Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 92 of 255
Found at i:28242923 original size:27 final size:27
Alignment explanation
Indices: 28242892--28243069 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28242882 TAAATTGTAC
28242892 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28242919 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28242945 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28242973 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28243001 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28243028 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28243055 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28243070 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28243006 original size:82 final size:81
Alignment explanation
Indices: 28242893--28243048 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28242883 AAATTGTACA
* *
28242893 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28242957 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28242974 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
28243039 TGCGAGTTGA
65 TGCGAATTGA
28243049 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28243060 original size:82 final size:81
Alignment explanation
Indices: 28242889--28243069 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
28242879 GATTAAATTG
* *
28242889 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28242954 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28242970 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28243034 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28243052 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28243070 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28255380 original size:42 final size:41
Alignment explanation
Indices: 28255279--28255436 Score: 165
Period size: 42 Copynumber: 3.7 Consensus size: 41
28255269 AACTCGTACA
* *
28255279 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATGACG
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AATCAAAT-ACG
** * *
28255322 ATGCCATTGTCTCAGACAAGGTCTTACACGAAGTCAAATACG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAA-TCAAATACG
* *
28255364 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCTCAAAT-CG
1 ATGCCAACGTCCCAGACATGGTCTTACAC--GAA--TCAAATACG
*
28255408 ATGCCAACGTCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACATGGTCTTACAC
28255437 AATAACTCAT
Statistics
Matches: 98, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
42 31 0.32
43 30 0.31
44 31 0.32
45 6 0.06
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (41 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAATCAAATACG
Found at i:28255422 original size:44 final size:42
Alignment explanation
Indices: 28255279--28255437 Score: 169
Period size: 43 Copynumber: 3.7 Consensus size: 42
28255269 AACTCGTACA
* **
28255279 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATGACG
1 ATGCCAACGTCCCAGACATGGTCTTACACATAATCAAAT-ACG
** * * *
28255322 ATGCCATTGTCTCAGACAAGGTCTTACACGA-AGTCAAATACG
1 ATGCCAACGTCCCAGACATGGTCTTACAC-ATAATCAAATACG
*
28255364 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCTCAAAT-CG
1 ATGCCAACGTCCCAGACATGGTCTTACACAT-AA--TCAAATACG
*
28255408 ATGCCAACGTCCCAGACGTGGTCTTACACA
1 ATGCCAACGTCCCAGACATGGTCTTACACA
28255438 ATAACTCATA
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
41 1 0.01
42 29 0.30
43 31 0.32
44 30 0.31
45 6 0.06
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACATAATCAAATACG
Found at i:28264794 original size:25 final size:25
Alignment explanation
Indices: 28264760--28264813 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
28264750 ATATGAGTCT
28264760 GTTGGATATTGATCCCACGAGGATG
1 GTTGGATATTGATCCCACGAGGATG
28264785 GTTGGATATTGATCCCACGAGGATG
1 GTTGGATATTGATCCCACGAGGATG
28264810 GTTG
1 GTTG
28264814 TATTTTGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.15, G:0.33, T:0.30
Consensus pattern (25 bp):
GTTGGATATTGATCCCACGAGGATG
Found at i:28274222 original size:11 final size:11
Alignment explanation
Indices: 28274201--28274234 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
28274191 TACAAAAATT
28274201 TAAATAATTAAA
1 TAAA-AATTAAA
28274213 TAAAAATTAAA
1 TAAAAATTAAA
*
28274224 TTAAAATTAAA
1 TAAAAATTAAA
28274235 ATTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTAAA
Found at i:28274228 original size:12 final size:13
Alignment explanation
Indices: 28274200--28274249 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
28274190 CTACAAAAAT
28274200 TTAAATAATTAAA
1 TTAAATAATTAAA
28274213 -TAAA-AATTAAA
1 TTAAATAATTAAA
28274224 TT-AA-AATTAAAA
1 TTAAATAATT-AAA
28274236 TTAAATAA-TAAA
1 TTAAATAATTAAA
28274248 TT
1 TT
28274250 TCATAAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 13 0.39
12 15 0.45
13 3 0.09
14 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAATAATTAAA
Found at i:28274241 original size:11 final size:11
Alignment explanation
Indices: 28274206--28274240 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
28274196 AAATTTAAAT
*
28274206 AATTAAATAAA
1 AATTAAATTAA
28274217 AATTAAATTAA
1 AATTAAATTAA
28274228 AATTAAAATTAA
1 AATT-AAATTAA
28274240 A
1 A
28274241 TAATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AATTAAATTAA
Found at i:28279958 original size:42 final size:42
Alignment explanation
Indices: 28279899--28280007 Score: 139
Period size: 43 Copynumber: 2.6 Consensus size: 42
28279889 GTTGATATTA
* *
28279899 CGTGTAAGACCATATCTGGGATATGACATTGATATGAAA-CTT
1 CGTGTAAGACCATATCTGGGATATGACATCGATATGAAATC-C
* * *
28279941 CGTGTAAGACCATATCTGGGCTATTGGCATCGATATGAGATCC
1 CGTGTAAGACCATATCTGGGATA-TGACATCGATATGAAATCC
*
28279984 CATGTAAGACCATATCTGGGATAT
1 CGTGTAAGACCATATCTGGGATAT
28280008 AGCATTGGTA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 23 0.40
43 34 0.59
44 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGATATGACATCGATATGAAATCC
Found at i:28280126 original size:20 final size:20
Alignment explanation
Indices: 28280098--28280136 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28280088 CAATGTTTAA
*
28280098 GTTGAGAAATACTATGGTAT
1 GTTGAGAAAGACTATGGTAT
* *
28280118 GTTGTGAAAGATTATGGTA
1 GTTGAGAAAGACTATGGTA
28280137 AGTTTCCAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (20 bp):
GTTGAGAAAGACTATGGTAT
Found at i:28281275 original size:30 final size:30
Alignment explanation
Indices: 28281239--28281298 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
28281229 GGGCGTGCAA
*
28281239 CCCTGTTTTGGTGAAAATTTTTCTGAGTGT
1 CCCTGTTTTGGTGAAAATTTTTCTAAGTGT
28281269 CCCTGTTTTGGTGAAAATTTTTCTAAGTGT
1 CCCTGTTTTGGTGAAAATTTTTCTAAGTGT
28281299 TGTAGAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.18, C:0.13, G:0.22, T:0.47
Consensus pattern (30 bp):
CCCTGTTTTGGTGAAAATTTTTCTAAGTGT
Found at i:28282621 original size:16 final size:17
Alignment explanation
Indices: 28282600--28282633 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
28282590 AAATATCATG
28282600 AAATAAAAA-CAAACAA
1 AAATAAAAATCAAACAA
28282616 AAATAAAAATCAAACAA
1 AAATAAAAATCAAACAA
28282633 A
1 A
28282634 CGCCATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.09
Consensus pattern (17 bp):
AAATAAAAATCAAACAA
Found at i:28283943 original size:19 final size:21
Alignment explanation
Indices: 28283919--28283965 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
28283909 AAATCAAATA
*
28283919 TTGCAACATCGG-TT-GGATG
1 TTGCAACATCGGATTCGAATG
*
28283938 TTGCAACATTGGATTCGAATG
1 TTGCAACATCGGATTCGAATG
28283959 TTGCAAC
1 TTGCAAC
28283966 TTTGCTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 2 0.08
21 11 0.46
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (21 bp):
TTGCAACATCGGATTCGAATG
Found at i:28285590 original size:12 final size:12
Alignment explanation
Indices: 28285573--28285599 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28285563 ATTCCGAAGT
28285573 ATATATATATAC
1 ATATATATATAC
28285585 ATATATATATAC
1 ATATATATATAC
28285597 ATA
1 ATA
28285600 AGTATGCCAT
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:28286113 original size:27 final size:27
Alignment explanation
Indices: 28286082--28286259 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28286072 TAAATTGTAC
28286082 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28286109 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28286135 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28286163 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28286191 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28286218 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28286245 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28286260 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28286196 original size:82 final size:81
Alignment explanation
Indices: 28286083--28286238 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28286073 AAATTGTACA
* *
28286083 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28286147 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28286164 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
28286229 TGCGAGTTGA
65 TGCGAATTGA
28286239 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28286250 original size:82 final size:81
Alignment explanation
Indices: 28286079--28286259 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
28286069 GATTAAATTG
* *
