTCCATTTTTAA-CCCG-A-TTTCACCAAAAATTACCATTTTACCCCCGA
4503323 GAGTCAAAGA
Statistics
Matches: 245, Mismatches: 30, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
57 11 0.04
58 100 0.41
59 122 0.50
60 8 0.03
61 4 0.02
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
Found at i:4503198 original size:30 final size:28
Alignment explanation
Indices: 4502980--4503264 Score: 129
Period size: 29 Copynumber: 9.8 Consensus size: 28
4502970 AAAACTTAAA
* *
4502980 AAAATTACATTTTAACCTCGATTTCACC
1 AAAATTCCATTTTAACCCCGATTTCACC
*
4503008 AAAAATTACTATTTT-ACCCCTGAACTTT--CC
1 -AAAATT-CCATTTTAACCCC-G-A-TTTCACC
* ** * *
4503038 AAAATTCCATTTTTGACCCTAATTTTACT
1 AAAATTCCA-TTTTAACCCCGATTTCACC
* *
4503067 AAAATTACCATTTTACCCCCGAACTTT--TC
1 AAAATT-CCATTTTAACCCCG-A-TTTCACC
*
4503096 AAAATTCCATTTTAACCCCAATTTCACC
1 AAAATTCCATTTTAACCCCGATTTCACC
* *
4503124 TAAAATTACTATTTTACCCCCGAACTTT--CC
1 -AAAATT-CCATTTTAACCCCG-A-TTTCACC
*
4503154 AAAATTCCATTTTTAATCCCGATTTCACC
1 AAAATTCCA-TTTTAACCCCGATTTCACC
* **
4503183 AAAAATTACCATTTTATCCTCAAACTTT--CC
1 -AAAATT-CCATTTTAACC-CCGA-TTTCACC
* *
4503213 AAAATTTCATTTTTAACCTCGATTTCACC
1 AAAATTCCA-TTTTAACCCCGATTTCACC
* *
4503242 AAAAATTACCGTTTTACCCCCGA
1 -AAAATT-CCATTTTAACCCCGA
4503265 ACCATTCAAA
Statistics
Matches: 192, Mismatches: 35, Indels: 57
0.68 0.12 0.20
Matches are distributed among these distances:
26 3 0.02
27 10 0.05
28 22 0.11
29 78 0.41
30 59 0.31
31 11 0.06
32 9 0.05
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAATTCCATTTTAACCCCGATTTCACC
Found at i:4516152 original size:21 final size:22
Alignment explanation
Indices: 4516121--4516172 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
4516111 ATCATATCTT
* *
4516121 ATTTAATTATT-TCATATTAAA
1 ATTTAAATATTATAATATTAAA
*
4516142 TTTTAAATATTATAATATTAAA
1 ATTTAAATATTATAATATTAAA
*
4516164 ATTAAAATA
1 ATTTAAATA
4516173 AATTCAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTAAATATTATAATATTAAA
Found at i:4523231 original size:6 final size:6
Alignment explanation
Indices: 4523220--4523249 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
4523210 CGGATCGAGT
4523220 TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA
1 TTGGGA TTGGGA TTGGGA TTGGGA TTGGGA
4523250 AGATGTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TTGGGA
Found at i:4525546 original size:17 final size:14
Alignment explanation
Indices: 4525502--4525553 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
4525492 TCATGTTATA
4525502 TTTTTATATTATTT
1 TTTTTATATTATTT
*
4525516 TTTATATCATTATTCT
1 TTTTTAT-ATTATT-T
*
4525532 TGTTTTATAATTATTA
1 T-TTTTAT-ATTATTT
4525548 TTTTTA
1 TTTTTA
4525554 ACTTATGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 6 0.19
15 11 0.35
16 3 0.10
17 11 0.35
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (14 bp):
TTTTTATATTATTT
Found at i:4537084 original size:27 final size:27
Alignment explanation
Indices: 4536942--4537090 Score: 69
Period size: 27 Copynumber: 5.4 Consensus size: 27
4536932 ATTTTTTTTG
*
4536942 TATAATTTAATATAATTATACATAAAA
1 TATAATTTAATATAATAATACATAAAA
* ** *
4536969 TATACTTTTTTTTAATAATTA-AT-AAA
1 TATAATTTAATATAATAA-TACATAAAA
* * *
4536995 T-TAATTGTAATTTTAATTACACATGAAATA
1 TATAATT-TAA-TATAATAATACAT-AAA-A
*
4537025 TTTTAAAATTTTAA-AT-ATAATA-AT-AAA
1 ---TATAA-TTTAATATAATAATACATAAAA
4537052 TAATAATTTAATATAATAATACATAAAA
1 T-ATAATTTAATATAATAATACATAAAA
*
4537080 TATAAATTAAT
1 TATAATTTAAT
4537091 CTAAAATTTG
Statistics
Matches: 89, Mismatches: 16, Indels: 34
0.64 0.12 0.24
Matches are distributed among these distances:
24 6 0.07
25 9 0.10
26 12 0.13
27 36 0.40
28 8 0.09
29 2 0.02
30 3 0.03
31 4 0.04
32 1 0.01
33 1 0.01
34 5 0.06
35 2 0.02
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (27 bp):
TATAATTTAATATAATAATACATAAAA
Found at i:4539845 original size:14 final size:14
Alignment explanation
Indices: 4539826--4539852 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4539816 TACCCACCAC
4539826 CCCTCTCTCTCTCT
1 CCCTCTCTCTCTCT
4539840 CCCTCTCTCTCTC
1 CCCTCTCTCTCTC
4539853 CCTCATTTCA
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:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (14 bp):
CCCTCTCTCTCTCT
Found at i:4539847 original size:12 final size:12
Alignment explanation
Indices: 4539830--4539856 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4539820 CACCACCCCT
4539830 CTCTCTCTCTCC
1 CTCTCTCTCTCC
4539842 CTCTCTCTCTCC
1 CTCTCTCTCTCC
4539854 CTC
1 CTC
4539857 ATTTCACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (12 bp):
CTCTCTCTCTCC
Found at i:4543146 original size:12 final size:13
Alignment explanation
Indices: 4543130--4543194 Score: 59
Period size: 12 Copynumber: 5.3 Consensus size: 13
4543120 TCAAAATCGA
4543130 ATTATTATATATT
1 ATTATTATATATT
4543143 -TTATTATA-ATT
1 ATTATTATATATT
* * *
4543154 GTATAGTAAATA-T
1 AT-TATTATATATT
4543167 ATTATTAT-TATT
1 ATTATTATATATT
4543179 ATTATTAT-TATT
1 ATTATTATATATT
4543191 ATTA
1 ATTA
4543195 GTAATTAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
11 5 0.12
12 30 0.70
13 7 0.16
14 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
ATTATTATATATT
Found at i:4543174 original size:3 final size:3
Alignment explanation
Indices: 4543166--4543194 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4543156 ATAGTAAATA
4543166 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4543195 GTAATTAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4543868 original size:6 final size:6
Alignment explanation
Indices: 4543857--4543886 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
4543847 AGACAGTATT
4543857 AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA
4543887 CATAAGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:4549511 original size:26 final size:26
Alignment explanation
Indices: 4549482--4549538 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
4549472 CAATAATTGG
4549482 AAAAAAAAAGTTTAGATAGTAAAGTA
1 AAAAAAAAAGTTTAGATAGTAAAGTA
4549508 AAAAAAAAAGTTTAGATAGTAAAGTA
1 AAAAAAAAAGTTTAGATAGTAAAGTA
4549534 AAAAA
1 AAAAA
4549539 TTCCATGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.21
Consensus pattern (26 bp):
AAAAAAAAAGTTTAGATAGTAAAGTA
Found at i:4561217 original size:480 final size:480
Alignment explanation
Indices: 4560316--4561279 Score: 1865
Period size: 480 Copynumber: 2.0 Consensus size: 480
4560306 GACTTGTTGC
*
4560316 GAAGGGATACAAGCAAAAGGTAGGAATTGACTATGACGAGGCGTTTGCTTCTGATGCAAGAATGG
1 GAAGGGATACAAGCAAAAGGTAGGAATTGACTATGACGAGGCGTTTGCTCCTGATGCAAGAATGG
4560381 AGACAATCCGATTACTCATTTTACAAGCTGCTCAATTCAAATGGCCGATATTTCAAATGGATGTC
66 AGACAATCCGATTACTCATTTTACAAGCTGCTCAATTCAAATGGCCGATATTTCAAATGGATGTC
*
4560446 AAGTCGGCATTCTTGAATGGTGTGCTCGAAGAAGATGTCTACATCGAATAACCACCCGGGTACAT
131 AAGTCGGCATTCTTGAATGGTGTGCTCGAAAAAGATGTCTACATCGAATAACCACCCGGGTACAT
* *
4560511 TAAAGTCGAAGAAGAGAAGAAGGTGTTAAAATTGAAGAAGGTACTTTACGGGTTGAAGCAAGCAC
196 TAAAGTCGAAGAAGAGAAGAAGGTGTTAAAATTGAAGAAGGCACTTTACGGGTTGAAACAAGCAC
4560576 CGTGGGCATGGAATACACGTATCGATACATATTTCAAGGAGAACGGGTTCAAGCAATGTCCCTAC
261 CGTGGGCATGGAATACACGTATCGATACATATTTCAAGGAGAACGGGTTCAAGCAATGTCCCTAC
4560641 GAGCATACTCTTTACGTAAAGAAGAATGGAGGTAACGTATTATTAGTTGCTCTTTATGTCGATGA
326 GAGCATACTCTTTACGTAAAGAAGAATGGAGGTAACGTATTATTAGTTGCTCTTTATGTCGATGA
4560706 CCTCATTTTTATGGGTAACAATGATGAGATGATAAAAGAATTTAAGGGCACAATGACTCGAGAAT
391 CCTCATTTTTATGGGTAACAATGATGAGATGATAAAAGAATTTAAGGGCACAATGACTCGAGAAT
4560771 TTGAGATGACAGATTTGGGCTTGAT
456 TTGAGATGACAGATTTGGGCTTGAT
4560796 GAAGGGATACAAGCAAAAGGTAGGAATTGACTATGACGAGGCGTTTGCTCCTGATGCAAGAATGG
1 GAAGGGATACAAGCAAAAGGTAGGAATTGACTATGACGAGGCGTTTGCTCCTGATGCAAGAATGG
*
4560861 AGACAATCCGATTACTCATTTTACAAGCTGCTCAATTCAAATGGTCGATATTTCAAATGGATGTC
66 AGACAATCCGATTACTCATTTTACAAGCTGCTCAATTCAAATGGCCGATATTTCAAATGGATGTC
4560926 AAGTCGGCATTCTTGAATGGTGTGCTCGAAAAAGATGTCTACATCGAATAACCACCCGGGTACAT
131 AAGTCGGCATTCTTGAATGGTGTGCTCGAAAAAGATGTCTACATCGAATAACCACCCGGGTACAT
4560991 TAAAGTCGAAGAAGAGAAGAAGGTGTTAAAATTGAAGAAGGCACTTTACGGGTTGAAACAAGCAC
196 TAAAGTCGAAGAAGAGAAGAAGGTGTTAAAATTGAAGAAGGCACTTTACGGGTTGAAACAAGCAC
*
4561056 CGTGGGCATGGAATACACGTATCGATACATATTTCAAGGAGAATGGGTTCAAGCAATGTCCCTAC
261 CGTGGGCATGGAATACACGTATCGATACATATTTCAAGGAGAACGGGTTCAAGCAATGTCCCTAC
4561121 GAGCATACTCTTTACGTAAAGAAGAATGGAGGTAACGTATTATTAGTTGCTCTTTATGTCGATGA
326 GAGCATACTCTTTACGTAAAGAAGAATGGAGGTAACGTATTATTAGTTGCTCTTTATGTCGATGA
4561186 CCTCATTTTTATGGGTAACAATGATGAGATGATAAAAGAATTTAAGGGCACAATGACTCGAGAAT
391 CCTCATTTTTATGGGTAACAATGATGAGATGATAAAAGAATTTAAGGGCACAATGACTCGAGAAT
*
4561251 TTGAGATGATAGATTTGGGCTTGAT
456 TTGAGATGACAGATTTGGGCTTGAT
4561276 GAAG
1 GAAG
4561280 TTTTTTTCTT
Statistics
Matches: 477, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
480 477 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (480 bp):
GAAGGGATACAAGCAAAAGGTAGGAATTGACTATGACGAGGCGTTTGCTCCTGATGCAAGAATGG
AGACAATCCGATTACTCATTTTACAAGCTGCTCAATTCAAATGGCCGATATTTCAAATGGATGTC
AAGTCGGCATTCTTGAATGGTGTGCTCGAAAAAGATGTCTACATCGAATAACCACCCGGGTACAT
TAAAGTCGAAGAAGAGAAGAAGGTGTTAAAATTGAAGAAGGCACTTTACGGGTTGAAACAAGCAC
CGTGGGCATGGAATACACGTATCGATACATATTTCAAGGAGAACGGGTTCAAGCAATGTCCCTAC
GAGCATACTCTTTACGTAAAGAAGAATGGAGGTAACGTATTATTAGTTGCTCTTTATGTCGATGA
