Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 123 of 168
Found at i:35728873 original size:108 final size:108
Alignment explanation
Indices: 35728677--35729085 Score: 667
Period size: 108 Copynumber: 3.8 Consensus size: 108
35728667 AAAAAAAAGG
*
35728677 AAAATATTTCAAAATAAGGCAATATTTTGCATTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
1 AAAAT-TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
*
35728742 GGTTCCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCA
65 GGTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCA
35728786 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
*
35728851 GTTTCGATTTCTCGTTCCACCAAATGACTTAATATCCTTTTCA
66 GTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCA
* *
35728894 AAAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
*
35728959 GTTTCGATTTCTCGTTCGACCAAAT-AGCTAAATATCCTTTTCAA
66 GTTTCGATTTCTCGTTCGACCAAATGA-CTTAATATCCTTTTC-A
* * * *
35729003 AAAACTTTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAACGTGCCCTAAGGTGCT
1 AAAA-TTTTC-AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT
*
35729068 GGGTTTCGATTTCACGTT
64 GGGTTTCGATTTCTCGTT
35729086 TAGCCAAATT
Statistics
Matches: 282, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
107 1 0.00
108 201 0.71
109 10 0.04
110 4 0.01
111 66 0.23
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (108 bp):
AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
GTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCA
Found at i:35731277 original size:39 final size:41
Alignment explanation
Indices: 35731221--35731324 Score: 122
Period size: 44 Copynumber: 2.5 Consensus size: 41
35731211 TTTCCTTATG
* *
35731221 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
*
35731261 C-ATTACGCTTCTATTCCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGC--C---TCTATTCCATTCAACCAAACAAAAGAATTAC
35731306 CTATTACGCCTCTATTCCA
1 CTATTACGCCTCTATTCCA
35731325 ATACGCATCT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
39 6 0.11
40 1 0.02
41 9 0.17
44 26 0.49
45 4 0.08
46 7 0.13
ACGTcount: A:0.36, C:0.32, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:35731301 original size:44 final size:46
Alignment explanation
Indices: 35731234--35731324 Score: 150
Period size: 44 Copynumber: 2.0 Consensus size: 46
35731224 TTACACCTCT
* *
35731234 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCTTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
35731278 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
35731324 A
1 A
35731325 ATACGCATCT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 23 0.53
45 4 0.09
46 16 0.37
ACGTcount: A:0.37, C:0.31, G:0.04, T:0.27
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:35731357 original size:16 final size:16
Alignment explanation
Indices: 35731308--35731361 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
35731298 AGAATTACCT
*
35731308 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
* * *
35731324 AATACGCATCTATTCC
1 ATTACACCTCTATTCC
35731340 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
35731356 ATTACA
1 ATTACA
35731362 GCGAACTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.28, C:0.33, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:35731540 original size:24 final size:26
Alignment explanation
Indices: 35731501--35731559 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
35731491 TAATTTTAAG
*
35731501 TATATTA-TTTATGATA-AATTGTTT
1 TATATTATTTTATGATATAAGTGTTT
35731525 TATATTATTTTA-GATATTAAGTGTTT
1 TATATTATTTTATGATA-TAAGTGTTT
*
35731551 TAAATTATT
1 TATATTATT
35731560 CCATATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 11 0.37
25 4 0.13
26 15 0.50
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (26 bp):
TATATTATTTTATGATATAAGTGTTT
Found at i:35731567 original size:26 final size:26
Alignment explanation
Indices: 35731520--35731569 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
35731510 TATGATAAAT
* **
35731520 TGTTTTATATTATTTTAGATATTAAG
1 TGTTTTAAATTATTCCAGATATTAAG
*
35731546 TGTTTTAAATTATTCCATATATTA
1 TGTTTTAAATTATTCCAGATATTA
35731570 TTTATGTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (26 bp):
TGTTTTAAATTATTCCAGATATTAAG
Found at i:35734438 original size:2 final size:2
Alignment explanation
Indices: 35734431--35734467 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35734421 TTTAGGTATT
35734431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35734468 GATCAGAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35735935 original size:3 final size:3
Alignment explanation
Indices: 35735927--35736006 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
35735917 AATCACGTCG
35735927 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35735975 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
35736007 TAAAAGTACA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:35736080 original size:21 final size:20
Alignment explanation
Indices: 35736054--35736095 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
35736044 CTAAACGTTT
35736054 AAAAAGGTA-AAGAAAGTAATA
1 AAAAAGGTAGAA-AAA-TAATA
35736075 AAAAAGGTAGAAAAATAATA
1 AAAAAGGTAGAAAAATAATA
35736095 A
1 A
35736096 TAAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 12 0.60
22 2 0.10
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAAAGGTAGAAAAATAATA
Found at i:35740409 original size:13 final size:13
Alignment explanation
Indices: 35740391--35740430 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
35740381 ATGTGCATAA
35740391 TATTATTTAAAAT
1 TATTATTTAAAAT
35740404 TATTATTTTAAAATT
1 TATTA-TTTAAAA-T
35740419 TATTA-TTAAAAT
1 TATTATTTAAAAT
35740431 AAAATTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 11 0.44
14 7 0.28
15 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTATTTAAAAT
Found at i:35740423 original size:15 final size:14
Alignment explanation
Indices: 35740391--35740425 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
35740381 ATGTGCATAA
35740391 TATTA-TTTAAAAT
1 TATTATTTTAAAAT
35740404 TATTATTTTAAAATT
1 TATTATTTTAAAA-T
35740419 TATTATT
1 TATTATT
35740426 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 7 0.35
15 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTATTTTAAAAT
Found at i:35748278 original size:33 final size:33
Alignment explanation
Indices: 35748240--35748303 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
35748230 ATATTTGTGT
35748240 TAGGTTATCAGCCTATGCTAAACCTTTATAATG
1 TAGGTTATCAGCCTATGCTAAACCTTTATAATG
35748273 TAGGTTATCAGCCTATGCTAAACCTTTATAA
1 TAGGTTATCAGCCTATGCTAAACCTTTATAA
35748304 CGACACATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (33 bp):
TAGGTTATCAGCCTATGCTAAACCTTTATAATG
Found at i:35752313 original size:7 final size:7
Alignment explanation
Indices: 35752301--35752342 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
35752291 GCTCAATATT
35752301 TTATTTA
1 TTATTTA
35752308 TTATTTA
1 TTATTTA
35752315 TTA-TTA
1 TTATTTA
35752321 -T-TTTA
1 TTATTTA
35752326 TTATTTA
1 TTATTTA
35752333 TTTATTTA
1 -TTATTTA
35752341 TT
1 TT
35752343 CATTCCGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 4 0.13
6 4 0.13
7 16 0.52
8 7 0.23
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTATTTA
Found at i:35752316 original size:11 final size:11
Alignment explanation
Indices: 35752300--35752342 Score: 54
Period size: 10 Copynumber: 3.9 Consensus size: 11
35752290 AGCTCAATAT
35752300 TTTATTTATTA
1 TTTATTTATTA
35752311 TTTA-TTATTA
1 TTTATTTATTA
35752321 TTT-TATTATTTA
1 TTTAT-TTA-TTA
35752333 TTTATTTATT
1 TTTATTTATT
35752343 CATTCCGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.32
11 9 0.32
12 9 0.32
13 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:35752325 original size:22 final size:22
Alignment explanation
Indices: 35752297--35752338 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
35752287 AAGAGCTCAA
35752297 TATTTTATT-TATTATTTATTAT
1 TATTTTATTAT-TTATTTATTAT
35752319 TATTTTATTATTTATTTATT
1 TATTTTATTATTTATTTATT
35752339 TATTCATTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
TATTTTATTATTTATTTATTAT
Found at i:35757443 original size:2 final size:2
Alignment explanation
Indices: 35757436--35757467 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35757426 TTCTATTTAG
35757436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35757468 TTAAAAATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35758114 original size:22 final size:22
Alignment explanation
Indices: 35758084--35758131 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
35758074 TTACCTTTTG
35758084 TTATAAATGATATACTACTA-TA
1 TTATAAATGAT-TACTACTATTA
* *
35758106 TTATCAATGGTTACTACTATTA
1 TTATAAATGATTACTACTATTA
35758128 TTAT
1 TTAT
35758132 TTTATAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (22 bp):
TTATAAATGATTACTACTATTA
Found at i:35758281 original size:31 final size:31
Alignment explanation
Indices: 35758246--35758304 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
35758236 ATTTTGACCT
35758246 TCAACATTTT-AAAAAGAGACGAATTTGATCA
1 TCAAC-TTTTCAAAAAGAGACGAATTTGATCA
**
35758277 TCAACTTTTCAAAAAGAGTTGAATTTGA
1 TCAACTTTTCAAAAAGAGACGAATTTGA
35758305 CTAACAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (31 bp):
TCAACTTTTCAAAAAGAGACGAATTTGATCA
Found at i:35759031 original size:28 final size:28
Alignment explanation
Indices: 35758992--35759053 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
35758982 TGGTCACTCA
*
35758992 TTTTATATTTTTAAAAATTAATTTTA-T
1 TTTTTTATTTTTAAAAATTAATTTTAGT
* *
35759019 TTTTTTATCTTTTTAGAATTAATTTTAGT
1 TTTTTTAT-TTTTAAAAATTAATTTTAGT
35759048 TTTTTT
1 TTTTTT
35759054 TCCTAGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 7 0.23
28 16 0.53
29 7 0.23
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (28 bp):
TTTTTTATTTTTAAAAATTAATTTTAGT
Found at i:35759031 original size:29 final size:29
Alignment explanation
Indices: 35758992--35759053 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
35758982 TGGTCACTCA
35758992 TTTTATATTTTTAAAAATTAATTTTA-TTT
1 TTTTATATTTTT-AAAATTAATTTTAGTTT
* *
35759021 TTTTATCTTTTTAGAATTAATTTTAGTTT
1 TTTTATATTTTTAAAATTAATTTTAGTTT
35759050 TTTT
1 TTTT
35759054 TCCTAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (29 bp):
TTTTATATTTTTAAAATTAATTTTAGTTT
Found at i:35762546 original size:21 final size:23
Alignment explanation
Indices: 35762516--35762557 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
35762506 ATAAAGGGCT
*
35762516 TTAATCGAAATTCA-AAATAACC
1 TTAATCGAAATTAAGAAATAACC
35762538 TTAA-CGAAATTAAGAAATAA
1 TTAATCGAAATTAAGAAATAA
35762558 AACCCGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (23 bp):
TTAATCGAAATTAAGAAATAACC
Found at i:35762608 original size:83 final size:83
Alignment explanation
Indices: 35762469--35762674 Score: 335
Period size: 83 Copynumber: 2.5 Consensus size: 83