28286079 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28286144 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28286160 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28286224 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28286242 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28286260 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28297308 original size:16 final size:16
Alignment explanation
Indices: 28297287--28297318 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28297277 TCAAAATGGG
*
28297287 GCCAAGGCACTAGCAA
1 GCCAAGGAACTAGCAA
28297303 GCCAAGGAACTAGCAA
1 GCCAAGGAACTAGCAA
28297319 AGAAGACTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.28, G:0.25, T:0.06
Consensus pattern (16 bp):
GCCAAGGAACTAGCAA
Found at i:28298438 original size:33 final size:33
Alignment explanation
Indices: 28298401--28298467 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
28298391 ATGTTATTGA
28298401 TAAGATTGTCGAAGACTTAGTTTTTGAAAGAGC
1 TAAGATTGTCGAAGACTTAGTTTTTGAAAGAGC
28298434 TAAGATTGTCGAAGACTTAGTTTTTGAAAGAGC
1 TAAGATTGTCGAAGACTTAGTTTTTGAAAGAGC
28298467 T
1 T
28298468 TCACACCTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (33 bp):
TAAGATTGTCGAAGACTTAGTTTTTGAAAGAGC
Found at i:28304319 original size:46 final size:46
Alignment explanation
Indices: 28304269--28304397 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
28304259 TGGTTGAGCA
* *
28304269 TCCGAACTCGTTGAGTTGAGTCCTAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
28304315 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
28304361 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28304398 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:28313340 original size:9 final size:9
Alignment explanation
Indices: 28313326--28313352 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
28313316 GCTCCAATAA
28313326 AATTGAAAG
1 AATTGAAAG
28313335 AATTGAAAG
1 AATTGAAAG
28313344 AATTGAAAG
1 AATTGAAAG
28313353 CTCAGTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (9 bp):
AATTGAAAG
Found at i:28317838 original size:37 final size:37
Alignment explanation
Indices: 28317788--28317866 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
28317778 TTATTACGAA
* * *
28317788 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
28317825 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
28317862 GTCTT
1 GTCTT
28317867 TAGTGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:28318063 original size:47 final size:47
Alignment explanation
Indices: 28317987--28318160 Score: 226
Period size: 47 Copynumber: 3.7 Consensus size: 47
28317977 CTTCGGGACT
* * * *
28317987 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTT-GGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGCCC
* *
28318034 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
*
28318081 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
* * *
28318128 TATCTCATATATGCA-TGTTCACATCCATCACAT
1 TATCACATATATACACT-TTCACATTCATCACAT
28318161 AGAATCCTAA
Statistics
Matches: 115, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
46 3 0.03
47 112 0.97
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
Found at i:28333425 original size:16 final size:16
Alignment explanation
Indices: 28333404--28333435 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28333394 TACATGGCTT
28333404 GAGTCCTTTTTGAGTG
1 GAGTCCTTTTTGAGTG
28333420 GAGTCCTTTTTGAGTG
1 GAGTCCTTTTTGAGTG
28333436 AGCTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.31, T:0.44
Consensus pattern (16 bp):
GAGTCCTTTTTGAGTG
Found at i:28335491 original size:26 final size:26
Alignment explanation
Indices: 28335451--28335501 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
28335441 GAGTTGGACC
* *
28335451 ATGTGAGGTTGAAACATGTTTTATTA
1 ATGTCAGGTTCAAACATGTTTTATTA
28335477 ATGTCAGGTTCAAACATGTTTTATT
1 ATGTCAGGTTCAAACATGTTTTATT
28335502 GTTGTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (26 bp):
ATGTCAGGTTCAAACATGTTTTATTA
Found at i:28337034 original size:18 final size:18
Alignment explanation
Indices: 28336998--28337035 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
28336988 CCAAAATCTT
*
28336998 ATTTTAATTCTTTTGTAC
1 ATTTTAATTCTTTTATAC
28337016 ATTTTAATT-TTATTATAC
1 ATTTTAATTCTT-TTATAC
28337034 AT
1 AT
28337036 ATTTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (18 bp):
ATTTTAATTCTTTTATAC
Found at i:28337780 original size:21 final size:21
Alignment explanation
Indices: 28337755--28337794 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28337745 TATTGCCTTC
28337755 AAATT-TTTTATTAAAATAAAA
1 AAATTATTTT-TTAAAATAAAA
*
28337776 AAATTATTTTTTACAATAA
1 AAATTATTTTTTAAAATAA
28337795 TTTAATTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATTATTTTTTAAAATAAAA
Found at i:28337812 original size:29 final size:30
Alignment explanation
Indices: 28337774--28337831 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
28337764 ATTAAAATAA
*
28337774 AAAAATTATTTT-TTACAATAATTTAATTAG
1 AAAAATTATTTTATGA-AATAATTTAATTAG
*
28337804 AAAAA-TATTTTATGAATTAATTTAATTA
1 AAAAATTATTTTATGAAATAATTTAATTA
28337832 TTATTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (30 bp):
AAAAATTATTTTATGAAATAATTTAATTAG
Found at i:28338255 original size:31 final size:31
Alignment explanation
Indices: 28338220--28338282 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
28338210 ATCAATGATT
28338220 TCACAAAAGCCAATAAAAAAACAATTTAACA
1 TCACAAAAGCCAATAAAAAAACAATTTAACA
28338251 TCACAAAAGCCAATAAAAAAACAATTTAACA
1 TCACAAAAGCCAATAAAAAAACAATTTAACA
28338282 T
1 T
28338283 AGATTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.60, C:0.19, G:0.03, T:0.17
Consensus pattern (31 bp):
TCACAAAAGCCAATAAAAAAACAATTTAACA
Found at i:28339874 original size:554 final size:554
Alignment explanation
Indices: 28338825--28339934 Score: 1898
Period size: 554 Copynumber: 2.0 Consensus size: 554
28338815 CATCACCGGA
28338825 CATAAACACATGCAATCGTATAAAACCAGGTCATGAATTTAAGTTCAAATTTAAAACTTTTCACA
1 CATAAACACATGCAATCGTATAAAACCAGGTCATGAATTTAAGTTCAAATTTAAAACTTTTCACA
* * *
28338890 TTTCATCTTAAAGTCCCTAATATGGGCCTACGAGGCCCAAATCATGCTTTGGAAACAATTCGGGA
66 TTTCATCTTAAAGTCCCTAATATGAGCCTACGAAGCCCAAATCATGCTTTGGAAACAATTCAGGA
* * ** * *
28338955 CCAAACCGAGAACTTTAGAACACTTTGAAAATTTTCATGAAAAACAGGGACACACTCCTGTGTGA
131 CCAAACCAAGAACTTTAGAAAACTTCAAAAAATTTCATGAAAAACAGGGACACACTCCCGTGTGA
* * * *
28339020 TATTAGGACATGGTCGTGTGGCTTGCATGGCCATGTCTCTAGCCCGTGCACTAATTTGACTTGTT
196 TATTAGGACATGGTCGTGTGGCTCGCATGGCCATGGCCCTAGCCCGTGCACTAATCTGACTTGTT
* *
28339085 GTTGCATACAAATTTACGTCACACATAGATATCACCACTCGTTCATCCACATATGTAAGCATACA
261 GTTGCATACAAATTTACGTCACACATAGATATCACCACTCATTCATCCACATATATAAGCATACA
* *
28339150 CATCCTTGAAATGCATCATCGTGGACTTATAATATAGCCAATATACCTACATCAAATGGCCTTAC
326 CATCCTTGAAATGCATCATCATAGACTTATAATATAGCCAATATACCTACATCAAATGGCCTTAC
* *
28339215 ACAACAATGAACTTTCAAATAGCATAGGCCAACATTTTAGGCCAAAACTATTATGACATATACAA
391 ACAACAATGAACTTTCAAATAGCATAGGCCAACATTTTAGGCCAAAACGATTATGACATATAAAA
*
28339280 AAATAACCATGTCCCCTATACATGCCATGACCTTAAGTATAAGAATCATCAATACCTAATTTGTT
456 AAATAACCAAGTCCCCTATACATGCCATGACCTTAAGTATAAGAATCATCAATACCTAATTTGTT
*
28339345 AGTTTGATAGTGTGATAGGTTCTCCAGTGACTTC
521 AGTTTGATAGTGTGATAGGTTCTCCAGCGACTTC
** *
28339379 CATAAACACATGCAATCGTATAAAACCAGGTCATGAATTTGCGTTCAAATTTCAAACTTTTCACA
1 CATAAACACATGCAATCGTATAAAACCAGGTCATGAATTTAAGTTCAAATTTAAAACTTTTCACA
*
28339444 TTTCATCTTAAAGTCCTTAATATGAGCCTACGAAGCCCAAATCATGCTTTGGAAACAATTCAGGA
66 TTTCATCTTAAAGTCCCTAATATGAGCCTACGAAGCCCAAATCATGCTTTGGAAACAATTCAGGA
* * *
28339509 CCAAACCAATAACTTTAGAAAACTTCAAAAAATTTCATGAAAAATAGGGGCACACTCCCGTGTGA
131 CCAAACCAAGAACTTTAGAAAACTTCAAAAAATTTCATGAAAAACAGGGACACACTCCCGTGTGA
**
28339574 TATTAGGACATGG-CTGTGTGGCTCGCATGGCCATGGCCCTAGCTTGTGCACTAATCTGACTTGT
196 TATTAGGACATGGTC-GTGTGGCTCGCATGGCCATGGCCCTAGCCCGTGCACTAATCTGACTTGT
*
28339638 TGTTGCGTACAAATTTACGTCACACATAGATATCACCACTCATTCATCCACATATATAAGCATAC
260 TGTTGCATACAAATTTACGTCACACATAGATATCACCACTCATTCATCCACATATATAAGCATAC
*
28339703 ACATCCTTGAAATGCATCATCATAGACTTATAATATAGGCAATATACCTACATCAAATGGCCTTA
325 ACATCCTTGAAATGCATCATCATAGACTTATAATATAGCCAATATACCTACATCAAATGGCCTTA
*
28339768 CACAACAGTGAACTTTCAAATAGCATAGGCCAACATTTTAGGCCAAAACGATTATGACATATAAA
390 CACAACAATGAACTTTCAAATAGCATAGGCCAACATTTTAGGCCAAAACGATTATGACATATAAA
28339833 AAAATAACCAAGTCCCCTATACATGCCATGACCTTAAGTATAAGAATCATCAATACCTAATTTGT
455 AAAATAACCAAGTCCCCTATACATGCCATGACCTTAAGTATAAGAATCATCAATACCTAATTTGT
*
28339898 TAGTTTGATAGTGTGATAGGTTCTCCGGCGACTTC
520 TAGTTTGATAGTGTGATAGGTTCTCCAGCGACTTC
28339933 CA
1 CA
28339935 ACCCCTAGCT
Statistics
Matches: 521, Mismatches: 34, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
553 1 0.00
554 520 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.29
Consensus pattern (554 bp):
CATAAACACATGCAATCGTATAAAACCAGGTCATGAATTTAAGTTCAAATTTAAAACTTTTCACA
TTTCATCTTAAAGTCCCTAATATGAGCCTACGAAGCCCAAATCATGCTTTGGAAACAATTCAGGA
CCAAACCAAGAACTTTAGAAAACTTCAAAAAATTTCATGAAAAACAGGGACACACTCCCGTGTGA
TATTAGGACATGGTCGTGTGGCTCGCATGGCCATGGCCCTAGCCCGTGCACTAATCTGACTTGTT
GTTGCATACAAATTTACGTCACACATAGATATCACCACTCATTCATCCACATATATAAGCATACA
CATCCTTGAAATGCATCATCATAGACTTATAATATAGCCAATATACCTACATCAAATGGCCTTAC
ACAACAATGAACTTTCAAATAGCATAGGCCAACATTTTAGGCCAAAACGATTATGACATATAAAA
AAATAACCAAGTCCCCTATACATGCCATGACCTTAAGTATAAGAATCATCAATACCTAATTTGTT
AGTTTGATAGTGTGATAGGTTCTCCAGCGACTTC
Found at i:28340969 original size:51 final size:51
Alignment explanation
Indices: 28340885--28341134 Score: 376
Period size: 51 Copynumber: 4.9 Consensus size: 51
28340875 CGGATGCACG
* **
28340885 GTGGCCTTCACATAGTACCACCCTTGTAG-CCAAAGCTATTTTATTTTCAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAAA
* * * *
28340936 GTAGCCTTCACATAATAACACACTTGTGTCCAAAGCTATTTTATTCAAAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* *
28340987 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTCATGCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* *
28341038 GTGGCCTTCACATAGTACCACACTTGTGTTCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
*
28341089 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGTTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
28341135 CTAAGGTTCA
Statistics
Matches: 178, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
50 1 0.01
51 177 0.99
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
Found at i:28342880 original size:39 final size:37
Alignment explanation
Indices: 28342803--28342889 Score: 88
Period size: 39 Copynumber: 2.3 Consensus size: 37
28342793 AGAATTATTT
* *
28342803 GAATATAATTTTATAAAATATAATTTAAATTTATAAA
1 GAATATAATTTTATAAAATAGAATTTAAATTTACAAA
28342840 GAATATATATTTATATAAAAT-GAATTTGAAAATTT-CAAA
1 GAATATA-ATTT-TATAAAATAGAATTT--AAATTTACAAA
*
28342879 GATTAATAATT
1 GAAT-ATAATT
28342890 CTATGCCAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
37 7 0.17
38 9 0.21
39 17 0.40
40 9 0.21
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (37 bp):
GAATATAATTTTATAAAATAGAATTTAAATTTACAAA
Found at i:28347346 original size:28 final size:28
Alignment explanation
Indices: 28347314--28347395 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
28347304 TTTGAATCAT
28347314 TCAATATTTCGTACACTAAGTGCCATTC
1 TCAATATTTCGTACACTAAGTGCCATTC
* *
28347342 TCAATATCTCGCACACTAAGTGCCATTC
1 TCAATATTTCGTACACTAAGTGCCATTC
* *
28347370 TCAATATTTTGTACACTGAGTGCCAT
1 TCAATATTTCGTACACTAAGTGCCAT
28347396 ATTTGATTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (28 bp):
TCAATATTTCGTACACTAAGTGCCATTC
Found at i:28366011 original size:27 final size:27
Alignment explanation
Indices: 28365952--28366103 Score: 223
Period size: 27 Copynumber: 5.6 Consensus size: 27
28365942 TAAATTGTAC
*
28365952 AGCACTAAGTGTGCGAGTTGGACTATGT
1 AGCACTAAGTGTGCGAATT-GACTATGT
28365980 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
28366007 TGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
28366034 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* *
28366062 AGCACTAAGTGTGCGAGTTGACTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
28366089 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28366104 GACTTAATAT
Statistics
Matches: 114, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
27 71 0.62
28 43 0.38
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:28366017 original size:55 final size:55
Alignment explanation
Indices: 28365952--28366103 Score: 234
Period size: 55 Copynumber: 2.8 Consensus size: 55
28365942 TAAATTGTAC
28365952 AGCACTAAGTGTGCGAGTTGGACTATGTAGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTT-GACTATGTAGCACTAAGTGTGCGAGATTGACTATGT
* * * *
28366007 TGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGATTGACTATGT
* *
28366062 AGCACTAAGTGTGCGAGTTGACTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
28366104 GACTTAATAT
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 24 0.27
55 64 0.73
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGATTGACTATGT
Found at i:28366066 original size:82 final size:82
Alignment explanation
Indices: 28365952--28366103 Score: 250
Period size: 82 Copynumber: 1.9 Consensus size: 82
28365942 TAAATTGTAC
* *
28365952 AGCACTAAGTGTGCGAGTTGGACTATGTAGCACTAAGTGTGCGAATTGACTATGTTGCACTAAGT
1 AGCACTAAGTGTGCGAGTTGGACTATGTAGCACTAAGTGTGCGAATTGACTATATAGCACTAAGT
28366017 GTGCGAATTGACTATGT
66 GTGCGAATTGACTATGT
* * * *
28366034 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGACTATATAGCACTGAGT
1 AGCACTAAGTGTGCGAGTTGGACTATGTAGCACTAAGTGTGCGAATTGACTATATAGCACTAAGT
28366099 GTGCG
66 GTGCG
28366104 GACTTAATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 64 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAGTTGGACTATGTAGCACTAAGTGTGCGAATTGACTATATAGCACTAAGT
GTGCGAATTGACTATGT
Found at i:28369269 original size:68 final size:64
Alignment explanation
Indices: 28369031--28369283 Score: 181
Period size: 68 Copynumber: 3.9 Consensus size: 64
28369021 ATATAGTTCG
** * * * * * *
28369031 GCTCTCTTGTAGACATGGTGAACACTTAGTACCACCCATGTGACCTAGC--CAGTTTAT-CTCGT
1 GCTCTCTTGTCTACATGATGTACACATAGCACCACACATGTGACCTAGCTACA-TATATCCT-GT
28369093 A
64 A
* * * * * * *
28369094 GCTCTCTTGTCTACATGGTGCCCTTCACCTGGAACCACGCATGCGACCTAGCTACATATATCCTG
1 GCTCTCTTGTCTACATGATG---TACACATAGCACCACACATGTGACCTAGCTACATATATCCTG
28369159 TA
63 TA
* * * * *
28369161 GCTCTCTTGTCTACATGGTGTACACATAGTATCACGCATGTGACCTAGCTACATCATAATGTCGT
1 GCTCTCTTGTCTACATGATGTACACATAGCACCACACATGTGACCTAGCTACAT-AT-A--TCCT
28369226 GTA
62 GTA
* * *
28369229 GCTCTCTTGTAC-ACATGATGTGCACTTAGCACCATACATGTGACCTAGCTACATA
1 GCTCTCTTGT-CTACATGATGTACACATAGCACCACACATGTGACCTAGCTACATA
28369284 CCATCAGTAT
Statistics
Matches: 155, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
63 18 0.12
64 28 0.18
65 2 0.01
66 23 0.15
67 28 0.18
68 55 0.35
69 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGATGTACACATAGCACCACACATGTGACCTAGCTACATATATCCTGTA
Found at i:28390930 original size:46 final size:46
Alignment explanation
Indices: 28390880--28391042 Score: 181
Period size: 46 Copynumber: 3.5 Consensus size: 46
28390870 TCCAAACTTA
**
28390880 TTGAGTTGAGTTTGAGTTCACTTATGGATGCGAATGTCCGAACTCG
1 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCG
* * *
28390926 TTGAGTTGAGTCCGAGTTCA-TGA--AATG-TAACTAGGCATCCGAACTCG
1 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCGAACTCG
* * *
28390973 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCG
1 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCG
28391019 TTGAGTTGAGTCCGAGTTCACTTA
1 TTGAGTTGAGTCCGAGTTCACTTA
28391043 GGGGCGGGTT
Statistics
Matches: 97, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 50 0.52
47 30 0.31
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.31
Consensus pattern (46 bp):
TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCG
Found at i:28398749 original size:18 final size:18
Alignment explanation
Indices: 28398712--28398750 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28398702 TTGGAAATCA
*
28398712 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
28398730 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
28398748 AAA
1 AAA
28398751 AATCATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:28410254 original size:40 final size:40
Alignment explanation
Indices: 28410210--28410395 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
28410200 GCTACTCATT
*
28410210 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
28410250 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
28410290 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
28410330 CAAATGCCTTC-GGATCTTAGTCCAGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28410371 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28410396 CATCATTCAA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 3 0.02
40 114 0.88
41 13 0.10
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28418176 original size:40 final size:40
Alignment explanation
Indices: 28418139--28418323 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
28418129 GCTACTCGTT
*
28418139 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
28418179 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
28418219 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
28418258 CAAATGCGTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28418299 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28418324 CATCATTCAA
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 78 0.62
41 13 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28418250 original size:79 final size:82
Alignment explanation
Indices: 28418139--28418323 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
28418129 GCTACTCGTT
* *
28418139 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
28418202 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* * **
28418219 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCGTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
28418282 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
28418299 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28418324 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:28423195 original size:3 final size:3
Alignment explanation
Indices: 28423187--28423226 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
28423177 AGCTTCTCTT
*
28423187 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28423227 AATTCACGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:28428934 original size:21 final size:22
Alignment explanation
Indices: 28428887--28428941 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
28428877 CATTCAAGAT
**
28428887 AAAATAATATATAAAACTCTTTA
1 AAAATAATATA-AAAACTAATTA
*
28428910 AAAATAATATAAAAAC-AATTC
1 AAAATAATATAAAAACTAATTA
28428931 AAAAT-ATATAA
1 AAAATAATATAA
28428942 TGTATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.21
21 7 0.24
22 5 0.17
23 11 0.38
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATAATATAAAAACTAATTA
Found at i:28429172 original size:15 final size:15
Alignment explanation
Indices: 28429148--28429193 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
28429138 ATATAAATAG
*
28429148 AAATAAAAATATAAT
1 AAATAGAAATATAAT
*
28429163 AAATAGAAATTTAAT
1 AAATAGAAATATAAT
