Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 46 of 91
Found at i:16017787 original size:31 final size:31
Alignment explanation
Indices: 16017752--16017893 Score: 266
Period size: 31 Copynumber: 4.6 Consensus size: 31
16017742 CTTTATTATT
*
16017752 TATTTCATGCACCACCTTATTCCTCCAATCC
1 TATTTCATGCACCACCTTATTCCTCAAATCC
16017783 TATTTCATGCACCACCTTATTCCTCAAATCC
1 TATTTCATGCACCACCTTATTCCTCAAATCC
*
16017814 TATTTCATGCACCACCTTATTCCTCCAATCC
1 TATTTCATGCACCACCTTATTCCTCAAATCC
16017845 TATTTCATGCACCACCTTATTCCTCAAATCC
1 TATTTCATGCACCACCTTATTCCTCAAATCC
16017876 TATTTCATGCACCACCTT
1 TATTTCATGCACCACCTT
16017894 CACCTTCTAT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 108 1.00
ACGTcount: A:0.24, C:0.37, G:0.04, T:0.36
Consensus pattern (31 bp):
TATTTCATGCACCACCTTATTCCTCAAATCC
Found at i:16018373 original size:19 final size:19
Alignment explanation
Indices: 16018335--16018373 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
16018325 AAATTTTTTA
**
16018335 AATAAAATAATATTTTAAT
1 AATAAAATAATATTAAAAT
16018354 AATAAAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
16018373 A
1 A
16018374 TTAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:16027984 original size:13 final size:13
Alignment explanation
Indices: 16027966--16027990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16027956 CCTGAGCTTG
16027966 GTGAAAAAAAACC
1 GTGAAAAAAAACC
16027979 GTGAAAAAAAAC
1 GTGAAAAAAAAC
16027991 TTTAAAGGTT
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:0.64, C:0.12, G:0.16, T:0.08
Consensus pattern (13 bp):
GTGAAAAAAAACC
Found at i:16046318 original size:23 final size:23
Alignment explanation
Indices: 16046267--16046322 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
16046257 CATACATATA
*
16046267 CTCATCATCATCTTGCACACCAT
1 CTCATCATCATCATGCACACCAT
* **
16046290 CCCATCATCATCATGCACACTGT
1 CTCATCATCATCATGCACACCAT
16046313 CTCATCATCA
1 CTCATCATCA
16046323 CCAGCTCACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.39, G:0.05, T:0.29
Consensus pattern (23 bp):
CTCATCATCATCATGCACACCAT
Found at i:16046364 original size:43 final size:42
Alignment explanation
Indices: 16046317--16046448 Score: 138
Period size: 43 Copynumber: 3.1 Consensus size: 42
16046307 CACTGTCTCA
* ** *
16046317 TCATCACCAGCTCACGCGCACTCCCTACTCGCACATGGCTGGG
1 TCATCACCAGCT-ATGCGCACTCCCTACTCGCACATAACCGGG
** *
16046360 TCATCATCTGGTTATGCGCACTCCCTACTCGCACATAACCGGG
1 TCATCA-CCAGCTATGCGCACTCCCTACTCGCACATAACCGGG
* * * *
16046403 TCATCATCGACCTATGCGCACTCCCTACTCGCACATAGCCGAG
1 TCATCA-CCAGCTATGCGCACTCCCTACTCGCACATAACCGGG
16046446 TCA
1 TCA
16046449 ATATAATTGC
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
43 72 0.96
44 3 0.04
ACGTcount: A:0.21, C:0.39, G:0.18, T:0.22
Consensus pattern (42 bp):
TCATCACCAGCTATGCGCACTCCCTACTCGCACATAACCGGG
Found at i:16049420 original size:43 final size:43
Alignment explanation
Indices: 16049387--16049492 Score: 178
Period size: 43 Copynumber: 2.5 Consensus size: 43
16049377 CTCCTTACTT
*
16049387 GCACATAG-TCGGATCATCATCAGCTCATGTGCACTCCCACACC
1 GCACATAGCTAGG-TCATCATCAGCTCATGTGCACTCCCACACC
16049430 GCACATAGCTAGGTCATCATCAGCTCATGTGCACTCCCACACC
1 GCACATAGCTAGGTCATCATCAGCTCATGTGCACTCCCACACC
*
16049473 GCACATAGCTGGGTCATCAT
1 GCACATAGCTAGGTCATCAT
16049493 TATCATACAA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
43 57 0.95
44 3 0.05
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.22
Consensus pattern (43 bp):
GCACATAGCTAGGTCATCATCAGCTCATGTGCACTCCCACACC
Found at i:16051085 original size:2 final size:2
Alignment explanation
Indices: 16051080--16051112 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16051070 TGTATATATA
16051080 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
16051113 TACATTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:16053354 original size:27 final size:27
Alignment explanation
Indices: 16053304--16053356 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
16053294 ACTTTATTTT
* *
16053304 CATCAAAATAATGCATGGTTTTACTTC
1 CATCAAAATAATACATGGTATTACTTC
* *
16053331 CATCAAAATAATACTTTGTATTACTT
1 CATCAAAATAATACATGGTATTACTT
16053357 TCATTTTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.40
Consensus pattern (27 bp):
CATCAAAATAATACATGGTATTACTTC
Found at i:16053360 original size:54 final size:54
Alignment explanation
Indices: 16053301--16053508 Score: 141
Period size: 54 Copynumber: 3.8 Consensus size: 54
16053291 CAAACTTTAT
* *
16053301 TTTCATCAAAATAATGCATGGTTTTACTTCCATCAAAATAATACTTTGTATTAC
1 TTTCATCAAAATAATACATTGTTTTACTTCCATCAAAATAATACTTTGTATTAC
* * * ** * * ** * * *
16053355 TTTCATTTTATTATTCCTTACA-AGTTTTATTTTCTTTCAAAATAATACATGGTTTTAC
1 TTTCA--TCA-AAAT-AATACATTGTTTTA-CTTCCATCAAAATAATACTTTGTATTAC
* * * * *
16053413 TTCCATCAAAATAATACCTTGTATTACTTTCATTAAAATAATA-TATTGTATTAC
1 TTTCATCAAAATAATACATTGTTTTACTTCCATCAAAATAATACT-TTGTATTAC
* * * *
16053467 TTTTATCAAAATAATACATTGCTTTGCTTTCATCAAAATAAT
1 TTTCATCAAAATAATACATTGTTTTACTTCCATCAAAATAAT
16053509 GCATTATATA
Statistics
Matches: 110, Mismatches: 37, Indels: 14
0.68 0.23 0.09
Matches are distributed among these distances:
54 62 0.56
55 7 0.06
56 4 0.04
57 8 0.07
58 29 0.26
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (54 bp):
TTTCATCAAAATAATACATTGTTTTACTTCCATCAAAATAATACTTTGTATTAC
Found at i:16053421 original size:27 final size:27
Alignment explanation
Indices: 16053391--16053513 Score: 149
Period size: 27 Copynumber: 4.6 Consensus size: 27
16053381 TTATTTTCTT
* * *
16053391 TCAAAATAATACATGGTTTTACTTCCA
1 TCAAAATAATACATTGTATTACTTTCA
*
16053418 TCAAAATAATACCTTGTATTACTTTCA
1 TCAAAATAATACATTGTATTACTTTCA
* * *
16053445 TTAAAATAATATATTGTATTACTTTTA
1 TCAAAATAATACATTGTATTACTTTCA
*
16053472 TCAAAATAATACATTGCT-TTGCTTTCA
1 TCAAAATAATACATTG-TATTACTTTCA
*
16053499 TCAAAATAATGCATT
1 TCAAAATAATACATT
16053514 ATATATATTA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
27 81 0.99
28 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (27 bp):
TCAAAATAATACATTGTATTACTTTCA
Found at i:16055959 original size:26 final size:24
Alignment explanation
Indices: 16055930--16055984 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
16055920 GCAACTCAAG
16055930 AATTCTAAACTTAATCTATTTTATTT
1 AATTCT-AACTTAATCTA-TTTATTT
* * *
16055956 AATTTCTCACTTTATTTATTTATTT
1 AA-TTCTAACTTAATCTATTTATTT
16055981 AATT
1 AATT
16055985 TACTGTCATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 2 0.08
25 9 0.36
26 10 0.40
27 4 0.16
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.58
Consensus pattern (24 bp):
AATTCTAACTTAATCTATTTATTT
Found at i:16059611 original size:28 final size:29
Alignment explanation
Indices: 16059568--16059634 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
16059558 ATGTCTATGG
* *
16059568 GTAATTTTTCAGTTTT-TGGGGCAAAAAT
1 GTAATTTTTCACTTTTAGGGGGCAAAAAT
* *
16059596 GTAATTTTTGACTTTTACGGGGGCAAAAGT
1 GTAATTTTTCACTTTTA-GGGGGCAAAAAT
*
16059626 GTAAATTTT
1 GTAATTTTT
16059635 AAAAATTACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 14 0.44
30 18 0.56
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.42
Consensus pattern (29 bp):
GTAATTTTTCACTTTTAGGGGGCAAAAAT
Found at i:16061590 original size:22 final size:21
Alignment explanation
Indices: 16061550--16061590 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
16061540 AGACAAGTGT
**
16061550 ATGGTGAAAATTTGGAAACAA
1 ATGGTGAAAATTTAAAAACAA
16061571 ATGGATGAAAATTTAAAAAC
1 ATGG-TGAAAATTTAAAAAC
16061591 GGACCAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (21 bp):
ATGGTGAAAATTTAAAAACAA
Found at i:16068081 original size:21 final size:21
Alignment explanation
Indices: 16068025--16068083 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
16068015 ACATATGGTT
* *
16068025 ATGTATCGATACAAGTTCATA
1 ATGTATTGATACAATTTCATA
16068046 ATGTATTGATACAATTTCATA
1 ATGTATTGATACAATTTCATA
16068067 ATGTATTGATACAATTT
1 ATGTATTGATACAATTT
16068084 TTTCAACACC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATTGATACAATTTCATA
Found at i:16072135 original size:80 final size:80
Alignment explanation
Indices: 16071853--16072145 Score: 342
Period size: 80 Copynumber: 3.7 Consensus size: 80
16071843 AGATTGTAAC
* * * * *
16071853 ATGTATGTGTTAAGCATA-TCATATACACTATGGTCTAAGCAT-TTAAGTGGTTTATCAGCTTAT
1 ATGTATGTGTTAAG-ATAGTCATATACACTATGGGCTAAGCATGTGAA-TGATTTATGAGGTTAT
* * *
16071916 GAAATGTATGTCGTGAG
64 GAAATGCATGCCATGAG
** * * * *
16071933 ATGTATGTGTCGAGATAGTCATATGCTCTATGGGCTACGCATGTGAATGACTTATGAGGTTATGA
1 ATGTATGTGTTAAGATAGTCATATACACTATGGGCTAAGCATGTGAATGATTTATGAGGTTATGA
16071998 AATGCATGCCATGAG
66 AATGCATGCCATGAG
*
16072013 ATGTATGTGTTAAGACAGTCATATACACTATGGGCTAAGCATGTGAATGATTTATGAGGTTATGA
