Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 65 of 103
Found at i:24357896 original size:86 final size:86
Alignment explanation
Indices: 24357750--24357929 Score: 299
Period size: 86 Copynumber: 2.1 Consensus size: 86
24357740 ATAAAAAACT
* * * * *
24357750 TATCTTTAACACTCGACATCAAAAGTCCAAGACTTGTTGATTAGGGATTCATCCATTTTTTTTTA
1 TATCTTTAACACTCAACATCAAAAGTCCAAGACTTGTCGATTAAGGATGCATCCAATTTTTTTTA
24357815 TTAAATAACCTTCCCATAACC
66 TTAAATAACCTTCCCATAACC
24357836 TATCTTTAACACTCAACATCAAAAG-CCTAAGACTTGTCGATTAAGGATGCATCCAATTTTTTTT
1 TATCTTTAACACTCAACATCAAAAGTCC-AAGACTTGTCGATTAAGGATGCATCCAATTTTTTTT
24357900 ATTAAATAACCTTCCCATAACC
65 ATTAAATAACCTTCCCATAACC
24357922 TATCTTTA
1 TATCTTTA
24357930 TCTATCTAGT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
85 2 0.02
86 86 0.98
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (86 bp):
TATCTTTAACACTCAACATCAAAAGTCCAAGACTTGTCGATTAAGGATGCATCCAATTTTTTTTA
TTAAATAACCTTCCCATAACC
Found at i:24366946 original size:15 final size:16
Alignment explanation
Indices: 24366928--24366957 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24366918 AAAAACAAAC
24366928 AAGAGCAA-AAAAGTA
1 AAGAGCAAGAAAAGTA
24366943 AAGAGCAAGAAAAGT
1 AAGAGCAAGAAAAGT
24366958 GTTCTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.07, G:0.23, T:0.07
Consensus pattern (16 bp):
AAGAGCAAGAAAAGTA
Found at i:24384802 original size:13 final size:13
Alignment explanation
Indices: 24384784--24384808 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24384774 ATTTTCAAAA
24384784 ATTTTATAAAATT
1 ATTTTATAAAATT
24384797 ATTTTATAAAAT
1 ATTTTATAAAAT
24384809 CTCATTTTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:24386019 original size:28 final size:29
Alignment explanation
Indices: 24385961--24386024 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
24385951 GTAAATTTTT
** *
24385961 AAAAATTACATTTTTACCCCCGTAAAGTG
1 AAAAATTACATTTTTACCCCCAAAAACTG
* *
24385990 AAAATTTACATTTTT-GCCCCAAAAACTG
1 AAAAATTACATTTTTACCCCCAAAAACTG
24386018 AAAAATT
1 AAAAATT
24386025 GCCCATAGAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCCCAAAAACTG
Found at i:24388424 original size:59 final size:58
Alignment explanation
Indices: 24388284--24388457 Score: 217
Period size: 59 Copynumber: 3.0 Consensus size: 58
24388274 TATGTCATTT
* * * * *
24388284 ATAATGTTTGACATCCATGATATTAGGGATCAAATACCTCAA-TTTTGGTGTC-AATTC
1 ATAATCTTTGACATCCATAATTTTAGGGATCAAATCCCT-AATTTTTGGTGTCAAATTA
* *
24388341 ATAATCTTTGACATCCATATTTTTAGGAATCAAATTCCCTAATTTTTGGTGTCAAATTA
1 ATAATCTTTGACATCCATAATTTTAGGGATCAAA-TCCCTAATTTTTGGTGTCAAATTA
* * *
24388400 ATAGTCTTTGACATTCATAATTTTAGGGATCAAATCCCTTGATTTTTGGTGTCAAATT
1 ATAATCTTTGACATCCATAATTTTAGGGATCAAATCCC-TAATTTTTGGTGTCAAATT
24388458 GAGCAACTTA
Statistics
Matches: 101, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
57 31 0.31
58 18 0.18
59 52 0.51
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (58 bp):
ATAATCTTTGACATCCATAATTTTAGGGATCAAATCCCTAATTTTTGGTGTCAAATTA
Found at i:24394728 original size:41 final size:41
Alignment explanation
Indices: 24394671--24394749 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
24394661 CATACTCAGC
24394671 TCATGTGCACTCCCTACACGCACAAAACAATATCATCATCA
1 TCATGTGCACTCCCTACACGCACAAAACAATATCATCATCA
* ***