35762459 TTAATATCGA
* *
35762469 AAATAAACCCCGATTCAACGAGGTAACAAATTAAGAAATAAAGGGCTTTAATCGAAATTCAAAAT
1 AAATAAAACCCGATTCAACAAGGTAACAAATTAAGAAATAAAGGGCTTTAATCGAAATTCAAAAT
* *
35762534 AACCTTAACGAAATTAAG
66 AACCTTAACCAAATTAAC
35762552 AAATAAAACCCGATTCAACAAGGTAACAAATTAAGAAATAAAGGGCTTTAATCGAAATTCAAAAT
1 AAATAAAACCCGATTCAACAAGGTAACAAATTAAGAAATAAAGGGCTTTAATCGAAATTCAAAAT
35762617 AACCTTAACCAAATTAAC
66 AACCTTAACCAAATTAAC
* *
35762635 AAAT-AAACCCTGATTCAACCAGGTAACAAATTCA-AAATAA
1 AAATAAAACCC-GATTCAACAAGGTAACAAATTAAGAAATAA
35762675 CCTTAACAAA
Statistics
Matches: 116, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
82 12 0.10
83 104 0.90
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (83 bp):
AAATAAAACCCGATTCAACAAGGTAACAAATTAAGAAATAAAGGGCTTTAATCGAAATTCAAAAT
AACCTTAACCAAATTAAC
Found at i:35762911 original size:12 final size:12
Alignment explanation
Indices: 35762889--35762952 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
35762879 AACAAACACC
35762889 CCAACCAAAAATG
1 CCAA-CAAAAATG
*
35762902 CTAACAAAAATG
1 CCAACAAAAATG
35762914 CCAAC-AAAATG
1 CCAACAAAAATG
* * *
35762925 CTAATAGAAATG
1 CCAACAAAAATG
35762937 CCAAC-AAAATG
1 CCAACAAAAATG
35762948 CCAAC
1 CCAAC
35762953 CAGAAATGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 19 0.45
12 20 0.48
13 3 0.07
ACGTcount: A:0.53, C:0.25, G:0.09, T:0.12
Consensus pattern (12 bp):
CCAACAAAAATG
Found at i:35762922 original size:11 final size:11
Alignment explanation
Indices: 35762896--35762952 Score: 69
Period size: 11 Copynumber: 5.0 Consensus size: 11
35762886 ACCCCAACCA
*
35762896 AAAATGCTAAC
1 AAAATGCCAAC
35762907 AAAAATGCCAAC
1 -AAAATGCCAAC
* *
35762919 AAAATGCTAAT
1 AAAATGCCAAC
35762930 AGAAATGCCAAC
1 A-AAATGCCAAC
35762942 AAAATGCCAAC
1 AAAATGCCAAC
35762953 CAGAAATGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
11 20 0.51
12 19 0.49
ACGTcount: A:0.54, C:0.21, G:0.11, T:0.14
Consensus pattern (11 bp):
AAAATGCCAAC
Found at i:35762926 original size:23 final size:23
Alignment explanation
Indices: 35762896--35762948 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
35762886 ACCCCAACCA
35762896 AAAATGCTAACAAAAATGCCAAC
1 AAAATGCTAACAAAAATGCCAAC
* *
35762919 AAAATGCTAATAGAAATGCCAAC
1 AAAATGCTAACAAAAATGCCAAC
35762942 AAAATGC
1 AAAATGC
35762949 CAACCAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.55, C:0.19, G:0.11, T:0.15
Consensus pattern (23 bp):
AAAATGCTAACAAAAATGCCAAC
Found at i:35763095 original size:23 final size:23
Alignment explanation
Indices: 35763069--35763158 Score: 101
Period size: 23 Copynumber: 3.8 Consensus size: 23
35763059 GGAATTCCAA
*
35763069 GAAATGAAATTGGGGATATTAGG
1 GAAATGAAATTGGGGAAATTAGG
* * *
35763092 GAAATAAAATCGGGGAAATTGGGG
1 GAAATGAAATTGGGGAAATT-AGG
*
35763116 GAAA-GAAAAATTTGGGAAATTAGG
1 GAAATG--AAATTGGGGAAATTAGG
35763140 GAAATGAAATTGGGGAAAT
1 GAAATGAAATTGGGGAAAT
35763159 CTGAGTGGGG
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
23 29 0.54
24 12 0.22
25 13 0.24
ACGTcount: A:0.44, C:0.01, G:0.33, T:0.21
Consensus pattern (23 bp):
GAAATGAAATTGGGGAAATTAGG
Found at i:35763522 original size:115 final size:115
Alignment explanation
Indices: 35763312--35763531 Score: 307
Period size: 115 Copynumber: 1.9 Consensus size: 115
35763302 TCAATCCTTT
* * * *
35763312 TGCGGCGTTTAAGTAAAAACGCCACTAAAATCGCAAACGAAAACGACTGCGTTTAGCAAAGACTT
1 TGCGGCGTTTAAGGAAAAACGCCACTAAAAGCGCAAACGAAAACGACGGCGTTTAGCAAACACTT
* * * *
35763377 AAAAATTAATTGCGGCATTTTTCATCAAAACGCCAGTAAAACTTACCATC
66 AAAAAATAATTGCGGCATTTATCATAAAAACGCCACTAAAACTTACCATC
** *
35763427 TGCGGCGTTT-AGGAACAAACGCCACTAAAAGCGCAAATTAAAACGACGGTGTTTAGCAAACACT
1 TGCGGCGTTTAAGGAA-AAACGCCACTAAAAGCGCAAACGAAAACGACGGCGTTTAGCAAACACT
* *
35763491 TAAAAAATAATTGCGGCGTTTATCGTAAAAACGCCACTAAA
65 TAAAAAATAATTGCGGCATTTATCATAAAAACGCCACTAAA
35763532 TACGCAAATT
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
114 4 0.04
115 87 0.96
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (115 bp):
TGCGGCGTTTAAGGAAAAACGCCACTAAAAGCGCAAACGAAAACGACGGCGTTTAGCAAACACTT
AAAAAATAATTGCGGCATTTATCATAAAAACGCCACTAAAACTTACCATC
Found at i:35763574 original size:75 final size:75
Alignment explanation
Indices: 35763427--35763684 Score: 378
Period size: 75 Copynumber: 3.4 Consensus size: 75
35763417 ACTTACCATC
*
35763427 TGCGGCGTTTA--GGAACAAACGCCACTAAAAGCGCAAATTAAAACGACGGTGTTTAGCAAACAC
1 TGCGGCGTTTATCGTAA-AAACGCCACTAAAA-CGCAAATTAAAACGACGGTGTTTAGCAAACAC
35763490 TTAAAAAATAAT
64 TTAAAAAATAAT
35763502 TGCGGCGTTTATCGTAAAAACGCCACTAAATACGCAAATTAAAACGACGGTGTTTAGC-AACACT
1 TGCGGCGTTTATCGTAAAAACGCCACTAAA-ACGCAAATTAAAACGACGGTGTTTAGCAAACACT
35763566 TAAAAAATAAT
65 TAAAAAATAAT
* * * *
35763577 TGCGGCGTTTATCGTAAAAACGCCACTAAAAATGCAAACTAAAACGACTGTGTTTAGCAAAGACT
1 TGCGGCGTTTATCGTAAAAACGCCACT-AAAACGCAAATTAAAACGACGGTGTTTAGCAAACACT
*
35763642 TAAAACATAAT
65 TAAAAAATAAT
* * *
35763653 TGCGGCGTTTATAGTAAAAATGACACTAAAAC
1 TGCGGCGTTTATCGTAAAAACGCCACTAAAAC
35763685 ATACATTTTA
Statistics
Matches: 168, Mismatches: 10, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
75 83 0.49
76 81 0.48
77 4 0.02
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (75 bp):
TGCGGCGTTTATCGTAAAAACGCCACTAAAACGCAAATTAAAACGACGGTGTTTAGCAAACACTT
AAAAAATAAT
Found at i:35763711 original size:113 final size:114
Alignment explanation
Indices: 35763592--35763848 Score: 338
Period size: 113 Copynumber: 2.3 Consensus size: 114
35763582 CGTTTATCGT
* * *
35763592 AAAAACGCCACTAAAAATGCAAACTAAAACGACTGTGTTTAGCAAAGACTTAAAACATAATTGCG
1 AAAAACGCCACTAAAAATGCAAATTAAAACGACTGCGTTTAGAAAAGACTTAAAACATAATTGCG
* *
35763657 GCGTTTATAGTAAAAATGACACTAAAACATACATTTTACGGTGTTTA-A
66 GCGTTTATAGTAAAAACGACACTAAAACATACATTTTACGGCGTTTAGA
* * *
35763705 AAAAACGCCAC-AAAGAATGCAATTTAGAACGACTGCGTTTAGAAAAGACTTCAAACATAATTGC
1 AAAAACGCCACTAAA-AATGCAAATTAAAACGACTGCGTTTAGAAAAGACTTAAAACATAATTGC
* * * ** * *
35763769 GGCGTTTATCGTAACAACGCCACTAAAATTTACCTTTTGCGGCGTTTATGA
65 GGCGTTTATAGTAAAAACGACACTAAAACATACATTTTACGGCGTTTA-GA
*
35763820 AAAAACGCCACTAAAAACGCAAATTAAAA
1 AAAAACGCCACTAAAAATGCAAATTAAAA
35763849 TTACTGCATT
Statistics
Matches: 122, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
112 3 0.02
113 93 0.76
115 23 0.19
116 3 0.02
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (114 bp):
AAAAACGCCACTAAAAATGCAAATTAAAACGACTGCGTTTAGAAAAGACTTAAAACATAATTGCG
GCGTTTATAGTAAAAACGACACTAAAACATACATTTTACGGCGTTTAGA
Found at i:35764185 original size:7 final size:7
Alignment explanation
Indices: 35764175--35764428 Score: 61
Period size: 7 Copynumber: 35.7 Consensus size: 7
35764165 AAGCTCCCAG
35764175 CTAAACC
1 CTAAACC
*
35764182 CTAAACA
1 CTAAACC
* *
35764189 ATAAACA
1 CTAAACC
* *
35764196 ATAAACA
1 CTAAACC
* *
35764203 ATAAACA
1 CTAAACC
35764210 CTAAACC
1 CTAAACC
*
35764217 ATAAACC
1 CTAAACC
*
35764224 C-ACACC
1 CTAAACC
* *
35764230 CTACACT
1 CTAAACC
35764237 CTAAACC
1 CTAAACC
* *
35764244 GTAAACA
1 CTAAACC
35764251 CTAATA--
1 CTAA-ACC
* *
35764257 TTAAATC
1 CTAAACC
*
35764264 ATAAACC
1 CTAAACC
* *
35764271 TTAAACT
1 CTAAACC
*
35764278 TTAAACC
1 CTAAACC
*
35764285 ATAAA-C
1 CTAAACC
**
35764291 CTCCACC
1 CTAAACC
35764298 CTAAACC
1 CTAAACC
* *
35764305 GTAAACA
1 CTAAACC
*
35764312 CTAAATC
1 CTAAACC
* *
35764319 GT-AAGC
1 CTAAACC
*
35764325 CAATAACC
1 CTA-AACC
*
35764333 CTTAAATC
1 C-TAAACC
*
35764341 CTAAGCC
1 CTAAACC
35764348 C-ATAACC
1 CTA-AACC
35764355 CTAAACC
1 CTAAACC
35764362 CTTAAACC
1 C-TAAACC
*
35764370 CTAATCC
1 CTAAACC
*
35764377 TTTAAACC
1 -CTAAACC
* *
35764385 TTAAATCT
1 CTAAA-CC
35764393 CTAAACC
1 CTAAACC
*
35764400 ATAAACC
1 CTAAACC
35764407 CTTAAACCC
1 C-TAAA-CC
35764416 CTAAACCC
1 CTAAA-CC
35764424 CTAAA
1 CTAAA
35764429 TCATAAACTA
Statistics
Matches: 184, Mismatches: 48, Indels: 29
0.70 0.18 0.11
Matches are distributed among these distances:
5 1 0.01
6 15 0.08
7 121 0.66
8 43 0.23
9 4 0.02
ACGTcount: A:0.45, C:0.32, G:0.02, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:35764345 original size:22 final size:22
Alignment explanation
Indices: 35764313--35764356 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35764303 CCGTAAACAC
*
35764313 TAAATCGTAAGCCAATAACCCT
1 TAAATCCTAAGCCAATAACCCT
*
35764335 TAAATCCTAAGCCCATAACCCT
1 TAAATCCTAAGCCAATAACCCT
35764357 AAACCCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.32, G:0.07, T:0.23
Consensus pattern (22 bp):
TAAATCCTAAGCCAATAACCCT
Found at i:35764369 original size:8 final size:8
Alignment explanation
Indices: 35764329--35764428 Score: 61
Period size: 8 Copynumber: 13.2 Consensus size: 8
35764319 GTAAGCCAAT
35764329 AACCCTTA
1 AACCCTTA
*
35764337 AATCC-TA
1 AACCCTTA
* *
35764344 AGCCCAT-
1 AACCCTTA
35764351 AACCC-TA
1 AACCCTTA
35764358 AACCCTTA
1 AACCCTTA
35764366 AACCC-TA
1 AACCCTTA
* *
35764373 ATCCTTTA
1 AACCCTTA
35764381 AA-CCTTA
1 AACCCTTA
*
35764388 AA-TCTCTA
1 AACCCT-TA
*
35764396 AA-CCATA
1 AACCCTTA
35764403 AACCCTTA
1 AACCCTTA
*
35764411 AACCCCTA
1 AACCCTTA
*
35764419 AACCCCTA
1 AACCCTTA
35764427 AA
1 AA
35764429 TCATAAACTA
Statistics
Matches: 73, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
6 1 0.01
7 31 0.42
8 41 0.56
ACGTcount: A:0.40, C:0.36, G:0.01, T:0.23
Consensus pattern (8 bp):
AACCCTTA
Found at i:35764371 original size:15 final size:15
Alignment explanation
Indices: 35764329--35764428 Score: 87
Period size: 15 Copynumber: 6.7 Consensus size: 15
35764319 GTAAGCCAAT
*
35764329 AACCCTTAAATCCTA
1 AACCCTTAAACCCTA
* *
35764344 AGCCCAT-AACCCTA
1 AACCCTTAAACCCTA
35764358 AACCCTTAAACCCTA
1 AACCCTTAAACCCTA
* * *
35764373 ATCCTTTAAACCTTA
1 AACCCTTAAACCCTA
* *
35764388 AA-TCTCTAAACCATA
1 AACCCT-TAAACCCTA
35764403 AACCCTTAAACCCCTA
1 AACCCTTAAA-CCCTA
*
35764419 AACCCCTAAA
1 AACCCTTAAA
35764429 TCATAAACTA
Statistics
Matches: 66, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
14 12 0.18
15 39 0.59
16 15 0.23
ACGTcount: A:0.40, C:0.36, G:0.01, T:0.23
Consensus pattern (15 bp):
AACCCTTAAACCCTA
Found at i:35764483 original size:22 final size:22
Alignment explanation
Indices: 35764451--35764493 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35764441 GATTAAACTG
35764451 TAAACCATAAGCC-ACTAACCCA
1 TAAACCATAAGCCTA-TAACCCA
*
35764473 TAAACCCTAAGCCTATAACCC
1 TAAACCATAAGCCTATAACCC
35764494 TTAGCTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.42, C:0.37, G:0.05, T:0.16
Consensus pattern (22 bp):
TAAACCATAAGCCTATAACCCA
Found at i:35764894 original size:15 final size:15
Alignment explanation
Indices: 35764874--35764902 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35764864 ATCTATAGCG
35764874 GCGCTTTTTCAAAAA
1 GCGCTTTTTCAAAAA
35764889 GCGCTTTTTCAAAA
1 GCGCTTTTTCAAAA
35764903 CTCATATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (15 bp):
GCGCTTTTTCAAAAA
Found at i:35765779 original size:18 final size:17
Alignment explanation