1 ATGTATGTGTTAAGATAGTCATATACACTATGGGCTAAGCATGTGAATGATTTATGAGGTTATGA
* *
16072078 AATGCATACCATAAG
66 AATGCATGCCATGAG
* * *
16072093 ATGTATGTGTGT-AGATAGTCATATACACTATAGGTTAGGCATGATG-ATGATTT
1 ATGTATGTGT-TAAGATAGTCATATACACTATGGGCTAAGCATG-TGAATGATTT
16072146 TTGGAAATGT
Statistics
Matches: 182, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
79 3 0.02
80 173 0.95
81 6 0.03
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (80 bp):
ATGTATGTGTTAAGATAGTCATATACACTATGGGCTAAGCATGTGAATGATTTATGAGGTTATGA
AATGCATGCCATGAG
Found at i:16084957 original size:42 final size:42
Alignment explanation
Indices: 16084899--16085073 Score: 181
Period size: 42 Copynumber: 4.2 Consensus size: 42
16084889 CAACTCATAT
* *
16084899 GCACTCCCACTAGCACAT-GGCTGGGTCAGCATCGGCTTATGC
1 GCACTCCCACTCGCACATAGTC-GGGTCAGCATCGGCTTATGC
* ** *
16084941 GCACTCCTACTCGCACATAGTCAAGTCAGCATCGGCTTATGT
1 GCACTCCCACTCGCACATAGTCGGGTCAGCATCGGCTTATGC
* * *
16084983 GCACTCCCCCTCACACATAGTCGGGTTAGCATCGGCTTATGC
1 GCACTCCCACTCGCACATAGTCGGGTCAGCATCGGCTTATGC
* * ** * * *
16085025 GCACTCCCCCTCGAACATAACCGGATTAGCATCGGCTTTTGC
1 GCACTCCCACTCGCACATAGTCGGGTCAGCATCGGCTTATGC
*
16085067 ACACTCC
1 GCACTCC
16085074 TACTAGTACA
Statistics
Matches: 112, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
42 110 0.98
43 2 0.02
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (42 bp):
GCACTCCCACTCGCACATAGTCGGGTCAGCATCGGCTTATGC
Found at i:16094321 original size:41 final size:41
Alignment explanation
Indices: 16094228--16094378 Score: 161
Period size: 41 Copynumber: 3.8 Consensus size: 41
16094218 ATATTGCCCG
* * **
16094228 TGTGCACGATGTGGGGGGTTGCACACGATGGCG-T-TAGC-
1 TGTGCACAATGTGGGGGGATGCACACGATGATGATATAGCT
*
16094266 TGTGCACAATGTGGGGGGATGCACACGATGATGATATCGCT
1 TGTGCACAATGTGGGGGGATGCACACGATGATGATATAGCT
*
16094307 TGTGCACAATGTGGGGGGATGCATAAAGCGATGAT-AT-TA-CT
1 TGTGCACAATGTGGGGGGATGC--ACA-CGATGATGATATAGCT
**
16094348 TGTGCATGATGTGGGGGGATGCACACGATGA
1 TGTGCACAATGTGGGGGGATGCACACGATGA
16094379 CTCCGGCTAT
Statistics
Matches: 97, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
38 35 0.36
39 3 0.03
40 3 0.03
41 44 0.45
42 1 0.01
43 4 0.04
44 7 0.07
ACGTcount: A:0.23, C:0.15, G:0.37, T:0.25
Consensus pattern (41 bp):
TGTGCACAATGTGGGGGGATGCACACGATGATGATATAGCT
Found at i:16094442 original size:53 final size:55
Alignment explanation
Indices: 16094384--16094488 Score: 171
Period size: 54 Copynumber: 1.9 Consensus size: 55
16094374 GATGACTCCG
*
16094384 GCTATGTGCATGATGT-GGGGAATGCACATGAGCT-GAGTGAGACGG-GGTGTCCA
1 GCTATGTGCACGATGTGGGGGAATGCACATGAGCTAG-GTGAGACGGTGGTGTCCA
16094437 GCTATGTGCACGATGTGGGGGAATGCACATGAGCTAGGTGAGACGGTGGTGT
1 GCTATGTGCACGATGTGGGGGAATGCACATGAGCTAGGTGAGACGGTGGTGT
16094489 ATGTGCTTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
53 15 0.31
54 27 0.56
55 6 0.12
ACGTcount: A:0.22, C:0.14, G:0.41, T:0.23
Consensus pattern (55 bp):
GCTATGTGCACGATGTGGGGGAATGCACATGAGCTAGGTGAGACGGTGGTGTCCA
Found at i:16098709 original size:105 final size:103
Alignment explanation
Indices: 16098560--16098759 Score: 276
Period size: 105 Copynumber: 1.9 Consensus size: 103
16098550 TTGCTGGAGT
* *
16098560 CATTGTGTGCACCCTCACATCGCACACAACAATGTCATCCTCCACACTCCCACACCCTGTCATCA
1 CATTGTGTGCACCCCCACATCACACACAACAATGTCATCCTCCACACTCCCACACCCTGTCATCA
* *
16098625 -TCGGCATGTGCATCCCCCACATCGCGCACAACTAATGC
66 CT-AGCAGGTGCATCCCCCACATCGCGCACAACTAATGC
* * ****
16098663 CATTGTGTGCAACCCCCACATCAACGCACAACAATGTCATCTTCCACACTTTTGCACCCTGTCAT
1 CATTGTGTGC-ACCCCCACATC-ACACACAACAATGTCATCCTCCACACTCCCACACCCTGTCAT
16098728 CACTAGCAGGTGCATCCCCCACATCGCGCACA
64 CACTAGCAGGTGCATCCCCCACATCGCGCACA
16098760 CACACAGTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
103 10 0.12
104 10 0.12
105 63 0.75
106 1 0.01
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.21
Consensus pattern (103 bp):
CATTGTGTGCACCCCCACATCACACACAACAATGTCATCCTCCACACTCCCACACCCTGTCATCA
CTAGCAGGTGCATCCCCCACATCGCGCACAACTAATGC
Found at i:16098814 original size:2 final size:2
Alignment explanation
Indices: 16098807--16098834 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16098797 TGCACAATAC
16098807 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
16098835 CAACATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16099603 original size:20 final size:20
Alignment explanation
Indices: 16099578--16099617 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16099568 AAAAGAAAAA
16099578 GAAGCTGCTAGAAAAATGAG
1 GAAGCTGCTAGAAAAATGAG
* *
16099598 GAAGCTGCTGGAGAAATGAG
1 GAAGCTGCTAGAAAAATGAG
16099618 ATATTTACGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.35, T:0.15
Consensus pattern (20 bp):
GAAGCTGCTAGAAAAATGAG
Found at i:16109329 original size:20 final size:18
Alignment explanation
Indices: 16109296--16109334 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
16109286 CACCATTGCC
16109296 TTCTTTGATTTCTTATTT
1 TTCTTTGATTTCTTATTT
*
16109314 TTCTTTGGAGTTTCTTCTTT
1 TTCTTT-GA-TTTCTTATTT
16109334 T
1 T
16109335 AGTAAGGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 2 0.11
20 10 0.56
ACGTcount: A:0.08, C:0.13, G:0.10, T:0.69
Consensus pattern (18 bp):
TTCTTTGATTTCTTATTT
Found at i:16113623 original size:73 final size:73
Alignment explanation
Indices: 16113536--16113726 Score: 194
Period size: 73 Copynumber: 2.6 Consensus size: 73
16113526 CAGAATGCTT
* *
16113536 TTAGTCAACTAACTTATTTCTTAGTCGACTAAGT-TGTCTCTGTTTTTTG-TTTCCAG-TTTCTG
1 TTAGTCAACTAACTTATTTCTTAGTCGACTAAGTCGGT-TCTG--TTTTGATGTCCAGATTTCTG
16113598 GCAGTGAGC-AC
63 GCAGT-AGCTAC
* * * * *
16113609 TTAGTCGACTAACTTACTTCTTGGTCAACTAAGTCGGTTCTGTTTTGATGTCTAGATTTCTGGCA
1 TTAGTCAACTAACTTATTTCTTAGTCGACTAAGTCGGTTCTGTTTTGATGTCCAGATTTCTGGCA
*
16113674 GTAGCTTC
66 GTAGCTAC
** **
16113682 TTAGTCAACTAACCCACTTT-TTAGTCGACTAAGTCTTTTCTGTTT
1 TTAGTCAACTAACTTA-TTTCTTAGTCGACTAAGTCGGTTCTGTTT
16113727 CTCAATATTC
Statistics
Matches: 97, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
71 5 0.05
72 8 0.08
73 80 0.82
74 4 0.04
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (73 bp):
TTAGTCAACTAACTTATTTCTTAGTCGACTAAGTCGGTTCTGTTTTGATGTCCAGATTTCTGGCA
GTAGCTAC
Found at i:16120228 original size:16 final size:15
Alignment explanation
Indices: 16120207--16120236 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16120197 TAAAATTTAG
16120207 ATTTTGATTCTTTTTT
1 ATTTTGATT-TTTTTT
16120223 ATTTTGATTTTTTT
1 ATTTTGATTTTTTT
16120237 GATATTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.03, G:0.07, T:0.77
Consensus pattern (15 bp):
ATTTTGATTTTTTTT
Found at i:16120495 original size:27 final size:25
Alignment explanation
Indices: 16120418--16120496 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 25
16120408 TATTTCAAAT
*
16120418 ATATCGATACATGTTCATGATGTATC
1 ATATAGATACATGTTCAT-ATGTATC
*
16120444 -TATACAT--ATGTTC--ATGTATC
1 ATATAGATACATGTTCATATGTATC
16120464 GATATAGATACATGTTCATAATGTATC
1 -ATATAGATACATGTTCAT-ATGTATC
16120491 AATATA
1 -ATATA
16120497 ATTTTTCCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
20 7 0.17
22 6 0.14
23 6 0.14
24 6 0.14
25 5 0.12
27 12 0.29
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (25 bp):
ATATAGATACATGTTCATATGTATC
Found at i:16121591 original size:80 final size:80
Alignment explanation
Indices: 16121479--16121784 Score: 402
Period size: 80 Copynumber: 3.8 Consensus size: 80
16121469 TGTAACATGT
* * * * *
16121479 ATGCCATGAGATGTATGAGTTAACCATA-TCATATACACTATGGGCTAAGTATGTGAGTGATTTA
1 ATGCCATGAGATGTATGTGTTGA-GATAGTCATATACACTATGAGCTAAGCATGTGAGTGATTTA
*
16121543 TGAGGTTATGAAATGT
65 TGAGGTTATGAAATGC
* * * *
16121559 ATGCCATGAGATGTATGTGCTGAGATAGTCATATATATTATGAGCTAAGCATGTGAGTGACTTAT
1 ATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGAGCTAAGCATGTGAGTGATTTAT
*
16121624 GAGATTATGAAATGC
66 GAGGTTATGAAATGC
* * *
16121639 ATGCCATGAGATGTAGGTGTTGAGATAGTCATATACACTATTAGCTAAGCATGTGAGTCATTTAT
1 ATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGAGCTAAGCATGTGAGTGATTTAT
*
16121704 GAGGTTGTGAAATGC
66 GAGGTTATGAAATGC
* * *
16121719 ATGCCATAAGATGTTTGTGTGGAGATAGTCATATACACTAT-AGGCTAAGCATGATGA-TGATTT
1 ATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGA-GCTAAGCATG-TGAGTGATTT
16121782 ATG
64 ATG
16121785 GAAATGTTAT
Statistics
Matches: 198, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
79 4 0.02
80 191 0.96
81 3 0.02
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.33
Consensus pattern (80 bp):
ATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGAGCTAAGCATGTGAGTGATTTAT
GAGGTTATGAAATGC
Found at i:16123331 original size:17 final size:17
Alignment explanation