CCTCATTTTTATGGGTAACAATGATGAGATGATAAAAGAATTTAAGGGCACAATGACTCGAGAAT
TTGAGATGACAGATTTGGGCTTGAT
Found at i:4563803 original size:21 final size:22
Alignment explanation
Indices: 4563774--4563819 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4563764 ATTGTTGTTA
* *
4563774 TTTGTTGTT-TTTTGCTGCCAT
1 TTTGATGTTGTTTTGCTACCAT
4563795 TTTGATGTTGTTTTGCTACCAT
1 TTTGATGTTGTTTTGCTACCAT
4563817 TTT
1 TTT
4563820 ATTGTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.09, C:0.13, G:0.17, T:0.61
Consensus pattern (22 bp):
TTTGATGTTGTTTTGCTACCAT
Found at i:4563825 original size:22 final size:22
Alignment explanation
Indices: 4563774--4563825 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
4563764 ATTGTTGTTA
*
4563774 TTTG-TTGTTTTTTGCTGCCAT
1 TTTGATTGTTTTTTGCTACCAT
4563795 TTTGA-TGTTGTTTTGCTACCAT
1 TTTGATTGTT-TTTTGCTACCAT
4563817 TTT-ATTGTT
1 TTTGATTGTT
4563826 ATTATTTGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.10, C:0.12, G:0.17, T:0.62
Consensus pattern (22 bp):
TTTGATTGTTTTTTGCTACCAT
Found at i:4572053 original size:2 final size:2
Alignment explanation
Indices: 4572046--4572081 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4572036 ACAAGCAAAG
4572046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4572082 ATCAACTGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4573681 original size:2 final size:2
Alignment explanation
Indices: 4573674--4573714 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4573664 GACGCTATCT
4573674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4573715 CAGTCACAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4582494 original size:17 final size:17
Alignment explanation
Indices: 4582472--4582505 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4582462 TTAAGAATTT
4582472 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
4582489 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
4582506 GTATCAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:4583363 original size:23 final size:23
Alignment explanation
Indices: 4583335--4583388 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
4583325 TCGTCCATCT
*
4583335 TGCTGACTAGACCTTCTGGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
* *
4583358 TGCTGACTAGATCTTTTAGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
4583381 TGCTGACT
1 TGCTGACT
4583389 GGATGCCACG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (23 bp):
TGCTGACTAGACCTTCTAGAAGC
Found at i:4584157 original size:12 final size:12
Alignment explanation
Indices: 4584124--4584158 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
4584114 TAAGCAACCA
*
4584124 TTTTCTTCTTCT
1 TTTTCTTCTTTT
4584136 TTTTC-TCTTTT
1 TTTTCTTCTTTT
4584147 TTTTCTTCTTTT
1 TTTTCTTCTTTT
4584159 CGAACCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTCTTCTTTT
Found at i:4584201 original size:38 final size:36
Alignment explanation
Indices: 4584132--4584220 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 36
4584122 CATTTTCTTC
* *
4584132 TTCTTTTTCTCTTTTTTTTCTTCTTTTCGAAC-CTT
1 TTCTTTTTTTCTTTTTTTTCTTCTTTACGAACACTT
* * *
4584167 TTGCTTTTTTTCTTTTTTTTGTTGTTCGTACGAACAGTT
1 TT-CTTTTTTTCTTTTTTTTCTTCTT--TACGAACACTT
4584206 TTCTTTTTTT-TTTTT
1 TTCTTTTTTTCTTTTT
4584221 ACTGTTCTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
35 2 0.04
36 20 0.44
37 5 0.11
38 14 0.31
39 4 0.09
ACGTcount: A:0.07, C:0.16, G:0.08, T:0.70
Consensus pattern (36 bp):
TTCTTTTTTTCTTTTTTTTCTTCTTTACGAACACTT
Found at i:4592594 original size:17 final size:17
Alignment explanation
Indices: 4592572--4592605 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4592562 TTAAGAATTT
4592572 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
4592589 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
4592606 GTATCAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:4602843 original size:2 final size:2
Alignment explanation
Indices: 4602836--4602864 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4602826 AATAGACACC
4602836 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4602865 TAGATATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4604338 original size:15 final size:17
Alignment explanation
Indices: 4604307--4604338 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4604297 ACACAATATG
4604307 GAGAAAATAATCCAAAA
1 GAGAAAATAATCCAAAA
4604324 GAGAAAA-AA-CCAAAA
1 GAGAAAATAATCCAAAA
4604339 CTCAAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.69, C:0.12, G:0.12, T:0.06
Consensus pattern (17 bp):
GAGAAAATAATCCAAAA
Found at i:4608309 original size:6 final size:6
Alignment explanation
Indices: 4608298--4608326 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4608288 ACACCTCTCT
4608298 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
4608327 TTCCCTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:4611471 original size:5 final size:5
Alignment explanation
Indices: 4611462--4611518 Score: 96
Period size: 5 Copynumber: 11.4 Consensus size: 5
4611452 ATTTGCCTCA
* *
4611462 CCATA CCATA CCATC CCATC CCATC CCATC CCATC CCATC CCATC CCATC
1 CCATC CCATC CCATC CCATC CCATC CCATC CCATC CCATC CCATC CCATC
4611512 CCATC CC
1 CCATC CC
4611519 TTACATCTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.23, C:0.58, G:0.00, T:0.19
Consensus pattern (5 bp):
CCATC
Found at i:4620495 original size:31 final size:30
Alignment explanation
Indices: 4620419--4620497 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
4620409 TTGTTATAGA
*
4620419 TTTAATCCTTATACTTTTAATTTGATCAAT
1 TTTAATCCTTATACTTTTAAATTGATCAAT
* * * * *
4620449 TTTAGTCTTTGTACTTTTCAAATTGGTTAAT
1 TTTAATCCTTATACTTTT-AAATTGATCAAT
*
4620480 TTTAATCCCTATACTTTT
1 TTTAATCCTTATACTTTT
4620498 TGACTTTTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 15 0.39
31 23 0.61
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.54
Consensus pattern (30 bp):
TTTAATCCTTATACTTTTAAATTGATCAAT
Found at i:4628893 original size:23 final size:23
Alignment explanation
Indices: 4628845--4628895 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
4628835 ATTTTGTTTG
* *
4628845 TTTGTGCAATTTTGATATTACTT
1 TTTGTGCAATGTTGATATGACTT
4628868 TTTGTAGCAATGTTGATATGACTT
1 TTTGT-GCAATGTTGATATGACTT
4628892 TTTG
1 TTTG
4628896 GTATTATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.22, C:0.08, G:0.18, T:0.53
Consensus pattern (23 bp):
TTTGTGCAATGTTGATATGACTT
Found at i:4631373 original size:33 final size:33
Alignment explanation
Indices: 4631286--4631373 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
4631276 AATATTATAC
* * *
4631286 TGTTGTTTTGGTGCTATATTTTTACTATTTTGGT
1 TGTTGTTTTCGTGTTAT-TTTTTACTATTTTGAT
* * * *
4631320 TGCTGTTTTTGTGTTGTTTTTTACTGTTTTGAT
1 TGTTGTTTTCGTGTTATTTTTTACTATTTTGAT
*
4631353 TGTTGTTTTCGTATTATTTTT
1 TGTTGTTTTCGTGTTATTTTT
4631374 GCTGTTATTT
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 31 0.70
34 13 0.30
ACGTcount: A:0.09, C:0.06, G:0.19, T:0.66
Consensus pattern (33 bp):
TGTTGTTTTCGTGTTATTTTTTACTATTTTGAT
Found at i:4631390 original size:15 final size:14
Alignment explanation
Indices: 4631372--4631415 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 14
4631362 CGTATTATTT
4631372 TTGCTGTTATTTTTG
1 TTGCTGTT-TTTTTG
4631387 TTGCTG--TTTTTG
1 TTGCTGTTTTTTTG
4631399 TTGCTGTTTTTGTTG
1 TTGCTGTTTTT-TTG
4631414 TT
1 TT
4631416 TTTAATGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.02, C:0.07, G:0.23, T:0.68
Consensus pattern (14 bp):
TTGCTGTTTTTTTG
Found at i:4631390 original size:68 final size:68
Alignment explanation
Indices: 4631311--4631457 Score: 183
Period size: 68 Copynumber: 2.2 Consensus size: 68
4631301 ATATTTTTAC
* * * *
4631311 TATTTTGGTTGCTGTTTTTG-TGTTGTTTTT-TACTGTTTTGATTGTTGTTTTCG-TATTATTTT
1 TATTTTTGTTGCTGTTTTTGTTGCTGTTTTTGT--TGTTTTGAATGTTGTTTT-GTTACTATTTT
*
4631373 TGCTGT
63 GGCTGT
* *
4631379 TATTTTTGTTGCTGTTTTTGTTGCTGTTTTTGTTGTTTTTAATGTTGTTTTGTTACTATTTTGGT
1 TATTTTTGTTGCTGTTTTTGTTGCTGTTTTTGTTGTTTTGAATGTTGTTTTGTTACTATTTTGGC
4631444 TGT
66 TGT
4631447 TATTTTTGTTG
1 TATTTTTGTTG
4631458 TTTGGATGGT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
67 1 0.01
68 58 0.84
69 9 0.13
70 1 0.01
ACGTcount: A:0.07, C:0.05, G:0.20, T:0.67
Consensus pattern (68 bp):
TATTTTTGTTGCTGTTTTTGTTGCTGTTTTTGTTGTTTTGAATGTTGTTTTGTTACTATTTTGGC
TGT
Found at i:4631396 original size:12 final size:12
Alignment explanation
Indices: 4631381--4631413 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
4631371 TTTGCTGTTA
4631381 TTTTTGTTGCTG
1 TTTTTGTTGCTG
4631393 TTTTTGTTGCTG
1 TTTTTGTTGCTG
4631405 TTTTTGTTG
1 TTTTTGTTG
4631414 TTTTTAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.06, G:0.24, T:0.70
Consensus pattern (12 bp):
TTTTTGTTGCTG
Found at i:4631446 original size:32 final size:32
Alignment explanation
Indices: 4631394--4631460 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
4631384 TTGTTGCTGT
* * *
4631394 TTTTGTTGCTGTTTTTGTTGTT-TTTAATGTTG
1 TTTTGTTACTATTTTGGTTGTTATTT-ATGTTG
*
4631426 TTTTGTTACTATTTTGGTTGTTATTTTTGTTG
1 TTTTGTTACTATTTTGGTTGTTATTTATGTTG
4631458 TTT
1 TTT
4631461 GGATGGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 27 0.90
33 3 0.10