24394712 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
1 TCATGTGCACTCCCTACACGCACAAAACAATATCATCA
24394750 CATGCACTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.27
Consensus pattern (41 bp):
TCATGTGCACTCCCTACACGCACAAAACAATATCATCATCA
Found at i:24395424 original size:2 final size:2
Alignment explanation
Indices: 24395417--24395444 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24395407 AAATCACTCA
24395417 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
24395445 ACACATCTAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:24401280 original size:103 final size:104
Alignment explanation
Indices: 24401119--24401309 Score: 303
Period size: 103 Copynumber: 1.8 Consensus size: 104
24401109 GTTCACCCAT
* * * *
24401119 TTTTCCTTTGACTTTTGAGCCCATTCTCTTTCTTTTTTCTTATAGAAGTCCCATAATTCTACCTT
1 TTTTCCTTTAACTTTTAAGCCCATTCTCTTTCTCTTTTCTTATAGAAGTCCCACAATTCTACCTT
24401184 TTTTAACATCAACTATTTTTTTTCTTCATATTTACCTGC
66 TTTTAACATCAACTATTTTTTTTCTTCATATTTACCTGC
* *
24401223 TTTTCCTTTAACTTTTAAG-CCATTCTCTTTCTCTTTTCTTCTAGAAGTCCCACAATTCTGCCTT
1 TTTTCCTTTAACTTTTAAGCCCATTCTCTTTCTCTTTTCTTATAGAAGTCCCACAATTCTACCTT
* *
24401287 TTTTAACATCAGCTCTTTTTTTT
66 TTTTAACATCAACTATTTTTTTT
24401310 TTCTTCATCC
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
103 62 0.78
104 17 0.22
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.52
Consensus pattern (104 bp):
TTTTCCTTTAACTTTTAAGCCCATTCTCTTTCTCTTTTCTTATAGAAGTCCCACAATTCTACCTT
TTTTAACATCAACTATTTTTTTTCTTCATATTTACCTGC
Found at i:24403113 original size:22 final size:22
Alignment explanation
Indices: 24403082--24403123 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
24403072 TTTTAAAAAT
* *
24403082 TTTTATCTCATAATACTTTTAA
1 TTTTACCTCATAACACTTTTAA
24403104 TTTTACCTCATAACACTTTT
1 TTTTACCTCATAACACTTTT
24403124 TTGTGATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTACCTCATAACACTTTTAA
Found at i:24403746 original size:13 final size:13
Alignment explanation
Indices: 24403728--24403755 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
24403718 TAATAATAAC
24403728 TTTTCAACCTATA
1 TTTTCAACCTATA
24403741 TTTTCAACCTATA
1 TTTTCAACCTATA
24403754 TT
1 TT
24403756 CTTAATTGGA
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:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTCAACCTATA
Found at i:24407118 original size:18 final size:18
Alignment explanation
Indices: 24407095--24407134 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24407085 GCTGAAATAT
*
24407095 TGTTTATGTATTTTGTTC
1 TGTTTATGTATTTTGTTA
* *
24407113 TGTTTATTTGTTTTGTTA
1 TGTTTATGTATTTTGTTA
24407131 TGTT
1 TGTT
24407135 GCTGATAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.03, G:0.17, T:0.70
Consensus pattern (18 bp):
TGTTTATGTATTTTGTTA
Found at i:24408019 original size:29 final size:29
Alignment explanation
Indices: 24407987--24408046 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
24407977 TTAAATTAGA
24407987 AGTTAGCAGGATGAAGAGTATTGAGAAAC
1 AGTTAGCAGGATGAAGAGTATTGAGAAAC
24408016 AGTTAGCAGGATGAAGAGTATTGAGAAAC
1 AGTTAGCAGGATGAAGAGTATTGAGAAAC
24408045 AG
1 AG
24408047 AACCAACTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.07, G:0.32, T:0.20
Consensus pattern (29 bp):
AGTTAGCAGGATGAAGAGTATTGAGAAAC
Found at i:24413530 original size:31 final size:31
Alignment explanation