Indices: 16123309--16123341 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16123299 TAAGCTAGAT
16123309 GTTGAATATGAT-AAAAG
1 GTTGAAT-TGATGAAAAG
16123326 GTTGAATTGATGAAAA
1 GTTGAATTGATGAAAA
16123342 AAAAGTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (17 bp):
GTTGAATTGATGAAAAG
Found at i:16132167 original size:43 final size:43
Alignment explanation
Indices: 16132108--16132239 Score: 216
Period size: 43 Copynumber: 3.1 Consensus size: 43
16132098 ACAATGTAAT
*
16132108 ATCATCA--TCATGTGCACTCCCTAC-TCGCACATAGCTGGGTC
1 ATCATCAGCTCATGTGCACTCCC-ACACCGCACATAGCTGGGTC
*
16132149 ATCATCAGCTCATGTGCACTCCCACACCTCACATAGCTGGGTC
1 ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
16132192 ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
1 ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
16132235 ATCAT
1 ATCAT
16132240 TATCACACAA
Statistics
Matches: 85, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
41 7 0.08
42 2 0.02
43 76 0.89
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (43 bp):
ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
Found at i:16141897 original size:38 final size:39
Alignment explanation
Indices: 16141796--16141901 Score: 126
Period size: 38 Copynumber: 2.7 Consensus size: 39
16141786 CACTCCCGGC
*
16141796 TCATGTACATCCCCCCACATCGTGCACATAGCCGGCACCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGG-ACCA
* * * *
16141836 TCATGTGCACCCCCCCACATCGTGCACA-ATCAGTG-CTA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAG-GACCA
*
16141874 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
16141902 CGGGCACTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
38 27 0.47
39 3 0.05
40 27 0.47
ACGTcount: A:0.24, C:0.42, G:0.15, T:0.20
Consensus pattern (39 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCAGGACCA
Found at i:16144695 original size:34 final size:32
Alignment explanation
Indices: 16144657--16144772 Score: 88
Period size: 34 Copynumber: 3.5 Consensus size: 32
16144647 AAAGGTTTCG
*
16144657 CTTGATCTCGTGAAAAAGAATTATAAAGGGTTTT
1 CTTGATCCCGT-AAAAAGAATTAT-AAGGGTTTT
* * *
16144691 CTTGATCCCGTAAAAAGCATTGTAAGGGTTTCA
1 CTTGATCCCGTAAAAAGAATTATAAGGGTTT-T
* * * * * * *
16144724 CTTAATCCAGTAAGAAGCTATTGTGAGGGTTTCG
1 CTTGATCCCGTAAAAAG-AATTATAAGGGTTT-T
16144758 CTTGATCCCGTAAAA
1 CTTGATCCCGTAAAA
16144773 GCTCATTTCT
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 8 0.12
33 24 0.36
34 35 0.52
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (32 bp):
CTTGATCCCGTAAAAAGAATTATAAGGGTTTT
Found at i:16144811 original size:20 final size:20
Alignment explanation
Indices: 16144786--16144825 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
16144776 CATTTCTTAG
16144786 TGTATTTGAAATTCCTTGGT
1 TGTATTTGAAATTCCTTGGT
16144806 TGTATTTGAAATTCCTTGGT
1 TGTATTTGAAATTCCTTGGT
16144826 GTTCCAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (20 bp):
TGTATTTGAAATTCCTTGGT
Found at i:16145950 original size:35 final size:35
Alignment explanation
Indices: 16145899--16145972 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
16145889 ATCAAGTAAT
* * * *
16145899 AACCTTCACAATGGTTTTTAATTGGCTTAATCACA
1 AACCCTCACAATGGTTTTTAATAGGCTCAACCACA
16145934 AACCCTCACAATGGTTTTTAATAGGCTCAACCACA
1 AACCCTCACAATGGTTTTTAATAGGCTCAACCACA
16145969 AACC
1 AACC
16145973 TTCATTAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.30
Consensus pattern (35 bp):
AACCCTCACAATGGTTTTTAATAGGCTCAACCACA
Found at i:16146676 original size:49 final size:49
Alignment explanation
Indices: 16146619--16146718 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
16146609 GGGTCAACTG
*
16146619 ACCATGCTTCAAAGATTGACTGGAGCTTTGTTTTCTTTAAGATTTGCAT
1 ACCATGCTTCAAAGATTGACTGAAGCTTTGTTTTCTTTAAGATTTGCAT
* *
16146668 ACCATGCTTCAAGGATTGACTGAAGGTTTGTTTTCTTTAAGATTTGCAT
1 ACCATGCTTCAAAGATTGACTGAAGCTTTGTTTTCTTTAAGATTTGCAT
16146717 AC
1 AC
16146719 ATTCTGCCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (49 bp):
ACCATGCTTCAAAGATTGACTGAAGCTTTGTTTTCTTTAAGATTTGCAT
Found at i:16155509 original size:20 final size:20
Alignment explanation
Indices: 16155484--16155529 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
16155474 TTTTGACCCC
16155484 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
16155504 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
16155524 ATTTGA
1 ATTTGA
16155530 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:16158417 original size:42 final size:42
Alignment explanation
Indices: 16158331--16158461 Score: 129
Period size: 43 Copynumber: 3.1 Consensus size: 42
16158321 CACTCTCCCA
* * * **
16158331 TCATCATCAAC-TCATGTGCACTCCCCACTAGCACATGGTTGGG
1 TCATCATCGACGT-ATGCGCACT-CCCACTAGCACATAGCCGGG
* * *
16158374 TCATCATCGGCTTATGCGCACTCCCACTTGCACATAGCCGGG
1 TCATCATCGACGTATGCGCACTCCCACTAGCACATAGCCGGG
* * *
16158416 TCAATCATCGACGTATGCACACTCCTACTCGCACATAGCCGGG
1 TC-ATCATCGACGTATGCGCACTCCCACTAGCACATAGCCGGG
16158459 TCA
1 TCA
16158462 ATATCATTAC
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
42 19 0.26
43 54 0.73
44 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (42 bp):
TCATCATCGACGTATGCGCACTCCCACTAGCACATAGCCGGG
Found at i:16158423 original size:43 final size:43
Alignment explanation
Indices: 16158348--16158463 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
16158338 CAACTCATGT
* ** * *
16158348 GCACTCCCCACTAGCACATGGTTGGGTC-ATCATCGGCTTATGC
1 GCACT-CCCACTAGCACATAGCCGGGTCAATCATCGACGTATGC
*
16158391 GCACTCCCACTTGCACATAGCCGGGTCAATCATCGACGTATGC
1 GCACTCCCACTAGCACATAGCCGGGTCAATCATCGACGTATGC
* * *
16158434 ACACTCCTACTCGCACATAGCCGGGTCAAT
1 GCACTCCCACTAGCACATAGCCGGGTCAAT
16158464 ATCATTACAC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 18 0.29
43 45 0.71
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.22
Consensus pattern (43 bp):
GCACTCCCACTAGCACATAGCCGGGTCAATCATCGACGTATGC
Found at i:16165323 original size:12 final size:12
Alignment explanation
Indices: 16165306--16165352 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
16165296 ATTTTTTAAT
16165306 TTCAAAAAAAAA
1 TTCAAAAAAAAA
16165318 TTCAAAAAAAAA
1 TTCAAAAAAAAA
*
16165330 -TAAAATTAAAAAA
1 TTCAAA--AAAAAA
16165343 TT-AAAAAAAA
1 TTCAAAAAAAA
16165353 TAAAAAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 9 0.29
12 12 0.39
13 9 0.29
14 1 0.03
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:16165329 original size:17 final size:16
Alignment explanation
Indices: 16165309--16165361 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
16165299 TTTTAATTTC
16165309 AAAAAAAAATTCAAAAA
1 AAAAAAAAATT-AAAAA
*
16165326 AAAATAAAATTAAAAA
1 AAAAAAAAATTAAAAA
16165342 ATTAAAAAAAA-TAAAAA
1 A--AAAAAAAATTAAAAA
16165359 AAA
1 AAA
16165362 GGTAACCCGC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 2 0.06
16 6 0.19
17 17 0.53
18 7 0.22
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAAAAAATTAAAAA
Found at i:16165348 original size:23 final size:24
Alignment explanation
Indices: 16165312--16165357 Score: 76
Period size: 23 Copynumber: 1.9 Consensus size: 24
16165302 TAATTTCAAA
16165312 AAAAAATTCAAAAAAAAATAAAATT
1 AAAAAATT-AAAAAAAAATAAAATT
16165337 AAAAAATT-AAAAAAAATAAAA
1 AAAAAATTAAAAAAAAATAAAA
16165358 AAAAGGTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
25 8 0.38
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (24 bp):
AAAAAATTAAAAAAAAATAAAATT
Found at i:16165359 original size:25 final size:25
Alignment explanation
Indices: 16165312--16165360 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
16165302 TAATTTCAAA
*
16165312 AAAAAATTCAAAAAAAAATAAAATT
1 AAAAAATTCAAAAAAAAAAAAAATT
*
16165337 AAAAAATTAAAAAAAATAAAAAAA
1 AAAAAATTCAAAAAAA-AAAAAAA
16165361 AGGTAACCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (25 bp):
AAAAAATTCAAAAAAAAAAAAAATT
Found at i:16165884 original size:13 final size:13
Alignment explanation
Indices: 16165866--16165908 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
16165856 CAATAAAAAC
16165866 TTTTCTTTATTTA
1 TTTTCTTTATTTA
*
16165879 TTTTCTTTAGTTA
1 TTTTCTTTATTTA
16165892 TTTT-TATTATTTA
1 TTTTCT-TTATTTA
16165905 TTTT
1 TTTT
16165909 ATTCTCTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 1 0.04
13 26 0.96
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTCTTTATTTA
Found at i:16167925 original size:41 final size:41
Alignment explanation
Indices: 16167868--16167949 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
16167858 GAAAGATGGA
16167868 CAAAAATCTTGTCAAAGTTGACACACTGTAGCAGTCTTGGT
1 CAAAAATCTTGTCAAAGTTGACACACTGTAGCAGTCTTGGT
16167909 CAAAAATCTTGTCAAAGTTGACACACTGTAGCAGTCTTGGT
1 CAAAAATCTTGTCAAAGTTGACACACTGTAGCAGTCTTGGT