ACGTcount: A:0.07, C:0.03, G:0.19, T:0.70
Consensus pattern (32 bp):
TTTTGTTACTATTTTGGTTGTTATTTATGTTG
Found at i:4631670 original size:38 final size:38
Alignment explanation
Indices: 4631590--4631671 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
4631580 AATATAATTT
* * * *
4631590 TTTTAATGTATTTTAAATTTATTTATTTTTAATGTTTG
1 TTTTAATGTATTTTAAATGTATTTATTATTAATGTATA
4631628 TTTTAATGT-TTTTAAATGTATTTGATATATT-ATGTATA
1 TTTTAATGTATTTTAAATGTATTT-AT-TATTAATGTATA
4631666 TTTTAA
1 TTTTAA
4631672 ATTTGTTGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 13 0.34
38 22 0.58
39 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (38 bp):
TTTTAATGTATTTTAAATGTATTTATTATTAATGTATA
Found at i:4635551 original size:19 final size:20
Alignment explanation
Indices: 4635524--4635562 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
4635514 TAAAATAGAT
* *
4635524 AATATATTTTAATTATGTTG
1 AATATATTTAAATAATGTTG
4635544 AATA-ATTTAAATAATGTTG
1 AATATATTTAAATAATGTTG
4635563 CTTTAGATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
AATATATTTAAATAATGTTG
Found at i:4641026 original size:10 final size:9
Alignment explanation
Indices: 4640995--4641037 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
4640985 CAATCAAAAC
4640995 GAGAGAGTT
1 GAGAGAGTT
*
4641004 GAGAGACTT
1 GAGAGAGTT
*
4641013 GAGAGTGTTT
1 GAGAGAG-TT
4641023 GAGAGAGTT
1 GAGAGAGTT
4641032 GAGAGA
1 GAGAGA
4641038 AGGATGTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.33, C:0.02, G:0.42, T:0.23
Consensus pattern (9 bp):
GAGAGAGTT
Found at i:4648111 original size:17 final size:17
Alignment explanation
Indices: 4648089--4648136 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
4648079 TTAAGGAGAT
4648089 AAAAATAAATAAATA-AG
1 AAAAATAAATAAA-ACAG
*
4648106 AAAAATAAACAAAACGAG
1 AAAAATAAATAAAAC-AG
*
4648124 AAAAATCAATAAA
1 AAAAATAAATAAA
4648137 CAAATCAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 1 0.04
17 12 0.46
18 13 0.50
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAATAAATAAAACAG
Found at i:4648137 original size:17 final size:17
Alignment explanation
Indices: 4648089--4648139 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
4648079 TTAAGGAGAT
*
4648089 AAAAATAAATAAATAAG
1 AAAAATAAATAAACAAG
* *
4648106 AAAAATAAACAAAACGAG
1 AAAAATAAA-TAAACAAG
*
4648124 AAAAATCAATAAACAA
1 AAAAATAAATAAACAA
4648140 ATCAGGAAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.75, C:0.08, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAATAAATAAACAAG
Found at i:4659527 original size:6 final size:6
Alignment explanation
Indices: 4659518--4659543 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4659508 TGTGTGTGTG
4659518 TTTGCT TTTGCT TTTGCT TTTGCT TT
1 TTTGCT TTTGCT TTTGCT TTTGCT TT
4659544 GGAGATATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (6 bp):
TTTGCT
Found at i:4668666 original size:3 final size:3
Alignment explanation
Indices: 4668658--4668697 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4668648 AGTGTAAGTA
4668658 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4668698 AAAGATAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4670996 original size:18 final size:16
Alignment explanation
Indices: 4670975--4671010 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
4670965 ATTTAAAATT
4670975 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
4670993 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
4671009 TT
1 TT
4671011 CTCATTCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:4681746 original size:49 final size:49
Alignment explanation
Indices: 4681684--4682071 Score: 212
Period size: 49 Copynumber: 7.9 Consensus size: 49
4681674 ATGTTCTTTA
* * * * *
4681684 GGTACAAGGTTCGTTGTTGCGACTTAAA-CATTTCCCTTTAAATCTTCGT
1 GGTACTAGATTCGTTGTTGCGGCTTAAATC-TTTCCCTTCATATCTTCGT
* * *
4681733 GGTACTAGATTCGTCGTTGGGGCTTAAATCTTT-CCTATCATATCCTCGT
1 GGTACTAGATTCGTTGTTGCGGCTTAAATCTTTCCCT-TCATATCTTCGT
* ** *
4681782 GGTACTGGATTCACTGTTGCGGCTTAAATCTTTCCCATCATATCTTCGT
1 GGTACTAGATTCGTTGTTGCGGCTTAAATCTTTCCCTTCATATCTTCGT
* * ** * * * *
4681831 GATACTAGGTTCGCCGTTGCAGCTTAAATCTTTCCCGTCAT-GCTTCTGA
1 GGTACTAGATTCGTTGTTGCGGCTTAAATCTTTCCCTTCATATCTTC-GT
** * * * * * * *
4681880 GGTAGAACG-TTTGCTATTGCGACTTAAACCTTTCCCTCCATATCTTCAT
1 GGTACTA-GATTCGTTGTTGCGGCTTAAATCTTTCCCTTCATATCTTCGT
* * ** * *
4681929 GGTACTGGATTTGCCGTTGCGGTTTAAATCTTTCCCTTCAT-GCTTC-T
1 GGTACTAGATTCGTTGTTGCGGCTTAAATCTTTCCCTTCATATCTTCGT
* * *** * * * *
4681976 AAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCATTCAAATCTTCGT
1 --GGTACTAGATTCGTTGTTGCGGCTTAAATCTTTCCCTTCATATCTTCGT
* * *** * * *
4682027 GGTATTGGATTCACCGTTGCTGCTTAAATCTTTCCCATAATATCT
1 GGTACTAGATTCGTTGTTGCGGCTTAAATCTTTCCCTTCATATCT
4682072 GCTAAGGTAC
Statistics
Matches: 258, Mismatches: 70, Indels: 22
0.74 0.20 0.06
Matches are distributed among these distances:
47 1 0.00
48 12 0.05
49 232 0.90
50 12 0.05
51 1 0.00
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (49 bp):
GGTACTAGATTCGTTGTTGCGGCTTAAATCTTTCCCTTCATATCTTCGT
Found at i:4681900 original size:98 final size:98
Alignment explanation
Indices: 4681700--4682062 Score: 315
Period size: 98 Copynumber: 3.7 Consensus size: 98
4681690 AGGTTCGTTG
* * * * * * **
4681700 TTGCGACTTAAACATTTCCCTTTAAATCTTCGTGGTACTAGATTCGTCGTTGGGGCTTAAATCTT
1 TTGCGACTTAAACCTTTCCCATCATATCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATCTT
** * * ** **
4681765 TCCTATCATATCCTCGT--GGTAC-TGGATTCACTG
66 TCCCGTCAT-GCTTC-TAAGGTACAACG-TTCACCA
* * *
4681798 TTGCGGCTTAAATCTTTCCCATCATATCTTCGTGATACTAGG-TTCGCCGTTGCAGCTTAAATCT
1 TTGCGACTTAAACCTTTCCCATCATATCTTCGTGGTACT-GGATTCGCCGTTGCAGCTTAAATCT
* * ** *
4681862 TTCCCGTCATGCTTCTGAGGTAGAACGTTTGCTA
65 TTCCCGTCATGCTTCTAAGGTACAACGTTCACCA
* * * *
4681896 TTGCGACTTAAACCTTTCCC-TCCATATCTTCATGGTACTGGATTTGCCGTTGCGGTTTAAATCT
1 TTGCGACTTAAACCTTTCCCAT-CATATCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATCT
* * *
4681960 TTCCCTTCATGCTTCTAAGGTACAAGGTTCACCG
65 TTCCCGTCATGCTTCTAAGGTACAACGTTCACCA
* * * *
4681994 TTGCGACTTAAACCTTT-CCATTCAAATCTTCGTGGTATTGGATTCACCGTTGCTGCTTAAATCT
1 TTGCGACTTAAACCTTTCCCA-TCATATCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATCT
4682058 TTCCC
65 TTCCC
4682063 ATAATATCTG
Statistics
Matches: 214, Mismatches: 43, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
96 1 0.00
97 8 0.04
98 202 0.94
99 3 0.01
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (98 bp):
TTGCGACTTAAACCTTTCCCATCATATCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATCTT
TCCCGTCATGCTTCTAAGGTACAACGTTCACCA
Found at i:4681963 original size:196 final size:195
Alignment explanation
Indices: 4681700--4682062 Score: 439
Period size: 196 Copynumber: 1.9 Consensus size: 195
4681690 AGGTTCGTTG
** * * *
4681700 TTGCGACTTAAACATTTCCCTTTAAATCTTCGTGGTACTAGATTCGTCGTTGGGGCTTAAATCTT
1 TTGCGACTTAAACATTTCCCTCCAAATCTTCATGGTACTAGATTCGCCGTTGCGGCTTAAATCTT
* * * * * *
4681765 T-CCTATCATATCCTCGT-GGTAC-TGGATTCACTGTTGCGGCTTAAATCTTTCCCA-TCATATC
66 TCCCT-TCAT-GCCTC-TAGGTACAAGG-TTCACCGTTGCGACTTAAACCTTT-CCATTCAAATC
*
4681826 TTCGTGATACTAGG-TTCGCCGTTGCAGCTTAAATCTTTCCCGTCATGCTTCTGAGGTAGAACGT
126 TTCGTGATA-TAGGATTCACCGTTGCAGCTTAAATCTTTCCCGTCATGCTTCTGAGGTAGAACGT
4681890 TTGCTA
190 TTGCTA
* * * * *
4681896 TTGCGACTTAAACCTTTCCCTCCATATCTTCATGGTACTGGATTTGCCGTTGCGGTTTAAATCTT
1 TTGCGACTTAAACATTTCCCTCCAAATCTTCATGGTACTAGATTCGCCGTTGCGGCTTAAATCTT
*
4681961 TCCCTTCATGCTTCTAAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCATTCAAATCTTCG
66 TCCCTTCATGCCTCT-AGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCATTCAAATCTTCG
* * *
4682026 TGGTATTGGATTCACCGTTGCTGCTTAAATCTTTCCC
130 TGATATAGGATTCACCGTTGCAGCTTAAATCTTTCCC
4682063 ATAATATCTG
Statistics
Matches: 140, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
194 1 0.01
195 9 0.06
196 125 0.89
197 5 0.04
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (195 bp):
TTGCGACTTAAACATTTCCCTCCAAATCTTCATGGTACTAGATTCGCCGTTGCGGCTTAAATCTT
TCCCTTCATGCCTCTAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCATTCAAATCTTCGT
GATATAGGATTCACCGTTGCAGCTTAAATCTTTCCCGTCATGCTTCTGAGGTAGAACGTTTGCTA
Found at i:4682070 original size:147 final size:145
Alignment explanation
Indices: 4681682--4682071 Score: 344
Period size: 147 Copynumber: 2.6 Consensus size: 145
4681672 TTATGTTCTT
** * * * *
4681682 TAGGTACAAGGTTCGTTGTTGCGACTTAAACATTTCCCTTTAAATCTTCGTGGTACTAGATTCGT
1 TAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTA-TGGATTCGC
* * * * *
4681747 CGTTGGGGCTTAAATCTTTCCTATCATATCCTCGTGGTACTGGATTCACTGTTGCGGCTTAAATC
65 CGTT-GCGCTTAAATCTTTCCCATCATATCTTCATGGTACTGGATTCACCGTTGCGGCTTAAATC
* *
4681812 TTTCCCATCATATCTTCG
129 TTTCCCTTCAT-GCTTCG
* * * * * *
4681830 T-GATACTAGGTTCGCCGTTGC-AGCTTAAATCTTTCCCGTC--ATGCTTCTGAGGTA-GAACGT
1 TAGGTACAAGGTTCGCCGTTGCGA-CTTAAACCTTTCCCTTCAAAT-CTTC-GTGGTATGGA--T
* ** * ** *
4681890 TTGCTATTGCGACTTAAACCTTTCCC-TCCATATCTTCATGGTACTGGATTTGCCGTTGCGGTTT
61 TCGCCGTTGCG-CTTAAATCTTTCCCAT-CATATCTTCATGGTACTGGATTCACCGTTGCGGCTT
4681954 AAATCTTTCCCTTCATGCTTC-
124 AAATCTTTCCCTTCATGCTTCG
* * *
4681975 TAAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCATTCAAATCTTCGTGGTATTGGATTCA
1 T-AGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTA-TGGATTCG