Indices: 24413494--24413566 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
24413484 AATTTTAAAA
24413494 TTACTACCCTAACCCTAACCCTATTACATTT
1 TTACTACCCTAACCCTAACCCTATTACATTT
24413525 TTACTACCCTAACCCTAACCCTATTACATTT
1 TTACTACCCTAACCCTAACCCTATTACATTT
24413556 TTACTACCCTA
1 TTACTACCCTA
24413567 TAATTACTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (31 bp):
TTACTACCCTAACCCTAACCCTATTACATTT
Found at i:24420979 original size:16 final size:19
Alignment explanation
Indices: 24420958--24420999 Score: 63
Period size: 16 Copynumber: 2.4 Consensus size: 19
24420948 TCTTAGAATT
24420958 TAAAATTTTA-TTTG-AC-
1 TAAAATTTTAGTTTGTACA
24420974 TAAAATTTTAGTTTGTACA
1 TAAAATTTTAGTTTGTACA
24420993 TAAAATT
1 TAAAATT
24421000 AAGACGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.43
17 4 0.17
18 2 0.09
19 7 0.30
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (19 bp):
TAAAATTTTAGTTTGTACA
Found at i:24431559 original size:22 final size:20
Alignment explanation
Indices: 24431532--24431581 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
24431522 TTTATTTTTG
24431532 ATTAATTTTATAATTATAATT
1 ATTAATTTTATAATT-TAATT
* *
24431553 ATATAATTTTATTATTTATTT
1 AT-TAATTTTATAATTTAATT
24431574 ATTAATTT
1 ATTAATTT
24431582 AAAAAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 8 0.31
22 12 0.46
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTAATTTTATAATTTAATT
Found at i:24432334 original size:20 final size:20
Alignment explanation
Indices: 24432311--24432352 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
24432301 GTGATAAATG
24432311 ATAAAAATATATT-TTTTATT
1 ATAAAAATA-ATTATTTTATT
*
24432331 ATAATAATAATTATTTTATT
1 ATAAAAATAATTATTTTATT
24432351 AT
1 AT
24432353 TTAATCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAAAAATAATTATTTTATT
Found at i:24432352 original size:23 final size:22
Alignment explanation
Indices: 24432311--24432357 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
24432301 GTGATAAATG
24432311 ATAAAAATATATTTTTTATTATA
1 ATAAAAATATATTTTTTATT-TA
*
24432334 ATAATAAT-TATTTTATTATTTA
1 ATAAAAATATATTTT-TTATTTA
24432356 AT
1 AT
24432358 CTTTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATAAAAATATATTTTTTATTTA
Found at i:24432491 original size:20 final size:18
Alignment explanation
Indices: 24432440--24432497 Score: 89
Period size: 18 Copynumber: 3.1 Consensus size: 18
24432430 TTTTATTTAA
*
24432440 TTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTC
24432458 TTTTTTTTTTTTTTTTTC
1 TTTTTTTTTTTTTTTTTC
24432476 TTTTTTTTTTGGTTTTTTTC
1 TTTTTTTTTT--TTTTTTTC
24432496 TT
1 TT
24432498 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
18 27 0.73
20 10 0.27
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.93
Consensus pattern (18 bp):
TTTTTTTTTTTTTTTTTC
Found at i:24432494 original size:1 final size:1
Alignment explanation
Indices: 24432440--24432485 Score: 83
Period size: 1 Copynumber: 46.0 Consensus size: 1
24432430 TTTTATTTAA
*
24432440 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
24432486 GGTTTTTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.02, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:24436416 original size:30 final size:31
Alignment explanation
Indices: 24436382--24436443 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