16167950 GCAATTACGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (41 bp):
CAAAAATCTTGTCAAAGTTGACACACTGTAGCAGTCTTGGT
Found at i:16171572 original size:20 final size:20
Alignment explanation
Indices: 16171549--16171589 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
16171539 ATCAAATCTC
*
16171549 ATTTCATTTCATATAAATCA
1 ATTTCATTTCATAAAAATCA
16171569 ATTTCATTTCATAAAAATCA
1 ATTTCATTTCATAAAAATCA
16171589 A
1 A
16171590 CAAGGCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTCATTTCATAAAAATCA
Found at i:16173964 original size:73 final size:73
Alignment explanation
Indices: 16173845--16173996 Score: 304
Period size: 73 Copynumber: 2.1 Consensus size: 73
16173835 TCATCTGGTA
16173845 CTCAACTTCCCACGTCATCTCCTCCATTCGAGCATTCTTCCATAACACCTTAACCATTGGGATGC
1 CTCAACTTCCCACGTCATCTCCTCCATTCGAGCATTCTTCCATAACACCTTAACCATTGGGATGC
16173910 TTTTATTC
66 TTTTATTC
16173918 CTCAACTTCCCACGTCATCTCCTCCATTCGAGCATTCTTCCATAACACCTTAACCATTGGGATGC
1 CTCAACTTCCCACGTCATCTCCTCCATTCGAGCATTCTTCCATAACACCTTAACCATTGGGATGC
16173983 TTTTATTC
66 TTTTATTC
16173991 CTCAAC
1 CTCAAC
16173997 ACTCAATACT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.22, C:0.35, G:0.09, T:0.34
Consensus pattern (73 bp):
CTCAACTTCCCACGTCATCTCCTCCATTCGAGCATTCTTCCATAACACCTTAACCATTGGGATGC
TTTTATTC
Found at i:16181031 original size:2 final size:2
Alignment explanation
Indices: 16181024--16181054 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16181014 ACTACTCTAC
16181024 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 T
16181055 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16181059 original size:2 final size:2
Alignment explanation
Indices: 16181054--16181098 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
16181044 TATATATATA
16181054 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
16181096 TG T
1 TG T
16181099 CCATATACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:16181126 original size:17 final size:17
Alignment explanation
Indices: 16181106--16181140 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
16181096 TGTCCATATA
16181106 CATTTAAGTGCCATCAT
1 CATTTAAGTGCCATCAT
16181123 CATTTAAGTGCCATCAT
1 CATTTAAGTGCCATCAT
16181140 C
1 C
16181141 CATCACTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (17 bp):
CATTTAAGTGCCATCAT
Found at i:16184601 original size:20 final size:20
Alignment explanation
Indices: 16184578--16184618 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
16184568 ATCAAATCTC
*
16184578 ATTTCATTTCATATAAATCA
1 ATTTCATTTCATAAAAATCA
16184598 ATTTCATTTCATAAAAATCA
1 ATTTCATTTCATAAAAATCA
16184618 A
1 A
16184619 CAAGGCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTCATTTCATAAAAATCA
Found at i:16189130 original size:10 final size:10
Alignment explanation
Indices: 16189115--16189139 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16189105 AATATTAAAT
16189115 TGAGAACAAG
1 TGAGAACAAG
16189125 TGAGAACAAG
1 TGAGAACAAG
16189135 TGAGA
1 TGAGA
16189140 TACATCCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.08, G:0.32, T:0.12
Consensus pattern (10 bp):
TGAGAACAAG
Found at i:16195271 original size:19 final size:19
Alignment explanation
Indices: 16195244--16195290 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
16195234 AACCAAAGAG
*
16195244 ATAAGATAAAATTTT-TAAA
1 ATAAAATAAAATTTTAT-AA
* *
16195263 ATAAAATAATATTTTATTA
1 ATAAAATAAAATTTTATAA
16195282 ATAAAATAA
1 ATAAAATAA
16195291 TATTAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAAAATAAAATTTTATAA
Found at i:16204932 original size:15 final size:16
Alignment explanation
Indices: 16204901--16204933 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
16204891 TATCAATATG
16204901 TCTTTCTTGCACAATTT
1 TCTTTCTTG-ACAATTT
16204918 TCTTTCTTG-CAATTT
1 TCTTTCTTGACAATTT
16204933 T
1 T
16204934 AGGCTGATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.58
Consensus pattern (16 bp):
TCTTTCTTGACAATTT
Found at i:16216582 original size:15 final size:15
Alignment explanation
Indices: 16216562--16216593 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16216552 TCAGTTTTGG
16216562 TATAGTTTCAATATA
1 TATAGTTTCAATATA
*
16216577 TATAGTTTTAATATA
1 TATAGTTTCAATATA
16216592 TA
1 TA
16216594 AAGATGTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATAGTTTCAATATA
Found at i:16227227 original size:11 final size:11
Alignment explanation
Indices: 16227211--16227238 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
16227201 CACTGTAGTT
16227211 TTTAAAACAAC
1 TTTAAAACAAC
16227222 TTTAAAACAAC
1 TTTAAAACAAC
16227233 TTTAAA
1 TTTAAA
16227239 CTTAAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (11 bp):
TTTAAAACAAC
Found at i:16227267 original size:22 final size:22
Alignment explanation
Indices: 16227252--16227311 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
16227242 AAAAGATCGA
16227252 ATCTTTAAAACCAAAAGCTCTG
1 ATCTTTAAAACCAAAAGCTCTG
*
16227274 ATCTTTAAAACTAAAAGCTCTG
1 ATCTTTAAAACCAAAAGCTCTG
*
16227296 ACCTTTAAAACCAAAA
1 ATCTTTAAAACCAAAA
16227312 ACTTTAATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.27
Consensus pattern (22 bp):
ATCTTTAAAACCAAAAGCTCTG
Found at i:16231716 original size:18 final size:18
Alignment explanation
Indices: 16231692--16231743 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
16231682 CTAGGCTGAA
16231692 CCTTCCTTTCTTTTTTCT
1 CCTTCCTTTCTTTTTTCT
* *
16231710 TCTTCCTCTTTCTTCCTTTCT
1 CCTT-C-CTTTCTT-TTTTCT
16231731 CCTT-CTTTCTTTT
1 CCTTCCTTTCTTTT
16231744 CTCCTTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
17 1 0.04
18 10 0.37
19 1 0.04
20 7 0.26
21 8 0.30
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (18 bp):
CCTTCCTTTCTTTTTTCT
Found at i:16231748 original size:22 final size:24
Alignment explanation
Indices: 16231708--16231752 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
16231698 TTTCTTTTTT
16231708 CTTCTTCCTCTTTCTTCCTTTCTC
1 CTTCTTCCTCTTTCTTCCTTTCTC
*
16231732 CTTCTTTCT-TTTC-TCCTTTCT
1 CTTCTTCCTCTTTCTTCCTTTCT
16231753 TCTTTCCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 4 0.20
24 8 0.40
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (24 bp):
CTTCTTCCTCTTTCTTCCTTTCTC
Found at i:16231771 original size:17 final size:15
Alignment explanation
Indices: 16231705--16231772 Score: 63
Period size: 15 Copynumber: 4.5 Consensus size: 15
16231695 TCCTTTCTTT
16231705 TTTCTTC-TTCCT-C
1 TTTCTTCTTTCCTCC
16231718 TTTCTTCCTTT-CTCC
1 TTTCTT-CTTTCCTCC
*
16231733 -TTCTTTCTTTTCTCC
1 TTTC-TTCTTTCCTCC
16231748 TTTCTTCTTTCCTCTC
1 TTTCTTCTTTCCTC-C
16231764 TTTGCTTCT
1 TTT-CTTCT
16231773 AAGCCGATCC
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
13 6 0.13
14 10 0.22
15 18 0.39
16 7 0.15
17 5 0.11
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.63
Consensus pattern (15 bp):
TTTCTTCTTTCCTCC
Found at i:16232859 original size:18 final size:19
Alignment explanation
Indices: 16232836--16232872 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
16232826 GTATTATTTT
16232836 ATTATTACTTTA-TCTAAA
1 ATTATTACTTTATTCTAAA
*
16232854 ATTATTATTTTATTCTAAA
1 ATTATTACTTTATTCTAAA
16232873 TTTTTCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTATTACTTTATTCTAAA
Found at i:16243391 original size:5 final size:5
Alignment explanation
Indices: 16243367--16243429 Score: 90
Period size: 5 Copynumber: 12.2 Consensus size: 5
16243357 TGGAGATAAG
* *
16243367 AAGAA GAGAA AGAGAGA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA GAGAA
1 AAGAA AAGAA A-AGA-A AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
16243419 AAGAA AAGAA A
1 AAGAA AAGAA A
16243430 TATATATATA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
5 44 0.85
6 6 0.12
7 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:16243501 original size:25 final size:25
Alignment explanation
Indices: 16243447--16243503 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
16243437 ATATGCATAC
*
16243447 AAATGGACATGGCCCAATAAGGAAAG
1 AAATGGGCATGGCCCAATAA-GAAAG
16243473 -AATGGGCATGGCCCAATTAA-AAAG
1 AAATGGGCATGGCCCAA-TAAGAAAG
16243497 AAATGGG
1 AAATGGG
16243504 AGAAGTCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.14
25 21 0.75
26 3 0.11
ACGTcount: A:0.44, C:0.14, G:0.28, T:0.14
Consensus pattern (25 bp):
AAATGGGCATGGCCCAATAAGAAAG
Found at i:16267984 original size:22 final size:23
Alignment explanation
Indices: 16267930--16267985 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
16267920 CTAACCTTCA
*
16267930 TTTCTCTTTTCTTCTTCCTCCTTT
1 TTTCTCTTTTCTCCTTCCT-CTTT
*
16267954 CTTC-C-TTTCTCCTTCCT-TTT
1 TTTCTCTTTTCTCCTTCCTCTTT
16267974 TTTCTCTTTTCT
1 TTTCTCTTTTCT
16267986 TCTTTTCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 6 0.22