Indices: 35765756--35765789 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35765746 TAAAAAATCT
35765756 TTATATATAAAGTTTATG
1 TTATATA-AAAGTTTATG
*
35765774 TTATATAAAATTTTAT
1 TTATATAAAAGTTTAT
35765790 ATACAAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TTATATAAAAGTTTATG
Found at i:35767344 original size:26 final size:26
Alignment explanation
Indices: 35767290--35767352 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
35767280 ACATATTTTC
* *
35767290 TCAAAATTTTACTAGGGGAAAAATCA
1 TCAAAATTTTACCAAGGGAAAAATCA
* * *
35767316 TCAAAATTTTACCAAGGGTAATATTA
1 TCAAAATTTTACCAAGGGAAAAATCA
*
35767342 TCAAAAGTTTA
1 TCAAAATTTTA
35767353 TTGGGGATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (26 bp):
TCAAAATTTTACCAAGGGAAAAATCA
Found at i:35772675 original size:83 final size:82
Alignment explanation
Indices: 35772484--35772733 Score: 430
Period size: 83 Copynumber: 3.0 Consensus size: 82
35772474 ATATCTCTCC
* * *
35772484 CACA-TGTGATTCATCCTAACAACTATATATTTGGTTTTTCTACTTAATTAAGTTGGTTATGCAA
1 CACAGTGTGATTCATCCTAACAACTATAAATTAGGTTTTTCTACTTAATTAAGCTGGTTATGCAA
35772548 AGTTTTTTTAATTTGTT
66 AGTTTTTTTAATTTGTT
*
35772565 CATAGTGTGATTCATCCTAACAACTATAAATTAGGTTTTTCTACTTAATTAAGCTGGTTATGCAA
1 CACAGTGTGATTCATCCTAACAACTATAAATTAGGTTTTTCTACTTAATTAAGCTGGTTATGCAA
35772630 AGTTTTTTTTAATTTGTT
66 AG-TTTTTTTAATTTGTT
* *
35772648 TACAGTGTGATTCATCCTAACAACTATAAATTAGGTTTTTCTACTTAATTAAGCTAGTTATGCAA
1 CACAGTGTGATTCATCCTAACAACTATAAATTAGGTTTTTCTACTTAATTAAGCTGGTTATGCAA
35772713 AGTTTTTTTAATTTGTT
66 AGTTTTTTTAATTTGTT
35772730 CACA
1 CACA
35772734 TGGGCAGCGT
Statistics
Matches: 159, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
81 3 0.02
82 77 0.48
83 79 0.50
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (82 bp):
CACAGTGTGATTCATCCTAACAACTATAAATTAGGTTTTTCTACTTAATTAAGCTGGTTATGCAA
AGTTTTTTTAATTTGTT
Found at i:35773358 original size:17 final size:17
Alignment explanation
Indices: 35773327--35773374 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
35773317 GAATTTAGAA
*
35773327 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
35773343 GAATTTTGTGATTTAGT
1 GAATTTTGTGATTTAGT
*
35773360 GAATTTTGCGATTTA
1 GAATTTTGTGATTTA
35773375 AAAAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.02, G:0.21, T:0.50
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:35774607 original size:46 final size:46
Alignment explanation
Indices: 35774551--35774687 Score: 157
Period size: 46 Copynumber: 3.0 Consensus size: 46
35774541 TGGCCAAGTA
* * **
35774551 TGAAACGTAGGTATGGTATTCCAGTGAAGAAAGTCATACTGAGTTG
1 TGAAAAGTAGGTATGGTATTCCAATGAAGAAAACCATACTGAGTTG
* **
35774597 TGAAAAGTAGGTATAGTATTTTAATGAAGAAAACCATACTGAGTTG
1 TGAAAAGTAGGTATGGTATTCCAATGAAGAAAACCATACTGAGTTG
* * ** * *
35774643 TGAAAAGTAGGAATGGTATTTCGGTAAAGAAAACCATACTAAGTT
1 TGAAAAGTAGGTATGGTATTCCAATGAAGAAAACCATACTGAGTT
35774688 ATAGCCTTGT
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (46 bp):
TGAAAAGTAGGTATGGTATTCCAATGAAGAAAACCATACTGAGTTG
Found at i:35782108 original size:145 final size:145
Alignment explanation
Indices: 35781864--35782148 Score: 525
Period size: 145 Copynumber: 2.0 Consensus size: 145
35781854 TTGGGGACAC
35781864 TATTTATACGGTGAGAAATGCTATGTGTATACAGATCATAAAAGTCTGAAGTATTTAATGACTCA
1 TATTTATACGGTGAGAAATGCTATGTGTATACAGATCATAAAAGTCTGAAGTATTTAATGACTCA
* *
35781929 GAAGGAGTTGAATTTAAAACAGAGACAGTGGTTCGAGTTGTTAAAAGATTATGATCTTGTTTTTG
66 GAAGAAGTTGAATTTAAAACAGAGACAGTGGTTCGAGTTGTTAAAAGATTATGATCTTGTTATTG
35781994 ATTACCACCCTGGAT
131 ATTACCACCCTGGAT
*
35782009 TATTTATACGGTGAGAAATGTTATGTGTATACAGATCATAAAAGTCTGAAGTATTTAATGACTCA
1 TATTTATACGGTGAGAAATGCTATGTGTATACAGATCATAAAAGTCTGAAGTATTTAATGACTCA
* *
35782074 GAAGAAGTTGAATTTAAGACAGAGACGGTGGTTCGAGTTGTTAAAAGATTATGATCTTGTTATTG
66 GAAGAAGTTGAATTTAAAACAGAGACAGTGGTTCGAGTTGTTAAAAGATTATGATCTTGTTATTG
35782139 ATTACCACCC
131 ATTACCACCC
35782149 GGAGAAAGCT
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
145 135 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (145 bp):
TATTTATACGGTGAGAAATGCTATGTGTATACAGATCATAAAAGTCTGAAGTATTTAATGACTCA
GAAGAAGTTGAATTTAAAACAGAGACAGTGGTTCGAGTTGTTAAAAGATTATGATCTTGTTATTG
ATTACCACCCTGGAT
Found at i:35783858 original size:17 final size:17
Alignment explanation
Indices: 35783821--35783869 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
35783811 GACTTTAGAA
*
35783821 GAATTTT-TGAATTAAT
1 GAATTTTGTGATTTAAT
*
35783837 GAATTTTGTGATTTAGT
1 GAATTTTGTGATTTAAT
*
35783854 GAATTTTGCGATTTAA
1 GAATTTTGTGATTTAA
35783870 AAAGAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (17 bp):
GAATTTTGTGATTTAAT
Found at i:35785159 original size:46 final size:46
Alignment explanation
Indices: 35785092--35785230 Score: 226
Period size: 46 Copynumber: 3.0 Consensus size: 46
35785082 CATGGCCAAG
*
35785092 TGTGAAACA-TAGGTATGGTATTCCAGTGAAGAAAACCATACTGAGT
1 TGTGAAA-AGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
35785138 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
35785184 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
35785230 T
1 T
35785231 ATAGCCTTGT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 1 0.01
46 86 0.99
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:35787375 original size:13 final size:13
Alignment explanation
Indices: 35787357--35787384 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35787347 AAATTCATTC
35787357 CTTACTTATTCAG
1 CTTACTTATTCAG
35787370 CTTACTTATTCAG
1 CTTACTTATTCAG
35787383 CT
1 CT
35787385 ATCAAGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.25, G:0.07, T:0.46
Consensus pattern (13 bp):
CTTACTTATTCAG
Found at i:35788989 original size:42 final size:42
Alignment explanation
Indices: 35788886--35789046 Score: 148
Period size: 42 Copynumber: 3.8 Consensus size: 42
35788876 CAACAGCTCG
* *
35788886 TACAATGCC-ATCGTCCCAAACATAGTCTTACATGTAATCAAA
1 TACAATGCCAAT-GTCCCAGACATGGTCTTACATGTAATCAAA
* * * *
35788928 TATCGATGCCACTGTCCCAGACAGGGTCTTACATG-AAGTCATA
1 TA-CAATGCCAATGTCCCAGACATGGTCTTACATGTAA-TCAAA
*
35788971 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAA
1 TACAATGCCAATGTCCCAGACATGGTCTTACATGT-AA--TCAAA
* * **
35789016 T-CGATGCCAACGTCCCAGATGTGGTCTTACA
1 TACAATGCCAATGTCCCAGACATGGTCTTACA
35789047 CGAAATCACA
Statistics
Matches: 97, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 32 0.33
43 31 0.32
44 29 0.30
45 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (42 bp):
TACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAA
Found at i:35811026 original size:18 final size:18
Alignment explanation
Indices: 35810992--35811024 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
35810982 AAAAATCACT
35810992 TTTATCTTTTTTATTTTC
1 TTTATCTTTTTTATTTTC
35811010 TTTA--TTTTTTATTTT
1 TTTATCTTTTTTATTTT
35811025 TTAAAATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.73
18 4 0.27
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTATCTTTTTTATTTTC
Found at i:35811422 original size:30 final size:30
Alignment explanation
Indices: 35811386--35811448 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
35811376 ACTTAACAAG
35811386 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
35811416 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
35811446 CAA
1 CAA
35811449 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:35815975 original size:5 final size:5
Alignment explanation
Indices: 35815965--35815992 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
35815955 ATAGAATTCA
35815965 AATCG AATCG AATCG AATCG AATCG AAT
1 AATCG AATCG AATCG AATCG AATCG AAT
35815993 ATATTTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (5 bp):
AATCG
Found at i:35816868 original size:9 final size:9
Alignment explanation
Indices: 35816850--35816886 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
35816840 TATAGTTTGA
35816850 TATTCGAAT
1 TATTCGAAT
*
35816859 TATTCAAAT
1 TATTCGAAT
*
35816868 TATTCGAGT
1 TATTCGAAT
35816877 TATTCGAAT
1 TATTCGAAT
35816886 T
1 T
35816887 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:35824335 original size:41 final size:40
Alignment explanation
Indices: 35824278--35824408 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 40
35824268 ACTTCTGAGG
*
35824278 TATGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGTA
1 TATGA-TTCATGTAAGACCATGTCTGGGACA-TGGCATCGTA
* *
35824320 TATGATTCATGTAAGACCCTGTCTGGGACAAGGGCATCGATA
1 TATGATTCATGTAAGACCATGTCTGGGAC-ATGGCATCG-TA
* * * * *
35824362 TGTGATAACATGTAAGACCATATCTGGGATATGGCATTGTA
1 TATGAT-TCATGTAAGACCATGTCTGGGACATGGCATCGTA
*
35824403 TGTGAT
1 TATGAT
35824409 ATATGTGTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
41 37 0.49
42 20 0.26
43 19 0.25
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (40 bp):
TATGATTCATGTAAGACCATGTCTGGGACATGGCATCGTA
Found at i:35827966 original size:26 final size:26
Alignment explanation
Indices: 35827937--35827991 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
35827927 TGGGGCACCT
*
35827937 CGCCCCAGCCATGACATCGGCAGCCC
1 CGCCCCAACCATGACATCGGCAGCCC
35827963 CGCCCCAACCATGACATCGGCAGCCC
1 CGCCCCAACCATGACATCGGCAGCCC
35827989 CGC
1 CGC
35827992 AAGGAGGCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.20, C:0.51, G:0.22, T:0.07
Consensus pattern (26 bp):
CGCCCCAACCATGACATCGGCAGCCC
Found at i:35830321 original size:21 final size:23
Alignment explanation
Indices: 35830292--35830349 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
35830282 ATTATAATAA
*
35830292 TAAATTATTACATTTTATTT-T-
1 TAAAATATTACATTTTATTTATC
*
35830313 TAAAATATTA-A-ATTATTTATC
1 TAAAATATTACATTTTATTTATC
*
35830334 TCAAATATTACATTTT
1 TAAAATATTACATTTT
35830350 TCTATTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 6 0.21
20 2 0.07
21 18 0.62
22 1 0.03
23 2 0.07
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAAATATTACATTTTATTTATC
Found at i:35831033 original size:12 final size:12
Alignment explanation
Indices: 35831016--35831040 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35831006 TCATAATCGA
35831016 TTAGTTAACATG
1 TTAGTTAACATG
35831028 TTAGTTAACATG
1 TTAGTTAACATG
35831040 T
1 T
35831041 GACAGTGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTAGTTAACATG
Found at i:35840529 original size:27 final size:27
Alignment explanation
Indices: 35840488--35840557 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
35840478 CATTTACGAA
* *
35840488 AAATAAATTACATTAAATATAGTAGTT
1 AAATAAATTATATTAAAGATAGTAGTT
*
35840515 AAATAAATTATATTAAAGATGGTAGTT
1 AAATAAATTATATTAAAGATAGTAGTT
35840542 AACAGTAAA-TATATTA
1 AA-A-TAAATTATATTA
35840558 TAATGATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 26 0.68
28 8 0.21
29 4 0.11
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (27 bp):
AAATAAATTATATTAAAGATAGTAGTT
Found at i:35840821 original size:13 final size:13
Alignment explanation
