Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008763.1 Hibiscus syriacus cultivar Beakdansim tig00111856_pilon, whole genome shotgun sequence
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: 72938
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:3629 original size:150 final size:150
Alignment explanation
Indices: 2844--3608 Score: 1350
Period size: 150 Copynumber: 5.1 Consensus size: 150
2834 GAGCAAGATG
* *
2844 ATAAGTCATTCGGGCCATCCATAAGACCTTCAAGCAAGATGTTTTCACATGTCTCTCAAAAAATG
1 ATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTCTCTCGAAAAATG
* * *
2909 ATAAAGGTTTCTTATTCGAATCCGAAAATTGAAATTTTTTAAAAGTAAGAAAGGTTGCTTACCTA
66 AGAAAGGTTTCTTATTCGAATCCGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
2974 GTAAACTATTTCCAAAATTT
131 GTAAACTATTTCCAAAATTT
*
2994 ATAAGTCCTTCGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTCTCTCGAAAAATG
1 ATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTCTCTCGAAAAATG
*
3059 ATAAAGGTTTCTTATTCGAATCCGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
66 AGAAAGGTTTCTTATTCGAATCCGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
*
3124 GTAAACTATTTTCAAAATTT
131 GTAAACTATTTCCAAAATTT
3144 ATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTCTCTCGAAAAATG
1 ATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTCTCTCGAAAAATG
*
3209 AGAAAGGTTTCTTATTCTAATCCGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
66 AGAAAGGTTTCTTATTCGAATCCGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
3274 GTAAACTATTTCCAAAATTT
131 GTAAACTATTTCCAAAATTT
* *
3294 ATAAGTCCTTCGGGCCATCCATAAGACCTTCGAGAAAGATGTTTTCACATGTCTCTCGAAAAATG
1 ATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTCTCTCGAAAAATG
*
3359 AGAAAGGTTTCTTATTCGAATCCAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
66 AGAAAGGTTTCTTATTCGAATCCGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
3424 GTAAACTATTTCCAAAATTT
131 GTAAACTATTTCCAAAATTT
*
3444 ATAAGTCATTTGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTCTCTCGAAAAATG
1 ATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTCTCTCGAAAAATG
** * ** *
3509 AGAAACATTTCTTATTCAAATTTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTA
66 AGAAAGGTTTCTTATTCGAATCCGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
3574 GTAAACTATTTCCAAAATTT
131 GTAAACTATTTCCAAAATTT
*
3594 ATAAGTCCTTCGGGC
1 ATAAGTCATTCGGGC
3609 TATCAGTAAG
Statistics
Matches: 589, Mismatches: 26, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
150 589 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (150 bp):
ATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTCTCTCGAAAAATG
AGAAAGGTTTCTTATTCGAATCCGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
GTAAACTATTTCCAAAATTT
Found at i:4025 original size:465 final size:466
Alignment explanation
Indices: 3444--4423 Score: 1622
Period size: 465 Copynumber: 2.1 Consensus size: 466
3434 TCCAAAATTT
* * * *
3444 ATAAGTCATTTGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTCTCTCGAAAAATG
1 ATAAGTCATTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCGAAAAATG
* *
3509 AGAAACATTTCTTATTCAAATTTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTA
66 AGAAACATTTCTCATTCAAATTTGAAAATTGAAATTGTTGAAAAATAAGAAAGGTTTCTTACCTA
*
3574 GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATAATTA
131 GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAATTA
* * *
3639 AATCCTTCGTGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTTGGGCCATCCATAAGAC
196 AATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGAC
* * *
3704 CTTTGGGTAGGATGTTTTCATAGGTATCTCGAAAAATGAAAAAGATTTCTAATTCAAATTTGAAA
261 CTTCGGGTAGGATGTTTTCACAGGTATATCGAAAAATGAAAAAGATTTCTAATTCAAATTTGAAA
* *
3769 ATTGAAATTGTTGAAAAGTAAGAAATATTTCTTACCTAGTAAACTATTTCCAAAATTTATAAGTC
326 ATTGAAATTGTTGAAAAGTAAGAAAGATTTCTTACCTAGTAAACAATTTCCAAAATTTATAAGTC
*
3834 ATTCGGGCCATC-GTAAGTCTTTCGAGCATGAT-ACTTAAATCCTTCGAGTCATATGTAAGTCTT
391 ATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA-TTAAATCATTCGAGTCATATGTAAGTCTT
3897 TCGAGCAAGATG
455 TCGAGCAAGATG
3909 ATAAGTCATTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCGAAAAATG
1 ATAAGTCATTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCGAAAAATG
**
3974 AGAAAGGTTTCTCATTCAAATTTGAAAATTGAAATTGTTGAAAAATAAGAAAGGTTTCTTACCTA
66 AGAAACATTTCTCATTCAAATTTGAAAATTGAAATTGTTGAAAAATAAGAAAGGTTTCTTACCTA
* **
4039 GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGTTGCTTA
131 GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAATTA
*
4104 AATCGTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGAC
196 AATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGAC
* * * * *
4169 CTTCGGGTAGGATGTTTTCACATGTCTATCGAAAATTGAGAAAGATTTCTCATTCAAATTTGAAA
261 CTTCGGGTAGGATGTTTTCACAGGTATATCGAAAAATGAAAAAGATTTCTAATTCAAATTTGAAA
* * *
4234 ATTGAAGTTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACAATTTCCAAAATTTATAAGTC
326 ATTGAAATTGTTGAAAAGTAAGAAAGATTTCTTACCTAGTAAACAATTTCCAAAATTTATAAGTC
* ** *
4299 CTTCTTGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGAGTCATCTGTAAGTCTTT
391 ATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGAGTCATATGTAAGTCTTT
4364 CGAGCAAGATG
456 CGAGCAAGATG
*
4375 ATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACA
1 ATAAGTCATTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACA
4424 GGTCCCTTTT
Statistics
Matches: 478, Mismatches: 35, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
465 370 0.77
466 107 0.22
467 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (466 bp):
ATAAGTCATTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCGAAAAATG
AGAAACATTTCTCATTCAAATTTGAAAATTGAAATTGTTGAAAAATAAGAAAGGTTTCTTACCTA
GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAATTA
AATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGAC
CTTCGGGTAGGATGTTTTCACAGGTATATCGAAAAATGAAAAAGATTTCTAATTCAAATTTGAAA
ATTGAAATTGTTGAAAAGTAAGAAAGATTTCTTACCTAGTAAACAATTTCCAAAATTTATAAGTC
ATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGAGTCATATGTAAGTCTTT
CGAGCAAGATG
Found at i:4134 original size:20 final size:19
Alignment explanation
Indices: 4060--4136 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 19
4050 CCAAAATTTA
* * *
4060 TAAGTCCTTCGGGCCATCAG
1 TAAGTCTTTCGAG-CATCTG
*
4080 TAAGTCTTTCGAGCATGTTG
1 TAAGTCTTTCGAGCAT-CTG
* *
4100 CTTAAATCGTTCGAGTCATCTG
1 --TAAGTCTTTCGAG-CATCTG
4122 TAAGTCTTTCGAGCA
1 TAAGTCTTTCGAGCA
4137 AGATGATAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
19 5 0.11
20 23 0.52
22 13 0.30
23 3 0.07
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (19 bp):
TAAGTCTTTCGAGCATCTG
Found at i:4188 original size:233 final size:233
Alignment explanation