28429178 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
28429194 ATAGATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 15 0.58
16 1 0.04
17 10 0.38
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:28429213 original size:15 final size:14
Alignment explanation
Indices: 28429186--28429256 Score: 56
Period size: 15 Copynumber: 4.9 Consensus size: 14
28429176 ATAATAGTAG
*
28429186 AAATATAAATAGAT
1 AAATAAAAATAGAT
28429200 AAATAAAAATTAGAT
1 AAATAAAAA-TAGAT
*
28429215 AAATAATAATAGTATT
1 AAATAAAAATAG-A-T
*
28429231 AGAATAACAA-A-AT
1 A-AATAAAAATAGAT
*
28429244 AAATAGAAATAGA
1 AAATAAAAATAGA
28429257 AACATAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
12 6 0.13
13 3 0.07
14 13 0.28
15 14 0.30
16 3 0.07
17 7 0.15
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.25
Consensus pattern (14 bp):
AAATAAAAATAGAT
Found at i:28438107 original size:8 final size:8
Alignment explanation
Indices: 28438094--28438123 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
28438084 GGCCGAAAAC
28438094 GGGCCAAT
1 GGGCCAAT
28438102 GGGCCAAT
1 GGGCCAAT
*
28438110 GGGCCAAC
1 GGGCCAAT
28438118 GGGCCA
1 GGGCCA
28438124 CTTTGGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.40, T:0.07
Consensus pattern (8 bp):
GGGCCAAT
Found at i:28441698 original size:40 final size:40
Alignment explanation
Indices: 28441468--28441699 Score: 288
Period size: 40 Copynumber: 5.8 Consensus size: 40
28441458 CATTTGAATG
* * * *
28441468 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
* * * * * *
28441508 TTATCCGGGCTAAGTCCTGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
* *
28441548 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
28441588 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
*
28441628 ATATCCGGGCTAAGACCCGAAGGCATTTGTGTGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
* * *
28441668 ATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
28441700 TTGTGGTTAT
Statistics
Matches: 177, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 175 0.99
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
Found at i:28445027 original size:30 final size:30
Alignment explanation
Indices: 28444991--28445057 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
28444981 TGCCTGGAAA
28444991 GGCACCGGTGTCCATTGGACCTTATAGGAT
1 GGCACCGGTGTCCATTGGACCTTATAGGAT
*
28445021 GGCACCGGTGTCTATTGGACCTTATAGGAT
1 GGCACCGGTGTCCATTGGACCTTATAGGAT
28445051 GGCACCG
1 GGCACCG
28445058 AAGGACTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.25
Consensus pattern (30 bp):
GGCACCGGTGTCCATTGGACCTTATAGGAT
Found at i:28453084 original size:20 final size:20
Alignment explanation
Indices: 28453055--28453103 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
28453045 TCATACGGGA
*
28453055 TTGCACTTCGGTGCCTCTAT
1 TTGCACTTCGATGCCTCTAT
* *
28453075 TTGCATTTCGATGCCTCTGT
1 TTGCACTTCGATGCCTCTAT
28453095 ATTGCACTT
1 -TTGCACTT
28453104 TGGCGCGTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.43
Consensus pattern (20 bp):
TTGCACTTCGATGCCTCTAT
Found at i:28462492 original size:30 final size:31
Alignment explanation
Indices: 28462456--28462519 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
28462446 TTTTCGAGCC
28462456 TAGGGGCAAAATCATAATTTTG-CAAAGGTT
1 TAGGGGCAAAATCATAATTTTGCCAAAGGTT
* * *
28462486 TAGGGGCATAATTATAATTTTGCCAAAGTTT
1 TAGGGGCAAAATCATAATTTTGCCAAAGGTT
28462517 TAG
1 TAG
28462520 TTAGGGAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (31 bp):
TAGGGGCAAAATCATAATTTTGCCAAAGGTT
Found at i:28463328 original size:47 final size:47
Alignment explanation
Indices: 28463274--28463395 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
28463264 GCATTAGCAC
*
28463274 TAAGACAATGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
28463321 TAAGACAAGGATACCATGTAAGACCATGTTTGGAGCATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *
28463368 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
28463396 CCAAGGCATG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:28463438 original size:54 final size:54
Alignment explanation
Indices: 28463382--28463581 Score: 217
Period size: 55 Copynumber: 3.7 Consensus size: 54
28463372 ATAAGGATAT
* *
28463382 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAAT
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAAAC
* * **
28463436 CATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGG-TCC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTATAAGGC-AAGGAAAC
* * * *
28463491 CAGGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAA-GAATAC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAA-AC
** * * *
28463544 CACATAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTC
28463582 AAAAGGAAAA
Statistics
Matches: 124, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
51 1 0.01
52 2 0.02
53 40 0.32
54 35 0.28
55 42 0.34
56 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.21
Consensus pattern (54 bp):
CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAAAC
Found at i:28463582 original size:53 final size:54
Alignment explanation
Indices: 28463385--28463581 Score: 211
Period size: 53 Copynumber: 3.6 Consensus size: 54
28463375 AGGATATCAT
* * *
28463385 GTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAA-ATCAT
1 GTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAA-GAATACCAC
* * * * *
28463439 GTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAA-AGGTCCCAG
1 GTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTATAAGGCAAGA-ATACCAC
* * *
28463494 GTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGAATACCAC
1 GTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGAATACCAC
* * * *
28463547 ATAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 GTAAGACCATGCCAAGACATGGCATTGATAAGTTC
28463582 AAAAGGAAAA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
53 44 0.36
54 33 0.27
55 44 0.36
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
GTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGAATACCAC
Found at i:28470022 original size:47 final size:47
Alignment explanation
Indices: 28469964--28470084 Score: 215
Period size: 47 Copynumber: 2.6 Consensus size: 47
28469954 GCATTGGCAC
28469964 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
28470011 TAAGACAAGGATACCATGTAAGACCATGTTTGGAGCATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *
28470058 TAAGATAAGGATATCATGTAAGACCAT
1 TAAGACAAGGATACCATGTAAGACCAT
28470085 TCCAAGGCAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.26
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:28470129 original size:54 final size:54
Alignment explanation
Indices: 28470064--28470260 Score: 204
Period size: 55 Copynumber: 3.6 Consensus size: 54
28470054 TTGGTAAGAT
* *
28470064 AAGGATATCATGTAAGACCATTCCAAGGCATGGTATTGATAAGTTCTATAAGGC
1 AAGGATATCATGTAAGACCATTCCAAGGCATGGCATTGATGAGTTCTATAAGGC
* *
28470118 AAGGAAATCATGTAAGACCATGT-CAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATATCATGTAAGACCAT-TCCAAGGCATGGCATTGATGAGTT-CTATAAGGC
** * * *
28470173 AAAGG-TCCCAGGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATATCATGTAAGACCATTCCAAGGCATGGCATTGATGAGTTCTATAAGGC
* * ** *
28470226 AAGAATACCACATAAGACCATGT-CAAGACATGGCA
1 AAGGATATCATGTAAGACCAT-TCCAAGGCATGGCA
28470261 ATGGTAAGTT
Statistics
Matches: 120, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
52 3 0.03
53 31 0.26
54 40 0.33
55 42 0.35
56 4 0.03
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
AAGGATATCATGTAAGACCATTCCAAGGCATGGCATTGATGAGTTCTATAAGGC
Found at i:28470246 original size:53 final size:54
Alignment explanation
Indices: 28470075--28470271 Score: 193
Period size: 53 Copynumber: 3.6 Consensus size: 54
28470065 AGGATATCAT
* * * * *
28470075 GTAAGACCATTCCAAGGCATGGTATTGATAAGTTCTATAAGGCAAGGAA-ATCAT
1 GTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAA-GAATACCAC
* * * * *
28470129 GTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAA-AGGTCCCAG
1 GTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTATAAGGCAAGA-ATACCAC
* * *
28470184 GTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGAATACCAC
1 GTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGAATACCAC
* * * *
28470237 ATAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 GTAAGACCATGCCAAGACATGGCATTGATAAGTTC
28470272 AAAAAGGAAA
Statistics
Matches: 119, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
53 44 0.37
54 31 0.26
55 44 0.37
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
GTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGAATACCAC
Found at i:28475896 original size:48 final size:48
Alignment explanation
Indices: 28475825--28476044 Score: 222
Period size: 48 Copynumber: 4.6 Consensus size: 48
28475815 AAACAAAGTA
*
28475825 CCAATGCCATGTCCCAGACATGGTCTTACATGAATCCACATATA-ATCC
1 CCAATGCCATGTCCCAGACATGGTCTTACAT-AATGCACATATACATCC
28475873 CCAATGCCATGTCCCAGACATGGTCTTAC--AATGGCACATATATCATCC
1 CCAATGCCATGTCCCAGACATGGTCTTACATAAT-GCACATATA-CATCC
* * * *
28475921 CCGATGCCATGTCCCAAACATGGTCTT--ATACAGGCACATATATCATCG
1 CCAATGCCATGTCCCAGACATGGTCTTACATA-ATGCACATATA-CATCC
** *
28475969 CC-ATGCCATGTCCCAGACATGGTCTTAC--ACGGCACATATATCATCG
1 CCAATGCCATGTCCCAGACATGGTCTTACATAATGCACATATA-CATCC
*** *
28476015 TTGATGCCATGTCCTAGACATGGTCTTACA
1 CCAATGCCATGTCCCAGACATGGTCTTACA
28476045 CAGGCACACT
Statistics
Matches: 152, Mismatches: 10, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
45 3 0.02
46 24 0.16
47 49 0.32
48 75 0.49