Indices: 35840805--35840829 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35840795 AAATTTTTAA
35840805 TTTTTAATTAATG
1 TTTTTAATTAATG
35840818 TTTTTAATTAAT
1 TTTTTAATTAAT
35840830 AACTCTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:35844430 original size:24 final size:24
Alignment explanation
Indices: 35844403--35844451 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
35844393 ATAATAAGTG
35844403 TGTGACTAGCTTTGGCTAAAAAAA
1 TGTGACTAGCTTTGGCTAAAAAAA
35844427 TGTGACTAGCTTTGGCTAAAAAAA
1 TGTGACTAGCTTTGGCTAAAAAAA
35844451 T
1 T
35844452 ACTTTTGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (24 bp):
TGTGACTAGCTTTGGCTAAAAAAA
Found at i:35845669 original size:21 final size:21
Alignment explanation
Indices: 35845645--35845690 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
35845635 GATTAATCAC
*
35845645 TCTTTTATGATTCTTGCCAAA
1 TCTTTTATGAATCTTGCCAAA
* * *
35845666 TCTTTTGTTAATCTTGTCAAA
1 TCTTTTATGAATCTTGCCAAA
35845687 TCTT
1 TCTT
35845691 GAACCCAGCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52
Consensus pattern (21 bp):
TCTTTTATGAATCTTGCCAAA
Found at i:35848868 original size:14 final size:16
Alignment explanation
Indices: 35848833--35848870 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
35848823 GCTTGCTCAA
35848833 ATATATGTGTTACATG
1 ATATATGTGTTACATG
*
35848849 ATATATGT-TTGCATG
1 ATATATGTGTTACATG
35848864 A-ATATGT
1 ATATATGT
35848871 AAATGCTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 7 0.33
16 8 0.38
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (16 bp):
ATATATGTGTTACATG
Found at i:35851557 original size:91 final size:88
Alignment explanation
Indices: 35851398--35851586 Score: 263
Period size: 91 Copynumber: 2.1 Consensus size: 88
35851388 AACCATTTTA
* * * *
35851398 TGGATAAACCACCAGTGTTGCAGGTTAATATGTTGTCAGTAGTTGTGAATACACAATGGGTTTAT
1 TGGATAAACCACAAGTGTTGCAGGTTAATATGCTGCCACTAGTTGTGAATACACAATGGGTTTAT
*
35851463 AGA-TAATAGTTTCCAGTATAAGTTG
66 AGATTAA-AGTTGCCAG--TAAGTTG
*
35851488 TGGATAAACCACAAGTGCTTGCAGGTTAATATGCTGCCACTAGTTGTGAATACACAATGGGTTTG
1 TGGATAAACCACAAGTG-TTGCAGGTTAATATGCTGCCACTAGTTGTGAATACACAATGGGTTTA
* *
35851553 TAGATTAAAGTTGCTAGTAATTTG
65 TAGATTAAAGTTGCCAGTAAGTTG
35851577 TGGATAAACC
1 TGGATAAACC
35851587 TCCAGTATTT
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
89 16 0.18
90 16 0.18
91 54 0.61
92 3 0.03
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (88 bp):
TGGATAAACCACAAGTGTTGCAGGTTAATATGCTGCCACTAGTTGTGAATACACAATGGGTTTAT
AGATTAAAGTTGCCAGTAAGTTG
Found at i:35854304 original size:13 final size:13
Alignment explanation
Indices: 35854286--35854313 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35854276 TAATAGAACT
35854286 TAAACTTACCATA
1 TAAACTTACCATA
35854299 TAAACTTACCATA
1 TAAACTTACCATA
35854312 TA
1 TA
35854314 CATTAGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAACTTACCATA
Found at i:35855040 original size:36 final size:36
Alignment explanation
Indices: 35854951--35855118 Score: 106
Period size: 36 Copynumber: 4.6 Consensus size: 36
35854941 AAAGTTTTAC
* * * **
35854951 GCCCAGCGCTAGTCGAATAAACTGAAAATG-GGTGTA
1 GCCCAGCGCTAGTCGGATAAACCGACAATGTCTTG-A
* *
35854987 -CCCTGCACTAGTCGGATAAACCGACAATGTCTTGA
1 GCCCAGCGCTAGTCGGATAAACCGACAATGTCTTGA
* * * * *
35855022 GCCTAGCGCTAGTTGGATAAACTGACGATGTCAAATATGT
1 GCCCAGCGCTAGTCGGATAAACCGACAATGTC---T-TGA
* * * * * *
35855062 GCCCAGCACTAGTCGAATAACCCAACAATGTTTTGC
1 GCCCAGCGCTAGTCGGATAAACCGACAATGTCTTGA
*
35855098 GCCCAGCGCTAGTTGGATAAA
1 GCCCAGCGCTAGTCGGATAAA
35855119 TTGACGATAT
Statistics
Matches: 98, Mismatches: 28, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
35 25 0.26
36 46 0.47
37 1 0.01
39 1 0.01
40 25 0.26
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (36 bp):
GCCCAGCGCTAGTCGGATAAACCGACAATGTCTTGA
Found at i:35855106 original size:76 final size:76
Alignment explanation
Indices: 35854991--35855302 Score: 318
Period size: 76 Copynumber: 4.1 Consensus size: 76
35854981 GGTGTACCCT
* * * * * *
35854991 GCACTAGTCGGATAAACCGACAATGTCTTGAGCCTAGCGCTAGTTGGATAAACTGACGATGTCAA
1 GCACTAGTCGAATAAACCAACAATGTCTTGCGCCCAGCGCTAATCGGATAAACTGACGATGTCAA
35855056 ATATGTGCCCA
66 ATATGTGCCCA
* * * * * *
35855067 GCACTAGTCGAATAACCCAACAATGTTTTGCGCCCAGCGCTAGTTGGATAAATTGACGATATCAA
1 GCACTAGTCGAATAAACCAACAATGTCTTGCGCCCAGCGCTAATCGGATAAACTGACGATGTCAA
* *
35855132 ATGTGTGTCCA
66 ATATGTGCCCA
* ** * ** * **
35855143 GCACTAGCCGAATAAACCAACAGCGTCTTGTGCCCAATGCTAATCGGATAAACCGAAAATGTCAA
1 GCACTAGTCGAATAAACCAACAATGTCTTGCGCCCAGCGCTAATCGGATAAACTGACGATGTCAA
35855208 ATATGTGCCCA
66 ATATGTGCCCA
* * * * * * * * *
35855219 GCACTACTCGGATAACCCGACAATATTTTGCACCCAGCGCTAATCGAATAAACTAACGATGTCAA
1 GCACTAGTCGAATAAACCAACAATGTCTTGCGCCCAGCGCTAATCGGATAAACTGACGATGTCAA
*
35855284 ATGTGTGCCCA
66 ATATGTGCCCA
*
35855295 ACACTAGT
1 GCACTAGT
35855303 TGGTTATACT
Statistics
Matches: 188, Mismatches: 48, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
76 188 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (76 bp):
GCACTAGTCGAATAAACCAACAATGTCTTGCGCCCAGCGCTAATCGGATAAACTGACGATGTCAA
ATATGTGCCCA
Found at i:35857731 original size:30 final size:29
Alignment explanation
Indices: 35857697--35857757 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
35857687 CCATAGAGGT
35857697 TTTCCTTTGACAGAGA-TTGCCACAAAGGCA
1 TTTCCTTT--CAGAGATTTGCCACAAAGGCA
*
35857727 TTTCCTTTTAGAGATTTGCCACAAAGGCA
1 TTTCCTTTCAGAGATTTGCCACAAAGGCA
35857756 TT
1 TT
35857758 CTTAAATAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 5 0.17
29 16 0.55
30 8 0.28
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (29 bp):
TTTCCTTTCAGAGATTTGCCACAAAGGCA
Found at i:35857864 original size:61 final size:61
Alignment explanation
Indices: 35857785--35857912 Score: 184
Period size: 61 Copynumber: 2.1 Consensus size: 61
35857775 ACGAAGGTTT
* ** * * *
35857785 TCCTTTACATTCAGTACTCGCCACAAAGGCTTTATTGTCTAGAGTTGTGCCACAAAGGCTA
1 TCCTTTACATTCAATACTCGCCACAAAGGCAATAGTGTCCAGAATTGTGCCACAAAGGCTA
* *
35857846 TCCTTTACATTCAATACTCGCCACAAAGGCAATCGTGTCCAGAATTGTGCCACAAAGGCTT
1 TCCTTTACATTCAATACTCGCCACAAAGGCAATAGTGTCCAGAATTGTGCCACAAAGGCTA
35857907 TCCTTT
1 TCCTTT
35857913 CCAGATTTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (61 bp):
TCCTTTACATTCAATACTCGCCACAAAGGCAATAGTGTCCAGAATTGTGCCACAAAGGCTA
Found at i:35857915 original size:29 final size:29
Alignment explanation
Indices: 35857829--35857939 Score: 91
Period size: 29 Copynumber: 3.8 Consensus size: 29
35857819 TTGTCTAGAG
* *
35857829 TTGTGCCACAAAGGCTATCCTTTACATTCAA
1 TTGTGCCACAAAGGCTATCCTTTCCA--GAA
** * * *
35857860 TACTCGCCACAAAGGCAATCGTGTCCAGAA
1 TTGT-GCCACAAAGGCTATCCTTTCCAGAA
* *
35857890 TTGTGCCACAAAGGCTTTCCTTTCCAGAT
1 TTGTGCCACAAAGGCTATCCTTTCCAGAA
*
35857919 TTGTG-C-CAAAGGCTATTCTTT
1 TTGTGCCACAAAGGCTATCCTTT
35857940 ACTAGTGTTT
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
27 13 0.21
28 1 0.02
29 25 0.40
30 4 0.06
31 2 0.03
32 18 0.29
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (29 bp):
TTGTGCCACAAAGGCTATCCTTTCCAGAA
Found at i:35857939 original size:27 final size:29
Alignment explanation
Indices: 35857804--35857926 Score: 86
Period size: 29 Copynumber: 4.1 Consensus size: 29
35857794 TTCAGTACTC
* * *
35857804 GCCACAAAGGCTTT-ATTGTCTAGAGTTGT
1 GCCACAAAGGCTTTCCTT-TCCAGAATTGT
* * * **
35857833 GCCACAAAGGCTATCCTTTACATTCAATACT
1 GCCACAAAGGCTTTCCTTTCCA--GAATTGT
** * *
35857864 CGCCACAAAGGCAATCGTGTCCAGAATTGT
1 -GCCACAAAGGCTTTCCTTTCCAGAATTGT
*
35857894 GCCACAAAGGCTTTCCTTTCCAGATTTGT
1 GCCACAAAGGCTTTCCTTTCCAGAATTGT
35857923 GCCA
1 GCCA
35857927 AAGGCTATTC
Statistics
Matches: 70, Mismatches: 20, Indels: 8
0.71 0.20 0.08
Matches are distributed among these distances:
29 43 0.61
30 6 0.09
31 3 0.04
32 18 0.26
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (29 bp):
GCCACAAAGGCTTTCCTTTCCAGAATTGT
Found at i:35859159 original size:2 final size:2
Alignment explanation
Indices: 35859152--35859176 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35859142 CGCCTTGCTC
35859152 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35859177 CCTTACCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35859437 original size:16 final size:16
Alignment explanation
Indices: 35859417--35859455 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
35859407 TTCCTTCATT
35859417 AGGTTTTTATCCT-ATA
1 AGGTTTTT-TCCTAATA
*
35859433 TGGTTTTTTCCTAATA
1 AGGTTTTTTCCTAATA
35859449 AGGTTTT
1 AGGTTTT
35859456 AACGAATGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (16 bp):
AGGTTTTTTCCTAATA
Found at i:35860795 original size:184 final size:184
Alignment explanation
Indices: 35860485--35860910 Score: 611
Period size: 184 Copynumber: 2.3 Consensus size: 184
35860475 TTATAATATT
* * *
35860485 AAATAAAATTTTATTATTATTTTGAAAATTAAAAAATAATATTTATATTTTAAAAAACATGTCAC
1 AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAATAATTATA-TTTAAAAAACATGTCAC
* * *
35860550 TTAGTACATAATTTGTGGCATAAATTACGCTTTTCTATAATATTACAACTTTCAGCTATGTTTAT
65 TTAGTACATAACTTGTGGCACAAATTACGCTTTTCTATAACATTACAACTTTCAGCTATGTTTAT
* * *
35860615 TCATTACAAATCTTTTCTAAAAGCTATGTTTATTTGAATAAATCTATTCAGATGC
130 TCATTACAAATCTTTTCTAAAAGCTACGCTTATTTGAATAAATCTATTCAGATGA
* * * * *
35860670 AAATAAAAATTTATTATTATTTTAAAAAATAAAAAATAAAAATTATGTTTAAAAAATATGTCATT
1 AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAATAATTATATTTAAAAAACATGTCACT
** * *
35860735 TAGTATGTAACTTGTGGCACAAGTTACGCTTTTTCT-TAACATTATAACTTTCAGCTATGTTTAT
66 TAGTACATAACTTGTGGCACAAATTACGC-TTTTCTATAACATTACAACTTTCAGCTATGTTTAT
* * * *
35860799 TCATTACGAATCTTTTTTTAAAGTTACGCTTATTTGAATAAATCTATTCAGATGA
130 TCATTACAAATCTTTTCTAAAAGCTACGCTTATTTGAATAAATCTATTCAGATGA
* *
35860854 AAATAAAAATTTATTTTTATTTTGAAAAATAAAAAATAATTATTATATTTAAAAAAC
1 AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAATAATTATATTTAAAAAAC
35860911 TTATTTGCAC
Statistics
Matches: 212, Mismatches: 28, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
184 165 0.78
185 47 0.22
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (184 bp):
AAATAAAAATTTATTATTATTTTGAAAAATAAAAAATAATAATTATATTTAAAAAACATGTCACT
TAGTACATAACTTGTGGCACAAATTACGCTTTTCTATAACATTACAACTTTCAGCTATGTTTATT
CATTACAAATCTTTTCTAAAAGCTACGCTTATTTGAATAAATCTATTCAGATGA
Found at i:35860899 original size:26 final size:27
Alignment explanation
Indices: 35860853--35860909 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
35860843 TATTCAGATG
* * * *
35860853 AAAATAAAAATTTATTTTTAT-TTTGA
1 AAAATAAAAAATAATTATTATATTTAA
35860879 AAAATAAAAAATAATTATTATATTTAA
1 AAAATAAAAAATAATTATTATATTTAA
35860906 AAAA
1 AAAA
35860910 CTTATTTGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
AAAATAAAAAATAATTATTATATTTAA
Found at i:35882349 original size:27 final size:27
Alignment explanation
Indices: 35882297--35882351 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
35882287 AATATATTGG
* *
35882297 TTTTATTTAATATTCAATAATTATATT