Indices: 3444--4423 Score: 1602
Period size: 233 Copynumber: 4.2 Consensus size: 233
3434 TCCAAAATTT
* * * *
3444 ATAAGTCATTTGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTCTCTCGAAAAATG
1 ATAAGTCATTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCGAAAAATG
* *
3509 AGAAACATTTCTTATTCAAATTTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTA
66 AGAAAGATTTCTCATTCAAATTTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTA
*
3574 GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATAATTA
131 GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAATTA
*
3639 AATCCTTCGTGTCATCTGTAAGTCTTTCGAGCAAGATG
196 AATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATG
* * * * * *
3677 ATAAGTCTTTTGGGCCATCCATAAGACCTTTGGGTAGGATGTTTTCATAGGTATCTCGAAAAATG
1 ATAAGTCATTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCGAAAAATG
* * **
3742 AAAAAGATTTCTAATTCAAATTTGAAAATTGAAATTGTTGAAAAGTAAGAAATATTTCTTACCTA
66 AGAAAGATTTCTCATTCAAATTTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTA
* *
3807 GTAAACTATTTCCAAAATTTATAAGTCATTCGGGCCATC-GTAAGTCTTTCGAGCATGATACTTA
131 GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAATTA
*
3871 AATCCTTCGAGTCATATGTAAGTCTTTCGAGCAAGATG
196 AATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATG
3909 ATAAGTCATTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCGAAAAATG
1 ATAAGTCATTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCGAAAAATG
* *
3974 AGAAAGGTTTCTCATTCAAATTTGAAAATTGAAATTGTTGAAAAATAAGAAAGGTTTCTTACCTA
66 AGAAAGATTTCTCATTCAAATTTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTA
* **
4039 GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGTTGCTTA
131 GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAATTA
*
4104 AATCGTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATG
196 AATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATG
* * * *
4142 ATAAGTCATTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGTCTATCGAAAATTG
1 ATAAGTCATTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCGAAAAATG
* *
4207 AGAAAGATTTCTCATTCAAATTTGAAAATTGAAGTTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
66 AGAAAGATTTCTCATTCAAATTTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTA
* ** *
4272 GTAAACAATTTCCAAAATTTATAAGTCCTTCTTGCCATCAGTAAGTCTTTCGAGCATGATGATTA
131 GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAATTA
*
4337 AATCATTCGAGTCATCTGTAAGTCTTTCGAGCAAGATG
196 AATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATG
*
4375 ATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACA
1 ATAAGTCATTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACA
4424 GGTCCCTTTT
Statistics
Matches: 694, Mismatches: 52, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
232 216 0.31
233 478 0.69
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (233 bp):
ATAAGTCATTCGGGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTCTCTCGAAAAATG
AGAAAGATTTCTCATTCAAATTTGAAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTCTTACCTA
GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAATTA
AATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATG
Found at i:5983 original size:6 final size:6
Alignment explanation
Indices: 5972--5998 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5962 TTAGCCCTAC
5972 TTTAAT TTTAAT TTTAAT TTTAAT TTT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTT
5999 TGCATGTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:12101 original size:12 final size:12
Alignment explanation
Indices: 12084--12156 Score: 57
Period size: 12 Copynumber: 6.1 Consensus size: 12
12074 AGGTATATTT
12084 TATTTTATTTAA
1 TATTTTATTTAA
12096 TATTTTA-TTAGA
1 TATTTTATTTA-A
12108 -ATTTTATTTAA
1 TATTTTATTTAA
*
12119 T-TATTTAATT-A
1 TAT-TTTATTTAA
12130 T-TTAATTATTTTAA
1 TATT--TTA-TTTAA
12144 TATTTTATTTAA
1 TATTTTATTTAA
12156 T
1 T
12157 TAATTTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
10 1 0.02
11 14 0.28
12 26 0.52
13 5 0.10
14 2 0.04
15 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:12124 original size:8 final size:8
Alignment explanation
Indices: 12111--12140 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
12101 TATTAGAATT
12111 TTATTTAA
1 TTATTTAA
12119 TTATTTAA
1 TTATTTAA
12127 TTATTTAA
1 TTATTTAA
12135 TTATTT
1 TTATTT
12141 TAATATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTATTTAA
Found at i:12147 original size:8 final size:9
Alignment explanation
Indices: 12114--12150 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
12104 TAGAATTTTA
12114 TTTAATTA-
1 TTTAATTAT
12122 TTTAATTA-
1 TTTAATTAT
12130 TTTAATTAT
1 TTTAATTAT
12139 TTTAA-TAT
1 TTTAATTAT
12147 TTTA
1 TTTA
12151 TTTAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 23 0.82
9 5 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTAATTAT
Found at i:12150 original size:25 final size:25
Alignment explanation
Indices: 12114--12166 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
12104 TAGAATTTTA
*
12114 TTTAATTATTTAATTATTTAATTAT
1 TTTAATTATTTAATTAATTAATTAT
* *
12139 TTTAA-TATTTTATTTAATTAATTTT
1 TTTAATTA-TTTAATTAATTAATTAT
12164 TTT
1 TTT
12167 GCAATTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTAATTATTTAATTAATTAATTAT
Found at i:12159 original size:16 final size:16
Alignment explanation
Indices: 12078--12164 Score: 58
Period size: 17 Copynumber: 5.4 Consensus size: 16
12068 AACTTAAGGT
12078 ATATTTTATTTTATTTA
1 ATATTTTA-TTTATTTA
*
12095 ATATTTTATTAGAATTT-
1 ATATTTTATT--TATTTA
*
12112 -TA-TTTAATTATTTA
1 ATATTTTATTTATTTA
*
12126 AT-TATTTAATTATTTTA
1 ATAT-TTTATTTA-TTTA
*
12143 ATATTTTATTTAATTA
1 ATATTTTATTTATTTA
12159 AT-TTTT
1 ATATTTT
12165 TTGCAATTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
13 4 0.07
15 10 0.18
16 17 0.30
17 21 0.37
18 5 0.09
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (16 bp):
ATATTTTATTTATTTA
Found at i:14240 original size:6 final size:6
Alignment explanation
Indices: 14195--14254 Score: 75
Period size: 6 Copynumber: 10.0 Consensus size: 6
14185 TATCTACTCC
* * * *
14195 TGATGA TGACGA TGACGA TGATGA TGACGA TGATGA TGATGA TGATGG
1 TGATGA TGATGA TGATGA TGATGA TGATGA TGATGA TGATGA TGATGA
*
14243 TGATGG TGATGA
1 TGATGA TGATGA
14255 GTAACAACCA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.30, C:0.05, G:0.37, T:0.28
Consensus pattern (6 bp):
TGATGA
Found at i:14246 original size:18 final size:18
Alignment explanation
Indices: 14195--14254 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
14185 TATCTACTCC
*
14195 TGATGATGACGATGACGA
1 TGATGATGACGATGATGA
14213 TGATGATGACGATGATGA
1 TGATGATGACGATGATGA
* * *
14231 TGATGATGATGGTGATGG
1 TGATGATGACGATGATGA
14249 TGATGA
1 TGATGA