*
4682040 CCGTTGCTGCTTAAATCTTTCCCATAATATCT
64 CCGTTGC-GCTTAAATCTTTCCCATCATATCT
4682072 GCTAAGGTAC
Statistics
Matches: 186, Mismatches: 40, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
145 4 0.02
146 12 0.06
147 158 0.85
148 8 0.04
149 4 0.02
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.38
Consensus pattern (145 bp):
TAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTATGGATTCGCC
GTTGCGCTTAAATCTTTCCCATCATATCTTCATGGTACTGGATTCACCGTTGCGGCTTAAATCTT
TCCCTTCATGCTTCG
Found at i:4682713 original size:112 final size:112
Alignment explanation
Indices: 4682507--4682718 Score: 273
Period size: 112 Copynumber: 1.9 Consensus size: 112
4682497 CTTATATCGT
* * * *
4682507 TTAGACCACTAACTGTCATTTCAATGCAAAAATGCTTGCATAGGGTTGTAAGGTGGATAAAATTG
1 TTAGACCACTAACTGTCACTTCAATGCAAAAATGCTTGAACAGGGTTGTAAGATGGATAAAATTG
* * *
4682572 AATTTTATTGGAGGCAAAGCTCGCGTGAATGAAAATATTAAGAATCA
66 AATTTGATTGAAGGCAAAGCTCGCATGAATGAAAATATTAAGAATCA
* * * * * * *
4682619 TTAGTCCACTAGCTGTTACTTCAATGCAAACATGCTTGAACATGGTTGTGAGATGGATGAAATTG
1 TTAGACCACTAACTGTCACTTCAATGCAAAAATGCTTGAACAGGGTTGTAAGATGGATAAAATTG
*
4682684 AATTTGATTGAAGGTAAAGC-CTGCATGAATGAAAA
66 AATTTGATTGAAGGCAAAGCTC-GCATGAATGAAAA
4682719 GGTCATTGGT
Statistics
Matches: 84, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
111 1 0.01
112 83 0.99
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (112 bp):
TTAGACCACTAACTGTCACTTCAATGCAAAAATGCTTGAACAGGGTTGTAAGATGGATAAAATTG
AATTTGATTGAAGGCAAAGCTCGCATGAATGAAAATATTAAGAATCA
Found at i:4687357 original size:29 final size:29
Alignment explanation
Indices: 4687322--4687377 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
4687312 TTGTCATGTC
*
4687322 ATTTCATAGAAAATGCAAATGATCATAAT
1 ATTTCATAGAAAATGCAAAGGATCATAAT
4687351 ATTTCATAGAAAATGCAAAGGATCATA
1 ATTTCATAGAAAATGCAAAGGATCATA
4687378 TATAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (29 bp):
ATTTCATAGAAAATGCAAAGGATCATAAT
Found at i:4688366 original size:11 final size:11
Alignment explanation
Indices: 4688344--4688385 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
4688334 TTTAAATTTT
4688344 TAAAAATAAAAA
1 TAAAAAT-AAAA
4688356 TAAAAATAAAA
1 TAAAAATAAAA
*
4688367 T-AAAATGAAA
1 TAAAAATAAAA
*
4688377 TGAAAATAA
1 TAAAAATAA
4688386 TCAAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 9 0.33
11 11 0.41
12 7 0.26
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:4690274 original size:12 final size:12
Alignment explanation
Indices: 4690257--4690282 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4690247 ACATTTTAAA
4690257 TTAATTTAAAAT
1 TTAATTTAAAAT
4690269 TTAATTTAAAAT
1 TTAATTTAAAAT
4690281 TT
1 TT
4690283 TTATTTTTTT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTAATTTAAAAT
Found at i:4690309 original size:17 final size:18
Alignment explanation
Indices: 4690286--4690321 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4690276 AAAATTTTTA
4690286 TTTTTTTGGGTTTTATTC
1 TTTTTTTGGGTTTTATTC
*
4690304 TTTTTTTGGTTTTTATTC
1 TTTTTTTGGGTTTTATTC
4690322 CCCAAGCCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.14, T:0.75
Consensus pattern (18 bp):
TTTTTTTGGGTTTTATTC
Found at i:4696428 original size:29 final size:29
Alignment explanation
Indices: 4696362--4696425 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
4696352 TCGAAACTCG
4696362 AAAAGTAAAAAGACTAACATTGATCAATT
1 AAAAGTAAAAAGACTAACATTGATCAATT
* *
4696391 CAAAAAGTAAAGAGACTAAGATTGATCAAATT
1 --AAAAGTAAAAAGACTAACATTGATC-AATT
4696423 AAA
1 AAA
4696426 GTATAAGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 3 0.10
31 23 0.77
32 4 0.13
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.22
Consensus pattern (29 bp):
AAAAGTAAAAAGACTAACATTGATCAATT
Found at i:4704575 original size:21 final size:21
Alignment explanation
Indices: 4704546--4704586 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4704536 GCATATCCAT
* * *
4704546 ATCACATTTATCAGGAAAAGG
1 ATCAAATTTATAAGAAAAAGG
4704567 ATCAAATTTATAAGAAAAAG
1 ATCAAATTTATAAGAAAAAG
4704587 AGAAGGAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (21 bp):
ATCAAATTTATAAGAAAAAGG
Found at i:4706953 original size:14 final size:15
Alignment explanation
Indices: 4706934--4706962 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4706924 AAGTATAGTA
4706934 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
4706948 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
4706963 GAGAGACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:4710779 original size:21 final size:21
Alignment explanation
Indices: 4710746--4710790 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4710736 GATTTTTTTA
4710746 TTTTGATACTTTATTTATATAT
1 TTTTGATACTTTATTTATAT-T
* *
4710768 TTTTTATA-TTTATTTCTATT
1 TTTTGATACTTTATTTATATT
4710788 TTT
1 TTT
4710791 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 10 0.48
22 7 0.33
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTGATACTTTATTTATATT
Found at i:4714348 original size:26 final size:24
Alignment explanation
Indices: 4714298--4714349 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 24
4714288 TTAAAATTAT
*
4714298 ATTTTTAAAAAAATGAAATTGAAA
1 ATTTTTAAAAAAATGAAATTAAAA
**
4714322 ATTTTTAAAATGAAATTTAATTAAAA
1 ATTTTTAAAA--AAATGAAATTAAAA
4714348 AT
1 AT
4714350 ATAAATGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 10 0.43
26 13 0.57
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (24 bp):
ATTTTTAAAAAAATGAAATTAAAA
Found at i:4723224 original size:23 final size:23
Alignment explanation
Indices: 4723197--4723245 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
4723187 ATTTTAGGGT
* *
4723197 AAATTTTGTATTTTATTTTGATA
1 AAATTTTATATTTTATTTTCATA
4723220 AAATTTTATATTTTATTTTCATA
1 AAATTTTATATTTTATTTTCATA
4723243 AAA
1 AAA
4723246 AAATTAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (23 bp):
AAATTTTATATTTTATTTTCATA
Found at i:4723419 original size:15 final size:15
Alignment explanation
Indices: 4723373--4723431 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 15
4723363 GTAATAAAAT
*
4723373 AATAA-TAAAATGTA
1 AATAATTAAAATATA
* * *
4723387 AGTGATTAAAACAT-
1 AATAATTAAAATATA
* *
4723401 AATATTTTAAATATA
1 AATAATTAAAATATA
4723416 AATAATTAAAATATA
1 AATAATTAAAATATA
4723431 A
1 A
4723432 TTTAACACAG
Statistics
Matches: 32, Mismatches: 11, Indels: 3
0.70 0.24 0.07
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (15 bp):
AATAATTAAAATATA
Found at i:4724869 original size:15 final size:16
Alignment explanation
Indices: 4724839--4724873 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
4724829 TTAAATTAAA
4724839 TAAATAATTAAAATAT
1 TAAATAATTAAAATAT
*
4724855 TAAAT-ATTTAAATAT
1 TAAATAATTAAAATAT
4724870 TAAA
1 TAAA
4724874 AACATTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATAATTAAAATAT
Found at i:4728370 original size:25 final size:25
Alignment explanation
Indices: 4728324--4728372 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
4728314 AGAGCCAAAC
** **
4728324 AAAATATGCCATGAAGGTAACATAT
1 AAAATATGCCACAAAGACAACATAT
4728349 AAAATATGCCACAAAGACAACATA
1 AAAATATGCCACAAAGACAACATA
4728373 CAGAATCACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.18
Consensus pattern (25 bp):
AAAATATGCCACAAAGACAACATAT
Found at i:4729170 original size:2 final size:2
Alignment explanation
Indices: 4729163--4729212 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
4729153 CTATTACCTT
*
4729163 CA CA CA CA CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
4729205 CA CA CA CA
1 CA CA CA CA
4729213 TATATATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:4730523 original size:61 final size:61
Alignment explanation
Indices: 4730407--4730523 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
4730397 AAATAAACTT
* * *
4730407 CAAATCTTGAACCCAAATAAAAAATTCCTAAATTAAGAACTCCCAATTTGAAAACCTCTTC
1 CAAATCTTAAACCCAAATAAAAAATTCCTAAATAAAGAACTCCCAAATTGAAAACCTCTTC
** * *
4730468 CAAATCTTAAACCCAAATCGAAAATTCCTAAATAAAGAACTCCTAAATTGGAAACC
1 CAAATCTTAAACCCAAATAAAAAATTCCTAAATAAAGAACTCCCAAATTGAAAACC
4730524 CATAAATCAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (61 bp):
CAAATCTTAAACCCAAATAAAAAATTCCTAAATAAAGAACTCCCAAATTGAAAACCTCTTC
Found at i:4733072 original size:48 final size:48
Alignment explanation
Indices: 4733001--4733097 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
4732991 TCTAACCCGA
4733001 ATCTAATTTAACCCGACCTATAAACACCTTTAAGCTCTACGTTTCGAC
1 ATCTAATTTAACCCGACCTATAAACACCTTTAAGCTCTACGTTTCGAC
4733049 ATCTAATTTAACCCGACCTATAAACACCTTTAAGCTCTACGTTTCGAC
1 ATCTAATTTAACCCGACCTATAAACACCTTTAAGCTCTACGTTTCGAC
4733097 A
1 A
4733098 ACTTCTTCCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.32, C:0.29, G:0.08, T:0.31
Consensus pattern (48 bp):
ATCTAATTTAACCCGACCTATAAACACCTTTAAGCTCTACGTTTCGAC
Found at i:4748505 original size:13 final size:13
Alignment explanation
Indices: 4748487--4748512 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4748477 AATATTAAAA
4748487 TATTAAATTTATT
1 TATTAAATTTATT
4748500 TATTAAATTTATT
1 TATTAAATTTATT
4748513 AAAAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTAAATTTATT
Found at i:4752372 original size:23 final size:23
Alignment explanation