21 1 0.04
22 16 0.59
23 1 0.04
24 3 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTCTCTTTTCTCCTTCCTCTTT
Found at i:16267995 original size:15 final size:15
Alignment explanation
Indices: 16267925--16267995 Score: 72
Period size: 15 Copynumber: 4.8 Consensus size: 15
16267915 CTAGGCTAAC
*
16267925 CTTCATTTCTCTTTT
1 CTTCTTTTCTCTTTT
* *
16267940 CTTC-TTCCTCCTTT
1 CTTCTTTTCTCTTTT
* * *
16267954 CTTCCTTTCTCCTTC
1 CTTCTTTTCTCTTTT
*
16267969 CTTTTTTTCTCTTTT
1 CTTCTTTTCTCTTTT
16267984 CTTCTTTTCTCT
1 CTTCTTTTCTCT
16267996 CTTTGCTTCC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
14 12 0.26
15 34 0.74
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (15 bp):
CTTCTTTTCTCTTTT
Found at i:16273349 original size:21 final size:23
Alignment explanation
Indices: 16273316--16273358 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
16273306 TACTTTTTTT
*
16273316 CACTTGTTTCCTTGAAT-TTTCA
1 CACTTGTTCCCTTGAATATTTCA
16273338 CACTT-TTCCCTTGAATATTTC
1 CACTTGTTCCCTTGAATATTTC
16273359 CACCTAGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.49
Consensus pattern (23 bp):
CACTTGTTCCCTTGAATATTTCA
Found at i:16275786 original size:24 final size:24
Alignment explanation
Indices: 16275754--16275805 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
16275744 AAAGAAGAAT
*
16275754 ATGGTAAGCATCTTGATGACGTAA
1 ATGGTAAGCATCTTAATGACGTAA
*
16275778 ATGGTAAGCATCTTAATGAGGTAA
1 ATGGTAAGCATCTTAATGACGTAA
16275802 ATGG
1 ATGG
16275806 CAAGAATGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.29
Consensus pattern (24 bp):
ATGGTAAGCATCTTAATGACGTAA
Found at i:16283656 original size:22 final size:22
Alignment explanation
Indices: 16283614--16283654 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
16283604 TACCTTTTGT
*
16283614 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
16283636 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
16283655 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:16283712 original size:11 final size:11
Alignment explanation
Indices: 16283680--16283706 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16283670 TATTCTTCTT
16283680 TTCTTCCTTTG
1 TTCTTCCTTTG
16283691 TTCTTCCTTTG
1 TTCTTCCTTTG
16283702 TTCTT
1 TTCTT
16283707 GTTTTGGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (11 bp):
TTCTTCCTTTG
Found at i:16284427 original size:42 final size:42
Alignment explanation
Indices: 16284369--16284458 Score: 164
Period size: 42 Copynumber: 2.1 Consensus size: 42
16284359 ACCATCCCAC
16284369 CATCATCAGCTCATGTGCACT-CCACATCGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACA-CGCACATAGCTGGGT
16284411 CATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGT
16284453 CATCAT
1 CATCAT
16284459 TATCACATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 42 0.89
43 5 0.11
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.23
Consensus pattern (42 bp):
CATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGT
Found at i:16303047 original size:14 final size:15
Alignment explanation
Indices: 16303023--16303052 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
16303013 TTTTTTCAGC
16303023 TAGATTCTTGTTAAT
1 TAGATTCTTGTTAAT
16303038 TAGATT-TTGTTAAT
1 TAGATTCTTGTTAAT
16303052 T
1 T
16303053 TTTAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (15 bp):
TAGATTCTTGTTAAT
Found at i:16304735 original size:39 final size:39
Alignment explanation
Indices: 16304678--16304789 Score: 118
Period size: 39 Copynumber: 2.9 Consensus size: 39
16304668 AGGCATTTGG
16304678 TTGTA-AAGGTTATGCTTGATCCTAAAAAGGCAGTGACTT
1 TTGTAGAA-GTTATGCTTGATCCTAAAAAGGCAGTGACTT
* * ** *
16304717 TTGTAGAAGTTATACTTGATCCTCAAAAGAAAATGACTT
1 TTGTAGAAGTTATGCTTGATCCTAAAAAGGCAGTGACTT
* * * **
16304756 TTGCAGAGGTTATGCTTCATCCTTGAAAGGCAGT
1 TTGTAGAAGTTATGCTTGATCCTAAAAAGGCAGT
16304790 CGCTTGTAAA
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
39 56 0.97
40 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (39 bp):
TTGTAGAAGTTATGCTTGATCCTAAAAAGGCAGTGACTT
Found at i:16308759 original size:42 final size:42
Alignment explanation
Indices: 16308711--16308870 Score: 257
Period size: 42 Copynumber: 3.8 Consensus size: 42
16308701 TATGCAACAA
* *
16308711 CTTATGTGTACTCCCACTCGCACATAGCCGGGTCAACAACGG
1 CTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGCAACGG
*
16308753 CTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGTAACGG
1 CTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGCAACGG
* *
16308795 CTTATGTGCACTCCCACTCGCACATAGCCGAGTCAGCAACGA
1 CTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGCAACGG
* *
16308837 CTTATGTGCACTCCTACTCGCACATAGCTGGGTC
1 CTTATGTGCACTCCCACTCGCACATAGCCGGGTC
16308871 CACATCAACA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 109 1.00
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.23
Consensus pattern (42 bp):
CTTATGTGCACTCCCACTCGCACATAGCCGGGTCAGCAACGG
Found at i:16315455 original size:42 final size:42
Alignment explanation
Indices: 16315388--16315509 Score: 199
Period size: 42 Copynumber: 2.9 Consensus size: 42
16315378 CATATGCAAT
* * **
16315388 GGCTTATGCGCACTCCTACTTGCACATAGTTGGGTCAACAAC
1 GGCTTATGCGCACTCCCACTCGCACATAGCCGGGTCAACAAC
*
16315430 GGCTTATGCGCACTCCCACTCGCACATAGCCGAGTCAACAAC
1 GGCTTATGCGCACTCCCACTCGCACATAGCCGGGTCAACAAC
16315472 GGCTTATGCGCACTCCCACTCGCACATAGCCGGGTCAA
1 GGCTTATGCGCACTCCCACTCGCACATAGCCGGGTCAA
16315510 TATCATTACA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.20
Consensus pattern (42 bp):
GGCTTATGCGCACTCCCACTCGCACATAGCCGGGTCAACAAC
Found at i:16316234 original size:19 final size:19
Alignment explanation
Indices: 16316193--16316234 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
16316183 GAAGAAGGAG
*
16316193 AAGAAGCTACTGGAGAATG
1 AAGAAGCTACTGGAGAATA
*
16316212 AAGAAGCTGCTGGAAGAA-A
1 AAGAAGCTACTGG-AGAATA
16316231 AAGA
1 AAGA
16316235 TATTTATAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.48, C:0.10, G:0.31, T:0.12
Consensus pattern (19 bp):
AAGAAGCTACTGGAGAATA
Found at i:16322036 original size:88 final size:87
Alignment explanation
Indices: 16321926--16322094 Score: 329
Period size: 88 Copynumber: 1.9 Consensus size: 87
16321916 CTAAGCCCAA
16321926 GCAAGCCTCTTTACGTAATCTAGTTCACCATCCCATCAATTTTTCATCACCATTACTAGACCACC
1 GCAAGCCTCTTTACGTAATCTAGTTCACCATCCCATCAATTTTTCATCACCATTACTAGACCACC
16321991 ATTTGTAATTTGCAACAGATCG
66 ATTTGTAATTTGCAACAGATCG
16322013 NGCAAGCCTCTTTACGTAATCTAGTTCACCATCCCATCAATTTTTCATCACCATTACTAGACCAC
1 -GCAAGCCTCTTTACGTAATCTAGTTCACCATCCCATCAATTTTTCATCACCATTACTAGACCAC
16322078 CATTTGTAATTTGCAAC
65 CATTTGTAATTTGCAAC
16322095 TAGACGTATT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (87 bp):
GCAAGCCTCTTTACGTAATCTAGTTCACCATCCCATCAATTTTTCATCACCATTACTAGACCACC
ATTTGTAATTTGCAACAGATCG
Found at i:16323252 original size:43 final size:43
Alignment explanation
Indices: 16323191--16323283 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 43
16323181 TGCAATATCA
*** *
16323191 TCATCATCAGTTCATGTGCACTCTTGCATCGCACATAGCTGGG
1 TCATCATCAGTTCATGTGCACTCCCACACCGCACATAGCTGGG
16323234 TCATCATCAGCTT-ATGTGCACTCCCACACCGCACATAGCTGGG
1 TCATCATCAG-TTCATGTGCACTCCCACACCGCACATAGCTGGG
16323277 TCATCAT
1 TCATCAT
16323284 TATCACACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 43 0.96
44 2 0.04
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (43 bp):
TCATCATCAGTTCATGTGCACTCCCACACCGCACATAGCTGGG
Found at i:16326201 original size:20 final size:21
Alignment explanation
Indices: 16326176--16326214 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
16326166 TATCTTATTT
*
16326176 TTCCAACACCTTC-TCTTCAC
1 TTCCAACAACTTCTTCTTCAC
16326196 TTCCAACAACTTCTTCTTC
1 TTCCAACAACTTCTTCTTC
16326215 TTCCTTCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.21, C:0.41, G:0.00, T:0.38
Consensus pattern (21 bp):
TTCCAACAACTTCTTCTTCAC
Found at i:16329174 original size:20 final size:20
Alignment explanation
Indices: 16329135--16329176 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
16329125 AGAAGAAGAA
*
16329135 GAAGAAGTTGCTAGAGAAAT
1 GAAGAAGTTGCTAGAAAAAT
* *
16329155 GAAGAAGTTGTTGGAAAAAT
1 GAAGAAGTTGCTAGAAAAAT
16329175 GA
1 GA
16329177 TATTTATAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.31, T:0.21
Consensus pattern (20 bp):
GAAGAAGTTGCTAGAAAAAT
Found at i:16331894 original size:35 final size:35
Alignment explanation
Indices: 16331855--16331939 Score: 136
Period size: 35 Copynumber: 2.5 Consensus size: 35
16331845 AGAGTGCGTG
*
16331855 TGATGATATTGAAATATGCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATATGCGTGTAGAGAGTGCACA
* *