1 TTTTATTAAATATTCAATAATAATATT
*
35882324 TTTTATTAAATATTTAA-ACATAATATT
1 TTTTATTAAATATTCAATA-ATAATATT
35882351 T
1 T
35882352 ACATTGTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTTATTAAATATTCAATAATAATATT
Found at i:35885214 original size:2 final size:2
Alignment explanation
Indices: 35885207--35885247 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
35885197 AAAGAATGCC
35885207 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35885248 AAAGCCATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35885575 original size:17 final size:17
Alignment explanation
Indices: 35885542--35885575 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35885532 TCACAAAAAA
*
35885542 AAATAAAAATAAAAAGG
1 AAATAAAAACAAAAAGG
*
35885559 AAATAAAAACAAGAAGG
1 AAATAAAAACAAAAAGG
35885576 GAGCAGATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.09
Consensus pattern (17 bp):
AAATAAAAACAAAAAGG
Found at i:35887128 original size:44 final size:44
Alignment explanation
Indices: 35886947--35887139 Score: 108
Period size: 44 Copynumber: 4.4 Consensus size: 44
35886937 CCACTGCCGA
* *
35886947 CCAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCATTGTAAC
1 CCAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGTAAC
* * * *** ** * *
35886990 CTCAGGGAGGTAAAATCTGCCATCTTCGGTCTACTCCACTACT-TC
1 C-CAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACT-GTAAC
* * * * * **
35887035 CTAGGGAGATAAGATTTGTAAT--CTTCAATCTATTCCACTGTTGC
1 CCAGGGAGAT-AGA-ATCTACTGGCTTCAATCTACTCCACTGTAAC
*
35887079 CCAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACTGTAAC
1 CCAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGTAAC
* *
35887122 CACAGGGAGGTAAAATCT
1 C-CAGGGAGATAGAATCT
35887140 GCCATCTTTG
Statistics
Matches: 106, Mismatches: 34, Indels: 18
0.67 0.22 0.11
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 24 0.23
44 55 0.52
45 20 0.19
46 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (44 bp):
CCAGGGAGATAGAATCTACTGGCTTCAATCTACTCCACTGTAAC
Found at i:35887885 original size:133 final size:133
Alignment explanation
Indices: 35886924--35887860 Score: 1421
Period size: 133 Copynumber: 7.1 Consensus size: 133
35886914 GATTTGCTAT
* * * * * *
35886924 TCTTCGATCGATTCCACTGCCGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCATTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAA
* * * * * * * * * ** *
35886989 CCTCAGGGAGGTAAAATCTGCCATCTTCGGTCTACTCCACT-ACT-TCCTAGGGAGATAAGATTT
66 CCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGTCTATGC-AGGAAGGCAAGATCT
*
35887052 GTAA
130 GAAA
* *
35887056 TCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAA
35887121 CCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTG
66 CCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTG
35887186 AAA
131 AAA
*
35887189 TCTTCAATCTATTCCGCTGCTGCCCAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAA
*
35887254 CCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCACTGTCTATGCAGGAAGGCAAGATCTG
66 CCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTG
35887319 AAA
131 AAA
* *
35887322 TCTTCAATCTATTCCGCTGCTGCCCAGGGAGATAGAATTAATAGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAA
35887387 CCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTG
66 CCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTG
35887452 AAA
131 AAA
* * * *
35887455 TCTTCAATCTATTCCGCTGCTGCCCAGGGAGATAGAATTACTAGCTTTAATGTACTCTATTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAA
*
35887520 CCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTG
66 CCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTG
35887585 AAA
131 AAA
35887588 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAA
* *
35887653 CCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATTTG
66 CCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTG
**
35887718 TTA
131 AAA
** ** *
35887721 TCTTTGATCTATTCCACTGCTGCCCAGGGA-AGTAGAATTACCGGCTTCAATGTACTCCACGGTA
1 TCTTCAATCTATTCCACTGCTGCCCAGGGAGA-TAGAATTACTAGCTTCAATGTACTCCACTGTA
* * * * *
35887785 ACCATAGAGAGGTAAAATATGCCATCTTTGATCTGCTCCACTGTCTATGCAGGAAGGCAAGATCT
65 ACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCT
**
35887850 GCTA
130 GAAA
35887854 TCTTCAA
1 TCTTCAA
35887861 CCTGCTCCAC
Statistics
Matches: 750, Mismatches: 52, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
132 95 0.13
133 653 0.87
134 2 0.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (133 bp):
TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAA
CCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTG
AAA
Found at i:35893587 original size:2 final size:2
Alignment explanation
Indices: 35893580--35893608 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
35893570 AAAGAATGCC
35893580 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35893609 AAAGCCATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35896454 original size:3 final size:3
Alignment explanation
Indices: 35896448--35896548 Score: 202
Period size: 3 Copynumber: 33.7 Consensus size: 3
35896438 CTTCATGTGC
35896448 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35896496 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35896544 ATT AT
1 ATT AT
35896549 CGCTATTACT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:35897677 original size:31 final size:32
Alignment explanation
Indices: 35897616--35897678 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
35897606 ATTCATTTCG
*
35897616 ACTCTTTTTCAAAAGGTTAATGATCAAATTTA
1 ACTCTTTTTCAAAAGGTTAAGGATCAAATTTA
* * *
35897648 ACTCTTTTT-AAAGGGTTGAGGGTCAAATTTA
1 ACTCTTTTTCAAAAGGTTAAGGATCAAATTTA
35897679 GCTAAAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (32 bp):
ACTCTTTTTCAAAAGGTTAAGGATCAAATTTA
Found at i:35902550 original size:26 final size:26
Alignment explanation
Indices: 35902521--35902571 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
35902511 TTTGAAATGG
*
35902521 AAAAAT-AATATGAATTTTACATTCAT
1 AAAAATGAATA-GAATTTTAAATTCAT
*
35902547 AAAAATGCATAGAATTTTAAATTCA
1 AAAAATGAATAGAATTTTAAATTCA
35902572 AAGTTGACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (26 bp):
AAAAATGAATAGAATTTTAAATTCAT
Found at i:35903337 original size:2 final size:2
Alignment explanation
Indices: 35903330--35903374 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
35903320 TTCGCAGTTT
35903330 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
35903373 TA
1 TA
35903375 CNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:35904208 original size:21 final size:21
Alignment explanation
Indices: 35904192--35904235 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35904182 AATAATTGAG
35904192 AATATATAATTATTAATTAAA
1 AATATATAATTATTAATTAAA
*
35904213 AATAATATAAATATT-ATTAAA
1 AAT-ATATAATTATTAATTAAA
35904234 AA
1 AA
35904236 ATAATATGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATATATAATTATTAATTAAA
Found at i:35904220 original size:22 final size:22
Alignment explanation
Indices: 35904195--35904242 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
35904185 AATTGAGAAT
*
35904195 ATATAATTATTAATT-AAAAATA
1 ATATAAATATT-ATTAAAAAATA
35904217 ATATAAATATTATTAAAAAATA
1 ATATAAATATTATTAAAAAATA
35904239 ATAT
1 ATAT
35904243 GGGTGATCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATAAATATTATTAAAAAATA
Found at i:35908707 original size:20 final size:21
Alignment explanation
Indices: 35908682--35908721 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
35908672 TCGTTAACTC
35908682 GATTTGACTCG-AAATTTTTT
1 GATTTGACTCGAAAATTTTTT
*
35908702 GATTTGATTCGAAAATTTTT
1 GATTTGACTCGAAAATTTTT
35908722 AAATGAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (21 bp):
GATTTGACTCGAAAATTTTTT
Found at i:35936882 original size:2 final size:2
Alignment explanation
Indices: 35936875--35936912 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
35936865 CCCCTCGTTC
*
35936875 CT CT CT CT CT CT CT CT CT CT CT CG CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
35936913 TTGAGCTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:35942673 original size:12 final size:12
Alignment explanation
Indices: 35942641--35942691 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
35942631 TAGCAATTAT
*
35942641 AATTGATTTTTAA
1 AATT-ATTTTAAA
35942654 AA-TATTTTAAA
1 AATTATTTTAAA
35942665 AATTATTTTTAAA
1 AATTA-TTTTAAA
* *
35942678 TATTTTTTTAAA
1 AATTATTTTAAA
35942690 AA
1 AA
35942692 AGCTTTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 9 0.28
12 11 0.34
13 12 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (12 bp):
AATTATTTTAAA
Found at i:35942684 original size:11 final size:11
Alignment explanation
Indices: 35942646--35942690 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
35942636 ATTATAATTG
35942646 ATTTTTAAAAT
1 ATTTTTAAAAT
*
35942657 ATTTTAAAAATT
1 ATTTTTAAAA-T
35942669 ATTTTTAAATAT
1 ATTTTTAAA-AT
*
35942681 TTTTTTAAAA
1 ATTTTTAAAA
35942691 AAGCTTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 10 0.34
12 18 0.62
13 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTTTAAAAT
Found at i:35948441 original size:9 final size:8
Alignment explanation
Indices: 35948421--35948474 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
35948411 AATGAAAATG
*
35948421 AAAAAAAT
1 AAAAAAAC
35948429 AAAAAAAC
1 AAAAAAAC
35948437 AAAAAAAC
1 AAAAAAAC
*
35948445 AAAAAGAAG
1 AAAAA-AAC
* *
35948454 AAAGAAAG
1 AAAAAAAC
35948462 AAAAAAATC
1 AAAAAAA-C
35948471 AAAA
1 AAAA
35948475 TCAAAATCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
8 29 0.74
9 10 0.26
ACGTcount: A:0.83, C:0.06, G:0.07, T:0.04
Consensus pattern (8 bp):
AAAAAAAC
Found at i:35948449 original size:25 final size:26
Alignment explanation
Indices: 35948421--35948474 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
35948411 AATGAAAATG
*
35948421 AAAAAAATAAAAAAACAAAAAAA-CA
1 AAAAAAAGAAAAAAACAAAAAAATCA
* * *
35948446 AAAAGAAGAAAGAAAGAAAAAAATCA
1 AAAAAAAGAAAAAAACAAAAAAATCA
35948472 AAA
1 AAA
35948475 TCAAAATCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.83, C:0.06, G:0.07, T:0.04
Consensus pattern (26 bp):
AAAAAAAGAAAAAAACAAAAAAATCA
Found at i:35950819 original size:43 final size:42
Alignment explanation
Indices: 35950703--35950819 Score: 112
Period size: 44 Copynumber: 2.7 Consensus size: 42
35950693 GAATATTTCA
* * *
35950703 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGACGCCT
1 GATCCTATCTCCCTGAAGTTACAGTGGAGCAGATCGACGCCT
* * *
35950745 GAGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAGGACACT
1 --GATCCTATCTCCCTGAAG-TTACAGTGGAGCAGATCGACG-C-CT
*
35950791 -ATCCTATCTCCCTGAAGTTATAGTGGAGC
1 GATCCTATCTCCCTGAAGTTACAGTGGAGC
35950820 GGATTAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
43 24 0.39
44 35 0.56
45 1 0.02
46 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (42 bp):
GATCCTATCTCCCTGAAGTTACAGTGGAGCAGATCGACGCCT