Indices: 4752341--4752392 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
4752331 CCATATTGAA
*
4752341 TTTTTAAAAAA-TATATATAAAT
1 TTTTTAAAAAAGAATATATAAAT
* *
4752363 TTTTTAAAAAAGAATTTATCAAT
1 TTTTTAAAAAAGAATATATAAAT
4752386 TTTTTAA
1 TTTTTAA
4752393 TTATTTTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTTTAAAAAAGAATATATAAAT
Found at i:4754051 original size:19 final size:21
Alignment explanation
Indices: 4754012--4754051 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
4754002 TTAATTGTAA
4754012 TTAATTAAATGAAAATGATAT
1 TTAATTAAATGAAAATGATAT
*
4754033 TTAA-TAAAT-AAAATTATAT
1 TTAATTAAATGAAAATGATAT
4754052 AGTTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 5 0.28
21 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
TTAATTAAATGAAAATGATAT
Found at i:4757747 original size:26 final size:22
Alignment explanation
Indices: 4757693--4757735 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
4757683 GCGCTTACTG
4757693 TTCAGCACTGTGTGTGCTTCTA
1 TTCAGCACTGTGTGTGCTTCTA
4757715 TTCAGCACTGTGTGTGCTTCT
1 TTCAGCACTGTGTGTGCTTCT
4757736 GTTTCCCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (22 bp):
TTCAGCACTGTGTGTGCTTCTA
Found at i:4760422 original size:18 final size:18
Alignment explanation
Indices: 4760399--4760441 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4760389 ATTTAAGGTG
*
4760399 TAATTAATTTAAAT-TTTT
1 TAATTAA-TTAAATCTATT
4760417 TAATTAATTAAATCTATT
1 TAATTAATTAAATCTATT
4760435 TAATTAA
1 TAATTAA
4760442 AAATATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAATCTATT
Found at i:4767983 original size:2 final size:2
Alignment explanation
Indices: 4767976--4768007 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4767966 AGCAGTTGCA
*
4767976 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4768008 TTTTTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4768710 original size:3 final size:3
Alignment explanation
Indices: 4768702--4768735 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4768692 GTATTAAAAG
4768702 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4768736 AACTGGGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4772121 original size:1 final size:1
Alignment explanation
Indices: 4772115--4772141 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
4772105 AAACAAATCT
4772115 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
4772142 ACCAACAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:4772590 original size:19 final size:18
Alignment explanation
Indices: 4772568--4772621 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
4772558 TAAAAAAACC
4772568 TATAATATTTAATTTTTAT
1 TATAATATTTAATTTTT-T
*
4772587 TATAATTTTTTAA-TTTTT
1 TATAA-TATTTAATTTTTT
4772605 T-TAATATATTAATTTTT
1 TATAATAT-TTAATTTTT
4772622 CTCTTTAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 2 0.07
17 7 0.23
18 6 0.20
19 9 0.30
20 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATAATATTTAATTTTTT
Found at i:4772609 original size:17 final size:18
Alignment explanation
Indices: 4772568--4772621 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
4772558 TAAAAAAACC
4772568 TATAATA-TTTAATTTTTAT
1 TATAATATTTTAA-TTTT-T
*
4772587 TATAATTTTTTAATTTTT
1 TATAATATTTTAATTTTT
*
4772605 T-TAATATATTAATTTTT
1 TATAATATTTTAATTTTT
4772622 CTCTTTAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 14 0.45
18 2 0.06
19 10 0.32
20 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATAATATTTTAATTTTT
Found at i:4776846 original size:141 final size:141
Alignment explanation
Indices: 4776553--4776862 Score: 405
Period size: 140 Copynumber: 2.2 Consensus size: 141
4776543 ATATTATTTT
* *
4776553 TATAATCTTAAAAATTAAATCTAAAAATTGTATGTAAAATATTATAATATACAAATTATTATTAC
1 TATAATCTTAAATATTAAATCT--AAA-T-TATGTAAAATATTATAATATAAAAATTATTATTAC
*
4776618 AAACTAAAAAAACAACATATTAAAACTATCTTAATCTATTCCTACAACTTAAACACAAATATAAC
62 AAACTAAAAAAACAACATATTAAAACTATCTTAATCTATTCCTACAACTTAAACACAAATACAAC
*
4776683 TTTAACAAATAAAAA
127 TTTAACAAACAAAAA
* *
4776698 TAAAATCTTAAATATTAAATCTAAA-TATGTAAAATATTATAATATAAAAATTATTATTACAAAT
1 TATAATCTTAAATATTAAATCTAAATTATGTAAAATATTATAATATAAAAATTATTATTACAAAC
* * * *
4776762 TAAAAAAA-ACCATACATTAAAACTGTCTTAATCTA-TCCTTACATCTTAAACGCAAATACAATC
66 TAAAAAAACAACAT--ATTAAAACTATCTTAATCTATTCC-TACAACTTAAACACAAATACAA-C
* *
4776825 TTT-ACTAACAACAA
127 TTTAACAAACAAAAA
4776839 TATAATCTT-AATATTAAATCTAAA
1 TATAATCTTAAATATTAAATCTAAA
4776863 ATTAACAATA
Statistics
Matches: 148, Mismatches: 13, Indels: 13
0.85 0.07 0.07
Matches are distributed among these distances:
139 4 0.03
140 63 0.43
141 54 0.36
142 4 0.03
143 3 0.02
145 20 0.14
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.34
Consensus pattern (141 bp):
TATAATCTTAAATATTAAATCTAAATTATGTAAAATATTATAATATAAAAATTATTATTACAAAC
TAAAAAAACAACATATTAAAACTATCTTAATCTATTCCTACAACTTAAACACAAATACAACTTTA
ACAAACAAAAA
Found at i:4780974 original size:22 final size:22
Alignment explanation
Indices: 4780933--4780973 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4780923 ACACTTTACT
*
4780933 TTTTTTAAAATAAATTAAAATA
1 TTTTTTAAAATAAATAAAAATA
4780955 TTTTTTAAAA-AAATAAAAA
1 TTTTTTAAAATAAATAAAAA
4780974 AATCATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTTTAAAATAAATAAAAATA
Found at i:4781137 original size:15 final size:15
Alignment explanation
Indices: 4781102--4781131 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4781092 AATTTTTAAC
4781102 ATTTAATTTCTTATT
1 ATTTAATTTCTTATT
*
4781117 ATTTAATTTTTTATT
1 ATTTAATTTCTTATT
4781132 TATTAAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTAATTTCTTATT
Found at i:4785369 original size:20 final size:19
Alignment explanation
Indices: 4785332--4785383 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
4785322 TATATTTTTT
4785332 AATTTATAAAAATGATTAA
1 AATTTATAAAAATGATTAA
* *
4785351 AATTTAATAAATATTATTAA
1 AATTT-ATAAAAATGATTAA
* *
4785371 AAATTAGAAAAAT
1 AATTTATAAAAAT
4785384 AAAAAATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (19 bp):
AATTTATAAAAATGATTAA
Found at i:4785384 original size:25 final size:26
Alignment explanation
Indices: 4785356--4785414 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
4785346 ATTAAAATTT
*
4785356 AATAAATATTATTAAAAAT-TAGAAA
1 AATAAATAATATTAAAAATATAGAAA
* * *
4785381 AATAAAAAATATTAATAATATATAAA
1 AATAAATAATATTAAAAATATAGAAA
*
4785407 AATTAATA
1 AATAAATA
4785415 GAAGGGCATA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (26 bp):
AATAAATAATATTAAAAATATAGAAA
Found at i:4788307 original size:17 final size:17
Alignment explanation
Indices: 4788285--4788320 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4788275 TTACTTCTTT
4788285 ACCCAAATGAAGAACAA
1 ACCCAAATGAAGAACAA
4788302 ACCCAAATGAAGAACAA
1 ACCCAAATGAAGAACAA
4788319 AC
1 AC
4788321 GATTAATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.25, G:0.11, T:0.06
Consensus pattern (17 bp):
ACCCAAATGAAGAACAA
Found at i:4795935 original size:10 final size:10
Alignment explanation
Indices: 4795920--4795949 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
4795910 CCAAAGCTTC
4795920 ATTTTAATAT
1 ATTTTAATAT
*
4795930 ATTTTAAAAT
1 ATTTTAATAT
4795940 ATTTTAATAT
1 ATTTTAATAT
4795950 GCACAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:4808006 original size:24 final size:21
Alignment explanation
Indices: 4807983--4808024 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4807973 ATAATGATAG
*
4807983 AGTAATTTATAAAAAAAATTAT
1 AGTAATTT-TAAAAAAAATGAT
*
4808005 AGTAATTTTAAAAAATATGA
1 AGTAATTTTAAAAAAAATGA
4808025 AAAACATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (21 bp):
AGTAATTTTAAAAAAAATGAT
Found at i:4808611 original size:20 final size:20
Alignment explanation
Indices: 4808560--4808602 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
4808550 TATAAAAAAT
*
4808560 AAAAGTCAAATTAATTTTCA
1 AAAAATCAAATTAATTTTCA
*
4808580 AAAAATCAAATTAATTTTTA
1 AAAAATCAAATTAATTTTCA
4808600 AAA
1 AAA
4808603 TTCTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAATCAAATTAATTTTCA
Found at i:4808639 original size:18 final size:18
Alignment explanation
Indices: 4808613--4808647 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4808603 TTCTAAATTT
*
4808613 TATATTTTTTTAAAAAAC
1 TATAATTTTTTAAAAAAC
4808631 TATAATTTTTTAAAAAA
1 TATAATTTTTTAAAAAA
4808648 ATCTAAAGAA
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TATAATTTTTTAAAAAAC
Found at i:4817671 original size:31 final size:32
Alignment explanation
Indices: 4817627--4817693 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
4817617 GTTCAATTGA
* *
4817627 TACTTAAACTTGAC-ATTTTTTCTTAATTTGG
1 TACTCAAACTTGACAATTTTTTCTTAAGTTGG
* *
4817658 TACTCAAAGTTGACAATTTTTTTTTAAGTTGG
1 TACTCAAACTTGACAATTTTTTCTTAAGTTGG
4817690 TACT
1 TACT
4817694 TAAATTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (32 bp):
TACTCAAACTTGACAATTTTTTCTTAAGTTGG
Found at i:4818047 original size:31 final size:32
Alignment explanation
Indices: 4817937--4818048 Score: 87
Period size: 31 Copynumber: 3.6 Consensus size: 32
4817927 AGTGTTTTGG
*
4817937 TATCAAATTAAGAA-AAAAAATGTCAAGTTCA-A
1 TATCAAATT--GAATAAAAAATATCAAGTTCAGA
* **
4817969 CTATCAAATTGGATCCAAAA-AT--AG-TCTAGA