16331890 TGATGATATTGAAATGTGTGTGTAGAGAGTGCACA
1 TGATGATATTGAAATATGCGTGTAGAGAGTGCACA
16331925 TGATGATATT-AAATA
1 TGATGATATTGAAATA
16331940 GTGTACATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 4 0.09
35 42 0.91
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (35 bp):
TGATGATATTGAAATATGCGTGTAGAGAGTGCACA
Found at i:16331947 original size:22 final size:23
Alignment explanation
Indices: 16331917--16331965 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
16331907 GTGTGTAGAG
16331917 AGTGCACATGATGATA-TTAAAT
1 AGTGCACATGATGATATTTAAAT
*
16331939 AGTGTACATGATGATATTTAAAT
1 AGTGCACATGATGATATTTAAAT
16331962 -GTGC
1 AGTGC
16331966 GTGTAAGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (23 bp):
AGTGCACATGATGATATTTAAAT
Found at i:16331950 original size:57 final size:60
Alignment explanation
Indices: 16331881--16332045 Score: 230
Period size: 57 Copynumber: 2.8 Consensus size: 60
16331871 TGCGTGTAGG
* *
16331881 GAGTGCACATGATGATATTGAAATGTGTGTGTAGAGAGTGCACATGATGATATT-AA-AT
1 GAGTGCACATGATGATATTGAAATGTGCGTGTAGAGAGTGCACATGATAATATTAAATAT
* *
16331939 -AGTGTACATGATGATATTTAAATGTGCGTGTA-AGGAGTGCACATGATAATATTGAAATAT
1 GAGTGCACATGATGATATTGAAATGTGCGTGTAGA-GAGTGCACATGATAATATT-AAATAT
* *
16331999 GAGTGCACATGATGAAATTGAAATGTGCGTGTAGGGAGTGCACATGA
1 GAGTGCACATGATGATATTGAAATGTGCGTGTAGAGAGTGCACATGA
16332046 GCTAAGTAAG
Statistics
Matches: 93, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
56 1 0.01
57 47 0.51
59 2 0.02
60 2 0.02
61 41 0.44
ACGTcount: A:0.35, C:0.08, G:0.28, T:0.30
Consensus pattern (60 bp):
GAGTGCACATGATGATATTGAAATGTGCGTGTAGAGAGTGCACATGATAATATTAAATAT
Found at i:16332009 original size:26 final size:26
Alignment explanation
Indices: 16331973--16332022 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
16331963 TGCGTGTAAG
16331973 GAGTGCACATGAT-AATATTGAAATAT
1 GAGTGCACATGATGAA-ATTGAAATAT
16331999 GAGTGCACATGATGAAATTGAAAT
1 GAGTGCACATGATGAAATTGAAAT
16332023 GTGCGTGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (26 bp):
GAGTGCACATGATGAAATTGAAATAT
Found at i:16338574 original size:2 final size:2
Alignment explanation
Indices: 16338567--16338600 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16338557 NNNNNNNNNN
16338567 AT 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 AT
16338601 GTTGCATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16340716 original size:42 final size:42
Alignment explanation
Indices: 16340664--16340789 Score: 180
Period size: 42 Copynumber: 3.0 Consensus size: 42
16340654 CAACTCATAT
* *
16340664 GCAATGGCTTATGCGCACTCCTACTCGCACATAGCTGGGTCA
1 GCAACGGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
* * * * *
16340706 GCAACGGCTTATGTGCAGTCCCACTTGCACATAGCCGAGTCA
1 GCAACGGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
*
16340748 GCAACTGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
1 GCAACGGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
16340790 ATATCATTAC
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.22
Consensus pattern (42 bp):
GCAACGGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCA
Found at i:16347603 original size:21 final size:20
Alignment explanation
Indices: 16347574--16347612 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
16347564 TGAGAGTTTC
*
16347574 TCGCAGCAGCGAGATTTCTTT
1 TCGCAGCAGAGAG-TTTCTTT
*
16347595 TCGCTGCAGAGAGTTTCT
1 TCGCAGCAGAGAGTTTCT
16347613 AGCTGCCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (20 bp):
TCGCAGCAGAGAGTTTCTTT
Found at i:16347901 original size:42 final size:42
Alignment explanation
Indices: 16347855--16347934 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
16347845 CATATGCAAT
*
16347855 GGCTTATGCACACTCTCACTCGCACATAGTCGGGTCAACAGC
1 GGCTTATGCACACTCTCACTCGCACATAGCCGGGTCAACAGC
* * *
16347897 GGCTTATGCGCACTCTTACTCGTACATAGCCGGGTCAA
1 GGCTTATGCACACTCTCACTCGCACATAGCCGGGTCAA
16347935 TATCATTACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.24
Consensus pattern (42 bp):
GGCTTATGCACACTCTCACTCGCACATAGCCGGGTCAACAGC
Found at i:16350362 original size:20 final size:20
Alignment explanation
Indices: 16350311--16350362 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
16350301 CTCCTCCACC
* *
16350311 TTCATGCTCTCAATGCCATT
1 TTCATGCTCCCAACGCCATT
** *
16350331 TTCACCCACCCAACGCCATT
1 TTCATGCTCCCAACGCCATT
16350351 TTCATGCTCCCA
1 TTCATGCTCCCA
16350363 TGCCATTTCA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.40, G:0.08, T:0.31
Consensus pattern (20 bp):
TTCATGCTCCCAACGCCATT
Found at i:16351555 original size:35 final size:35
Alignment explanation
Indices: 16351516--16351588 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
16351506 GGAGTGCGTG
16351516 TGATGATATTGAAATGTGTGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGTGTGTAGGGAGTGCACA
***
16351551 TGATGATATTGCCTTGTGTGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGTGTGTAGGGAGTGCACA
16351586 TGA
1 TGA
16351589 GCTGAGTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.25, C:0.08, G:0.34, T:0.33
Consensus pattern (35 bp):
TGATGATATTGAAATGTGTGTGTAGGGAGTGCACA
Found at i:16353750 original size:54 final size:54
Alignment explanation
Indices: 16353544--16353752 Score: 337
Period size: 54 Copynumber: 3.9 Consensus size: 54
16353534 CATCATATGC
* *
16353544 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACATCCT
1 ATCTCACCCGGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCCT
* *
16353598 ATCTCACCCGGCTCATGTGCATCCCACCACATCGTGCACATAGCTGGACATCCC
1 ATCTCACCCGGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCCT
* * *
16353652 ATCTCACTCGGCTCATGTGCATCCCACCACATTGTGTACATAGCCGGACATCCT
1 ATCTCACCCGGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCCT
* *
16353706 ATCTCAGCCGGCTCATGTGCATCCCACTACATCGTGCACATAGCCGG
1 ATCTCACCCGGCTCATGTGCATCCCACCACATCGTGCACATAGCCGG
16353753 CTAGTATCAC
Statistics
Matches: 141, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 141 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.22
Consensus pattern (54 bp):
ATCTCACCCGGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCCT
Found at i:16355453 original size:35 final size:32
Alignment explanation
Indices: 16355414--16355524 Score: 109
Period size: 35 Copynumber: 3.3 Consensus size: 32
16355404 AAACCCAAAG
16355414 TGGTTTTTCAAAGGCTCAACCATAACCTTTCACAA
1 TGGTTTTTCAAAGGCTCAACCA-AACC--TCACAA
* ** *
16355449 TGGTTTTTTACGGGCTCAACCAAAAC-CA-AA
1 TGGTTTTTCAAAGGCTCAACCAAACCTCACAA
16355479 GTGGTTTTTCAAAGGCTCAACCACAACCTACAACAA
1 -TGGTTTTTCAAAGGCTCAACCA-AACCT-C-ACAA
16355515 TGGTTTTTCA
1 TGGTTTTTCA
16355525 CGAGATCAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
30 2 0.03
31 21 0.34
32 3 0.05
34 4 0.06
35 30 0.48
36 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (32 bp):
TGGTTTTTCAAAGGCTCAACCAAACCTCACAA
Found at i:16355468 original size:67 final size:67
Alignment explanation
Indices: 16355370--16355544 Score: 248
Period size: 66 Copynumber: 2.6 Consensus size: 67
16355360 GCTTAGCCAA
* *
16355370 AACCTTTCACAATAG-TTTTTACCGGGATCAACTAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTTA-CGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
*
16355434 CAT
65 CAC
*
16355437 AACCTTTCACAATGGTTTTTTACGGGCTCAACCAAAA-CCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTTACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
16355501 AC
66 AC
* * *
16355503 AACC-TACAACAATGGTTTTTCACGAGATCAACCAAAACCCAA
1 AACCTTTC-ACAATGGTTTTTTACGGGATCAACCAAAACCCAA
16355545 CAACTAACTT
Statistics
Matches: 97, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
65 2 0.02
66 58 0.60
67 31 0.32
68 6 0.06
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTTACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
AC
Found at i:16355487 original size:31 final size:31
Alignment explanation
Indices: 16355397--16355506 Score: 105
Period size: 31 Copynumber: 3.4 Consensus size: 31
16355387 TTTACCGGGA
*
16355397 TCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAA-CCAAAGTGGTTTTTCAAAGGC
* * **
16355429 TCAACCATAACCTTTCACAA-TGGTTTTTTACGGGC
1 TCAACCA-AAAC---CA-AAGTGGTTTTTCAAAGGC
16355464 TCAACCAAAACCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCAAAGTGGTTTTTCAAAGGC
*
16355495 TCAACCACAACC
1 TCAACCAAAACC
16355507 TACAACAATG
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
30 2 0.03
31 25 0.40
32 7 0.11
33 2 0.03
34 3 0.05
35 21 0.34
36 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (31 bp):
TCAACCAAAACCAAAGTGGTTTTTCAAAGGC
Found at i:16358654 original size:13 final size:14
Alignment explanation
Indices: 16358636--16358664 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
16358626 ATTAGGAAGT