Found at i:35950907 original size:41 final size:44
Alignment explanation
Indices: 35950795--35950947 Score: 131
Period size: 44 Copynumber: 3.5 Consensus size: 44
35950785 GACACTATCC
* *
35950795 TATCTCCCTGAAGTTATAGTGGAGC-GGATT-AAAATA-AAGGATCC-
1 TATCTCCCTGAAGTTACAGTGGAGCAGG-TTGAACATACAA-G--CCT
* ** *
35950839 TATCTCTCTGAAGTTACAGCAGAGCAGG-T-CACATA-AAGCCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGGTTGAACATACAAGCCT
* * *
35950880 TATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATACAAGTCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGGTTGAACATACAAGCCT
*
35950924 TATCTCCCTGAGGTTACAGTGGAG
1 TATCTCCCTGAAGTTACAGTGGAG
35950948 TAGACCGAAG
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
40 2 0.02
41 24 0.27
42 2 0.02
43 11 0.12
44 48 0.54
45 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGGTTGAACATACAAGCCT
Found at i:35951021 original size:19 final size:19
Alignment explanation
Indices: 35950997--35951034 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
35950987 AGCGGAGCAG
35950997 ATCGAGGACACTATCCTAT
1 ATCGAGGACACTATCCTAT
35951016 ATCGAGGACACTATCCTAT
1 ATCGAGGACACTATCCTAT
35951035 CTCCCTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (19 bp):
ATCGAGGACACTATCCTAT
Found at i:35951170 original size:44 final size:44
Alignment explanation
Indices: 35951115--35951409 Score: 158
Period size: 44 Copynumber: 6.6 Consensus size: 44
35951105 CACATAAAGC
*
35951115 CTTATCTCCCTGAAGTTACAGTGGGGCAAGTTGAATATGCAAGT
1 CTTATCTCCCTGAAGTTACAGTGGAGCAAGTTGAATATGCAAGT
* * ** *
35951159 CTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAAT-TTC-AGAT
1 CTTATCTCCCTGAAGTTACAGTGGAGCA-A--GTTGAATATGCAAG-T
* * * **** **
35951205 CTTATCACCCTG-AGATTACAGAGGAGC-AGATCGAAGCCACAAAC
1 CTTATCTCCCTGAAG-TTACAGTGGAGCAAG-TTGAATATGCAAGT
* *
35951249 CTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAGT
1 CTTATCTCCCTGAAGTTACAGTGGAGCAAGTTGAATATGCAAGT
* * * ** *
35951293 CTTATCTTCCTGAGGTTACAGTGGAGTAGACCGAAGAAT-TTC-AGAT
1 CTTATCTCCCTGAAGTTACAGTGGAGCA-A--GTTGAATATGCAAG-T
* * *
35951339 CTTATCTCCCTGAGGTTACAGTGGAGC-AGATTGGAGCTA-GTAA-T
1 CTTATCTCCCTGAAGTTACAGTGGAGCAAG-TT-GA-ATATGCAAGT
* *
35951383 CCTATCTCCCCGAAGTTACAGTGGAGC
1 CTTATCTCCCTGAAGTTACAGTGGAGC
35951410 GGATTAAAAT
Statistics
Matches: 186, Mismatches: 46, Indels: 38
0.69 0.17 0.14
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 107 0.58
45 11 0.06
46 53 0.28
47 10 0.05
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTACAGTGGAGCAAGTTGAATATGCAAGT
Found at i:35951194 original size:237 final size:237
Alignment explanation
Indices: 35950779--35951238 Score: 875
Period size: 237 Copynumber: 1.9 Consensus size: 237
35950769 AGCGGAGCAG
35950779 ATCGAGGACACTATCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAAGGATCCTATCT
1 ATCGAGGACACTATCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAAGGATCCTATCT
*
35950844 CTCTGAAGTTACAGCAGAGCAGGTCACATAAAGCCTTATCTCCCTGAAGTTACAGTGGGGCAGGT
66 CTCTGAAGTTACAGCAGAGCAGGTCACATAAAGCCTTATCTCCCTGAAGTTACAGTGGGGCAAGT
35950909 TGAATATACAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATC
131 TGAATATACAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATC
* *
35950974 TCCCTGAGATTACAGCGGAGCAGATCGAGGACACTATCCTAT
196 ACCCTGAGATTACAGAGGAGCAGATCGAGGACACTATCCTAT
*
35951016 ATCGAGGACACTATCCTATCTCCCTGAAGTTATAGTTGAGCGGATTAAAATAAAGGATCCTATCT
1 ATCGAGGACACTATCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAAGGATCCTATCT
35951081 CTCTGAAGTTACAGCAGAGCAGGTCACATAAAGCCTTATCTCCCTGAAGTTACAGTGGGGCAAGT
66 CTCTGAAGTTACAGCAGAGCAGGTCACATAAAGCCTTATCTCCCTGAAGTTACAGTGGGGCAAGT
*
35951146 TGAATATGCAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATC
131 TGAATATACAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATC
35951211 ACCCTGAGATTACAGAGGAGCAGATCGA
196 ACCCTGAGATTACAGAGGAGCAGATCGA
35951239 AGCCACAAAC
Statistics
Matches: 218, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
237 218 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (237 bp):
ATCGAGGACACTATCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAAGGATCCTATCT
CTCTGAAGTTACAGCAGAGCAGGTCACATAAAGCCTTATCTCCCTGAAGTTACAGTGGGGCAAGT
TGAATATACAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATC
ACCCTGAGATTACAGAGGAGCAGATCGAGGACACTATCCTAT
Found at i:35951216 original size:46 final size:46
Alignment explanation
Indices: 35951158--35951542 Score: 239
Period size: 44 Copynumber: 8.7 Consensus size: 46
35951148 AATATGCAAG
*
35951158 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTTCAGA
* * * * * *
35951204 TCTTATCACCCTGAGATTACAGAGGAGCAGATCGAAGCCA---CAAA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAG-AATTTCAGA
* * * ** *
35951248 CCTTATCTCCCTGAAGTTACAGTGGGGCAG---GTTGAATATGCA-A
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAAT-TTCAGA
* *
35951291 GTCTTATCTTCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGA
1 -TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTTCAGA
** * * *
35951338 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGGAG-CTAGT-A-A
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAAT-TTCAGA
* * * * ** **
35951382 TCCTATCTCCCCGAAGTTACAGTGGAGCGGA-TTAA-AA-TAAAGGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTTCA-GA
* * * * * * * *
35951426 TCTCATCTCTCTGAAGTTACAGTAGAGTAGATC--A-CA--TCAGG
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTTCAGA
* *
35951467 TCTTATCTCCCTGAGGTTACAGTGGAGTAAACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTTCAGA
* *
35951513 TCTTACCTCCCTGAGGTTACAATGGAGCAG
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAG
35951543 GTCAAAGGTG
Statistics
Matches: 254, Mismatches: 64, Indels: 42
0.71 0.18 0.12
Matches are distributed among these distances:
40 1 0.00
41 30 0.12
42 2 0.01
43 6 0.02
44 108 0.43
45 2 0.01
46 98 0.39
47 7 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (46 bp):
TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTTCAGA
Found at i:35951269 original size:134 final size:135
Alignment explanation
Indices: 35951114--35951406 Score: 473
Period size: 134 Copynumber: 2.2 Consensus size: 135
35951104 TCACATAAAG
35951114 CCTTATCTCCCTGAAGTTACAGTGGGGCAAGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACA
1 CCTTATCTCCCTGAAGTTACAGTGGGGCAAGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACA
35951179 GTGGAGTAGACCGAAGAATTTCAGATCTTATCACCCTGAGATTACAGAGGAGCAGATCGAAGCCA
66 GTGGAGTAGACCGAAGAATTTCAGATCTTATCACCCTGAGATTACAGAGGAGCAGATCGAAGCCA
35951244 -CAAA
131 GCAAA
* *
35951248 CCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAGTCTTATCTTCCTGAGGTTACA
1 CCTTATCTCCCTGAAGTTACAGTGGGGCAAGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACA
* * * * * *
35951313 GTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGGAGCTA
66 GTGGAGTAGACCGAAGAATTTCAGATCTTATCACCCTGAGATTACAGAGGAGCAGATCGAAGCCA
* *
35951378 GTAAT
131 GCAAA
*
35951383 CC-TATCTCCCCGAAGTTACAGTGG
1 CCTTATCTCCCTGAAGTTACAGTGG
35951407 AGCGGATTAA
Statistics
Matches: 147, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
134 143 0.97
135 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (135 bp):
CCTTATCTCCCTGAAGTTACAGTGGGGCAAGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACA
GTGGAGTAGACCGAAGAATTTCAGATCTTATCACCCTGAGATTACAGAGGAGCAGATCGAAGCCA
GCAAA
Found at i:35951445 original size:134 final size:134
Alignment explanation
Indices: 35951114--35951493 Score: 420
Period size: 134 Copynumber: 2.9 Consensus size: 134
35951104 TCACATAAAG
* * * * * * *
35951114 CCTTATCTCCCTGAAGTTACAGTGGGGCAAGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACA
1 CCTTATCTCCCCGAAGTTACAGTGGAGCAGGTTGAAAATGAAAGTCTCATCTCTCTGAGGTTACA
* * *
35951179 GTGGAGTAGACCGAAGAATTTCAGATCTTATCACCCTGAGATTACAGAGGAGCAGATCGAAGCCA
66 GTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGCCA
35951244 CAAA
131 CAAA
* * * * *
35951248 CCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAGTCTTATCT-TCCTGAGGTTAC
1 CCTTATCTCCCCGAAGTTACAGTGGAGCAGGTTGAAAATGAAAGTCTCATCTCT-CTGAGGTTAC
* * *
35951312 AGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGGAGCT
65 AGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGCC
* *
35951377 AGTAAT
130 A-CAAA
*
35951383 CC-TATCTCCCCGAAGTTACAGTGGAGC-GGATT-AAAAT-AAAGGATCTCATCTCTCTGAAGTT
1 CCTTATCTCCCCGAAGTTACAGTGGAGCAGG-TTGAAAATGAAA-G-TCTCATCTCTCTGAGGTT
* * * *
35951444 ACAGTAGAGTAGATC--A-CA--TCAGGTCTTATCTCCCTGAGGTTACAGTGGAG
63 ACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAG
35951494 TAAACCGAAG
Statistics
Matches: 220, Mismatches: 20, Indels: 17
0.86 0.08 0.07
Matches are distributed among these distances:
129 31 0.14
131 1 0.00
132 3 0.01
133 7 0.03
134 173 0.79
135 5 0.02
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (134 bp):
CCTTATCTCCCCGAAGTTACAGTGGAGCAGGTTGAAAATGAAAGTCTCATCTCTCTGAGGTTACA
GTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGCCA
CAAA
Found at i:35951791 original size:40 final size:40
Alignment explanation
Indices: 35951561--35952136 Score: 480
Period size: 40 Copynumber: 13.7 Consensus size: 40
35951551 TGTTAGATCC
**
35951561 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAA-TCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATC----ACATC-AAGTCT
* * * * * *
35951605 TATCTTCCTAAGCAGTAGTGAAGCAAATTTAAGCCA-CCAGTCC
1 TATCTCCCTAAGCAGTAGTGGAGCAGA--TCA--CATCAAGTCT
* * ** *
35951648 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCC
1 TATCTCCCTAAGCAGTAGTGGAGCAGATC--ACAT-CAAG-TCT
* * *
35951692 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAT-ATGGTAGATCC
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCA----AG-TCT
*
35951736 TATCTCCCTAAGCAGTAGTGGAGCAGATCACACCAAGTCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCT
** * * *
35951776 TATCTCCCTAAGCAGTAGTGAAGCAGACAGAAAAAACCAA-TCC
1 TATCTCCCTAAGCAGTAGTG--G-AG-CAGATCACATCAAGTCT
** * * * *
35951819 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCATAGATCT
1 TATCTCCCT-AAGCAGTAGTGGAGCAGA-TCACATCA-AG-TCT
35951863 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCT
35951903 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCT
* **
35951943 TATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCGATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAA--G-TCT
35951986 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCT
* * **
35952026 TATCTTCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCGATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAA--G-TCT
*
35952069 TATCTCTCTAAGCAGTAGTGGAGCAGATCACATCAAGTCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCT
35952109 TATCTCCCTAAGCAGTAGTGGAGCAGAT
1 TATCTCCCTAAGCAGTAGTGGAGCAGAT
35952137 GAAAGAAACC
Statistics
Matches: 444, Mismatches: 54, Indels: 72
0.78 0.09 0.13
Matches are distributed among these distances:
39 2 0.00
40 162 0.36
41 16 0.04
42 16 0.04
43 122 0.27