49 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (48 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATAATGCACATATACATCC
Found at i:28476086 original size:143 final size:141
Alignment explanation
Indices: 28475828--28476096 Score: 339
Period size: 143 Copynumber: 1.9 Consensus size: 141
28475818 CAAAGTACCA
*
28475828 ATGCCATGTCCCAGACATGGTCTTACATGAATCCACATATAATCCCCAATGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACG-A-CCACATATAATCCCCAATGCCATGTCCCAGACA
* *
28475893 TGGTCTTACAATGGCACATATATCATCCCCGATGCCATGTCCCAAACATGGTCTTATACAGGCAC
64 TGGTCTTACAATGGCACATATATCATCCCCAATGCCATGTCCCAAACATGGTCTTACACAGGCAC
28475958 ATATATCATCGCC
129 ATATATCATCGCC
* **** *
28475971 ATGCCATGTCCCAGACATGGTCTTACACG-GCACATATATCATCGTTGATGCCATGTCCTAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACGACCACATATA--ATCCCCAATGCCATGTCCCAGACA
* *
28476035 TGGTCTTACACA-GGCACACT-TCTCGGAT-GCCAATGCCATGTCCCAAACATGGTCTTACACAG
64 TGGTCTTACA-ATGGCACA-TATATC--ATCCCCAATGCCATGTCCCAAACATGGTCTTACACAG
28476097 AATCTCATTT
Statistics
Matches: 109, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
140 8 0.07
142 38 0.35
143 61 0.56
144 2 0.02
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (141 bp):
ATGCCATGTCCCAGACATGGTCTTACACGACCACATATAATCCCCAATGCCATGTCCCAGACATG
GTCTTACAATGGCACATATATCATCCCCAATGCCATGTCCCAAACATGGTCTTACACAGGCACAT
ATATCATCGCC
Found at i:28487321 original size:79 final size:81
Alignment explanation
Indices: 28487183--28487367 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
28487173 TTGAATGATG
* *
28487183 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
28487247 TGTGCAAGATACTA-A
66 TGTGCAAGATACTATA
* * * **
28487262 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
* *
28487324 TTTGTGCGAGTTACTATA
64 TTTGTGCAAGATACTATA
* *
28487342 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28487368 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCAAGATACTATA
Found at i:28487374 original size:40 final size:40
Alignment explanation
Indices: 28487183--28487367 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
28487173 TTGAATGATG
* * * * *
28487183 TCCGGGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
28487223 TCCGGACTAAGAT-CCGAAGGCATTTGTGCAAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
28487263 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28487302 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28487343 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28487368 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 34 0.27
40 82 0.65
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28487389 original size:79 final size:79
Alignment explanation
Indices: 28487236--28487400 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
28487226 GGACTAAGAT
* **
28487236 CCGAAGGCATTTGTGCAAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCAAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28487301 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
28487315 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCAAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28487378 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28487394 CCGAAGG
1 CCGAAGG
28487401 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCAAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28495214 original size:39 final size:41
Alignment explanation
Indices: 28495113--28495296 Score: 206
Period size: 39 Copynumber: 4.6 Consensus size: 41
28495103 TTGAATGATG
* *
28495113 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
28495153 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
28495193 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
28495232 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
28495271 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28495297 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.01
39 69 0.55
40 43 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:28495249 original size:79 final size:80
Alignment explanation
Indices: 28495113--28495296 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
28495103 TTGAATGATG
*
28495113 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
28495177 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
28495192 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
28495254 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
28495271 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28495297 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 49 0.54
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
GTGCGAGATACTATA
Found at i:28495319 original size:78 final size:79
Alignment explanation
Indices: 28495166--28495329 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 79
28495156 GGACTAAGAT
* **
28495166 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28495231 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
28495245 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28495307 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28495323 CCGAAGG
1 CCGAAGG
28495330 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 38 0.51
79 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28502780 original size:79 final size:81
Alignment explanation
Indices: 28502644--28502828 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
28502634 TTGAATGATG
* *
28502644 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
28502708 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
28502723 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
28502785 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
28502803 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28502829 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:28502842 original size:40 final size:40
Alignment explanation
Indices: 28502645--28502828 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
28502635 TGAATGATGT
* * * *
28502645 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
28502685 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
28502725 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
28502763 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
28502804 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28502829 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:28502850 original size:79 final size:79
Alignment explanation
Indices: 28502697--28502861 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
28502687 GGACTAAGAT
* * **
28502697 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28502762 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
28502776 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28502839 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28502855 CCGAAGG
1 CCGAAGG
28502862 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28514539 original size:20 final size:18
Alignment explanation
Indices: 28514502--28514552 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
28514492 CTATAGCAAC
28514502 TCACAATTT-CAATTATT
1 TCACAATTTACAATTATT
28514519 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
*
28514539 TTACAACTTTACAA
1 TCACAA-TTTACAA
28514553 AATAGCCCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 4 0.14
20 16 0.55
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:28523951 original size:20 final size:20
Alignment explanation
Indices: 28523926--28523971 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28523916 ATTGGGCCTT
28523926 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
28523946 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
28523965 GCCCATA
1 GCCCATA
28523972 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:28523980 original size:19 final size:20
Alignment explanation
Indices: 28523938--28523981 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
28523928 CCATATTAAC
** *
28523938 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
28523958 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
28523977 ACAGT
1 ACAGT
28523982 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:28527611 original size:43 final size:43
Alignment explanation
Indices: 28527553--28527718 Score: 199
Period size: 43 Copynumber: 3.9 Consensus size: 43
28527543 ATTATCGAGA
* * *
28527553 TGTGATTGCATGTAAGAACATGCCTGGGACATTGGCATTGTAT
1 TGTGATTACGTGTAAGAACATGTCTGGGACATTGGCATTGTAT
* * *
28527596 TGTGCTTACGTGTAAGAACATGTCGGGGACACTGGCATTGTAT
1 TGTGATTACGTGTAAGAACATGTCTGGGACATTGGCATTGTAT
* * *
28527639 TGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCGT-T
1 TGTGATTACGTGTAAGAACATGTCTGGGACATTGGCATTGTAT
* * * *
28527681 ATATGATTTCGTGGAAGACCATGTCTGGGACATTGGCA
1 -TGTGATTACGTGTAAGAACATGTCTGGGACATTGGCA
28527719 CCGATATGTG
Statistics
Matches: 106, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 1 0.01
43 105 0.99
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTGATTACGTGTAAGAACATGTCTGGGACATTGGCATTGTAT
Found at i:28527744 original size:43 final size:43
Alignment explanation
Indices: 28527649--28527745 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 43
28527639 TGTGATTATG
* * ** *
28527649 TGTAAGACCATGTCTGGGACATTGGCATCGTTATATGATTTCG
1 TGTAAGACCATGTCTGGGACATTGGCACCGATATATGATAACA
* *
28527692 TGGAAGACCATGTCTGGGACATTGGCACCGATATGTGATAACA
1 TGTAAGACCATGTCTGGGACATTGGCACCGATATATGATAACA
*
28527735 TGTACGACCAT
1 TGTAAGACCAT
28527746 ATTTGGGATA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCACCGATATATGATAACA
Found at i:28527744 original size:86 final size:85
Alignment explanation