16358636 TTTCATTATC-AGA
1 TTTCATTATCTAGA
16358649 TTTCATTATCTAGA
1 TTTCATTATCTAGA
16358663 TT
1 TT
16358665 ATCTTCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTCATTATCTAGA
Found at i:16378428 original size:28 final size:28
Alignment explanation
Indices: 16378367--16378428 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
16378357 GTTGGGTGGT
* * *
16378367 GAAAAATTACAATTTTGCCCTTAGGGTG
1 GAAAAATGACAATTTTGCCCTTAGGCTC
* * *
16378395 GCAAAATGACTATTTTGCCCTTATGCTC
1 GAAAAATGACAATTTTGCCCTTAGGCTC
16378423 GAAAAA
1 GAAAAA
16378429 ATGCCGAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (28 bp):
GAAAAATGACAATTTTGCCCTTAGGCTC
Found at i:16386963 original size:38 final size:39
Alignment explanation
Indices: 16386865--16386970 Score: 126
Period size: 38 Copynumber: 2.7 Consensus size: 39
16386855 CACTCCCGGC
*
16386865 TCATGTACATCCCCCCACATCGTGCACATAGCCGGCACCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGG-ACCA
* * * *
16386905 TCATGTGCATCCCCCCACATCATGCACA-ATCAGTG-CTA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAG-GACCA
*
16386943 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
16386971 CGGGCACTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
38 27 0.47
39 3 0.05
40 27 0.47
ACGTcount: A:0.25, C:0.41, G:0.14, T:0.21
Consensus pattern (39 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCAGGACCA
Found at i:16397495 original size:54 final size:54
Alignment explanation
Indices: 16397412--16397621 Score: 330
Period size: 54 Copynumber: 3.9 Consensus size: 54
16397402 CACCAGATGC
* * **
16397412 ATCTCACCCAGCTCATGTGCATCCAACCACATCGTGCACATAATCAAACATCCT
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACATCCT
* *
16397466 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACGTAGTCGGACATTCT
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACATCCT
* *
16397520 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCCC
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACATCCT
* *
16397574 ATCTCACCCGGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGA
1 ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGA
16397622 TAGTATTACC
Statistics
Matches: 145, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 145 1.00
ACGTcount: A:0.25, C:0.39, G:0.15, T:0.21
Consensus pattern (54 bp):
ATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACATCCT
Found at i:16422084 original size:27 final size:28
Alignment explanation
Indices: 16422027--16422083 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
16422017 GGAAAAATGT
16422027 CCTGGTGGTGGAAAATTACAATTTTACC
1 CCTGGTGGTGGAAAATTACAATTTTACC
*
16422055 CCTGG-GGTGGCAAAATTACCATTTTACC
1 CCTGGTGGTGG-AAAATTACAATTTTACC
16422083 C
1 C
16422084 TTTTACTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (28 bp):
CCTGGTGGTGGAAAATTACAATTTTACC
Found at i:16422155 original size:20 final size:20
Alignment explanation
Indices: 16422138--16422175 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
16422128 CCTCAAATCT
16422138 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
16422158 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
16422176 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:16423237 original size:35 final size:35
Alignment explanation
Indices: 16423157--16423251 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 35
16423147 GCTCTTATCA
* * * ** *
16423157 ATGATCTATTCTCTGCCCGTTGTTTTGGCACGTGC
1 ATGATCTGTTCTCTGCCTGTTGCTTTCACAAGTGC
*
16423192 ATGATATGTTCTCTGCCTGTTGCTTTCACAAGTGC
1 ATGATCTGTTCTCTGCCTGTTGCTTTCACAAGTGC
* *
16423227 GTGATCTGTTCTCCGCCTGTTGCTT
1 ATGATCTGTTCTCTGCCTGTTGCTT
16423252 CAGGACGCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (35 bp):
ATGATCTGTTCTCTGCCTGTTGCTTTCACAAGTGC
Found at i:16430012 original size:47 final size:47
Alignment explanation
Indices: 16429938--16430030 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 47
16429928 TGCTGCCAAT
*
16429938 TTGTGCAAAAAAATTGGAACTATTTGCTGCCAATTTGTGCAGAAAAA
1 TTGTCCAAAAAAATTGGAACTATTTGCTGCCAATTTGTGCAGAAAAA
* * *
16429985 TTGTCCAAAAAAATTGGAGCTGTTTGCTGCCAATTTGTGTAGAAAA
1 TTGTCCAAAAAAATTGGAACTATTTGCTGCCAATTTGTGCAGAAAA
16430031 TTAGACAGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (47 bp):
TTGTCCAAAAAAATTGGAACTATTTGCTGCCAATTTGTGCAGAAAAA
Found at i:16430242 original size:19 final size:22
Alignment explanation
Indices: 16430169--16430249 Score: 123
Period size: 22 Copynumber: 3.8 Consensus size: 22
16430159 GAGAGGAAAG
*
16430169 GAAGAGAGGAAGCCACGGTGAT
1 GAAGAGAGGAAGCCACGGTGGT
*
16430191 GAAGAGAGGAAGCCATGGTGGT
1 GAAGAGAGGAAGCCACGGTGGT
16430213 GAAGAGAGGAAGCCACGGTGGT
1 GAAGAGAGGAAGCCACGGTGGT
16430235 G-A-AG-GGAAGCCACGG
1 GAAGAGAGGAAGCCACGG
16430250 GCTGGAAAGA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.20
20 2 0.04
21 1 0.02
22 42 0.75
ACGTcount: A:0.33, C:0.14, G:0.44, T:0.09
Consensus pattern (22 bp):
GAAGAGAGGAAGCCACGGTGGT
Found at i:16430357 original size:26 final size:25
Alignment explanation
Indices: 16430328--16430391 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
16430318 GAAATGAAAA
16430328 AATAAATAAATAAATGGGCATGACCC
1 AATAAA-AAATAAATGGGCATGACCC
* * * *
16430354 AATAGAAAATAAGTGGGCATGGCCT
1 AATAAAAAATAAATGGGCATGACCC
*
16430379 AATAAGAAATAAA
1 AATAAAAAATAAA
16430392 AATAAATGGG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 26 0.84
26 5 0.16
ACGTcount: A:0.52, C:0.11, G:0.19, T:0.19
Consensus pattern (25 bp):
AATAAAAAATAAATGGGCATGACCC
Found at i:16433912 original size:2 final size:2
Alignment explanation
Indices: 16433907--16433957 Score: 84
Period size: 2 Copynumber: 25.0 Consensus size: 2
16433897 AAAACCTCTC
*
16433907 TA TA TA GTA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16433950 TA TA TA TA
1 TA TA TA TA
16433958 CACGAATGCC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:16434060 original size:36 final size:36
Alignment explanation
Indices: 16434020--16434145 Score: 198
Period size: 36 Copynumber: 3.5 Consensus size: 36
16434010 TAGCCGGAGT
** *
16434020 CATCATGTGCACCCCCACATCGTGCACAGCTAATAC
1 CATCATGTGCACCCCCACATCACGCACAGCTAATGC
16434056 CATCATGTGCACCCCCACATCACGCACAGCTAATGC
1 CATCATGTGCACCCCCACATCACGCACAGCTAATGC
* *
16434092 CATCATGTGCACCCCCACATCACACACAACTAATGC
1 CATCATGTGCACCCCCACATCACGCACAGCTAATGC
*
16434128 CATCATGTACACCCCCAC
1 CATCATGTGCACCCCCAC
16434146 TGTAAAATTT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 84 1.00
ACGTcount: A:0.29, C:0.42, G:0.11, T:0.17
Consensus pattern (36 bp):
CATCATGTGCACCCCCACATCACGCACAGCTAATGC
Found at i:16434771 original size:11 final size:11
Alignment explanation
Indices: 16434755--16434788 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
16434745 ATGAAAAGTC
16434755 AGCCCATTTAA
1 AGCCCATTTAA
16434766 AGCCCATTTAA
1 AGCCCATTTAA
*
16434777 ACCCCATATTAA
1 AGCCCAT-TTAA
16434789 GTGATGTCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.38, C:0.29, G:0.06, T:0.26
Consensus pattern (11 bp):
AGCCCATTTAA
Found at i:16444271 original size:38 final size:38
Alignment explanation
Indices: 16444228--16444335 Score: 180
Period size: 38 Copynumber: 2.8 Consensus size: 38
16444218 AAACTGCCCA
* *
16444228 TGTGCACGATGTGGGGGGATGAACACGATGGCACTAAT
1 TGTGCACGATGTGGGGGGATGCACACGATGACACTAAT
*
16444266 TGTGCACTATGTGGGGGGATGCACACGATGACACTAAT
1 TGTGCACGATGTGGGGGGATGCACACGATGACACTAAT
*
16444304 TGTGCACGATGTGGGGGGATGCACATGATGAC
1 TGTGCACGATGTGGGGGGATGCACACGATGAC
16444336 CCCGGCTATG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.22
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGCACACGATGACACTAAT
Found at i:16444419 original size:8 final size:8
Alignment explanation
Indices: 16444406--16444432 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
16444396 AGTATTTTTC
16444406 TATGTATA
1 TATGTATA
16444414 TATGTATA
1 TATGTATA
16444422 TATGTATA
1 TATGTATA
16444430 TAT
1 TAT
16444433 ATGTTTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (8 bp):
TATGTATA
Found at i:16446521 original size:36 final size:36
Alignment explanation
Indices: 16446481--16446575 Score: 127
Period size: 36 Copynumber: 2.6 Consensus size: 36
16446471 GAGTCATCGT
16446481 GTGCACCCCCACATCGCGCACAGCTAATACCATCAC
1 GTGCACCCCCACATCGCGCACAGCTAATACCATCAC
** * * * *
16446517 GTGCACCCCTGCACCGCACACAGCTAATGCCATCAT
1 GTGCACCCCCACATCGCGCACAGCTAATACCATCAC
*
16446553 GTGCATCCCCACATCGCGCACAG
1 GTGCACCCCCACATCGCGCACAG
16446576 GCAATATCAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.25, C:0.43, G:0.17, T:0.15
Consensus pattern (36 bp):
GTGCACCCCCACATCGCGCACAGCTAATACCATCAC
Found at i:16446587 original size:36 final size:35
Alignment explanation