14255 GTAACAACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.30, C:0.05, G:0.37, T:0.28
Consensus pattern (18 bp):
TGATGATGACGATGATGA
Found at i:14557 original size:34 final size:33
Alignment explanation
Indices: 14480--14558 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
14470 TTTTGTTAAT
14480 TTTGTTTA-TTACCATTTAATACCAGTTATTGTAA
1 TTTGTTTATTTACCATTTAAT--CAGTTATTGTAA
*
14514 TTT-TTTATTTACCATTTAAT-ATTTATTGTAA
1 TTTGTTTATTTACCATTTAATCAGTTATTGTAA
14545 GTTTGTTGTATTTA
1 -TTTGTT-TATTTA
14559 ATATTATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
31 10 0.25
32 3 0.08
33 6 0.15
34 21 0.52
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.57
Consensus pattern (33 bp):
TTTGTTTATTTACCATTTAATCAGTTATTGTAA
Found at i:20952 original size:26 final size:26
Alignment explanation
Indices: 20916--20970 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
20906 ACTAACTGCA
20916 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
20942 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
20968 TAT
1 TAT
20971 CACTTCGGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.36
Consensus pattern (26 bp):
TATGGTGGGCACGACCTTATGTGTAT
Found at i:22906 original size:14 final size:14
Alignment explanation
Indices: 22889--22916 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22879 GTATACTAAC
22889 ATTGGTATGTTATG
1 ATTGGTATGTTATG
22903 ATTGGTATGTTATG
1 ATTGGTATGTTATG
22917 TGTACTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (14 bp):
ATTGGTATGTTATG
Found at i:23265 original size:47 final size:47
Alignment explanation
Indices: 23211--23578 Score: 171
Period size: 54 Copynumber: 7.1 Consensus size: 47
23201 ATCTTATGTG
* *
23211 GATGAATAATCGTTTCGACACTAAGTGTACATTTCATGAAATTCATC
1 GATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGAAATTCATC
* * * *
23258 GATGAATAACCATTTCGGCACTAAGTGTGCATTTCATGGAACTCATACTATGTG
1 GATGAATAACCGTTTCGACACTAAGTGTGCATTTCAT-GAA---ATTC-A--TC
* * *
23312 GATGAATAACCGTTTCGACACTAAGTGTGCATTCCACGGAATTCATCC
1 GATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGAAATTCAT-C
* * * * * *
23360 TATGTGGATGAATAACCTTTTCGGCACTATGTGTGCATCTCATGGACTTCATCC
1 ------GATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGAAATTCAT-C
* ** * *
23414 TATGTTGATGAATAACCGTTTTGGTACTAAGTGTGCATTCCATGGAATTCATCCTATGC
1 ------GATGAATAACCGTTTCGACACTAAGTGTGCATTTCAT-GAA---ATTC-AT-C
* * * *
23473 GGATGAATAACTGTTTCGGCACTAAGTGTGCATTCCAAGAAATTCATC
1 -GATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGAAATTCATC
* * *
23521 ATATGTGGAAGAATAACCGTTTCGACATTAAGTGTGCATTTCATGGAATTCATC
1 -------GATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGAAATTCATC
23575 -ATGA
1 GATGA
23579 GTTGATGAAT
Statistics
Matches: 251, Mismatches: 45, Indels: 51
0.72 0.13 0.15
Matches are distributed among these distances:
46 3 0.01
47 34 0.14
48 4 0.02
49 3 0.01
50 6 0.02
51 3 0.01
52 1 0.00
53 5 0.02
54 185 0.74
55 2 0.01
58 2 0.01
59 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (47 bp):
GATGAATAACCGTTTCGACACTAAGTGTGCATTTCATGAAATTCATC
Found at i:23340 original size:54 final size:54
Alignment explanation
Indices: 23258--23574 Score: 429
Period size: 54 Copynumber: 5.9 Consensus size: 54
23248 GAAATTCATC
* * * *
23258 GATGAATAACCATTTCGGCACTAAGTGTGCATTTCATGGAACTCATACTATGTG
1 GATGAATAACCGTTTCGGCACTAAGTGTGCATTCCATGGAATTCATCCTATGTG
* *
23312 GATGAATAACCGTTTCGACACTAAGTGTGCATTCCACGGAATTCATCCTATGTG
1 GATGAATAACCGTTTCGGCACTAAGTGTGCATTCCATGGAATTCATCCTATGTG
* * * *
23366 GATGAATAACCTTTTCGGCACTATGTGTGCA-TCTCATGGACTTCATCCTATGTT
1 GATGAATAACCGTTTCGGCACTAAGTGTGCATTC-CATGGAATTCATCCTATGTG
* * *
23420 GATGAATAACCGTTTTGGTACTAAGTGTGCATTCCATGGAATTCATCCTATGCG
1 GATGAATAACCGTTTCGGCACTAAGTGTGCATTCCATGGAATTCATCCTATGTG
* * * *
23474 GATGAATAACTGTTTCGGCACTAAGTGTGCATTCCAAGAAATTCATCATATGTG
1 GATGAATAACCGTTTCGGCACTAAGTGTGCATTCCATGGAATTCATCCTATGTG
* * * *
23528 GAAGAATAACCGTTTCGACATTAAGTGTGCATTTCATGGAATTCATC
1 GATGAATAACCGTTTCGGCACTAAGTGTGCATTCCATGGAATTCATC
23575 ATGAGTTGAT
Statistics
Matches: 228, Mismatches: 33, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
53 2 0.01
54 224 0.98
55 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (54 bp):
GATGAATAACCGTTTCGGCACTAAGTGTGCATTCCATGGAATTCATCCTATGTG
Found at i:23417 original size:108 final size:107
Alignment explanation
Indices: 23123--23574 Score: 467
Period size: 108 Copynumber: 4.3 Consensus size: 107
23113 ACCAAATAGG
* * * * * * ** *
23123 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATATCCGTTTCAACA-TTA-TGTG
1 CACTAAGTGTGCATTCCATGGAATTCATCCTATGCGGATGAATAACCTTTTCGGCACTAAGTGTG
* ** * * *
23186 CACTCCACAGAATTCATCTTATGTGGATGAATAATCGTTTCGA
66 CA-TTCATGGACTTCATCCTATGTGGATGAATAACCGTTTCGA
* * * *
23229 CACTAAGTGTACATTTCAT-GAA---ATTC-AT-C-GATGAATAACCATTTCGGCACTAAGTGTG
1 CACTAAGTGTGCATTCCATGGAATTCATCCTATGCGGATGAATAACCTTTTCGGCACTAAGTGTG
*
23287 CATTTCATGGAAC-TCATACTATGTGGATGAATAACCGTTTCGA
66 CA-TTCATGG-ACTTCATCCTATGTGGATGAATAACCGTTTCGA
* * *
23330 CACTAAGTGTGCATTCCACGGAATTCATCCTATGTGGATGAATAACCTTTTCGGCACTATGTGTG
1 CACTAAGTGTGCATTCCATGGAATTCATCCTATGCGGATGAATAACCTTTTCGGCACTAAGTGTG
* * *
23395 CATCTCATGGACTTCATCCTATGTTGATGAATAACCGTTTTGG
66 CAT-TCATGGACTTCATCCTATGTGGATGAATAACCGTTTCGA
*
23438 TACTAAGTGTGCATTCCATGGAATTCATCCTATGCGGATGAATAA-CTGTTTCGGCACTAAGTGT
1 CACTAAGTGTGCATTCCATGGAATTCATCCTATGCGGATGAATAACCT-TTTCGGCACTAAGTGT
* * * * *
23502 GCATTCCAAGAAATTCATCATATGTGGAAGAATAACCGTTTCGA
65 GCATT-CATGGACTTCATCCTATGTGGATGAATAACCGTTTCGA
* *
23546 CATTAAGTGTGCATTTCATGGAATTCATC
1 CACTAAGTGTGCATTCCATGGAATTCATC
23575 ATGAGTTGAT
Statistics
Matches: 288, Mismatches: 44, Indels: 26
0.80 0.12 0.07
Matches are distributed among these distances:
99 16 0.06
100 2 0.01
101 54 0.19
102 7 0.02
105 6 0.02
106 19 0.07
107 6 0.02
108 178 0.62
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (107 bp):
CACTAAGTGTGCATTCCATGGAATTCATCCTATGCGGATGAATAACCTTTTCGGCACTAAGTGTG
CATTCATGGACTTCATCCTATGTGGATGAATAACCGTTTCGA
Found at i:23498 original size:162 final size:161
Alignment explanation
Indices: 23121--23590 Score: 587
Period size: 162 Copynumber: 3.0 Consensus size: 161
23111 TTACCAAATA
* * * * *
23121 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATATCCGTTTCAACA-TTA-TG
1 GGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTG
* * * * *
23184 TGCACTCCACAGAATTCATCTTATGTGGATGAATAATCGTTTCGACACTAAGTGTACATTTCATG
66 TGCATTCCACGGAATTCATCATATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCATG
*
23249 AAATTCAT-C-----GATGAATAACCATTTC
131 GAATTCATCCTAGTTGATGAATAACCATTTC
* *
23274 GGCACTAAGTGTGCATTTCATGGAACTCATACTATGTGGATGAATAACCGTTTCGACACTAAGTG
1 GGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTG
* * * * *
23339 TGCATTCCACGGAATTCATCCTATGTGGATGAATAACCTTTTCGGCACTATGTGTGCATCTCATG
66 TGCATTCCACGGAATTCATCATATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCATG
* * *
23404 GACTTCATCCTATGTTGATGAATAACCGTTTT
131 GAATTCATCCTA-GTTGATGAATAACCATTTC
* * * * *
23436 GGTACTAAGTGTGCATTCCATGGAATTCATCCTATGCGGATGAATAACTGTTTCGGCACTAAGTG
1 GGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTG
* * * *
23501 TGCATTCCAAGAAATTCATCATATGTGGAAGAATAACCGTTTCGACATTAAGTGTGCATTTCATG
66 TGCATTCCACGGAATTCATCATATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCATG
*
23566 GAATTCATCATGAGTTGATGAATAA
131 GAATTCATCCT-AGTTGATGAATAA
23591 TCGTAAAGGA
Statistics
Matches: 269, Mismatches: 38, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
153 52 0.19
154 2 0.01
155 64 0.24
156 1 0.00
162 149 0.55
163 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (161 bp):
GGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTG
TGCATTCCACGGAATTCATCATATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCATG
GAATTCATCCTAGTTGATGAATAACCATTTC
Found at i:23575 original size:54 final size:54
Alignment explanation
Indices: 23258--23704 Score: 420
Period size: 54 Copynumber: 8.2 Consensus size: 54
23248 GAAATTCATC
* * *
23258 GATGAATAACCATTTCGGCACTAAGTGTGCATTTCATGGAACTCAT-ACTATGTG
1 GATGAATAACCGTTTCGGCACTAAGTGTGCATTCCATGGAATTCATCA-TATGTG
* * *
23312 GATGAATAACCGTTTCGACACTAAGTGTGCATTCCACGGAATTCATCCTATGTG
1 GATGAATAACCGTTTCGGCACTAAGTGTGCATTCCATGGAATTCATCATATGTG
* * * * *
23366 GATGAATAACCTTTTCGGCACTATGTGTGCA-TCTCATGGACTTCATCCTATGTT
1 GATGAATAACCGTTTCGGCACTAAGTGTGCATTC-CATGGAATTCATCATATGTG
* * * *
23420 GATGAATAACCGTTTTGGTACTAAGTGTGCATTCCATGGAATTCATCCTATGCG
1 GATGAATAACCGTTTCGGCACTAAGTGTGCATTCCATGGAATTCATCATATGTG
* * *
23474 GATGAATAACTGTTTCGGCACTAAGTGTGCATTCCAAGAAATTCATCATATGTG
1 GATGAATAACCGTTTCGGCACTAAGTGTGCATTCCATGGAATTCATCATATGTG
* * * * *
23528 GAAGAATAACCGTTTCGACATTAAGTGTGCATTTCATGGAATTCATCATGA-GTT
1 GATGAATAACCGTTTCGGCACTAAGTGTGCATTCCATGGAATTCATCAT-ATGTG
* *** * * * * * *
23582 GATGAATAATCGTAAAGGAACTATGTGTGTAAATCCACGGAATTCATCAT-TAGTT
1 GATGAATAACCGTTTCGGCACTAAGTGTG-CATTCCATGGAATTCATCATAT-GTG
* * * * * * *
23637 GATGAATAATCG-TACAGGCACTATGTGTGTAAATCCACGGAATTCATCATGA-GTT
1 GATGAATAACCGTTTC-GGCACTAAGTGTG-CATTCCATGGAATTCATCAT-ATGTG
23692 GATGAATAACCGT
1 GATGAATAACCGT
23705 ACAGACACTA
Statistics
Matches: 331, Mismatches: 51, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
53 2 0.01
54 248 0.75
55 81 0.24
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (54 bp):
GATGAATAACCGTTTCGGCACTAAGTGTGCATTCCATGGAATTCATCATATGTG
Found at i:23586 original size:108 final size:106
Alignment explanation
Indices: 23195--23701 Score: 426
Period size: 108 Copynumber: 4.7 Consensus size: 106
23185 GCACTCCACA
* * * * *
23195 GAATTCATCTTATGTGGATGAATAATCGTTTCGACACTAAGTGTACATTTCATGAAATTCATC--
1 GAATTCATCATATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTCCATGGAATTCATCAT
* *
23258 ----GATGAATAACCATTTCGGCACTAAGTGTGCATTTCATG
66 GAGTGATGAATAA-CTTTTCGGCACTAAGTGTGCATTCCATG
* * *
23296 GAACTCAT-ACTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTCCACGGAATTCATCC
1 GAATTCATCA-TATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTCCATGGAATTCATCA
*
23360 T-ATGTGGATGAATAACCTTTTCGGCACTATGTGTGCA-TCTCATG
65 TGA-GT-GATGAATAA-CTTTTCGGCACTAAGTGTGCATTC-CATG
* * * * **
23404 GACTTCATCCTATGTTGATGAATAACCGTTTTGGTACTAAGTGTGCATTCCATGGAATTCATCCT
1 GAATTCATCATATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTCCATGGAATTCAT-C-
* *
23469 ATGCG-GATGAATAACTGTTTCGGCACTAAGTGTGCATTCCAAG
64 ATGAGTGATGAATAACT-TTTCGGCACTAAGTGTGCATTCCATG
* * * *
23512 AAATTCATCATATGTGGAAGAATAACCGTTTCGACATTAAGTGTGCATTTCATGGAATTCATCAT
1 GAATTCATCATATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTCCATGGAATTCATCAT
* *** * * * * *
23577 GAGTTGATGAATAATCGTAAAGGAACTATGTGTGTAAATCCACG
66 GAG-TGATGAATAA-CTTTTCGGCACTAAGTGTG-CATTCCATG
* * * * * * * *
23621 GAATTCATCAT-TAGTTGATGAATAATCG-TACAGGCACTATGTGTGTAAATCCACGGAATTCAT
1 GAATTCATCATAT-GTGGATGAATAACCGTTTC-GACACTAAGTGTG-CATTCCATGGAATTCAT
23684 CATGAGTTGATGAATAAC
63 CATGAG-TGATGAATAAC
23702 CGTACAGACA
Statistics
Matches: 330, Mismatches: 54, Indels: 36
0.79 0.13 0.09
Matches are distributed among these distances:
101 55 0.17
106 4 0.01
107 4 0.01
108 192 0.58
109 43 0.13
110 32 0.10
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (106 bp):
GAATTCATCATATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTCCATGGAATTCATCAT
GAGTGATGAATAACTTTTCGGCACTAAGTGTGCATTCCATG
Found at i:23769 original size:55 final size:55
Alignment explanation
Indices: 23565--23775 Score: 325
Period size: 55 Copynumber: 3.8 Consensus size: 55
23555 TGCATTTCAT
* *
23565 GGAATTCATCATGAGTTGATGAATAATCGTAAAGGAACTATGTGTGTAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAATCGTACAGGCACTATGTGTGTAAATCCAC
*
23620 GGAATTCATCATTAGTTGATGAATAATCGTACAGGCACTATGTGTGTAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAATCGTACAGGCACTATGTGTGTAAATCCAC
* *
23675 GGAATTCATCATGAGTTGATGAATAACCGTACAGACACTATGTGTGTAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAATCGTACAGGCACTATGTGTGTAAATCCAC
* * * *
23730 AGAATTCATCATGAGTTGATGAACTACT-GTAGAGGCACTACGTGTG
1 GGAATTCATCATGAGTTGATGAA-TAATCGTACAGGCACTATGTGTG
23776 CATCATAATA
Statistics
Matches: 143, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
55 141 0.99
56 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.29
Consensus pattern (55 bp):
GGAATTCATCATGAGTTGATGAATAATCGTACAGGCACTATGTGTGTAAATCCAC
Found at i:24249 original size:45 final size:46
Alignment explanation
Indices: 24198--24284 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
24188 GATGTGTGAT
* * *
24198 AATGTATAACT-TTGTATA-AAAGGTATGAAAGGATGTCATAAATGA
1 AATGTATAA-TATCGTATAGAAAGGCATGAAAGGATGCCATAAATGA
*
24243 AATGTATAATATCGTATAGAAGGGCATGAAAGGATGCCATAA
1 AATGTATAATATCGTATAGAAAGGCATGAAAGGATGCCATAA
24285 TTAAAATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 1 0.03
45 15 0.42
46 20 0.56
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.28
Consensus pattern (46 bp):
AATGTATAATATCGTATAGAAAGGCATGAAAGGATGCCATAAATGA
Found at i:24354 original size:46 final size:45
Alignment explanation
Indices: 24265--24354 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 45
24255 CGTATAGAAG
* * * *
24265 GGCATGAAAGGATGCCATAATTAAAATTCATATGAGTGCATTATT
1 GGCATGAAAGAATGCCATAATGAAAATGCATACGAGTGCATTATT
*
24310 GGCATGAAAGAATGTCATAAATGAAAATGCATAACG-GTGCATTAT
1 GGCATGAAAGAATGCCAT-AATGAAAATGCAT-ACGAGTGCATTAT
24355 AAGTATGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
45 16 0.42
46 20 0.53
47 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (45 bp):