24436372 TATTAATTAT
* * *
24436382 AAAGACTTATTTGACTTAAAATAAAAA-ATA
1 AAAGACGTATTTAACTCAAAATAAAAATATA
24436412 AAAGACGTATTTAACTCAAAATAAAAATATA
1 AAAGACGTATTTAACTCAAAATAAAAATATA
24436443 A
1 A
24436444 GGGTTGATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.27
Consensus pattern (31 bp):
AAAGACGTATTTAACTCAAAATAAAAATATA
Found at i:24436864 original size:17 final size:17
Alignment explanation
Indices: 24436844--24436878 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
24436834 TTCTAGAATC
24436844 TTTTCT-TTTTATTCCTT
1 TTTTCTCTTTT-TTCCTT
24436861 TTTTCTCTTTTTTCCTT
1 TTTTCTCTTTTTTCCTT
24436878 T
1 T
24436879 GAAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTCTCTTTTTTCCTT
Found at i:24438566 original size:30 final size:30
Alignment explanation
Indices: 24438530--24438587 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
24438520 ATTATTAATC
24438530 ATAAAGGTTTATTTGACACAAAATAAAATT
1 ATAAAGGTTTATTTGACACAAAATAAAATT
*
24438560 ATAAAGGTTTATTTGACTCAAAATAAAA
1 ATAAAGGTTTATTTGACACAAAATAAAA
24438588 ATAAAATGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (30 bp):
ATAAAGGTTTATTTGACACAAAATAAAATT
Found at i:24441539 original size:22 final size:20
Alignment explanation
Indices: 24441497--24441540 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
24441487 TTTCTCTTTT
*
24441497 AACTTTCTTTTTTGTTTCAA
1 AACTTTCTTTTTTATTTCAA
*
24441517 AACTTTTTATTTTTATTTACAA
1 AACTTTCT-TTTTTATTT-CAA
24441539 AA
1 AA
24441541 TTATGAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 8 0.40
22 5 0.25
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (20 bp):
AACTTTCTTTTTTATTTCAA
Found at i:24449582 original size:28 final size:27
Alignment explanation
Indices: 24449517--24449588 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
24449507 AGCAAAATTA
* *
24449517 TTGAACATGGCATGTAGAAATTTTTTT
1 TTGAAAATGGCATGTAGAAATTTTCTT
* * *
24449544 TTCAAGATGGCGTGTAGAAATATTTCTT
1 TTGAAAATGGCATGTAGAAAT-TTTCTT
*
24449572 TTGAAAATGGCTTGTAG
1 TTGAAAATGGCATGTAG
24449589 CACACTATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 18 0.49
28 19 0.51
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.40
Consensus pattern (27 bp):
TTGAAAATGGCATGTAGAAATTTTCTT
Found at i:24450149 original size:21 final size:21
Alignment explanation
Indices: 24450125--24450168 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
24450115 AGCGACACTT
* *
24450125 GAGGACAACACTATGATGTTC
1 GAGGACAACACTACGATGCTC
**
24450146 GAGGATGACACTACGATGCTC
1 GAGGACAACACTACGATGCTC
24450167 GA
1 GA
24450169 AGATAATACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.20
Consensus pattern (21 bp):
GAGGACAACACTACGATGCTC
Found at i:24453147 original size:71 final size:70
Alignment explanation
Indices: 24453014--24453147 Score: 173
Period size: 71 Copynumber: 1.9 Consensus size: 70
24453004 ACACACCGCG
* * *
24453014 CTTGTAGATGTCATTTACATCTTCTTGTCACACGCCATTTCAAAGAAGTTGTATATTGTTACATG
1 CTTGTAGATGTCATTTACATCTTCTCGTCACACGCCATTTCAAAGAAGTTGTATAATATTACATG
24453079 CTATT
66 CTATT
** *
24453084 CTTGTTAGATGTTGTTTACATCTTCTCGTCACACGCCATTTCACAA-ACGTCT-TATAATATTAC
1 CTTG-TAGATGTCATTTACATCTTCTCGTCACACGCCATTTCA-AAGAAGT-TGTATAATATTAC
24453147 A
63 A
24453148 CGCCATGGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