44 124 0.28
45 1 0.00
46 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (40 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCT
Found at i:35952004 original size:83 final size:83
Alignment explanation
Indices: 35951556--35952158 Score: 630
Period size: 83 Copynumber: 7.1 Consensus size: 83
35951546 AAAGGTGTTA
** *
35951556 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAA-TCTTATCTTCCTAAGCAG
1 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGATC----ACATC-AAGTCTTATCTCCCTAAGCAG
* * *** **
35951620 TAGTGAAGCAAATTTAAGCCACC
61 TAGTGGAGCAGACGAAAGAAACC
* * ** *
35951643 -AGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAG
1 GA-TCCTATCTCCCTAAGCAGTAGTGGAGCAGATC--ACAT-CAAG-TCTTATCTCCCTAAGCAG
* * **
35951707 TAGTGGAGCAGGTCAAATATGGTA--
61 TAGTGGAGCA-GACGAA-A-GAAACC
*
35951731 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCACACCAAGTCTTATCTCCCTAAGCAGTAGTG
1 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTG
*
35951796 AAGCAGACAGAAA-AAACC
66 GAGCAGAC-GAAAGAAACC
* ** * * * *
35951814 AATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCATAGATCTTATCTCCCTAAGCAGT
1 GATCCTATCTCCCT-AAGCAGTAGTGGAGCAGA-TCACATCA-AG-TCTTATCTCCCTAAGCAGT
* **
35951879 AGTGGAGCAGATC-ACATCAA--
62 AGTGGAGCAGA-CGAAAGAAACC
*
35951899 G-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTG
1 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTG
35951963 GAGCAGACGAAAGAAACC
66 GAGCAGACGAAAGAAACC
* *
35951981 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTTCCTAAGCAGTAGTG
1 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTG
35952046 GAGCAGACGAAAGAAACC
66 GAGCAGACGAAAGAAACC
* *
35952064 GATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTG
1 GATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTG
*
35952129 GAGCAGATGAAAGAAACC
66 GAGCAGACGAAAGAAACC
*
35952147 AATCCTATCTCC
1 GATCCTATCTCC
35952159 TGAAGTTACA
Statistics
Matches: 438, Mismatches: 57, Indels: 46
0.81 0.11 0.09
Matches are distributed among these distances:
79 1 0.00
80 34 0.08
81 3 0.01
82 7 0.02
83 199 0.45
84 53 0.12
85 10 0.02
86 7 0.02
87 87 0.20
88 33 0.08
89 2 0.00
90 2 0.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (83 bp):
GATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTG
GAGCAGACGAAAGAAACC
Found at i:35952021 original size:123 final size:123
Alignment explanation
Indices: 35951555--35952136 Score: 536
Period size: 123 Copynumber: 4.6 Consensus size: 123
35951545 CAAAGGTGTT
** *
35951555 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGACGGCGAATCTTATCTTCCTAAGCA
1 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGA--AAG-ATCTTATCTCCCTAAGCA
* * * * * *
35951619 GTAGTGAAGCAAATTTAAGCCA-CCAGTCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGAT
62 GTAGTGGAGCAGA--TCA--CATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAA-AT
**
35951683 GGT
122 -CA
* * ** *
35951686 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAATATGGTAGATCCTATCTCCCTAAGCAG
1 AGATCCTATCTCCCTAAGCAGTAGTGGAGCA-GACGAA-A-GAAAGATCTTATCTCCCTAAGCAG
* * *
35951751 TAGTGGAGCAGATCACACCAAGTCTTATCTCCCTAAGCAGTAGTGAAGCAGA-CAGAAA-AA
63 TAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA-AAATCA
* ** * * **
35951811 ACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAA-ATCATAGATCTTATCTCCCTAAG
1 A--GATCCTATCTCCCT-AAGCAGTAGTGGAGCAGACGAAAGA--A-AGATCTTATCTCCCTAAG
*
35951875 CAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCA
60 CAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAATCA
*
35951938 AG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCGATCTTATCTCCCTAAGCAGT
1 AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAA--GATCTTATCTCCCTAAGCAGT
* * **
35952002 AGTGGAGCAGATCACATCAAGTCTTATCTTCCTAAGCAGTAGTGGAGCAGA-CGAAAGAA
64 AGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAATCA
* * * **
35952061 ACCGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATC-ACATCAAG-TCTTATCTCCCTAAGCAG
1 A--GATCCTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAAGATCTTATCTCCCTAAGCAG
35952124 TAGTGGAGCAGAT
63 TAGTGGAGCAGAT
35952137 GAAAGAAACC
Statistics
Matches: 382, Mismatches: 47, Indels: 52
0.79 0.10 0.11
Matches are distributed among these distances:
121 1 0.00
122 2 0.01
123 123 0.32
124 13 0.03
125 2 0.01
126 36 0.09
127 94 0.25
128 45 0.12
129 2 0.01
131 59 0.15
132 3 0.01
133 1 0.00
134 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (123 bp):
AGATCCTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAATCA
Found at i:35957389 original size:12 final size:13
Alignment explanation
Indices: 35957372--35957402 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
35957362 TCAATCTTTC
35957372 TATTTTTA-TTTT
1 TATTTTTATTTTT
35957384 TATTTTTATTTTT
1 TATTTTTATTTTT
35957397 TATTTT
1 TATTTT
35957403 GTAAACGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:35957390 original size:7 final size:6
Alignment explanation
Indices: 35957372--35957402 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
35957362 TCAATCTTTC
35957372 TATTTT TATTTT TATTTT TATTTTT TATTTT
1 TATTTT TATTTT TATTTT TA-TTTT TATTTT
35957403 GTAAACGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:35958331 original size:30 final size:30
Alignment explanation
Indices: 35958290--35958346 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
35958280 TAATTCCAAG
* * *
35958290 TTTTATTATATATGTATATATATACATATC
1 TTTTATAATATATATATATAAATACATATC
35958320 TTTTATAATATATATATATAAATACAT
1 TTTTATAATATATATATATAAATACAT
35958347 GCACATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (30 bp):
TTTTATAATATATATATATAAATACATATC
Found at i:35960906 original size:22 final size:22
Alignment explanation
Indices: 35960878--35960945 Score: 109
Period size: 22 Copynumber: 3.1 Consensus size: 22
35960868 TCTATAAAAT
35960878 TGGCTAACGTACTAAGCTCTCA
1 TGGCTAACGTACTAAGCTCTCA
35960900 TGGCTAACGTACTAAGCTCTCA
1 TGGCTAACGTACTAAGCTCTCA
** *
35960922 TGTTTCACGTACTAAGCTCTCA
1 TGGCTAACGTACTAAGCTCTCA
35960944 TG
1 TG
35960946 TTTGAACAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (22 bp):
TGGCTAACGTACTAAGCTCTCA
Found at i:35966472 original size:128 final size:128
Alignment explanation
Indices: 35966241--35966473 Score: 378
Period size: 128 Copynumber: 1.8 Consensus size: 128
35966231 ATCAGTGAAT
* * *
35966241 ATTATAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCAAG
1 ATTATAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAGACGACGAATCTTATCTTCAAG
* * *
35966306 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAA
66 TGTAAGGAAGCAAATTGAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAA
*
35966369 ATTATAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCGAAGACGACGAATCTTATCTTCAAG
1 ATTATAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAGACGACGAATCTTATCTTCAAG
*
35966434 TGTAAGGAAGCAAATTGAAGCCGATAA-TCCTATCTCCCTG
66 TGTAAGGAAGCAAATTGAAGCC-ACAAGTCCTATCTCCCTG
35966474 AAGTTATAGT
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
128 93 0.97
129 3 0.03
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (128 bp):
ATTATAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAGACGACGAATCTTATCTTCAAG
TGTAAGGAAGCAAATTGAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAA
Found at i:35966707 original size:133 final size:133
Alignment explanation
Indices: 35966549--35966826 Score: 477
Period size: 133 Copynumber: 2.1 Consensus size: 133
35966539 CATCAGGTCT
* *
35966549 TATCTCCCTGAAGTTGCAACGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAACAGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTAAAGTTGCAGTG
35966614 GGACAGATCGAAGATGACAAATCTTATCTCCCTGAAGTTACAGTCGAGCAGATTGAAGCCGA-TA
66 GGACAGATCGAAGATGACAAATCTTATCTCCCTGAAGTTACAGTCGAGCAGATTGAAGCC-ATTA
35966678 ATCC
130 ATCC
* *
35966682 TATCTCCTTGAAGTTGCAGCAGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTAAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAACAGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTAAAGTTGCAGTG
* * *
35966747 GGGCAGATCGAAGATGACAAATCTTATCTCCCTGAAGTTACAGTGGAGCGGATTGAAGCCATTAA
66 GGACAGATCGAAGATGACAAATCTTATCTCCCTGAAGTTACAGTCGAGCAGATTGAAGCCATTAA
35966812 TCC
131 TCC
35966815 TATCTCCCTGAA
1 TATCTCCCTGAA
35966827 ATTACAGTGG
Statistics
Matches: 136, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
132 1 0.01
133 135 0.99
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (133 bp):
TATCTCCCTGAAGTTGCAACAGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTAAAGTTGCAGTG
GGACAGATCGAAGATGACAAATCTTATCTCCCTGAAGTTACAGTCGAGCAGATTGAAGCCATTAA
TCC
Found at i:35966860 original size:133 final size:133
Alignment explanation
Indices: 35966549--35966878 Score: 430
Period size: 133 Copynumber: 2.5 Consensus size: 133
35966539 CATCAGGTCT
* * * * * *
35966549 TATCTCCCTGAAGTTGCAACGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAATTACAGCAGAGCAGACTAAGTAAGCAGATCTTATCCCCCTGAAGTTGCAGTG
35966614 GGACAGATCGAAGATGACAAATCTTATCTCCCTGAAGTTACAGTCGAGCAGATTGAAGCCGATAA
66 GGACAGATCGAAGATGACAAATCTTATCTCCCTGAAGTTACAGTCGAGCAGATTGAAGCCGATAA
35966679 TCC
131 TCC
* * * * * *
35966682 TATCTCCTTGAAGTTGCAGCAGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTAAAGTTGCAGTG
1 TATCTCCCTGAAATTACAGCAGAGCAGACTAAGTAAGCAGATCTTATCCCCCTGAAGTTGCAGTG
* * *
35966747 GGGCAGATCGAAGATGACAAATCTTATCTCCCTGAAGTTACAGTGGAGCGGATTGAAGCC-ATTA
66 GGACAGATCGAAGATGACAAATCTTATCTCCCTGAAGTTACAGTCGAGCAGATTGAAGCCGA-TA
35966811 ATCC
130 ATCC
** * * * * *
35966815 TATCTCCCTGAAATTACAGTGGAGCGGATTAAAGTAA-TAGATCTTATCTCTCTGAAGTTGCAGT
1 TATCTCCCTGAAATTACAGCAGAGCAGACT-AAGTAAGCAGATCTTATCCCCCTGAAGTTGCAGT
35966879 AGAGTGGATC
Statistics
Matches: 175, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
132 1 0.01
133 169 0.97
134 5 0.03
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.26
Consensus pattern (133 bp):
TATCTCCCTGAAATTACAGCAGAGCAGACTAAGTAAGCAGATCTTATCCCCCTGAAGTTGCAGTG
GGACAGATCGAAGATGACAAATCTTATCTCCCTGAAGTTACAGTCGAGCAGATTGAAGCCGATAA
TCC
Found at i:35967057 original size:217 final size:218
Alignment explanation
Indices: 35966694--35967111 Score: 626
Period size: 217 Copynumber: 1.9 Consensus size: 218
35966684 TCTCCTTGAA
* * * **
35966694 GTTGCAGCAGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTAAAGTTGCAGTGGGGCAGATCGAA
1 GTTGCAGCAGAGCAGACTGAGAAAACAAGTCTTATCCCCCTAAAGTCACAGTGGGGCAGATCGAA
* * * *
35966759 GATGACAAATCTTATCTCCCTGAAGTTACAGTGGAGCGGATTGAAGCCATTAATCCTATCTCCCT
66 GAAGACAAATCCTATCTCCCTCAAGTTACAGTGGAGCAGATTGAAGCCATTAATCCTATCTCCCT
**
35966824 GAAATTACAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATC
131 GAAATTACAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC
35966889 GCATCAGGTCTTATCTCTATGAG
196 GCATCAGGTCTTATCTCTATGAG
**
35966912 GTTGCAGTGGAGCAGACTGAGAAAACAAGTCTTATCCCCCTAAAGTCACAGTGGGGCAGA-CTGA
1 GTTGCAGCAGAGCAGACTGAGAAAACAAGTCTTATCCCCCTAAAGTCACAGTGGGGCAGATC-GA