GGCATGAAAGAATGCCATAATGAAAATGCATACGAGTGCATTATT
Found at i:28780 original size:54 final size:54
Alignment explanation
Indices: 28698--29449 Score: 859
Period size: 54 Copynumber: 13.9 Consensus size: 54
28688 CACAAATAGG
* * *
28698 CACTAAGTGTGCATTTCACAGAATTCATCCTAGGTGGATGAATAACCATTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * *
28752 CACTAAGTGTGCATTCCACGGAATTCATCCTATGTGCATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* ** * *
28806 CACTAAGTGTGCATTTAACGGAATTTGTCCTAGGTGGATGACTAACCGTTTC-A
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * *
28859 GTACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATAAATAACTGTTTCGA
1 -CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * * * *
28914 CACTAAGTGTGTATTCCATGAAATTCATCCTATGTGGATGAATAACTGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * *
28968 CACTATGTGTGCATTTCACGGACTTTATCCTATGTGGATGAATAATCGTTTCGGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC-GA
* * **
29023 -ACTAAGTGTGCCTTCCACGGAATTCATCCTATGTGGATGAATAATTGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* ** * *
29076 CACTAAGTGTGCATTTAACGGAATTTGTCCTAGGTGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * *
29130 TACTAAGTATGCATTTCACGAAATTCATCCTATGTGGATAAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * * *
29184 CACTAAGTGTGTATTCCATGAAATTCATCCTATGTGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * * *
29238 CACTATGTGTGCATTTCACGGACTTCATCCTATGTAGATGAATAATCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * * *
29292 CACTAAGTGTGCATTCCACGGAATTCATCCTATGTGGACGAATAACTGTTTTGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * *
29346 CACTAAGTGTGCATTTCACGGAATTCAT--TATGAGTTGATGAATAACCG-TACAGT
1 CACTAAGTGTGCATTTCACGGAATTCATCCTAT--GTGGATGAATAACCGTTTC-GA
* ** * *
29400 CACTATGTGTGCAAATCAACGGAATTCATCATGA-GTTGATGAATAACCGT
1 CACTAAGTGTGCATTTC-ACGGAATTCATCCT-ATGTGGATGAATAACCGT
29450 ATAAGCACTA
Statistics
Matches: 590, Mismatches: 96, Indels: 22
0.83 0.14 0.03
Matches are distributed among these distances:
52 3 0.01
53 3 0.01
54 554 0.94
55 28 0.05
57 1 0.00
58 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
Found at i:29437 original size:55 final size:55
Alignment explanation
Indices: 29362--29622 Score: 334
Period size: 55 Copynumber: 4.8 Consensus size: 55
29352 GTGTGCATTT
*
29362 CACGGAATTCATTATGAGTTGATGAATAACCGTACAGTCACTATGTGTGCAAATC
1 CACGGAATTCATCATGAGTTGATGAATAACCGTACAGTCACTATGTGTGCAAATC
* *
29417 AACGGAATTCATCATGAGTTGATGAATAACCGTATAAG-CACTA--TGTGCAAATC
1 CACGGAATTCATCATGAGTTGATGAATAACCGTA-CAGTCACTATGTGTGCAAATC
* * *
29470 CATGGAATTCATCCTGGGTTGATGAATAACCGTACA-TGCACTATGTGTGCAAATC
1 CACGGAATTCATCATGAGTTGATGAATAACCGTACAGT-CACTATGTGTGCAAATC
* * * * *
29525 CACGTAATTCATCATGGGTTGATGAATAACCATACAGGCTCTATGTGTGCAAATC
1 CACGGAATTCATCATGAGTTGATGAATAACCGTACAGTCACTATGTGTGCAAATC
* * *
29580 CACAGAATTCATCATGAGTTGATGAACT-ACTGTATAGTCACTA
1 CACGGAATTCATCATGAGTTGATGAA-TAACCGTACAGTCACTA
29623 CGTATGCATC
Statistics
Matches: 177, Mismatches: 22, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
52 1 0.01
53 45 0.25
55 128 0.72
56 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (55 bp):
CACGGAATTCATCATGAGTTGATGAATAACCGTACAGTCACTATGTGTGCAAATC
Found at i:29503 original size:108 final size:109
Alignment explanation
Indices: 29345--29622 Score: 348
Period size: 108 Copynumber: 2.6 Consensus size: 109
29335 AACTGTTTTG
* * *
29345 GCACTAAGTGTGC-ATTTCACGGAATTCATTATGAGTTGATGAATAACCGTACAGTCACTATGTG
1 GCACT-AGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGTCACTATGTG
* *
29409 TGCAAATCAACGGAATTCATCATGAGTTGATGAATAACCGTATAA
65 TGCAAATCAACGGAATTCATCATGAGTTGATGAATAACCATACAA
* * *
29454 GCACTA-TGTGCAAATCCATGGAATTCATCCTGGGTTGATGAATAACCGTACA-TGCACTATGTG
1 GCACTAGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGT-CACTATGTG
* * * *
29517 TGCAAATCCACGTAATTCATCATGGGTTGATGAATAACCATACAG
65 TGCAAATCAACGGAATTCATCATGAGTTGATGAATAACCATACAA
* * * *
29562 GCTCTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAACT-ACTGTATAGTCACTA
1 GCACTA-GTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA-TAACCGTACAGTCACTA
29623 CGTATGCATC
Statistics
Matches: 144, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
107 6 0.04
108 88 0.61
109 5 0.03
110 43 0.30
111 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (109 bp):
GCACTAGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGTCACTATGTGT
GCAAATCAACGGAATTCATCATGAGTTGATGAATAACCATACAA
Found at i:29975 original size:68 final size:68
Alignment explanation
Indices: 29895--30098 Score: 284
Period size: 68 Copynumber: 3.0 Consensus size: 68
29885 AAGATTAATA
* * * *
29895 GCCTACCTGTGCATTTGATAGAAAGGTGTCAATTATGACAGTTAGATGAAAGGCTGAGTGCCTTT
1 GCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGACAGTTACATGAAAGGCTAAGTGCCTTT
29960 GAG
66 GAG
* * * *
29963 GCCTAGCTGTGCATTTGACAGAAAAGTGTGAATTATGTCAGTTACATGAAAGGTTAAGTGCCTTT
1 GCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGACAGTTACATGAAAGGCTAAGTGCCTTT
30028 GAG
66 GAG
* * * *
30031 GCCTAGCTGGGCATTTGACAGAAAGGTGTCAATTATGCCAGTTATATG-AAGGACTAAATGCCTT
1 GCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGACAGTTACATGAAAGG-CTAAGTGCCTT
30095 TGAG
65 TGAG
30099 TAAAAGACTA
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 4 0.03
68 116 0.97
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (68 bp):
GCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGACAGTTACATGAAAGGCTAAGTGCCTTT
GAG
Found at i:33724 original size:15 final size:15
Alignment explanation
Indices: 33704--33735 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
33694 CATAATGTTT
33704 TTCATGTGTTGATTA
1 TTCATGTGTTGATTA
33719 TTCATGTGTTGATTA
1 TTCATGTGTTGATTA
33734 TT
1 TT
33736 AGAAAGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (15 bp):
TTCATGTGTTGATTA
Found at i:36046 original size:30 final size:30
Alignment explanation
Indices: 36012--36073 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
36002 AAGTTTATAT
*
36012 CAACACTATAGTGTATAAAGACACTTAGTG
1 CAACACTATAGTGTATAAAGACACTAAGTG
* * *
36042 CAACACTATAGTGTGTAAGGGCACTAAGTG
1 CAACACTATAGTGTATAAAGACACTAAGTG
36072 CA
1 CA
36074 TATGGTGGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (30 bp):
CAACACTATAGTGTATAAAGACACTAAGTG
Found at i:36110 original size:26 final size:26
Alignment explanation
Indices: 36074--36128 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
36064 ACTAAGTGCA
*
36074 TATGGTGGGCACAACCTTATGTGTAT
1 TATGGTGGGCACAACCATATGTGTAT
* *
36100 TATGGTGGGCACGACCATGTGTGTAT
1 TATGGTGGGCACAACCATATGTGTAT
36126 TAT
1 TAT
36129 CACTTCGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.35
Consensus pattern (26 bp):