Indices: 28527552--28527745 Score: 201
Period size: 86 Copynumber: 2.3 Consensus size: 85
28527542 TATTATCGAG
* * * * * *
28527552 ATGTGATTGCATGTAAGAACATGCCTGGGACATTGGCATTGTATTGTGCTTACGTGTAAGAACAT
1 ATGTGATTACATGTAAGACCATGCCTGGGACATTGGCATCGTATTATGATTACGTGGAAGAACAT
**
28527617 GTCGGGGACACTGGCATTGT
66 GTCGGGGACACTGGCACCGT
** * * *
28527637 ATTGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCGT-TATATGATTTCGTGGAAGACC
1 A-TGTGATTACATGTAAGACCATGCCTGGGACATTGGCATCGTAT-TATGATTACGTGGAAGAAC
* *
28527701 ATGTCTGGGACATTGGCACCGAT
64 ATGTCGGGGACACTGGCACCG-T
* *
28527724 ATGTGATAACATGTACGACCAT
1 ATGTGATTACATGTAAGACCAT
28527746 ATTTGGGATA
Statistics
Matches: 87, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
85 2 0.02
86 83 0.95
87 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (85 bp):
ATGTGATTACATGTAAGACCATGCCTGGGACATTGGCATCGTATTATGATTACGTGGAAGAACAT
GTCGGGGACACTGGCACCGT
Found at i:28528125 original size:13 final size:13
Alignment explanation
Indices: 28528107--28528133 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28528097 GAAGTAATCG
28528107 CACACGGGCGTGT
1 CACACGGGCGTGT
28528120 CACACGGGCGTGT
1 CACACGGGCGTGT
28528133 C
1 C
28528134 CCTGCTGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:28548618 original size:3 final size:3
Alignment explanation
Indices: 28548610--28548929 Score: 187
Period size: 3 Copynumber: 107.3 Consensus size: 3
28548600 TAATTTAATA
* * * *
28548610 TAT TAT TAT TAC TAT TAT TAT T-T TAC TAT TAC TAT CTAA TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
* * * * * *
28548654 TAT TAT TAC TAT TAT TGT TAT T-T TAC TAT TAT AAT T-T AACG TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
28548698 TAT TAT TAT TACT T-T TAT TAT TAT TAT TAT TAT TAT TATT TAC TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * * *
28548744 TAT TACT TA- TAT TCGT TAG TAT CAT TAT TAAT T-T TACC T-T TAT T-T
1 TAT TA-T TAT TAT T-AT TAT TAT TAT TAT T-AT TAT TA-T TAT TAT TAT
* * * * * *
28548789 TCTT TAC TAT TAT TTT TAT TAT CAT TAAT TAT TAT TAT TAT AAA TA-
1 T-AT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* * * * *
28548835 TAT TAT TAT TAT TAC TAT TAT TAC TAT TTT TAT TAC TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
28548883 TAC TAT TAC TAC TAT TAT TA- TAT TGT TAT TAT TAC TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28548929 T
1 T
28548930 TTTACCTATT
Statistics
Matches: 238, Mismatches: 57, Indels: 44
0.70 0.17 0.13
Matches are distributed among these distances:
2 22 0.09
3 194 0.82
4 22 0.09
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:28548660 original size:44 final size:44
Alignment explanation
Indices: 28548610--28548730 Score: 145
Period size: 44 Copynumber: 2.7 Consensus size: 44
28548600 TAATTTAATA
*
28548610 TATTATTATTACTATTATTATTTTACTATTACT-ATCTAATATAT
1 TATTATTATTACTATTATTATTTTACTATTA-TAATCTAACATAT
* * * * *
28548654 TATTATTACTATTATTGTTATTTTACTATTATAATTTAACGTAT
1 TATTATTATTACTATTATTATTTTACTATTATAATCTAACATAT
* *
28548698 TATTATTATTACTTTTATTATTATTATTATTAT
1 TATTATTATTACTATTATTATT-TTACTATTAT
28548731 TATTATTTAC
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
43 1 0.02
44 54 0.84
45 9 0.14
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.60
Consensus pattern (44 bp):
TATTATTATTACTATTATTATTTTACTATTATAATCTAACATAT
Found at i:28552601 original size:15 final size:15
Alignment explanation
Indices: 28552562--28552618 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
28552552 AGTGAAATGT
* *
28552562 ACTTAAATTTTCAAT
1 ACTTAATTTTTCAAC
28552577 ACTTAATTTTTCAAC
1 ACTTAATTTTTCAAC
** *
28552592 ACTTTTTTTTTTCATC
1 AC-TTAATTTTTCAAC
28552608 ACTTAATTTTT
1 ACTTAATTTTT
28552619 TTAGTTTATC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 22 0.65
16 12 0.35
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (15 bp):
ACTTAATTTTTCAAC
Found at i:28552617 original size:16 final size:16
Alignment explanation
Indices: 28552569--28552619 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
28552559 TGTACTTAAA
*
28552569 TTTTCAATACTTAA-T
1 TTTTCAACACTTAATT
**
28552584 TTTTCAACACTTTTTT
1 TTTTCAACACTTAATT
*
28552600 TTTTCATCACTTAATT
1 TTTTCAACACTTAATT
28552616 TTTT
1 TTTT
28552620 TAGTTTATCA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTCAACACTTAATT
Found at i:28553815 original size:11 final size:11
Alignment explanation
Indices: 28553792--28553822 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
28553782 CCTTTTATGC
28553792 TTTTATT-TTA
1 TTTTATTATTA
28553802 TTTTATTATTA
1 TTTTATTATTA
28553813 TTTTATTATT
1 TTTTATTATT
28553823 TTTCCAAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:28555038 original size:31 final size:31
Alignment explanation
Indices: 28555003--28555064 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
28554993 TATAATTAAG
28555003 TTAGTAGATAGTTATGAATAAGATTTTATTC
1 TTAGTAGATAGTTATGAATAAGATTTTATTC
28555034 TTAGTAGATAGTTATGAATAAGATTTTATTC
1 TTAGTAGATAGTTATGAATAAGATTTTATTC
28555065 AAATTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.45
Consensus pattern (31 bp):
TTAGTAGATAGTTATGAATAAGATTTTATTC
Found at i:28555915 original size:13 final size:13
Alignment explanation
Indices: 28555897--28555921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28555887 CCAAGAACAC
28555897 GCCCGTGTCCCTA
1 GCCCGTGTCCCTA
28555910 GCCCGTGTCCCT
1 GCCCGTGTCCCT
28555922 CACACGGCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.48, G:0.24, T:0.24
Consensus pattern (13 bp):
GCCCGTGTCCCTA
Found at i:28566249 original size:22 final size:22
Alignment explanation
Indices: 28566221--28566265 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
28566211 TGGTAGATCG
28566221 AACGTATAAAGCTGAAGAACTT
1 AACGTATAAAGCTGAAGAACTT
28566243 AACGTATAAAGCTGAAGAACTT
1 AACGTATAAAGCTGAAGAACTT
28566265 A
1 A
28566266 GTAAAGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (22 bp):
AACGTATAAAGCTGAAGAACTT
Found at i:28571831 original size:22 final size:22
Alignment explanation
Indices: 28571791--28571865 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
28571781 TTTGTTGTTG
*
28571791 TTTGTTGCTG-TTTAGCTACCAT
1 TTTGTTGTTGTTTTA-CTACCAT
* *
28571813 TTTGTTGTTGTTTTCCTACCAA
1 TTTGTTGTTGTTTTACTACCAT
* * * * *
28571835 TTTGCTATTATATTACTACTAT
1 TTTGTTGTTGTTTTACTACCAT
28571857 TTTGTTGTT
1 TTTGTTGTT
28571866 ATTGTTTAGA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
22 37 0.93
23 3 0.08
ACGTcount: A:0.16, C:0.15, G:0.13, T:0.56
Consensus pattern (22 bp):
TTTGTTGTTGTTTTACTACCAT
Found at i:28577657 original size:44 final size:43
Alignment explanation
Indices: 28577583--28577744 Score: 154
Period size: 42 Copynumber: 3.8 Consensus size: 43
28577573 GTTGGTATTA
* * *
28577583 ATCTGAA-TTATCGTGTAATACCGTGTCTGGGACACAGGCATTG
1 ATCTGAATTTA-CGTGTAAGACCATGTCTGGGACACAGGCATCG
*
28577626 ATTTGAAATTTACGTGTAAGACCATGTCTGGGACATC-GGCATCG
1 ATCTG-AATTTACGTGTAAGACCATGTCTGGGACA-CAGGCATCG
* * * *
28577670 TATCTG-ATTT-CGTATAAGACCCTGTCTGGGATAGAGGCATCG
1 -ATCTGAATTTACGTGTAAGACCATGTCTGGGACACAGGCATCG
* *
28577712 ATACTGAA-TTACATGTAAGACCACGTCTGGGAC
1 AT-CTGAATTTACGTGTAAGACCATGTCTGGGAC
28577745 GTTGGCATTA
Statistics
Matches: 97, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
41 2 0.02
42 32 0.33
43 26 0.27
44 29 0.30
45 8 0.08
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (43 bp):
ATCTGAATTTACGTGTAAGACCATGTCTGGGACACAGGCATCG
Found at i:28577894 original size:18 final size:18
Alignment explanation
Indices: 28577867--28577907 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
28577857 TATCGTACTT
*
28577867 AATTTCTGAATATGAAAG
1 AATTTTTGAATATGAAAG
28577885 AATTTTTGAATATGAAAG
1 AATTTTTGAATATGAAAG
28577903 -ATTTT
1 AATTTT
28577908 GTTTATGCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.41
Consensus pattern (18 bp):
AATTTTTGAATATGAAAG
Found at i:28581339 original size:17 final size:18
Alignment explanation
Indices: 28581304--28581344 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
28581294 CAAAATTATT
28581304 AAAAAAATAGAAAATTCTA
1 AAAAAAATA-AAAATTCTA
28581323 GAAAAAAAT-AAAA-TCTA
1 -AAAAAAATAAAAATTCTA
28581340 AAAAA
1 AAAAA
28581345 TATTGAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.24
17 4 0.19
18 4 0.19
20 8 0.38
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (18 bp):
AAAAAAATAAAAATTCTA
Found at i:28585222 original size:30 final size:31
Alignment explanation
Indices: 28585188--28585256 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
28585178 TGGCCCAAGA
* *
28585188 GTAAATACTG-AAAATTTGAGGGATTAA-AGT
1 GTAAATA-TGAAAAATTTGAAGGACTAATAGT
28585218 GTAAATATGAAAAATTTGAAGGACTAATAGT
1 GTAAATATGAAAAATTTGAAGGACTAATAGT
*
28585249 GAAAATAT
1 GTAAATAT
28585257 TTTAAGGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 2 0.06
30 22 0.65
31 10 0.29
ACGTcount: A:0.48, C:0.03, G:0.20, T:0.29
Consensus pattern (31 bp):
GTAAATATGAAAAATTTGAAGGACTAATAGT
Found at i:28585521 original size:8 final size:8
Alignment explanation
Indices: 28585510--28585534 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28585500 TTTAATAAGA
28585510 TATTTTAT
1 TATTTTAT
28585518 TATTTTAT
1 TATTTTAT
28585526 TATTTTAT
1 TATTTTAT
28585534 T
1 T
28585535 TAGTCTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:28592619 original size:40 final size:40
Alignment explanation
Indices: 28592556--28592736 Score: 269
Period size: 40 Copynumber: 4.6 Consensus size: 40
28592546 ATTCAGATTG
28592556 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
28592595 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