1 -TATCAAATTGAATAAAAAATATCAAGTTC-AGA
4817999 TATCAAATT--ATGAAAAAATATCAAGTTCAGA
1 TATCAAATTGAAT-AAAAAATATCAAGTTCAGA
4818030 TATCAAATTGAATAAAAAA
1 TATCAAATTGAATAAAAAA
4818049 ATTAGGTACC
Statistics
Matches: 63, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
27 2 0.03
28 6 0.10
29 14 0.22
30 1 0.02
31 17 0.27
32 12 0.19
33 11 0.17
ACGTcount: A:0.53, C:0.11, G:0.10, T:0.27
Consensus pattern (32 bp):
TATCAAATTGAATAAAAAATATCAAGTTCAGA
Found at i:4828687 original size:3 final size:3
Alignment explanation
Indices: 4828679--4828740 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
4828669 TATGAAGTAG
4828679 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGGA A-A AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA
* *
4828723 AGG AGG AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA
4828741 GAAAATTTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
2 4 0.07
3 48 0.87
4 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4830973 original size:15 final size:17
Alignment explanation
Indices: 4830953--4830985 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
4830943 TCAGAAACAC
4830953 TTTTGAGA-AAAA-TAT
1 TTTTGAGATAAAAGTAT
4830968 TTTTGAGATAAAAGTAT
1 TTTTGAGATAAAAGTAT
4830985 T
1 T
4830986 ATTAAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (17 bp):
TTTTGAGATAAAAGTAT
Found at i:4834175 original size:14 final size:14
Alignment explanation
Indices: 4834153--4834203 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
4834143 CAAAATATAA
*
4834153 TTTGTTTTTTAGAT
1 TTTGATTTTTAGAT
* * *
4834167 TTTGATTTTGAAAA
1 TTTGATTTTTAGAT
*
4834181 TTTGTTTTTTAGAT
1 TTTGATTTTTAGAT
4834195 TTTGATTTT
1 TTTGATTTT
4834204 GAAAATTAAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.67
Consensus pattern (14 bp):
TTTGATTTTTAGAT
Found at i:4834191 original size:28 final size:28
Alignment explanation
Indices: 4834151--4834210 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
4834141 ATCAAAATAT
4834151 AATTTGTTTTTTAGATTTTGATTTTGAA
1 AATTTGTTTTTTAGATTTTGATTTTGAA
4834179 AATTTGTTTTTTAGATTTTGATTTTGAA
1 AATTTGTTTTTTAGATTTTGATTTTGAA
4834207 AATT
1 AATT
4834211 AATTTAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (28 bp):
AATTTGTTTTTTAGATTTTGATTTTGAA
Found at i:4835324 original size:19 final size:19
Alignment explanation
Indices: 4835281--4835339 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
4835271 ATTACAAAAT
* *
4835281 AATTCAAAATAAATTTCAA
1 AATTCAAAATAATTTTTAA
4835300 AGATTCAAAATAATTTTTAA
1 A-ATTCAAAATAATTTTTAA
*
4835320 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTTTTAA
4835338 AA
1 AA
4835340 ATTCCAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.25
19 10 0.28
20 17 0.47
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (19 bp):
AATTCAAAATAATTTTTAA
Found at i:4835340 original size:19 final size:19
Alignment explanation
Indices: 4835281--4835348 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
4835271 ATTACAAAAT
*
4835281 AATTCAAAATAAATTTCAAA
1 AATTCAAAAT-AATTTTAAA
* *
4835301 GATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTTAAA
4835320 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TAAA
4835339 AATTCCAAAA
1 AATT-CAAAA
4835349 ATTATCTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 4 0.10
19 23 0.56
20 14 0.34
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:4838917 original size:57 final size:57
Alignment explanation
Indices: 4838828--4839347 Score: 507
Period size: 57 Copynumber: 8.8 Consensus size: 57
4838818 ACCTGTTTGA
* * **
4838828 GAAAAAAAATCAAAATTTTTTGGTGTTAGCCATCAAATGATCGACACCCTCTTTTCTC
1 GAAAAAAAAT-TAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTC
* * *
4838886 GAAAAAAAATTACATTTTTAGGTGTTGGCCATCAAATGGCCGACA-CCTATTTTTCTC
1 GAAAAAAAATTAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCT-CTTTTCTC
* * * * * *
4838943 G-AAAAAAATTACATTTTTGGGTTTTGGACATCAAATGGTCGACACTCTCTTTTCTC
1 GAAAAAAAATTAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTC
4838999 GAGAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCC-CATTTTCTC
1 GA-AAAAAAA-TT-AAA-TTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTC-TTTTCTC
** * * *
4839060 -AAAAAAATATTGCATTTTTGGGTGTTGGCCATCAAATGGTCGACATCGCC-CTATTCTC
1 GAAAAAAA-ATTAAATTTTTTGGTGTTGGCCATCAAATGGCCGACA-C-CCTCTTTTCTC
*
4839118 GAGAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTC
1 GA-AAAAAAA-TT--AAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTC
** * * *
4839179 -AAAAAAATATTGCATTTTTGGGTGTTGGCCATCAAATGGTCGACATCGCC-CTATTCTC
1 GAAAAAAA-ATTAAATTTTTTGGTGTTGGCCATCAAATGGCCGACA-C-CCTCTTTTCTC
*
4839237 GAGAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTTTTTCTC
1 GA-AAAAAAA-TT-AAA-TTTTTTGGTGTTGGCCATCAAATGGCCGACA-CCCTCTTTTCTC
* * *
4839299 GAGAAAAAATTTCAAATTTTTTTGGTGTTGGTCAT-AAATGGCCAACACC
1 GA-AAAAAAATT-AAA-TTTTTTGGTGTTGGCCATCAAATGGCCGACACC
4839348 AACTTCTCCT
Statistics
Matches: 392, Mismatches: 44, Indels: 51
0.80 0.09 0.10
Matches are distributed among these distances:
56 50 0.13
57 98 0.25
58 33 0.08
59 29 0.07
60 36 0.09
61 71 0.18
62 75 0.19
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (57 bp):
GAAAAAAAATTAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTC
Found at i:4839355 original size:119 final size:118
Alignment explanation
Indices: 4838842--4839308 Score: 662
Period size: 119 Copynumber: 4.0 Consensus size: 118
4838832 AAAAATCAAA
* * * *
4838842 ATTTTTTGGTGTTAGCCATCAAATGATCGACA-C-CCTCTTTTCTCGA-AAAAAAA-TT-ACA-T
1 ATTTTTGGGTGTTGGCCATCAAATGGTCGACATCGCC-C-TTTCTCGAGAAAAAAATTTCAAATT
* ** * *
4838901 TTTTAGGTGTTGGCCATCAAATGGCCGACACCTATTTTTCTCGAAAAAA-ATTAC
64 TTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTTTTCTCAAAAAAATATTGC
* * * *
4838955 ATTTTTGGGTTTTGGACATCAAATGGTCGACACTC-TCTTTTCTCGAGAAAAAAATTTCAAATTT
1 ATTTTTGGGTGTTGGCCATCAAATGGTCGACA-TCGCCCTTTCTCGAGAAAAAAATTTCAAATTT
*
4839019 TTTTGGTGTTGGCCATCAAATGGCCGACACCCCATTTTCTCAAAAAAATATTGC
65 TTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTTTTCTCAAAAAAATATTGC
*
4839073 ATTTTTGGGTGTTGGCCATCAAATGGTCGACATCGCCCTATTCTCGAGAAAAAAATTTCAAAATT
1 ATTTTTGGGTGTTGGCCATCAAATGGTCGACATCGCCCT-TTCTCGAGAAAAAAATTTCAAATTT
*
4839138 TTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTTTTCTCAAAAAAATATTGC
65 TTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTTTTCTCAAAAAAATATTGC
4839192 ATTTTTGGGTGTTGGCCATCAAATGGTCGACATCGCCCTATTCTCGAGAAAAAAATTTCAAATTT
1 ATTTTTGGGTGTTGGCCATCAAATGGTCGACATCGCCCT-TTCTCGAGAAAAAAATTTCAAATTT
4839257 TTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTTTTTCTCGAGAAAAAAT
65 TTTTGGTGTTGGCCATCAAATGGCCGACACCCC-TTTTTCTC-A-AAAAAAT
4839309 TTCAAATTTT
Statistics
Matches: 320, Mismatches: 22, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
113 35 0.11
114 7 0.02
115 4 0.01
116 2 0.01
117 47 0.15
118 36 0.11
119 174 0.54
120 7 0.02
121 1 0.00
122 7 0.02
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (118 bp):
ATTTTTGGGTGTTGGCCATCAAATGGTCGACATCGCCCTTTCTCGAGAAAAAAATTTCAAATTTT
TTTGGTGTTGGCCATCAAATGGCCGACACCCCTTTTTCTCAAAAAAATATTGC
Found at i:4840227 original size:30 final size:30
Alignment explanation
Indices: 4840193--4840258 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
4840183 GAAAGAAAAA
*
4840193 TTAAAATATACAA-GAAATT-CGAAATTAAAT
1 TTAAAATA-AAAATGAAATTAC-AAATTAAAT
4840223 TTAAAATAAAAATGAAATTACAAATTAAAT
1 TTAAAATAAAAATGAAATTACAAATTAAAT
4840253 TTAAAA
1 TTAAAA
4840259 AGTAAAGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 3 0.09
30 29 0.88
31 1 0.03
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (30 bp):
TTAAAATAAAAATGAAATTACAAATTAAAT
Found at i:4842498 original size:21 final size:20
Alignment explanation
Indices: 4842474--4842512 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4842464 CATAATATGA
4842474 CGGATGAAACTCGATCAACGG
1 CGGAT-AAACTCGATCAACGG
* *
4842495 CGGATAAAGTCGGTCAAC
1 CGGATAAACTCGATCAAC
4842513 AGTGATCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.15
Consensus pattern (20 bp):
CGGATAAACTCGATCAACGG
Found at i:4842531 original size:10 final size:10
Alignment explanation
Indices: 4842506--4842559 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
4842496 GGATAAAGTC
*
4842506 GGTCAACAGT
1 GGTCAACGGT
*
4842516 GATCAACGGT
1 GGTCAACGGT
* *
4842526 GGTCAATGGC
1 GGTCAACGGT
*
4842536 GGTCAACGAT
1 GGTCAACGGT
*
4842546 GGTCAACGGC
1 GGTCAACGGT
4842556 GGTC
1 GGTC
4842560 TCGGGACGTT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.35, T:0.19
Consensus pattern (10 bp):
GGTCAACGGT
Found at i:4842541 original size:20 final size:20
Alignment explanation
Indices: 4842518--4842559 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4842508 TCAACAGTGA
* *
4842518 TCAACGGTGGTCAATGGCGG
1 TCAACGATGGTCAACGGCGG
4842538 TCAACGATGGTCAACGGCGG
1 TCAACGATGGTCAACGGCGG
4842558 TC
1 TC
4842560 TCGGGACGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.36, T:0.19
Consensus pattern (20 bp):
TCAACGATGGTCAACGGCGG
Found at i:4842949 original size:89 final size:89
Alignment explanation
Indices: 4842734--4843451 Score: 966
Period size: 89 Copynumber: 8.1 Consensus size: 89
4842724 TGATAAAAAT
4842734 TATAAT-ATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAA
1 TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAA
* *
4842798 CA-TTTAAAATATGATAAAAATT-TTA
66 CACATT---ATATGATAAAAATTATAA
* *
4842823 -AT-ATAATAATAATAATTTTTATTTAAAGCTATAAAATTAATAAATAATATATTATCAAATCAA
1 TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAA
4842886 CACATTATATGATAAAAATTATAA
66 CACATTATATGATAAAAATTATAA
* * *
4842910 TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATACTGGATTGTCAAATCAA
1 TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAA
*
4842975 CACATTATATAATAAAAATTATAA
66 CACATTATATGATAAAAATTATAA
*
4842999 TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAA
1 TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAA
*
4843064 CA-TTTAAAATATGATAAAAATTATAATA
66 CACATT---ATATGATAAAAATTAT-A-A
*
4843092 TAATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATATATTATCAAATCA
1 T-ATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCA
4843157 ACACATTATATGAT-AAAA--AT--
65 ACACATTATATGATAAAAATTATAA
*
4843177 TATAAT-ATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTAATATCAAATCAA
1 TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAA
*
4843241 CACATTATATGATAAAAATTGTAATA
66 CACATTATATGATAAAAATTAT-A-A
* *
4843267 TAATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCGAATCA
1 T-ATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCA
4843332 ACACATTATATGATAAAAATTAT-A
65 ACACATTATATGATAAAAATTATAA
* * * *
4843356 -AT-ATAATAATAATAATTTGTACTTT-AA-ATATGAAAATTTGATAAACAATGTATTGTCAAAT
1 TATAATAATAATAATAATTTTTA-TTTAAAGATAT-AAAA-TTAATAAATAATGTATTATCAAAT
* * * * *
4843417 TAACACAATATTTGATATAAATTGTAA
63 CAACACATTATATGATAAAAATTATAA
4843444 TATAATAA
1 TATAATAA
4843452 CTATATTTTT
Statistics
Matches: 569, Mismatches: 33, Indels: 53
0.87 0.05 0.08
Matches are distributed among these distances:
83 69 0.12
84 9 0.02
85 5 0.01
86 39 0.07
87 50 0.09
88 65 0.11
89 151 0.27
90 5 0.01
91 24 0.04
92 84 0.15
93 2 0.00
94 64 0.11
95 2 0.00
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (89 bp):
TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAA
CACATTATATGATAAAAATTATAA
Found at i:4843003 original size:17 final size:17
Alignment explanation
Indices: 4842981--4843016 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4842971 TCAACACATT
*
4842981 ATATAATAAAAATTATA
1 ATATAATAAAAATAATA
*
4842998 ATATAATAATAATAATA
1 ATATAATAAAAATAATA
4843015 AT
1 AT
4843017 TTTTATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATAATAAAAATAATA
Found at i:4843194 original size:266 final size:272
Alignment explanation
Indices: 4842734--4843371 Score: 1038
Period size: 266 Copynumber: 2.4 Consensus size: 272
4842724 TGATAAAAAT
*
4842734 TATAAT-ATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAA
1 TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAA
*
4842798 CATTTAAAATATGATAAAAA-T-T--T-TAAT-ATAATAATAATAATTTTTATTTAAAGCTATAA
66 CATTTAAAATATGATAAAAATTATAATATAATAATAATAATAATAATTTTTATTTAAAGATATAA
4842857 AATTAATAAATAATATATTATCAAATCAACACATTATATGATAAAAATTATAATATAATAATAAT
131 AATTAATAAATAATATATTATCAAATCAACACATTATATGATAAAAA-TAT-ATATAATAATAAT
* * *
4842922 AATAATTTTTATTTAAAGATATAAAATTAATAAATACTGGATTGTCAAATCAACACATTATATAA
194 AATAATTTTTATTTAAAGATATAAAATTAATAAATAATGGAATATCAAATCAACACATTATATAA
4842987 TAAAAATTAT-A-A
259 TAAAAATTATAATA
4842999 TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAA
1 TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAA
4843064 CATTTAAAATATGATAAAAATTATAATATAATAATAATAATAATAATTTTTATTTAAAGATATAA
66 CATTTAAAATATGATAAAAATTATAATATAATAATAATAATAATAATTTTTATTTAAAGATATAA
4843129 AATTAATAAATAATATATTATCAAATCAACACATTATATGAT-AAAA-AT-TATAAT-ATAATAA
131 AATTAATAAATAATATATTATCAAATCAACACATTATATGATAAAAATATATATAATAATAATAA
* *
4843190 TAATTTTTATTTAAAGATATAAAATTAATAAATAATGTAATATCAAATCAACACATTATATGATA
196 TAATTTTTATTTAAAGATATAAAATTAATAAATAATGGAATATCAAATCAACACATTATATAATA
*
4843255 AAAATTGTAATA
261 AAAATTATAATA
*
4843267 TAATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCGAATCA
1 T-ATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCA
*
4843332 ACACATT---ATATGATAAAAATTATAATATAATAATAATAAT
65 ACA-TTTAAAATATGATAAAAATTATAATATAATAATAATAAT
4843372 TTGTACTTTA
Statistics
Matches: 352, Mismatches: 10, Indels: 20
0.92 0.03 0.05
Matches are distributed among these distances:
265 6 0.02
266 151 0.43
267 41 0.12
268 3 0.01
269 67 0.19
270 3 0.01
271 8 0.02
272 73 0.21
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (272 bp):
TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAA
CATTTAAAATATGATAAAAATTATAATATAATAATAATAATAATAATTTTTATTTAAAGATATAA
AATTAATAAATAATATATTATCAAATCAACACATTATATGATAAAAATATATATAATAATAATAA
TAATTTTTATTTAAAGATATAAAATTAATAAATAATGGAATATCAAATCAACACATTATATAATA
AAAATTATAATA
Found at i:4843333 original size:175 final size:176
Alignment explanation
Indices: 4842735--4843451 Score: 993
Period size: 177 Copynumber: 4.0 Consensus size: 176
4842725 GATAAAAATT
4842735 ATAAT-ATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAAC
1 ATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAAC
* * *
4842799 A-TTTAAAATATGATAAAAATTTTAATATAATAATAATAATTTTTATTTAAAGCTATAAAATTAA
66 ACATT---ATATGATAAAAATTAT-A-ATAATAATAATAATTTTTATTTAAAGATATAAAATTAA
*
4842863 TAAATAATATATTATCAAATCAACACATTATATGATAAAAATTAT-A-AT-
126 TAAATAATGTATTATCAAATCAACACATTATATGATAAAAATTATAATATA
* * *
4842911 ATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATACTGGATTGTCAAATCAAC
1 ATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAAC
*
4842976 ACATTATATAATAAAAATTATAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAA
66 ACATTATATGAT-AAAA--AT--TATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAA
* *
4843041 TAAATAATGTATTGTCAAATCAACA-TTTAAAATATGATAAAAATTATAATATA
126 TAAATAATGTATTATCAAATCAACACATT---ATATGATAAAAATTATAATATA
*
4843094 ATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATATATTATCAAATCAAC
1 ATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAAC
4843159 ACATTATATGATAAAAATTATAAT-ATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
66 ACATTATATGATAAAAATTATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
* *
4843223 AATGTAATATCAAATCAACACATTATATGATAAAAATTGTAATATA
131 AATGTATTATCAAATCAACACATTATATGATAAAAATTATAATATA
* *
4843269 ATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCGAATCAAC
1 ATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAAC
* *
4843334 ACATTATATGATAAAAATTATAATATAATAATAATAATTTGTACTTT-AA-ATATGAAAATTTGA
66 ACATTATATGATAAAAATTAT-A-ATAATAATAATAATTTTTA-TTTAAAGATAT-AAAA-TTAA
* * * * * * *
4843397 TAAACAATGTATTGTCAAATTAACACAATATTTGATATAAATTGTAATATA
126 TAAATAATGTATTATCAAATCAACACATTATATGATAAAAATTATAATATA
4843448 ATAA
1 ATAA
4843452 CTATATTTTT
Statistics
Matches: 490, Mismatches: 31, Indels: 37
0.88 0.06 0.07
Matches are distributed among these distances:
175 110 0.22
176 10 0.02
177 123 0.25
178 93 0.19
179 55 0.11
180 20 0.04
181 1 0.00
182 6 0.01
183 72 0.15
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (176 bp):
ATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTATCAAATCAAC
ACATTATATGATAAAAATTATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
AATGTATTATCAAATCAACACATTATATGATAAAAATTATAATATA
Found at i:4847496 original size:119 final size:118
Alignment explanation
Indices: 4847284--4847668 Score: 505
Period size: 119 Copynumber: 3.3 Consensus size: 118
4847274 GGAGAAGTTA
* *
4847284 GTGTCGACCATTTGATGGCCAACACCAAAAAAATTTAAAATTTTTTTCTCGAGAAAAAGAGATGT
1 GTGTCGACCATTTGATGGCCAACACC-AAAAAATTTTAAATTTTTTTCTCGAGAAAAAGAGGTGT
** *
4847349 CGGCCATTTGATGGCCAATGCCCAAAAATGCAATTTATTTTTTAGAAAAAAGGGG
65 CGGCCATTTGATGGCCAACACCCAAAAATGCAATTT-TTTTTTAGAGAAAAGGGG
* *
4847404 GTGTCGGCTATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAGAAAAAGAGGTGTC
1 GTGTCGACCATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAGAAAAAGAGGTGTC
* * * *
4847469 GGCCATTTGATGGCTAACACTCAAAAATACAA-TTTTTTTT-GAGAAAAGAGG
66 GGCCATTTGATGGCCAACACCCAAAAATGCAATTTTTTTTTAGAGAAAAGGGG
* * *
4847520 GTGTCGGCCATTTGATGGCCAACACAAAAAAATTTTGAATTTTTTTCTC-A-AACAGAA-A-GTG
1 GTGTCGACCATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAGAA-A-AAGAGGTG
*** * * *
4847581 TCGGCCATGCAATGGCCAACACCCAAAAATGTAATTTTTTTTCA-AGAAAATGGG
64 TCGGCCATTTGATGGCCAACACCCAAAAATGCAATTTTTTTTTAGAGAAAAGGGG
4847635 GTGTCGACCATTTGATGGCCAACACCAAAAAATT
1 GTGTCGACCATTTGATGGCCAACACCAAAAAATT
4847669 GTATTTTTTT
Statistics
Matches: 235, Mismatches: 26, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
114 32 0.14
115 50 0.21
116 57 0.24
117 6 0.03
118 2 0.01
119 64 0.27
120 24 0.10
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (118 bp):
GTGTCGACCATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAGAAAAAGAGGTGTC
GGCCATTTGATGGCCAACACCCAAAAATGCAATTTTTTTTTAGAGAAAAGGGG
Found at i:4847609 original size:58 final size:55
Alignment explanation
Indices: 4847283--4847679 Score: 286
Period size: 58 Copynumber: 6.8 Consensus size: 55
4847273 AGGAGAAGTT
*
4847283 AGTGTCGACCATTTGATGGCCAACACCAAAAAAATTTAAAATTTTTTTCTCGAGAAA-AA
1 AGTGTCGGCCATTTGATGGCCAACACC-AAAAAATTT--AATTTTTTT-TC-AGAAAGAA
** * ** *
4847342 GAGATGTCGGCCATTTGATGGCCAATGCCCAAAAATGCAATTTATTTTTTAGAAA-AA