TATGGTGGGCACAACCATATGTGTAT
Found at i:37573 original size:39 final size:38
Alignment explanation
Indices: 37530--37619 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 38
37520 GGAGCTTGTG
* * *
37530 GTAAGGACTTACCCTGAGCATAAAGCCAAAGAGTCTGC
1 GTAAGGACTTACCCCGAGCACAAAGCCAAAGAGCCTGC
* *
37568 AGTAAGGACTTACCCCGAGCACAAAGCCGAGGAGCCTGC
1 -GTAAGGACTTACCCCGAGCACAAAGCCAAAGAGCCTGC
37607 GCTAAGGACTTAC
1 G-TAAGGACTTAC
37620 AAGTCATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
38 1 0.02
39 44 0.98
ACGTcount: A:0.32, C:0.27, G:0.26, T:0.16
Consensus pattern (38 bp):
GTAAGGACTTACCCCGAGCACAAAGCCAAAGAGCCTGC
Found at i:41439 original size:198 final size:198
Alignment explanation
Indices: 41087--41486 Score: 529
Period size: 198 Copynumber: 2.0 Consensus size: 198
41077 CTTTTTACTA
* * * ** *
41087 TGACTAAATAATTTTGTTGCAATTTGTTATTGTTAAAGAATATTATTTGTCACAATATTTTATAA
1 TGACTAAATAATTTTGTTACAATTTATTATTGTGAAAGAATATTACGTATCACAATATTTTATAA
* * * * * *
41152 TGAGAAATTAATATTTTTTTATAAATTGCTATTTTGATTAAATAAAATTTTCTCAATTTTTTATT
66 TGAGAAATTAATATTATATTATAAATTACTATTTTGAATAAATAAAATTTTCTAAAATTTTTATT
* * * *
41217 TTGACAAATGTTAGGACGAAATAAATTTGACATAACTTTTTATTTTGACTAAATTTAAC-ATGTT
131 TTGAAAAATATTAGGACAAAATAAATTTGACATAAATTTTTATTTTGACTAAATTT-ACTATGTT
41281 ATTG
195 ATTG
* * *
41285 TGACTAAATCATTTTGTTACAATTTATTATTGTGAAAGAATATTACGTATCACAATTTTTTATGA
1 TGACTAAATAATTTTGTTACAATTTATTATTGTGAAAGAATATTACGTATCACAATATTTTATAA
* *
41350 TGAGAAATTAATA-TATATTATAAATTATTTTTTTAGAATAAAT-AAATTTGTC-AAAATTTTTA
66 TGAGAAATTAATATTATATTATAAATTACTATTTT-GAATAAATAAAATTT-TCTAAAATTTTTA
* *
41412 TTTTGAAAAAATATTATGACAAAATAAATTTGGCATAAATTTTTATTTTGACTAAATTTACTATG
129 TTTTG-AAAAATATTAGGACAAAATAAATTTGACATAAATTTTTATTTTGACTAAATTTACTATG
41477 TTATTG
193 TTATTG
41483 TGAC
1 TGAC
41487 AAAAATAACC
Statistics
Matches: 175, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
197 37 0.21
198 138 0.79
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (198 bp):
TGACTAAATAATTTTGTTACAATTTATTATTGTGAAAGAATATTACGTATCACAATATTTTATAA
TGAGAAATTAATATTATATTATAAATTACTATTTTGAATAAATAAAATTTTCTAAAATTTTTATT
TTGAAAAATATTAGGACAAAATAAATTTGACATAAATTTTTATTTTGACTAAATTTACTATGTTA
TTG
Found at i:44471 original size:5 final size:5
Alignment explanation
Indices: 44461--44532 Score: 50
Period size: 5 Copynumber: 15.6 Consensus size: 5
44451 TTAGATATAA
* * **
44461 AAAAT AAAAT AAAAT -AAAT -AAAT AAATT CAACC AAAAT AAAA- AGAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT
44509 AAAAT -AAAT -AAAT -AAAT -AAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
44533 GCATAGAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
4 25 0.45
5 30 0.54
6 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:44481 original size:4 final size:4
Alignment explanation
Indices: 44457--44532 Score: 52
Period size: 4 Copynumber: 18.2 Consensus size: 4
44447 CATGTTAGAT
44457 ATAA A-AA ATAAA ATAAA ATAA ATAA ATAA ATTCAA CCA-AA AT-A A-AA
1 ATAA ATAA AT-AA AT-AA ATAA ATAA ATAA A-T-AA --ATAA ATAA ATAA
*
44503 AGAA ATAAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA AT-AA ATAA ATAA ATAA ATAA ATAA A
44533 GCATAGAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 20
0.74 0.01 0.24
Matches are distributed among these distances:
3 8 0.13
4 34 0.56
5 16 0.26
6 2 0.03
8 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:45319 original size:34 final size:35
Alignment explanation
Indices: 45243--45341 Score: 137
Period size: 34 Copynumber: 2.8 Consensus size: 35
45233 AGTAGAACTC
45243 TATCCTATTTTTAGGAGTTTGAATCCTAACAAAATTT
1 TATCCTATTTTTAGGAGTTTGAATCCT-A-AAAATTT
* *
45280 CATCCTATTTTTAGGAGTTTGAATCCT-GAAATTT
1 TATCCTATTTTTAGGAGTTTGAATCCTAAAAATTT
**
45314 TATCCTATTTTTAGGAGTTCAAATCCTA
1 TATCCTATTTTTAGGAGTTTGAATCCTA
45342 GTAGGACGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
34 30 0.54
37 26 0.46
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.43
Consensus pattern (35 bp):
TATCCTATTTTTAGGAGTTTGAATCCTAAAAATTT
Found at i:46188 original size:105 final size:105
Alignment explanation
Indices: 45890--46550 Score: 947
Period size: 105 Copynumber: 6.3 Consensus size: 105
45880 CATTGTTCCA
* * ** *
45890 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* ** * * * *
45954 CCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
45996 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
46056 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
46096 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* *
46161 AGAGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
46201 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
46266 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
46306 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
46371 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
46411 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTCGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
* * * *
46476 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
46517 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
46551 CGCGGATGGC
Statistics
Matches: 513, Mismatches: 32, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
100 83 0.16
101 1 0.00
102 7 0.01
104 5 0.01
105 307 0.60
106 85 0.17
107 3 0.01
109 22 0.04
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:47275 original size:36 final size:35
Alignment explanation
Indices: 47226--47466 Score: 176
Period size: 36 Copynumber: 6.9 Consensus size: 35
47216 GATTTTGTGT
* *
47226 TTCAAGAGTAACTGTCTCAAGATAGACGAAAATTGA
1 TTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTGA
47262 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTGA
* * * *
47297 GTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGT
1 -TT-CAAGAGAAACTGTCTCAAGAGAGAC-AAAATTGA
* * ** *
47335 TTCAA-AGAAAACATAT-TC---A-A-A-TATTTTGT
1 TTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATTGA
* * * *
47364 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTGA
*
47400 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTGA
* *
47435 TTTCAAGGGAAACTTTCTCAAGAGAGACAAAA
1 -TTCAAGAGAAACTGTCTCAAGAGAGACAAAA
47467 ATCTTCTAGT
Statistics
Matches: 167, Mismatches: 21, Indels: 34
0.75 0.09 0.15
Matches are distributed among these distances:
28 2 0.01
29 17 0.10
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 12 0.07
36 98 0.59
37 29 0.17
38 3 0.02
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (35 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTGA
Found at i:47973 original size:18 final size:18
Alignment explanation
Indices: 47946--47981 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
47936 TGATGAATCC
* *