* * *
35966976 AGAAG-CAAATCCTATCTCCCTCAGGTTGCAGTGGAGCAGATTGAAGTCGA-TAATCCTATCTCC
65 AGAAGACAAATCCTATCTCCCTCAAGTTACAGTGGAGCAGATTGAAG-CCATTAATCCTATCTCC
* * *
35967039 TTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA
129 CTGAAATTACAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA
35967104 TCGCATCA
194 TCGCATCA
35967112 AGCCTTGCCG
Statistics
Matches: 179, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
217 118 0.66
218 61 0.34
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (218 bp):
GTTGCAGCAGAGCAGACTGAGAAAACAAGTCTTATCCCCCTAAAGTCACAGTGGGGCAGATCGAA
GAAGACAAATCCTATCTCCCTCAAGTTACAGTGGAGCAGATTGAAGCCATTAATCCTATCTCCCT
GAAATTACAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC
GCATCAGGTCTTATCTCTATGAG
Found at i:35967080 original size:44 final size:44
Alignment explanation
Indices: 35966464--35967104 Score: 351
Period size: 44 Copynumber: 14.7 Consensus size: 44
35966454 CCGATAATCC
** * * *
35966464 TATCTCCCTGAAGTTATAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAACAGATCT
* * * ** * *
35966508 TACCTCTCTGAAGTTGCAGT--AG-AG-TGGATCTCATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGT-AACAGATCT
** * *
35966549 TATCTCCCTGAAGTTGCAACGGAGCAGACTG-AGTAAGCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAA-CAGATCT
* * * *
35966593 TATCCCCCTGAAGTTGCAGTGG-GACAGATCGAAGATGACAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAG-TAACAGATCT
* * ** * *
35966638 TATCTCCCTGAAGTTACAGTCGAGCAGATTGAAGCCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TAACAGATCT
* ** * *
35966682 TATCTCCTTGAAGTTGCAGCAGAGCAGACTG-AGTAAGCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAA-CAGATCT
* * * * * *
35966726 TATCCCCCTAAAGTTGCAGTGGGGCAGATCGAAGATGACAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TAACAGATCT
* * * ** *
35966771 TATCTCCCTGAAGTTACAGTGGAGCGGATTGAAGCCATTA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TAACAGATCT
* * * * *
35966815 TATCTCCCTGAAATTACAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAACAGATCT
* * ** * * *
35966859 TATCTCTCTGAAGTTGCAGTAGAGTGGATCGCA-T--CAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAACAGATCT
** * * *
35966900 TATCTCTATGAGGTTGCAGTGGAGCAGACTG-AGAAAACA-AGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TAACAGA-TCT
* * ** * * * *
35966944 TATCCCCCTAAAGTCACAGTGGGGCAGACTGAAG-AAGCAAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAA-CAGATCT
* * * * *
35966988 TATCTCCCTCAGGTTGCAGTGGAGCAGATTGAAGTCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGT-AACAGATCT
* * * *
35967032 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAACAGATCT
* *
35967076 TATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT
35967105 CGCATCAAGC
Statistics
Matches: 448, Mismatches: 123, Indels: 52
0.72 0.20 0.08
Matches are distributed among these distances:
40 4 0.01
41 52 0.12
42 3 0.01
43 16 0.04
44 288 0.64
45 79 0.18
46 6 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTAACAGATCT
Found at i:35972762 original size:3 final size:3
Alignment explanation
Indices: 35972748--35972781 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
35972738 TGTATATTCC
*
35972748 ATT ATA ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
35972782 GTCTTTAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:35978008 original size:14 final size:14
Alignment explanation
Indices: 35977989--35978015 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35977979 TGAATGTACC
35977989 ATTTTTGGTACATA
1 ATTTTTGGTACATA
35978003 ATTTTTGGTACAT
1 ATTTTTGGTACAT
35978016 GCCATTTCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (14 bp):
ATTTTTGGTACATA
Found at i:35978945 original size:15 final size:16
Alignment explanation
Indices: 35978914--35978947 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
35978904 TAATATTAAT
35978914 AAACTAAAAAAATTGA
1 AAACTAAAAAAATTGA
*
35978930 AAACTCAAAAAA-TGA
1 AAACTAAAAAAATTGA
35978945 AAA
1 AAA
35978948 AACTCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.15
Consensus pattern (16 bp):
AAACTAAAAAAATTGA
Found at i:35979939 original size:4 final size:4
Alignment explanation
Indices: 35979930--35980200 Score: 282
Period size: 4 Copynumber: 66.0 Consensus size: 4
35979920 CCCAAGAGAA
*
35979930 TATG TATG TACG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
35979978 TATG TATG TATG TATG TATG TATG TATG TATG TATG TACG TA-G TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *** * * * *
35980025 TACG CTA-G -AGGTG CTCATGGG CCGGG CCATG -A-G CACCTC TAATG TACG
1 TATG -TATG TA--TG -T-AT--G -TATG -TATG TATG TA--TG T-ATG TATG
* * *
35980073 CATG TATG TACG TATG TACG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
35980121 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
35980169 TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
35980201 CGGAAAAACC
Statistics
Matches: 232, Mismatches: 20, Indels: 30
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.01
3 5 0.02
4 211 0.91
5 9 0.04
6 1 0.00
7 1 0.00
8 3 0.01
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (4 bp):
TATG
Found at i:35982883 original size:18 final size:18
Alignment explanation
Indices: 35982862--35982917 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
35982852 GTCTATTTTC
*
35982862 TTTTCTTTTATTATTATT
1 TTTTCTTTTATTTTTATT
*
35982880 TTTTCTTTTATTTTTA-A
1 TTTTCTTTTATTTTTATT
35982897 TTTTCTGTTTATTTTTATT
1 TTTTCT-TTTATTTTTATT
35982916 TT
1 TT
35982918 CTTAGACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.18
18 25 0.76
19 2 0.06
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTCTTTTATTTTTATT
Found at i:35982899 original size:7 final size:6
Alignment explanation
Indices: 35982867--35982917 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
35982857 TTTTCTTTTC
* * * *
35982867 TTTTAT TATTAT TTTT-T CTTTTAT TTTTAA TTTTCT GTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
35982915 TTT
1 TTT
35982918 CTTAGACTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
5 1 0.03
6 33 0.94
7 1 0.03
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:35987961 original size:27 final size:27
Alignment explanation
Indices: 35987919--35988195 Score: 297
Period size: 27 Copynumber: 10.2 Consensus size: 27
35987909 AGAGGTTAAT
* * *
35987919 AAATGATCGAACTACCCCCATAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * *
35987946 AAATGACCAAATTACCCCCAGAAGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* *
35987973 AAATAACCGAATTACCCCCACATGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * *
35988000 AAATGATCGAATTACTCCCACAGGATA
1 AAATGACCGAATTACCCCCACAGGGTA
*
35988027 AAATGACCGAATTACCCTCACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * *
35988054 ACATGACAGAATTACCCTCACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* *
35988081 AAATAACCGAATTATCCCCACAGGGTA
1 AAATGACCGAATTACCCCCACAGGGTA
* * * *
35988108 AAATAACCAAATTACCCCTACAGGCTA
1 AAATGACCGAATTACCCCCACAGGGTA
* *
35988135 AAAT-AGCTGAATTACCCCTCATAGGGTA
1 AAATGA-CCGAATTACCCC-CACAGGGTA
*
35988163 AAATGACCGAATTACCCCCA-TGGGATA
1 AAATGACCGAATTACCCCCACAGGG-TA
35988190 AAATGA
1 AAATGA
35988196 ACAAAATACC
Statistics
Matches: 210, Mismatches: 36, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
26 4 0.02
27 184 0.88
28 21 0.10
29 1 0.00
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (27 bp):
AAATGACCGAATTACCCCCACAGGGTA
Found at i:35988682 original size:5 final size:5
Alignment explanation
Indices: 35988654--35988718 Score: 89
Period size: 5 Copynumber: 13.2 Consensus size: 5
35988644 TTTTTATGTT
*
35988654 TTATA -TATA TTATT TTAT- TATATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA
*
35988703 TTGTA TTATA TTATA T
1 TTATA TTATA TTATA T
35988719 AAGTAAAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
4 5 0.09
5 48 0.89
6 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:35989491 original size:113 final size:113
Alignment explanation
Indices: 35989333--35989585 Score: 373
Period size: 113 Copynumber: 2.2 Consensus size: 113
35989323 AAAATGAGCA
** * *
35989333 TTAGCGGCGTTTTTCAGCAAGCGCCACAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGTTT
1 TTAGCGGCGTTTTTCAAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCATTTTCTGAGTTT
* *
35989398 TTGGGGCTTTAGTGACGTTTTTTAAAAAGCGTCGCTAATGCATGGGGCT
66 TAGGGGCTTTAGTGACGTTTTTTAAAAAGCGTCGCTAAAGCAT-GGGCT
* * *
35989447 TTAGCGGCATTTTCCAAAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGTCATTTTTTGAGTTT
1 TTAGCGGCGTTTTTCAAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCATTTTCTGAGTTT
* *
35989511 TAGGGGCTTTAGTGGCGTTTTTTAAAAAGCGTCGCTAAAGTATGGGCT
66 TAGGGGCTTTAGTGACGTTTTTTAAAAAGCGTCGCTAAAGCATGGGCT
**
35989559 TTAGCGGCGTTTTTGGAAAAGCGCCGC
1 TTAGCGGCGTTTTTCAAAAAGCGCCGC
35989586 TAATGCTATT
Statistics
Matches: 124, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
112 28 0.23
113 74 0.60
114 22 0.18
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (113 bp):
TTAGCGGCGTTTTTCAAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCATTTTCTGAGTTT
TAGGGGCTTTAGTGACGTTTTTTAAAAAGCGTCGCTAAAGCATGGGCT
Found at i:35989899 original size:21 final size:20
Alignment explanation
Indices: 35989869--35989957 Score: 70
Period size: 21 Copynumber: 4.2 Consensus size: 20
35989859 GAGTTACTAT
*
35989869 TTTAAGGTTTATAGATTATGG
1 TTTAA-GTTTATAGATTAAGG
* *
35989890 TTTATAGTTTATGCGTTTAAGG
1 TTTA-AGTTTAT-AGATTAAGG
* * * *
35989912 TTTAAGGGTTATGGTTTATGG
1 TTTAA-GTTTATAGATTAAGG
35989933 TTTAAGATTTATAGATTAAGG
1 TTTAAG-TTTATAGATTAAGG
35989954 TTTA
1 TTTA
35989958 GGGGTTAGGG
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.02
21 37 0.69
22 16 0.30
ACGTcount: A:0.27, C:0.01, G:0.24, T:0.48
Consensus pattern (20 bp):
TTTAAGTTTATAGATTAAGG
Found at i:35989943 original size:14 final size:14
Alignment explanation
Indices: 35989869--35989944 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
35989859 GAGTTACTAT
*
35989869 TTTAAGGTTTATAGA
1 TTTATGGTTTA-AGA
35989884 -TTATGGTTTATAG-
1 TTTATGGTTTA-AGA
*
35989897 TTTATGCGTTTAAGG
1 TTTATG-GTTTAAGA
* * * *
35989912 TTTAAGGGTTATGG
1 TTTATGGTTTAAGA
35989926 TTTATGGTTTAAGA
1 TTTATGGTTTAAGA
35989940 TTTAT
1 TTTAT
35989945 AGATTAAGGT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
14 40 0.80
15 10 0.20
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.50
Consensus pattern (14 bp):
TTTATGGTTTAAGA
Found at i:35990018 original size:21 final size:21
Alignment explanation
Indices: 35989994--35990058 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
35989984 TAAGAGTTAA
*
35989994 GGGTTATGGTTTATGGTTTAT
1 GGGTTAGGGTTTATGGTTTAT
* *
35990015 GGGTTGGGGTTTAAT-GTTTAG
1 GGGTTAGGGTTT-ATGGTTTAT
*
35990036 GGGTTAGGGGTTTAAGGTTTAT
1 GGGTTA-GGGTTTATGGTTTAT
35990058 G
1 G
35990059 TTTTATGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (21 bp):
GGGTTAGGGTTTATGGTTTAT
Done.