28592635 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
28592675 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* **
28592715 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
28592737 TACTTGGTTT
Statistics
Matches: 130, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
39 29 0.22
40 101 0.78
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.22
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:28598130 original size:3 final size:3
Alignment explanation
Indices: 28598122--28598154 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28598112 ATTCAATACC
28598122 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28598155 CTTACCGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28598802 original size:17 final size:19
Alignment explanation
Indices: 28598768--28598805 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
28598758 AAACCTTTAA
28598768 TTTTCTCTTTTCTTCTTTC
1 TTTTCTCTTTTCTTCTTTC
28598787 TTTTCTC-TTT-TTCTTTC
1 TTTTCTCTTTTCTTCTTTC
28598804 TT
1 TT
28598806 CCTTCCCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTCTTTTCTTCTTTC
Found at i:28601773 original size:24 final size:24
Alignment explanation
Indices: 28601741--28601811 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
28601731 CTGTCAGGAG
28601741 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
28601765 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
28601789 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
28601812 GGAAATCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.35, C:0.01, G:0.38, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:28601823 original size:48 final size:48
Alignment explanation
Indices: 28601741--28601834 Score: 111
Period size: 48 Copynumber: 1.9 Consensus size: 48
28601731 CTGTCAGGAG
** * *
28601741 AGGATTTAGGAGTTGATAAGGGATAGGATTTAGGAGTTGAT-AAGGGAT
1 AGGATTTAGGAGCAGATAAGGGA-AGGATCTAGGAGCTGATCAAGGGAT
28601789 AGGATTTAGGAGCAGATAAGGG-AGGAAATCTAGGAGCTGATCAAGG
1 AGGATTTAGGAGCAGATAAGGGAAGG--ATCTAGGAGCTGATCAAGG
28601835 AACAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
46 3 0.08
48 32 0.82
49 4 0.10
ACGTcount: A:0.35, C:0.04, G:0.37, T:0.23
Consensus pattern (48 bp):
AGGATTTAGGAGCAGATAAGGGAAGGATCTAGGAGCTGATCAAGGGAT
Found at i:28602112 original size:58 final size:58
Alignment explanation
Indices: 28602047--28602164 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
28602037 CTTCCTTCCA
28602047 TTATTTTTAAGACTATAGCCGATTGCCTCAAATCTCGAAATCCCGAAAACTTGACTCC
1 TTATTTTTAAGACTATAGCCGATTGCCTCAAATCTCGAAATCCCGAAAACTTGACTCC
28602105 TTATTTTTAAGACTATAGCCGATTGCCTCAAATCTCGAAATCCCGAAAACTTGACTCC
1 TTATTTTTAAGACTATAGCCGATTGCCTCAAATCTCGAAATCCCGAAAACTTGACTCC
28602163 TT
1 TT
28602165 TTGTACCGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (58 bp):
TTATTTTTAAGACTATAGCCGATTGCCTCAAATCTCGAAATCCCGAAAACTTGACTCC
Found at i:28603092 original size:27 final size:27
Alignment explanation
Indices: 28603052--28603163 Score: 111
Period size: 27 Copynumber: 4.1 Consensus size: 27
28603042 AGGAAGCGTC
* *
28603052 CTGGTGGCTATGCCACAATTATTTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
28603079 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
* * *
28603106 TTGGTGGATCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
28603134 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
28603160 CTGG
1 CTGG
28603164 CAGCCATGCT
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
26 8 0.11
27 46 0.66
28 16 0.23
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.39
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:28603158 original size:54 final size:54
Alignment explanation
Indices: 28603053--28603159 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
28603043 GGAAGCGTCC
* * * *
28603053 TGGTGGCTATGCCACAATTATTTGATCTGGTGGCTCTGCCACATATTTCTGTTT
1 TGGTGGATATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTT
* * *
28603107 TGGTGGATCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 TGGTGGATATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
28603160 CTGGCAGCCA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 27 0.60
55 18 0.40
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (54 bp):
TGGTGGATATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTT
Found at i:28606483 original size:14 final size:14
Alignment explanation
Indices: 28606464--28606491 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28606454 CTGAGTTAAA
28606464 AACTAGACCAACAT
1 AACTAGACCAACAT
28606478 AACTAGACCAACAT
1 AACTAGACCAACAT
28606492 TCTTGCAGCA
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:0.50, C:0.29, G:0.07, T:0.14
Consensus pattern (14 bp):
AACTAGACCAACAT
Found at i:28619561 original size:64 final size:64
Alignment explanation
Indices: 28619493--28619613 Score: 183
Period size: 65 Copynumber: 1.9 Consensus size: 64
28619483 TTTTGAATTA
* *
28619493 AGAAAAT-AAACATA-TTTAAAATAACATAAAAATGCCAAAATAACACCAACTTATTCTTTATGC
1 AGAAAATGAAACATACTTAAAAACAACAT-AAAATGCCAAAATAACACCAACTT-TTCTTTATGC
28619556 G
64 G
*
28619557 AGAAAATGAAACATACTTAAAAACAACATAAAATGCTAAAATAACACCAACTTTTCT
1 AGAAAATGAAACATACTTAAAAACAACATAAAATGCCAAAATAACACCAACTTTTCT
28619614 AATGATTCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
64 11 0.21
65 30 0.58
66 11 0.21
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.25
Consensus pattern (64 bp):
AGAAAATGAAACATACTTAAAAACAACATAAAATGCCAAAATAACACCAACTTTTCTTTATGCG
Found at i:28625238 original size:26 final size:26
Alignment explanation
Indices: 28625205--28625258 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
28625195 GTTTAAGGAC
28625205 TAAAATGAAACTAAGTTTAAGATGTG
1 TAAAATGAAACTAAGTTTAAGATGTG
28625231 TAAAATGAAACTAAGTTTAAGATGTG
1 TAAAATGAAACTAAGTTTAAGATGTG
28625257 TA
1 TA
28625259 CTCCCGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (26 bp):
TAAAATGAAACTAAGTTTAAGATGTG
Found at i:28631455 original size:39 final size:40
Alignment explanation
Indices: 28631362--28631528 Score: 275
Period size: 39 Copynumber: 4.2 Consensus size: 40
28631352 TATGTGCATA
*
28631362 GCATTCGTGCAGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
**
28631402 GCATTCGTATGGGTTATTATAACCGGGTTAAGT-CCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
28631441 GTATTCGTGCGGGTTATTATAACCGGGTTAAGT-CCAAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
28631480 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
28631520 GCATTCGTG
1 GCATTCGTG
28631529 ATGGTTGTTA
Statistics
Matches: 117, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
39 73 0.62
40 44 0.38
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:28631462 original size:79 final size:79
Alignment explanation
Indices: 28631362--28631528 Score: 273
Period size: 79 Copynumber: 2.1 Consensus size: 79
28631352 TATGTGCATA
* *
28631362 GCATTCGTGCAGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTATGGGTTATTATAACCG
1 GCATTCGTGCAGGTTATTATAACCGGGTTAAGT-CCAAAGGCATTCGTACGGGTTATTATAACCG
28631427 GGTTAAGT-CCGAAG
65 GGTTAAGTCCCGAAG
* * *
28631441 GTATTCGTGCGGGTTATTATAACCGGGTTAAGTCCAAAGGCATTCGTGCGGGTTATTATAACCGG
1 GCATTCGTGCAGGTTATTATAACCGGGTTAAGTCCAAAGGCATTCGTACGGGTTATTATAACCGG
28631506 GTTAAGTCCCGAAG
66 GTTAAGTCCCGAAG
28631520 GCATTCGTG
1 GCATTCGTG
28631529 ATGGTTGTTA
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
78 36 0.44
79 45 0.56
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (79 bp):
GCATTCGTGCAGGTTATTATAACCGGGTTAAGTCCAAAGGCATTCGTACGGGTTATTATAACCGG
GTTAAGTCCCGAAG
Found at i:28654280 original size:62 final size:62
Alignment explanation
Indices: 28654205--28654332 Score: 238
Period size: 62 Copynumber: 2.1 Consensus size: 62
28654195 ATGTCATGAC
*
28654205 ATTAGGTTACCGAGATGTGATTACATGTAAGACCATGTTTAGGACATTGGCATTGTATTGTG
1 ATTAGGTTACCGAGATGTGATCACATGTAAGACCATGTTTAGGACATTGGCATTGTATTGTG
*
28654267 ATTAGGTTACCGAGATGTGATCACATGTAAGACCATGTTTGGGACATTGGCATTGTATTGTG
1 ATTAGGTTACCGAGATGTGATCACATGTAAGACCATGTTTAGGACATTGGCATTGTATTGTG
28654329 ATTA
1 ATTA
28654333 CATATAAGAC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (62 bp):
ATTAGGTTACCGAGATGTGATCACATGTAAGACCATGTTTAGGACATTGGCATTGTATTGTG
Found at i:28654343 original size:43 final size:44
Alignment explanation
Indices: 28654282--28654474 Score: 196
Period size: 43 Copynumber: 4.5 Consensus size: 44
28654272 GTTACCGAGA
* *
28654282 TGTGATCACATGTAAGACCATGTTTGGGACATTGGCATTG-TAT
1 TGTGATTACATGTAAGACCATGTTTGGGACATTGGCATCGTTAT
*
28654325 TGTGATTACATATAAGACCATGTTTGGGACATTGGCATCGTTAT
1 TGTGATTACATGTAAGACCATGTTTGGGACATTGGCATCGTTAT
* * * * *
28654369 T-CGATTACGTGTAAGACCATGTATGGGACATCGGCTTCGTTAT
1 TGTGATTACATGTAAGACCATGTTTGGGACATTGGCATCGTTAT
* * * * * * * **
28654412 T-CGATTTCGTGTAAGACCCTGTCTGGGACAGTGGTATCAATA-
1 TGTGATTACATGTAAGACCATGTTTGGGACATTGGCATCGTTAT
*
28654454 TGTGATAACATGTAAGACCAT
1 TGTGATTACATGTAAGACCAT
28654475 ATCTGGGATA
Statistics
Matches: 125, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.01
43 120 0.96
44 4 0.03
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (44 bp):
TGTGATTACATGTAAGACCATGTTTGGGACATTGGCATCGTTAT
Found at i:28657691 original size:21 final size:21
Alignment explanation
Indices: 28657665--28657707 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28657655 ACAAAACGGT
28657665 ACTAATTCAAGACCAAGCAAC
1 ACTAATTCAAGACCAAGCAAC
* **
28657686 ACTAATTTAAGGTCAAGCAAC
1 ACTAATTCAAGACCAAGCAAC
28657707 A
1 A
28657708 ACATTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.23, G:0.12, T:0.19
Consensus pattern (21 bp):
ACTAATTCAAGACCAAGCAAC