47946 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
47964 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
47982 TTGATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:48397 original size:22 final size:22
Alignment explanation
Indices: 48372--48422 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
48362 TTGTGTTTGG
*
48372 TCAAGGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
48394 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
48416 TCAAAGG
1 TCAAAGG
48423 ATTGATGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:49083 original size:23 final size:22
Alignment explanation
Indices: 49056--49135 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
49046 TTTTTGTCCC
49056 TTTTTCTTTTTGATTTTTGCTCT
1 TTTTTCTTTTTG-TTTTTGCTCT
* * *
49079 TTTTTCCTTTTGTTCTTGTTTCT
1 TTTTTCTTTTTGTTTTTG-CTCT
*
49102 CTTTTTCTTTGTTTTTTTTGCT-T
1 -TTTTTCTTT-TTGTTTTTGCTCT
*
49125 CTTTTCTTTTT
1 TTTTTCTTTTT
49136 TGTTCTTGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
21 2 0.04
22 13 0.28
23 15 0.33
24 9 0.20
25 7 0.15
ACGTcount: A:0.01, C:0.15, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTTTCTTTTTGTTTTTGCTCT
Found at i:49089 original size:16 final size:17
Alignment explanation
Indices: 49070--49123 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
49060 TCTTTTTGAT
*
49070 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
49086 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
*
49103 TTTTTCT-TTGTTT-T-
1 TTTTGCTCTTGTTTCTC
49117 TTTTGCT
1 TTTTGCT
49124 TCTTTTCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 6 0.19
15 1 0.03
16 19 0.59
17 6 0.19
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:53605 original size:5 final size:5
Alignment explanation
Indices: 53595--53680 Score: 62
Period size: 5 Copynumber: 18.6 Consensus size: 5
53585 TAGATATAAA
* * * **
53595 AAAAT AAAAT AAAAT -AAAT AAAAT -AAAT -AAAT ATATT CAACC AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
53642 AAAA- AGAAAT AAAAT AAAAT -AAAT -AAAT -AAAT -AAAT AAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
53681 GCATAGAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
4 29 0.43
5 37 0.55
6 1 0.01
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:53615 original size:4 final size:4
Alignment explanation
Indices: 53590--53680 Score: 53
Period size: 4 Copynumber: 21.2 Consensus size: 4
53580 CATTTTAGAT
* *
53590 ATAA AAAA ATAAA ATAAA ATAA ATAAA ATAA ATAA ATATA TTCAA CCA-AA
1 ATAA ATAA AT-AA AT-AA ATAA AT-AA ATAA ATAA ATA-A AT-AA --ATAA
*
53640 AT-A A-AA AGAA ATAAA ATAAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA AT-AA AT-AA ATAA ATAA ATAA ATAA ATAA A
53681 GCATAGAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
3 5 0.07
4 39 0.54
5 27 0.38
6 1 0.01
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:54473 original size:34 final size:35
Alignment explanation
Indices: 54395--54495 Score: 143
Period size: 34 Copynumber: 2.9 Consensus size: 35
54385 ATAGTAGAAC
54395 TCTATCCTATTTTTAGGAGTTTGAATCCTAACAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCT-A-AAAAT
*
54432 T-TCATCCTATTTTTAGGAGTTTGAATCCT-GAAAT
1 TCT-ATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
*
54466 TCTATCCTATTTTTAGGAGTTCGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
54496 GTAGGACGAA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
34 30 0.51
35 1 0.02
36 1 0.02
37 27 0.46
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
Found at i:57733 original size:20 final size:20
Alignment explanation
Indices: 57705--57742 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57695 AACTCTACCT
57705 CCTGAATCTAAATGATATGA
1 CCTGAATCTAAATGATATGA
* *
57725 CCTGGATCTGAATGATAT
1 CCTGAATCTAAATGATAT
57743 CGCCTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (20 bp):
CCTGAATCTAAATGATATGA
Found at i:61871 original size:39 final size:39
Alignment explanation
Indices: 61810--61978 Score: 180
Period size: 39 Copynumber: 4.3 Consensus size: 39
61800 AAAGACATAG
* * * *
61810 GGTAAGGACTTACCTTGTGCACAAAGCAGAGGAGCTTGC
1 GGTAAGAACTTACCATGAGCACAAAGCAGAGGAGCATGC
* * * *
61849 GGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGC
1 GGTAAGAACTTACCATGAGCACAAAGCAGAGGAGCATGC
* ** *
61888 AGTAAGAACTTACCATGAGCACAAAGTTGAGAAGCATGC
1 GGTAAGAACTTACCATGAGCACAAAGCAGAGGAGCATGC
* *
61927 GTTAAGAACTTACCATGAGCACAAAGCCA-ATGAGCATGC
1 GGTAAGAACTTACCATGAGCACAAAG-CAGAGGAGCATGC
61966 GGTACA-AACTTAC
1 GGTA-AGAACTTAC
61979 AAGCCATAGA
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
39 109 0.99
40 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.18
Consensus pattern (39 bp):
GGTAAGAACTTACCATGAGCACAAAGCAGAGGAGCATGC
Found at i:64252 original size:104 final size:104
Alignment explanation
Indices: 64072--64279 Score: 416
Period size: 104 Copynumber: 2.0 Consensus size: 104
64062 ACTGAGATGA
64072 TGCGGAATTTGTTCGTGGCTACCCTTTCAGTCTCTGTGAGGGTGTTCCCACTGCCGTGTCTCACG
1 TGCGGAATTTGTTCGTGGCTACCCTTTCAGTCTCTGTGAGGGTGTTCCCACTGCCGTGTCTCACG
64137 GTCTCTGGCTCAACATCCCGGATTATGATGCTCCGACTC
66 GTCTCTGGCTCAACATCCCGGATTATGATGCTCCGACTC
64176 TGCGGAATTTGTTCGTGGCTACCCTTTCAGTCTCTGTGAGGGTGTTCCCACTGCCGTGTCTCACG
1 TGCGGAATTTGTTCGTGGCTACCCTTTCAGTCTCTGTGAGGGTGTTCCCACTGCCGTGTCTCACG
64241 GTCTCTGGCTCAACATCCCGGATTATGATGCTCCGACTC
66 GTCTCTGGCTCAACATCCCGGATTATGATGCTCCGACTC
64280 AGCTTGTCAA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.13, C:0.30, G:0.25, T:0.32
Consensus pattern (104 bp):
TGCGGAATTTGTTCGTGGCTACCCTTTCAGTCTCTGTGAGGGTGTTCCCACTGCCGTGTCTCACG
GTCTCTGGCTCAACATCCCGGATTATGATGCTCCGACTC
Found at i:65464 original size:20 final size:20
Alignment explanation
Indices: 65439--65476 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
65429 CCAAATTTGC
65439 AACGCGAATATGTAAATCGT
1 AACGCGAATATGTAAATCGT
*
65459 AACGCGAATCTGTAAATC
1 AACGCGAATATGTAAATC
65477 ACGTTGCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (20 bp):
AACGCGAATATGTAAATCGT
Found at i:65507 original size:20 final size:20
Alignment explanation
Indices: 65482--65566 Score: 109
Period size: 20 Copynumber: 4.2 Consensus size: 20
65472 AAATCACGTT
65482 GCGATTTCCAAATTCGCAAC
1 GCGATTTCCAAATTCGCAAC
65502 GCGATTTCCAAATTCGCAAC
1 GCGATTTCCAAATTCGCAAC
*
65522 ACTGAATTT-CAAATTCGCAAC
1 GC-G-ATTTCCAAATTCGCAAC
* **
65543 TCGATTTCTGAATTCGCAAC
1 GCGATTTCCAAATTCGCAAC
65563 GCGA
1 GCGA
65567 ATTTTGTTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
19 4 0.07
20 35 0.61
21 14 0.25
22 4 0.07
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (20 bp):
GCGATTTCCAAATTCGCAAC
Found at i:65622 original size:40 final size:40
Alignment explanation