1 -AG-TGTCGGCCATTTGATGGCCAACACCAAAAAATTTAATTT-TTTTTCAGAAAGAA
*
4847399 AGGGGGTGTCGGCTATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAGAAA-AA
1 A----GTGTCGGCCATTTGATGGCCAACACCAAAAAA-TTT-AATTTTTTT-TC-AGAAAGAA
* ** * *
4847461 GAGGTGTCGGCCATTTGATGGCTAACACTC-AAAAATACAATTTTTTTTGAGAAAAGAG
1 -A-GTGTCGGCCATTTGATGGCCAACAC-CAAAAAATTTAATTTTTTTTCAG-AAAGAA
* *
4847519 GGTGTCGGCCATTTGATGGCCAACACAAAAAAATTTTGAATTTTTTTCTCA-AACAGAA
1 AGTGTCGGCCATTTGATGGCCAACACCAAAAAA-TTT-AATTTTTTT-TCAGAA-AGAA
*** * * *
4847577 AGTGTCGGCCATGCAATGGCCAACACCCAAAAATGTAATTTTTTTTCAAGAAA-ATGG
1 AGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTAATTTTTTTTC-AGAAAGA--A
* *
4847634 GGTGTCGACCATTTGATGGCCAACACCAAAAAATTGT-ATTTTTTTT
1 AGTGTCGGCCATTTGATGGCCAACACCAAAAAATT-TAATTTTTTTT
4847680 GACAAGAAGC
Statistics
Matches: 271, Mismatches: 42, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
55 3 0.01
56 43 0.16
57 55 0.20
58 56 0.21
59 34 0.13
60 43 0.16
61 29 0.11
62 7 0.03
63 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (55 bp):
AGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTAATTTTTTTTCAGAAAGAA
Found at i:4860713 original size:2 final size:2
Alignment explanation
Indices: 4860700--4860738 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
4860690 TTGAAAACGA
*
4860700 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG CAG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG
4860739 CAGCACCCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4863011 original size:4 final size:4
Alignment explanation
Indices: 4863002--4863063 Score: 80
Period size: 4 Copynumber: 16.8 Consensus size: 4
4862992 TATTTTTAAC
4863002 TTTA TTTA TTTA TTTA -TT- TTTA TTTA TTTA TTTA -TT- TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
4863046 TTTA TCTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTT
4863064 GAATAAATAC
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
3 11 0.22
4 40 0.78
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:4863023 original size:18 final size:18
Alignment explanation
Indices: 4863002--4863063 Score: 106
Period size: 18 Copynumber: 3.4 Consensus size: 18
4862992 TATTTTTAAC
4863002 TTTATTTATTTATTTATT
1 TTTATTTATTTATTTATT
4863020 TTTATTTATTTATTTATT
1 TTTATTTATTTATTTATT
*
4863038 TTTATTTATTTATCTATT
1 TTTATTTATTTATTTATT
4863056 TATTATTT
1 T-TTATTT
4863064 GAATAAATAC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
18 36 0.86
19 6 0.14
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTATTTATTTATT
Found at i:4863030 original size:22 final size:22
Alignment explanation
Indices: 4862992--4863063 Score: 94
Period size: 22 Copynumber: 3.2 Consensus size: 22
4862982 GGCCCAATTC
4862992 TATTTTTAACTTTATTTATTTATT
1 TATTTTT-A-TTTATTTATTTATT
4863016 TATTTTTATTTATTTATTTATT
1 TATTTTTATTTATTTATTTATT
*
4863038 T-TTATTTATTTATCTATTTA-T
1 TATT-TTTATTTATTTATTTATT
4863059 TATTT
1 TATTT
4863064 GAATAAATAC
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
21 5 0.11
22 32 0.71
23 1 0.02
24 7 0.16
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (22 bp):
TATTTTTATTTATTTATTTATT
Found at i:4869644 original size:19 final size:19
Alignment explanation
Indices: 4869602--4869646 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4869592 TGTTTTTAAC
* *
4869602 TTTATTTATTTCTTTTATT
1 TTTATTTATTTCATCTATT
4869621 TTTATTTATTT-ATCTATT
1 TTTATTTATTTCATCTATT
4869639 TATTATTT
1 T-TTATTT
4869647 GAATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTATTTATTTCATCTATT
Found at i:4870695 original size:29 final size:28
Alignment explanation
Indices: 4870667--4870775 Score: 101
Period size: 30 Copynumber: 3.6 Consensus size: 28
4870657 TGTTTTATTT
* *
4870667 TAAAATTATATTTTTACCCTCAAACATTTC
1 TAAAATT-TAATTTGACCCTCAAAC-TTTC
*
4870697 AAAAATTTGAATTTGACCCCTCAAACTTTC
1 TAAAATTT-AATTTGA-CCCTCAAACTTTC
*
4870727 TAAAATTCCAATTTGACCCTCAAACTTTTC
1 TAAAATT-TAATTTGACCCTCAAAC-TTTC
* *
4870757 AAAAATTCAAATTTGACCC
1 TAAAATT-TAATTTGACCC
4870776 AGTTTTAATG
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
29 10 0.15
30 49 0.72
31 9 0.13
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.36
Consensus pattern (28 bp):
TAAAATTTAATTTGACCCTCAAACTTTC
Found at i:4870732 original size:30 final size:31
Alignment explanation
Indices: 4870683--4870775 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 31
4870673 TATATTTTTA
**
4870683 CCCTCAAACATTTCAAAAATTTGAATTTGAC
1 CCCTCAAACATTTCAAAAATTCAAATTTGAC
* *
4870714 CCCTCAAAC-TTTCTAAAATTCCAATTTGA-
1 CCCTCAAACATTTCAAAAATTCAAATTTGAC
*
4870743 CCCTCAAACTTTTCAAAAATTCAAATTTGAC
1 CCCTCAAACATTTCAAAAATTCAAATTTGAC
4870774 CC
1 CC
4870776 AGTTTTAATG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
29 9 0.16
30 35 0.64
31 11 0.20
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (31 bp):
CCCTCAAACATTTCAAAAATTCAAATTTGAC
Found at i:4873701 original size:21 final size:23
Alignment explanation
Indices: 4873677--4873730 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 23
4873667 AATAAATGCT
4873677 TTAAAATTATTTTT-T-AAAAAA
1 TTAAAATTATTTTTGTGAAAAAA
*
4873698 TTAAAATTATTTTTGTGAAATAA
1 TTAAAATTATTTTTGTGAAAAAA
4873721 -TAAAATTATT
1 TTAAAATTATT
4873731 AAATAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 14 0.47
22 11 0.37
23 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
TTAAAATTATTTTTGTGAAAAAA
Found at i:4873809 original size:27 final size:27
Alignment explanation
Indices: 4873779--4873833 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
4873769 ATTTCCTTCC
4873779 TTCATCATCTCACATCTTAAATCATCA
1 TTCATCATCTCACATCTTAAATCATCA
**
4873806 TTCATCATCTCTTATCTTAAATCATCA
1 TTCATCATCTCACATCTTAAATCATCA
4873833 T
1 T
4873834 CAACTCCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (27 bp):
TTCATCATCTCACATCTTAAATCATCA
Found at i:4874726 original size:121 final size:121
Alignment explanation
Indices: 4874583--4874826 Score: 452
Period size: 121 Copynumber: 2.0 Consensus size: 121
4874573 AAACCTTAAA
4874583 TTAACACACTCAGATTGGATCAATTTTCTGGGTTCTGAAAATGTGTTTTTATCTTTTCCACTCAA
1 TTAACACACTCAGATTGGATCAATTTTCTGGGTTCTGAAAATGTGTTTTTATCTTTTCCACTCAA
* *
4874648 ATAGAACATAACTACTCATACGTTTTTGGGTAAATATTTAGGATTTTCTATTTCAT
66 ACAGAACATAACTACTCATACGTTTTTGGGTAAATATTTAAGATTTTCTATTTCAT
*
4874704 TTAACACACTCAGATTGGATCAATTTTCTGGGTTCTGGAAATGTGTTTTTATCTTTTCCACTCAA
1 TTAACACACTCAGATTGGATCAATTTTCTGGGTTCTGAAAATGTGTTTTTATCTTTTCCACTCAA
*
4874769 ACAGGACATAACTACTCATACGTTTTTGGGTAAATATTTAAGATTTTCTATTTCAT
66 ACAGAACATAACTACTCATACGTTTTTGGGTAAATATTTAAGATTTTCTATTTCAT
4874825 TT
1 TT
4874827 GGGAAAAAAA
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 119 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (121 bp):
TTAACACACTCAGATTGGATCAATTTTCTGGGTTCTGAAAATGTGTTTTTATCTTTTCCACTCAA
ACAGAACATAACTACTCATACGTTTTTGGGTAAATATTTAAGATTTTCTATTTCAT
Found at i:4875017 original size:31 final size:29
Alignment explanation
Indices: 4874971--4875051 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 29
4874961 ACTGGAAATT
*
4874971 AAAATTATTTAATAATTTTATTATTTCAAA
1 AAAATAATTTAATAATTTTA-TATTTCAAA
*
4875001 AAAATAATGTTAATAATTTTATATTTTAAA
1 AAAATAAT-TTAATAATTTTATATTTCAAA
4875031 AAAATAATTTCAATAATTTTA
1 AAAATAATTT-AATAATTTTA
4875052 AAATCATTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
29 2 0.04
30 33 0.70
31 12 0.26
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (29 bp):
AAAATAATTTAATAATTTTATATTTCAAA
Found at i:4884004 original size:17 final size:16
Alignment explanation
Indices: 4883955--4884005 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
4883945 ATAATTTTTT
4883955 TTTGTTATATCAATTT-
1 TTTGTTATAT-AATTTA
* *
4883971 TTTTTTATA-AATATA
1 TTTGTTATATAATTTA
4883986 TTTGTTATATAATGTTA
1 TTTGTTATATAAT-TTA
4884003 TTT
1 TTT
4884006 TTACCTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 11 0.39
17 5 0.18
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (16 bp):
TTTGTTATATAATTTA
Found at i:4895964 original size:2 final size:2
Alignment explanation
Indices: 4895957--4896005 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
4895947 GTTTGTTGAG
4895957 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4895999 TC TC TC T
1 TC TC TC T
4896006 GGGTGCCGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4898305 original size:6 final size:6
Alignment explanation
Indices: 4898294--4898326 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
4898284 TTGCTGTGAA
4898294 CCCC-C CCCC-C CCCCAC CCCCAC CCCCAC CCCCA
1 CCCCAC CCCCAC CCCCAC CCCCAC CCCCAC CCCCA
4898327 TGTCTTCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 9 0.33
6 18 0.67
ACGTcount: A:0.12, C:0.88, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCCAC
Found at i:4903632 original size:13 final size:13
Alignment explanation
Indices: 4903616--4903665 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
4903606 ACCAAACATG
4903616 TTGACTTTGACTA
1 TTGACTTTGACTA
*
4903629 TTGACCATTGACT-
1 TTGA-CTTTGACTA
*
4903642 TTGACTTTGA-GA
1 TTGACTTTGACTA
4903654 GTTGACTTTGAC
1 -TTGACTTTGAC
4903666 CAAACATGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
12 5 0.17
13 18 0.60
14 7 0.23
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (13 bp):
TTGACTTTGACTA
Done.