Found at i:28661485 original size:49 final size:50
Alignment explanation
Indices: 28661281--28661591 Score: 217
Period size: 49 Copynumber: 6.5 Consensus size: 50
28661271 TATGTGTGCT
* *
28661281 AGTGTAAGACATGTCTGGGACAT-GCATCGACCAC--AT-TATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGAGCACTGATAGATGAGAGCC
* * * *
28661327 AGTGTAAGACATGTCTGGGGCAT-GCATCG-GCATTG--AGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGGCATCGAGCACTGATAGATGAGAGCC
* * * * *
28661373 AGTGTAAGACATGTCTAGGACAT-GCATC-AGC-CTCGAGATAT-ACAAGCT
1 AGTGTAAGACATGTCTGGGACATGGCATCGAGCACT-GATAGATGA-GAGCC
* *
28661421 AGTGTAAGACTTGTCTGGGACATGGCATTGA-CACTGATAGATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGAGCACTGATAGATGAGAGCC
* * * * * * *
28661470 AGTGTAAGACCTGTCTGGGACACGTCAT-TAGC-CTCGATATATGAAAGTC
1 AGTGTAAGACATGTCTGGGACATGGCATCGAGCACT-GATAGATGAGAGCC
* * ** **
28661519 AGTGTAAGACCTGTTTGGGACATGGCATCGA-CTTTGAT-G-TGCTAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGAGCACTGATAGATGAGAGCC
*
28661566 AGTGTAAGACCATGTCTGTGACATGG
1 AGTGTAAGA-CATGTCTGGGACATGG
28661592 TGTCGGCATC
Statistics
Matches: 210, Mismatches: 38, Indels: 32
0.75 0.14 0.11
Matches are distributed among these distances:
45 3 0.01
46 64 0.30
47 15 0.07
48 43 0.20
49 79 0.38
50 6 0.03
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (50 bp):
AGTGTAAGACATGTCTGGGACATGGCATCGAGCACTGATAGATGAGAGCC
Found at i:28661541 original size:98 final size:95
Alignment explanation
Indices: 28661327--28661588 Score: 262
Period size: 98 Copynumber: 2.7 Consensus size: 95
28661317 TATGAGAGCC
* * * * * * * *
28661327 AGTGTAAGACATGTCTGGGGCAT-GCATCGGCATTGA-GACGAGAGCTAGTGTAAGACATGTCTA
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACACTGATG-TGAGAGCCAGTGTAAGACCTGTCTG
*
28661390 GGACATGCATCAGCCTCGAGATATACAAGCT
65 GGACACGCATCAGCCTCGAGATATACAAGCT
* *
28661421 AGTGTAAGACTTGTCTGGGACATGGCATTGACACTGATAGATGAGAGCCAGTGTAAGACCTGTCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACACTGAT-G-TGAGAGCCAGTGTAAGACCTGTCT
* *
28661486 GGGACACGTCATTAGCCTCGATATATGA-AAG-T
64 GGGACACG-CATCAGCCTCGAGATAT-ACAAGCT
* ** **
28661518 CAGTGTAAGACCTGTTTGGGACATGGCATCGACTTTGATGTGCTAGCCAGTGTAAGACCATGTCT
1 -AGTGTAAGACCTGTCTGGGACATGGCATCGACACTGATGTGAGAGCCAGTGTAAGACC-TGTCT
*
28661583 GTGACA
64 GGGACA
28661589 TGGTGTCGGC
Statistics
Matches: 141, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
94 21 0.15
95 10 0.07
96 17 0.12
97 41 0.29
98 51 0.36
99 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (95 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACACTGATGTGAGAGCCAGTGTAAGACCTGTCTGG
GACACGCATCAGCCTCGAGATATACAAGCT
Found at i:28668507 original size:17 final size:19
Alignment explanation
Indices: 28668480--28668518 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
28668470 GCCATTTCTA
28668480 GGCGATGTAGG-CCACACG
1 GGCGATGTAGGACCACACG
*
28668498 GGCG-TGTAGGACCACATG
1 GGCGATGTAGGACCACACG
28668516 GGC
1 GGC
28668519 CTGCATTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.21, C:0.26, G:0.41, T:0.13
Consensus pattern (19 bp):
GGCGATGTAGGACCACACG
Found at i:28668664 original size:27 final size:27
Alignment explanation
Indices: 28668634--28668850 Score: 224
Period size: 27 Copynumber: 8.1 Consensus size: 27
28668624 CCCTAAATTA
*
28668634 ATAAAATGAATGTTTTGCCCTTATGTG
1 ATAAAATGATTGTTTTGCCCTTATGTG
28668661 ATAAAATGATTGTTTTGCCCTTATGTG
1 ATAAAATGATTGTTTTGCCCTTATGTG
* *
28668688 GTAAAATGATTGTTTTTCCCTTATGTG
1 ATAAAATGATTGTTTTGCCCTTATGTG
**
28668715 ATAAAATGATTGTTTTGCTGTTATGT-
1 ATAAAATGATTGTTTTGCCCTTATGTG
* * *
28668741 AGTAAAATGACTGCTTTT-CCATTAGGTG
1 A-TAAAATGATTG-TTTTGCCCTTATGTG
* * * * *
28668769 GTAAGATAAATGTTTTTCCCTTATGTG
1 ATAAAATGATTGTTTTGCCCTTATGTG
* *
28668796 GTAAAATGATTGTTTTGCCCTTATATG
1 ATAAAATGATTGTTTTGCCCTTATGTG
* * * *
28668823 GTAATATGACTGTTTTTCCC-TATGTG
1 ATAAAATGATTGTTTTGCCCTTATGTG
28668849 AT
1 AT
28668851 GTATATATAT
Statistics
Matches: 159, Mismatches: 27, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
26 11 0.07
27 144 0.91
28 4 0.03
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (27 bp):
ATAAAATGATTGTTTTGCCCTTATGTG
Found at i:28668840 original size:81 final size:81
Alignment explanation
Indices: 28668634--28668841 Score: 272
Period size: 81 Copynumber: 2.6 Consensus size: 81
28668624 CCCTAAATTA
* * * * * * * *
28668634 ATAAAATGAATGTTTTGCCCTTATGTGATAAAATGATTGTTTTGCCCTTATGTGGTAAAATGATT
1 ATAAAATGATTGTTTTGCCCTTATGTGGTAAAATGACTGTTTTTCCATTAGGTGGTAAAATAAAT
28668699 GTTTTTCCCTTATGTG
66 GTTTTTCCCTTATGTG
** * * *
28668715 ATAAAATGATTGTTTTGCTGTTATGTAGTAAAATGACTGCTTTTCCATTAGGTGGTAAGATAAAT
1 ATAAAATGATTGTTTTGCCCTTATGTGGTAAAATGACTGTTTTTCCATTAGGTGGTAAAATAAAT
28668780 GTTTTTCCCTTATGTG
66 GTTTTTCCCTTATGTG
* * *
28668796 GTAAAATGATTGTTTTGCCCTTATATGGTAATATGACTGTTTTTCC
1 ATAAAATGATTGTTTTGCCCTTATGTGGTAAAATGACTGTTTTTCC
28668842 CTATGTGATG
Statistics
Matches: 107, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 107 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (81 bp):
ATAAAATGATTGTTTTGCCCTTATGTGGTAAAATGACTGTTTTTCCATTAGGTGGTAAAATAAAT
GTTTTTCCCTTATGTG
Found at i:28669185 original size:18 final size:18
Alignment explanation
Indices: 28669162--28669205 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
28669152 ACATGTATTC
28669162 TGTTACTGCACTGAT-TAT
1 TGTTACTGCACT-ATGTAT
28669180 TGTTACTGCACTATGTAT
1 TGTTACTGCACTATGTAT
28669198 TGTTACTG
1 TGTTACTG
28669206 TATTGGGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.45
Consensus pattern (18 bp):
TGTTACTGCACTATGTAT
Found at i:28670391 original size:20 final size:21
Alignment explanation
Indices: 28670354--28670392 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
28670344 AAGGATTAAT
28670354 ATGTATAAATATTAAAAATTC
1 ATGTATAAATATTAAAAATTC
28670375 ATGT-TAAAT-TTATAAAAT
1 ATGTATAAATATTA-AAAAT
28670393 GATGGTGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (21 bp):
ATGTATAAATATTAAAAATTC
Found at i:28672957 original size:25 final size:25
Alignment explanation
Indices: 28672907--28672957 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
28672897 CCCTTATAAT
* *
28672907 GTGAAAATGACATTTTTGCCCCTAG
1 GTGAAAATGACATTTATACCCCTAG
*
28672932 GTGAAAATGAC-TATTATACCCTTAG
1 GTGAAAATGACAT-TTATACCCCTAG
28672957 G
1 G
28672958 GTTATGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (25 bp):
GTGAAAATGACATTTATACCCCTAG
Found at i:28673085 original size:25 final size:25
Alignment explanation
Indices: 28673057--28673125 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 25
28673047 AGGAAGTGCT
* *
28673057 AAAGGGCTATGCCCCAGTTTACCGA
1 AAAGGGCTTTGCCCCAGTTTACCAA
* *
28673082 AAAGGGCTTTGCCCTAGTTTATCAA
1 AAAGGGCTTTGCCCCAGTTTACCAA
28673107 AAAGGGCTTTGCCCCAGTT
1 AAAGGGCTTTGCCCCAGTT
28673126 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAGGGCTTTGCCCCAGTTTACCAA
Found at i:28673138 original size:24 final size:24
Alignment explanation
Indices: 28673057--28673152 Score: 72
Period size: 25 Copynumber: 3.9 Consensus size: 24
28673047 AGGAAGTGCT
* *
28673057 AAAG-GGCTATGCCCCAGTTTACCGA
1 AAAGAGGCTTTGCCCCAG-TTATC-A
*
28673082 AAAG-GGCTTTGCCCTAGTTTATCA
1 AAAGAGGCTTTGCCCCAG-TTATCA
*
28673106 AAA-AGGGCTTTGCCCCAGTTATTA
1 AAAGA-GGCTTTGCCCCAGTTATCA
**
28673130 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAGAGGCTTTGCC-CCAGTTAT
28673153 ATGATAAAAG
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
24 19 0.32
25 41 0.68
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAGAGGCTTTGCCCCAGTTATCA
Found at i:28673382 original size:31 final size:31
Alignment explanation
Indices: 28673347--28673430 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
28673337 CGTTTATAGT
28673347 AAAGGCTTCGGCCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* * * *
28673378 AAAGGCTTCTGCCTAGTGGTATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
28673409 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
28673431 CTGAGATTGA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 4 0.09
31 42 0.91
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:28683627 original size:4 final size:4
Alignment explanation
Indices: 28683618--28683662 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
28683608 ATCCAAGTCA
28683618 AAAT AAAT AAAT AAAT AAGAT AAAT AAAAT AGAAT -AAT AAAT AAA
1 AAAT AAAT AAAT AAAT AA-AT AAAT -AAAT A-AAT AAAT AAAT AAA
28683663 ATATCAGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 3 0.08
4 23 0.62
5 11 0.30
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:28683663 original size:17 final size:17
Alignment explanation
Indices: 28683618--28683665 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
28683608 ATCCAAGTCA
28683618 AAATAAAT-AAATAAAT
1 AAATAAATAAAATAAAT
28683634 AAGATAAATAAAATAGAAT
1 AA-ATAAATAAAATA-AAT
28683653 -AATAAATAAAATA
1 AAATAAATAAAATA
28683666 TCAGAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.07
17 18 0.62
18 6 0.21
19 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
AAATAAATAAAATAAAT
Found at i:28683673 original size:17 final size:17
Alignment explanation
Indices: 28683619--28683674 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
28683609 TCCAAGTCAA
*
28683619 AATAAATAAATAAATAAG
1 AATAAATAAA-ATATAAG
* *
28683637 -ATAAATAAAATAGAAT
1 AATAAATAAAATATAAG
*
28683653 AATAAATAAAATATCAG
1 AATAAATAAAATATAAG
28683670 AATAA
1 AATAA
28683675 TAAGGAAGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 4 0.13
17 27 0.87
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (17 bp):
AATAAATAAAATATAAG
Done.