Indices: 65494--65622 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 40
65484 GATTTCCAAA
* * * *
65494 TTCGCAACGCGATTTCCAAATTCGCAACACTGAATTTCAAA
1 TTCGCAACTCGATTTTCAAATTCGCAACAC-GAATTTTAAT
* * *
65535 TTCGCAACTCGA-TTTCTGAATTCGCAACGCGAATTTT-GT
1 TTCGCAACTCGATTTTC-AAATTCGCAACACGAATTTTAAT
* *
65574 TGTAGCAACTTGATTTTCAAATTCGCAACACGAATTTTAAT
1 T-TCGCAACTCGATTTTCAAATTCGCAACACGAATTTTAAT
65615 TTCGCAAC
1 TTCGCAAC
65623 AGGTTTTAGT
Statistics
Matches: 71, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
39 1 0.01
40 42 0.59
41 28 0.39
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (40 bp):
TTCGCAACTCGATTTTCAAATTCGCAACACGAATTTTAAT
Found at i:65623 original size:20 final size:20
Alignment explanation
Indices: 65491--65623 Score: 85
Period size: 20 Copynumber: 6.6 Consensus size: 20
65481 TGCGATTTCC
* *
65491 AAATTCGCAACGCG-ATTTCC
1 AAATTCGCAACACGAATTT-T
*
65511 AAATTCGCAACACTGAATTTC
1 AAATTCGCAACAC-GAATTTT
*
65532 AAATTCGCAACTCG-ATTTCT
1 AAATTCGCAACACGAATTT-T
* *
65552 GAATTCGCAACGCGAATTTT
1 AAATTCGCAACACGAATTTT
** * **
65572 -GTTGTAGCAACTTG-ATTTT
1 AAAT-TCGCAACACGAATTTT
65591 CAAATTCGCAACACGAATTTT
1 -AAATTCGCAACACGAATTTT
*
65612 AATTTCGCAACA
1 AAATTCGCAACA
65624 GGTTTTAGTT
Statistics
Matches: 89, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
19 10 0.11
20 51 0.57
21 24 0.27
22 4 0.04
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (20 bp):
AAATTCGCAACACGAATTTT
Found at i:66432 original size:12 final size:12
Alignment explanation
Indices: 66411--66444 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
66401 ACCACATTTC
*
66411 CAATACCAAACA
1 CAATATCAAACA
66423 CAATATCAAACA
1 CAATATCAAACA
*
66435 CAATCTCAAA
1 CAATATCAAA
66445 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:66586 original size:24 final size:24
Alignment explanation
Indices: 66565--66611 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
66555 AGGCAATATT
66565 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
* *
66589 CGGACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
66612 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:66616 original size:24 final size:24
Alignment explanation
Indices: 66570--66623 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
66560 ATATTCGAAA
66570 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
66594 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
66618 TTTGAT
1 TTTGAT
66624 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:68866 original size:12 final size:12
Alignment explanation
Indices: 68849--68895 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
68839 AGCAAAAGGA
68849 AATCAAAATCGC
1 AATCAAAATCGC
**
68861 AATCAAAATCAA
1 AATCAAAATCGC
*
68873 AATCAAAATCCC
1 AATCAAAATCGC
*
68885 AATCACAATCG
1 AATCAAAATCG
68896 ACTTCACCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.53, C:0.26, G:0.04, T:0.17
Consensus pattern (12 bp):
AATCAAAATCGC
Found at i:68870 original size:6 final size:6
Alignment explanation
Indices: 68848--68882 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
68838 AAGCAAAAGG
* *
68848 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
68883 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:69099 original size:29 final size:29
Alignment explanation
Indices: 69062--69117 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
69052 GATTTTTTTG
* *
69062 TTGCGATTGTTGCGAAAGTCAAATTCGCA
1 TTGCAATTGTTGCAAAAGTCAAATTCGCA
69091 TTGCAATTGTTGCAAAAGTCAAATTCG
1 TTGCAATTGTTGCAAAAGTCAAATTCG
69118 AAATACGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (29 bp):
TTGCAATTGTTGCAAAAGTCAAATTCGCA
Found at i:69169 original size:20 final size:20
Alignment explanation
Indices: 69142--69192 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
69132 CAACGTGAAG
69142 TTGACTTTCGCGTTGCAAAT
1 TTGACTTTCGCGTTGCAAAT
* * *
69162 TTGGCTTTCACGTTGCGAAT
1 TTGACTTTCGCGTTGCAAAT
69182 TTGACTTTCGC
1 TTGACTTTCGC
69193 AACCATCGCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCAAAT
Found at i:69362 original size:13 final size:12
Alignment explanation
Indices: 69344--69373 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
69334 TTATTTACAC
69344 ATCAATTAAACAA
1 ATCAATTAAAC-A
69357 ATCAATTAAACA
1 ATCAATTAAACA
69369 ATCAA
1 ATCAA
69374 AAAATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (12 bp):
ATCAATTAAACA
Found at i:69369 original size:50 final size:50
Alignment explanation
Indices: 69303--69411 Score: 164
Period size: 50 Copynumber: 2.2 Consensus size: 50
69293 ATCAACTTTT
69303 ACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAA
1 ACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAA
* *** * *
69353 ACAAATCAATTAAACAATCAAAAAATAATTCTTATTTCCTCATCAATTAA
1 ACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAA
69403 ACAAATCAA
1 ACAAATCAA
69412 CTTTTACAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.27
Consensus pattern (50 bp):
ACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAA
Found at i:70634 original size:21 final size:21
Alignment explanation
Indices: 70598--70701 Score: 113
Period size: 21 Copynumber: 5.0 Consensus size: 21
70588 CAAACGGTGG
*
70598 GAGGGACCTC-TGAACGATGA
1 GAGGGGCCTCTTGAACGATGA
* * *
70618 TAGGGGCCTCTTGAACGGTGG
1 GAGGGGCCTCTTGAACGATGA
*
70639 GAGGGGCCTCTTGAATGATGA
1 GAGGGGCCTCTTGAACGATGA
* *
70660 TAGGGGCCTCTTGAATGAT-A
1 GAGGGGCCTCTTGAACGATGA
*
70680 GGAGAGGCCTCTTGAACGATGA
1 -GAGGGGCCTCTTGAACGATGA
70702 CAGGTGATTC
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 9 0.13
21 59 0.86
22 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.22
Consensus pattern (21 bp):
GAGGGGCCTCTTGAACGATGA
Found at i:70672 original size:42 final size:42
Alignment explanation
Indices: 70590--70701 Score: 163
Period size: 42 Copynumber: 2.7 Consensus size: 42
70580 CGGGCTCTCA
*
70590 AACGGTGGGAGGGACCTC-TGAACGATGATAGGGGCCTCTTG
1 AACGGTGGGAGGGGCCTCTTGAACGATGATAGGGGCCTCTTG
*
70631 AACGGTGGGAGGGGCCTCTTGAATGATGATAGGGGCCTCTTG
1 AACGGTGGGAGGGGCCTCTTGAACGATGATAGGGGCCTCTTG
* * * *
70673 AATGATAGGAGAGGCCTCTTGAACGATGA
1 AACGGTGGGAGGGGCCTCTTGAACGATGA
70702 CAGGTGATTC
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 17 0.27
42 46 0.73
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
AACGGTGGGAGGGGCCTCTTGAACGATGATAGGGGCCTCTTG
Found at i:71020 original size:21 final size:21
Alignment explanation
Indices: 70996--71035 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
70986 ATAGATATGC
*
70996 TACCTCATCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
71017 TACCTCACCACGTAAAGTA
1 TACCTCACCACGTAAAGTA
71036 CCATTGTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.23
Consensus pattern (21 bp):
TACCTCACCACGTAAAGTAGA
Done.