Indices: 16446475--16446588 Score: 122
Period size: 36 Copynumber: 3.2 Consensus size: 35
16446465 TAGCTGGAGT
*
16446475 CATCGTGTGCACCCCCACATCGCGCACAGCTAATAC
1 CATCATGTGCA-CCCCACATCGCGCACAGCTAATAC
* * * * *
16446511 CATCACGTGCACCCCTGCACCGCACACAGCTAATGC
1 CATCATGTGCACCCC-ACATCGCGCACAGCTAATAC
*
16446547 CATCATGTGCATCCCCACATCGCGCACAGGC-AATAT
1 CATCATGTGCA-CCCCACATCGCGCACA-GCTAATAC
16446583 CATCAT
1 CATCAT
16446589 TCACACTCCC
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
35 4 0.06
36 53 0.84
37 6 0.10
ACGTcount: A:0.26, C:0.40, G:0.16, T:0.18
Consensus pattern (35 bp):
CATCATGTGCACCCCACATCGCGCACAGCTAATAC
Found at i:16450918 original size:38 final size:40
Alignment explanation
Indices: 16450831--16450937 Score: 146
Period size: 38 Copynumber: 2.7 Consensus size: 40
16450821 CACACCCGAC
* *
16450831 TCATGTACATCCCCCAACATCGTGCACATAGCCGGCGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCCAGCGCCA
* * *
16450871 TCGTGTACATCCCCCCACATCGTGCACA-A-TCAGTGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCCAGCGCCA
*
16450909 TCATGTACATCCCCCCACATTGTGCACAT
1 TCATGTACATCCCCCCACATCGTGCACAT
16450938 GGGCATTATC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
38 32 0.54
39 1 0.02
40 26 0.44
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCCAGCGCCA
Found at i:16460867 original size:63 final size:63
Alignment explanation
Indices: 16460768--16460923 Score: 231
Period size: 63 Copynumber: 2.5 Consensus size: 63
16460758 GGATGTAACT
** ** * * *
16460768 GTGCATGTGCGGAGTGGGCAGTGCACATGCTGGTTGAATGATGAGGTTTCGATAGTTACGACC
1 GTGCATGTGCGGAGTGGGCAGTGCACATGCCCGTTGAATGACAAGGCTGCGATAATTACGACC
* *
16460831 GTGCATGTGCGGAGTGGGCAGTGCACATGCCCGTTGAATGACAATGCTGCGATAATTACTACC
1 GTGCATGTGCGGAGTGGGCAGTGCACATGCCCGTTGAATGACAAGGCTGCGATAATTACGACC
16460894 GTGCATGTGCGGAGTGGGCAGTGCACATGC
1 GTGCATGTGCGGAGTGGGCAGTGCACATGC
16460924 TAGTAATGAT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 84 1.00
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.24
Consensus pattern (63 bp):
GTGCATGTGCGGAGTGGGCAGTGCACATGCCCGTTGAATGACAAGGCTGCGATAATTACGACC
Found at i:16465755 original size:22 final size:22
Alignment explanation
Indices: 16465730--16465778 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
16465720 TCGCTATAGC
*
16465730 GAGAATCCATTTTCGCTGCAGT
1 GAGAATCCATTTTCACTGCAGT
* *
16465752 GAGAATTCTTTTTCACTGCAGT
1 GAGAATCCATTTTCACTGCAGT
*
16465774 AAGAA
1 GAGAA
16465779 ACAGGGCTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (22 bp):
GAGAATCCATTTTCACTGCAGT
Found at i:16467680 original size:29 final size:29
Alignment explanation
Indices: 16467615--16467681 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
16467605 TATGTAAAAG
*
16467615 CTAAAATGATGTTGTGCATACAGTTGGCA
1 CTAAAATGATATTGTGCATACAGTTGGCA
* *
16467644 C-ATGAATGATATTGTGCATA-TGTTTGGCA
1 CTA-AAATGATATTGTGCATACAG-TTGGCA
16467673 CTAAAATGA
1 CTAAAATGA
16467682 GTATGATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
28 2 0.06
29 28 0.90
30 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (29 bp):
CTAAAATGATATTGTGCATACAGTTGGCA
Found at i:16468983 original size:22 final size:22
Alignment explanation
Indices: 16468942--16468980 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16468932 GCTAGGCTAA
16468942 TAATGTTAATGTGAATATGAGT
1 TAATGTTAATGTGAATATGAGT
16468964 TAATG-TAATG-GAA-ATGA
1 TAATGTTAATGTGAATATGA
16468981 TGACACTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 5 0.29
22 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (22 bp):
TAATGTTAATGTGAATATGAGT
Found at i:16469428 original size:49 final size:49
Alignment explanation
Indices: 16469327--16469499 Score: 184
Period size: 49 Copynumber: 3.5 Consensus size: 49
16469317 ACCATTCGTG
* * * * * * * *
16469327 GATGGTTCCGGACGATGGTGTGATATGAGATATGTATCTTCCATCCAAA
1 GATGATTCCGGACAATGATATGATGTGAGATATGTATGTTCCGTCCATA
** * * *
16469376 GATGATTTTGGACAATGATATGATGTGAGATATGTCTGTTCTGTCCGTA
1 GATGATTCCGGACAATGATATGATGTGAGATATGTATGTTCCGTCCATA
* *
16469425 GATGATTCCGGACAATGATATGATGTGAGGTATGTATGTTCCGTCCATG
1 GATGATTCCGGACAATGATATGATGTGAGATATGTATGTTCCGTCCATA
* * *
16469474 GATGATTCCAGACGATGTTATGATGT
1 GATGATTCCGGACAATGATATGATGT
16469500 TGATTATGCA
Statistics
Matches: 101, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 101 1.00
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.34
Consensus pattern (49 bp):
GATGATTCCGGACAATGATATGATGTGAGATATGTATGTTCCGTCCATA
Found at i:16472921 original size:38 final size:38
Alignment explanation
Indices: 16472835--16472945 Score: 168
Period size: 38 Copynumber: 2.9 Consensus size: 38
16472825 AACTCATGTA
***
16472835 CATCCCCCCACATCGTGCACATAGCTGGAGTCATCGTGTG
1 CATCCCCCCACATCGTGCACA-AGCAATA-TCATCGTGTG
*
16472875 CATCCCCCCACATCGTGCACAAGCAATATCATTGTGTG
1 CATCCCCCCACATCGTGCACAAGCAATATCATCGTGTG
16472913 CATCCCCCCACATCGTGCACAAGCAATATCATC
1 CATCCCCCCACATCGTGCACAAGCAATATCATC
16472946 ACCCACATTC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 41 0.62
39 4 0.06
40 21 0.32
ACGTcount: A:0.25, C:0.37, G:0.16, T:0.22
Consensus pattern (38 bp):
CATCCCCCCACATCGTGCACAAGCAATATCATCGTGTG
Found at i:16474585 original size:38 final size:36
Alignment explanation
Indices: 16474542--16474614 Score: 128
Period size: 38 Copynumber: 2.0 Consensus size: 36
16474532 AGAAGCTGGT
16474542 GGTCAGCTGGAGAGAAGAGGAAGAAGAAAAAAAAAAA
1 GGTCAGCTGGAGAGAAGAGGAAG-AGAAAAAAAAAAA
16474579 GNGTCAGCTGGAGAGAAGAGGAAGAGAAAAAAAAAA
1 G-GTCAGCTGGAGAGAAGAGGAAGAGAAAAAAAAAA
16474615 GAAAAGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 13 0.37
38 22 0.63
ACGTcount: A:0.55, C:0.05, G:0.33, T:0.05
Consensus pattern (36 bp):
GGTCAGCTGGAGAGAAGAGGAAGAGAAAAAAAAAAA
Found at i:16474613 original size:5 final size:5
Alignment explanation
Indices: 16474606--16474666 Score: 83
Period size: 5 Copynumber: 12.8 Consensus size: 5
16474596 GAGGAAGAGA
* *
16474606 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG --AAG AGAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
16474654 AAAAG AAAA- AAAA
1 AAAAG AAAAG AAAA
16474667 TATATATATA
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
3 3 0.06
4 4 0.08
5 45 0.87
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:16474644 original size:28 final size:26
Alignment explanation
Indices: 16474603--16474666 Score: 101
Period size: 28 Copynumber: 2.4 Consensus size: 26
16474593 GAAGAGGAAG
16474603 AGAAAAAAAAAAGAAAAGAAAAGAAA
1 AGAAAAAAAAAAGAAAAGAAAAGAAA
*
16474629 AGAAAAGAAAAGAAGAGAAGAAAAGAAA
1 AGAAAA-AAAA-AAGAAAAGAAAAGAAA
16474657 AGAAAAAAAA
1 AGAAAAAAAA
16474667 TATATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 6 0.17
27 8 0.23
28 21 0.60
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (26 bp):
AGAAAAAAAAAAGAAAAGAAAAGAAA
Found at i:16482517 original size:22 final size:22
Alignment explanation
Indices: 16482475--16482515 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
16482465 TACCTTTTGT
*
16482475 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
16482497 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
16482516 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:16484388 original size:35 final size:35
Alignment explanation
Indices: 16484321--16484516 Score: 241
Period size: 35 Copynumber: 5.6 Consensus size: 35
16484311 ACTCAGCCAA
* * * *
16484321 TGTGCACTCCCTGCACGCACA-AGGCAATATCATCG
1 TGTGCACTCCCTACTCGCACACA-TCAACATCATCG
* *
16484356 TGTGCACTCCCTACTCGCGCACATCAACATCATTG
1 TGTGCACTCCCTACTCGCACACATCAACATCATCG
* * *
16484391 TGTGGACTCCCTACTCGCACACATCAACATCACCA
1 TGTGCACTCCCTACTCGCACACATCAACATCATCG
* **
16484426 TGCGCACTCCCTACTCGCACACATCAACATCATAT
1 TGTGCACTCCCTACTCGCACACATCAACATCATCG
*
16484461 TGTGCACTCCCTACTCGCACACATCAACATCATCT
1 TGTGCACTCCCTACTCGCACACATCAACATCATCG
* *
16484496 TGTGCACTCTCTACTCACACA
1 TGTGCACTCCCTACTCGCACA
16484517 TCTCAATATC
Statistics
Matches: 140, Mismatches: 20, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
35 139 0.99
36 1 0.01
ACGTcount: A:0.26, C:0.38, G:0.12, T:0.23
Consensus pattern (35 bp):
TGTGCACTCCCTACTCGCACACATCAACATCATCG
Found at i:16494341 original size:52 final size:52
Alignment explanation
Indices: 16494259--16494361 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
16494249 TGCACTGCAG
* *
16494259 TGGTACTATATTATGAATGTAGGCCTAGTTGATCATCTTTAGGCTAGAGAAA
1 TGGTACTATATTATGAATGTAGGCCAAGTTGATCATCCTTAGGCTAGAGAAA
16494311 TGGTACTATATTATGAATGTAGGCCAAGTTGATCATCCTTAGGCTAGAGAA
1 TGGTACTATATTATGAATGTAGGCCAAGTTGATCATCCTTAGGCTAGAGAA
16494362 CTATGTATGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (52 bp):
TGGTACTATATTATGAATGTAGGCCAAGTTGATCATCCTTAGGCTAGAGAAA
Done.