70 4 0.07
71 48 0.87
72 3 0.05
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (70 bp):
CTTGTAGATGTCATTTACATCTTCTCGTCACACGCCATTTCAAAGAAGTTGTATAATATTACATG
CTATT
Found at i:24457215 original size:42 final size:41
Alignment explanation
Indices: 24457141--24457282 Score: 187
Period size: 42 Copynumber: 3.4 Consensus size: 41
24457131 ACGGCTTATG
* * *
24457141 CGCATATAGCCAGGTCAGCAACGACTTATGTGCACT-CTCACT
1 CGCACATAGCCGGGTCAGCAAAG-CTTATGTGCACTCCT-ACT
* *
24457183 CACACATAGCCGGGTCAGCAATAGCTTGTGTGCACTCCTACT
1 CGCACATAGCCGGGTCAGCAA-AGCTTATGTGCACTCCTACT
*
24457225 CGCACATAGCCGGGTCAGCAACGGCTTATGTGCACTCCTACT
1 CGCACATAGCCGGGTCAGCAA-AGCTTATGTGCACTCCTACT
24457267 CGCACATAGCCGGGTC
1 CGCACATAGCCGGGTC
24457283 CAAATCAACA
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
42 86 0.97
43 3 0.03
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.22
Consensus pattern (41 bp):
CGCACATAGCCGGGTCAGCAAAGCTTATGTGCACTCCTACT
Found at i:24467061 original size:213 final size:213
Alignment explanation
Indices: 24466666--24467109 Score: 572
Period size: 213 Copynumber: 2.1 Consensus size: 213
24466656 TACTTATTTG
* ** **
24466666 TTACATGCCATGAATGAATCCTAAATGGCACGTTGTTACACAATATGCCATGTTGAGTATGCGAT
1 TTACATGCCATGAATAAATCCTAAATCCCACGTTGTTACACAATATGCCATGCCGAGTATGCGAT
*
24466731 TTTAACATTACACGCCATACATGTAATGCTAAGCTAGACCTAAAAACAATTAACCCATAATATGC
66 TTTAACACTACACGCCATACATGTAATGCTAAGCTAGACCTAAAAACAATTAACCCATAATATGC
* ** * *
24466796 ATCACGTTAGATAGAAAAAATTTATTGTTGTTACATGCTATGCAGACCAAGTAAAATATTGTTAC
131 ATCACG-CAGATAGAAAAAACGTATTATTGTTACACGCTATGCAGACCAAGTAAAATATTGTTAC
** *
24466861 ACGTGATGCCTATATATTC
195 ACGCCATACCTATATATTC
* * *
24466880 TTACACGCCATGAATAAATCCTAAA-CCCACGTTGTTACACGATATGCCATGCCGAGTATGCG-G
1 TTACATGCCATGAATAAATCCTAAATCCCACGTTGTTACACAATATGCCATGCCGAGTATGCGAT
* * *** *
24466943 TTTATACACTACACGCCATACATGTAATGTTGAGCTAGACCTAAAAATGGTTAACCCATAATGTG
66 TTTA-ACACTACACGCCATACATGTAATGCTAAGCTAGACCTAAAAACAATTAACCCATAATATG
* *
24467008 CAATACAC-CAGATA-AAAGAAACGTATTATTGTTACACGCTATGCAGACCAAGTACAATGTTGT
130 C-AT-CACGCAGATAGAAA-AAACGTATTATTGTTACACGCTATGCAGACCAAGTAAAATATTGT
*
24467071 TACACGCCATACCTATATGTTC
192 TACACGCCATACCTATATATTC
*
24467093 TTACATGCCATGTATAA
1 TTACATGCCATGAATAA
24467110 TTACTTATTT
Statistics
Matches: 198, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
212 7 0.04
213 163 0.82
214 25 0.13
215 3 0.02
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (213 bp):
TTACATGCCATGAATAAATCCTAAATCCCACGTTGTTACACAATATGCCATGCCGAGTATGCGAT
TTTAACACTACACGCCATACATGTAATGCTAAGCTAGACCTAAAAACAATTAACCCATAATATGC
ATCACGCAGATAGAAAAAACGTATTATTGTTACACGCTATGCAGACCAAGTAAAATATTGTTACA
CGCCATACCTATATATTC
Found at i:24467775 original size:23 final size:23
Alignment explanation
Indices: 24467748--24468051 Score: 224
Period size: 23 Copynumber: 13.2 Consensus size: 23
24467738 AAATTTATGA
24467748 CGTGTCACATATTCTCATCATGG
1 CGTGTCACATATTCTCATCATGG
* *
24467771 TGTGTCACATATTC-CTTCCATGG
1 CGTGTCACATATTCTCAT-CATGG
*
24467794 CATGTCACATATTCTCATCATGG
1 CGTGTCACATATTCTCATCATGG
* * *
24467817 AGTTTCACATATTC-CTTCCATGG
1 CGTGTCACATATTCTCAT-CATGG
* * *
24467840 CGTGTCGCATATTCTCACCATGA
1 CGTGTCACATATTCTCATCATGG
* * * * *
24467863 AGTCTCACATATTTTCACCATGA
1 CGTGTCACATATTCTCATCATGG
* * * * **
24467886 CATCTCACATATTCCCTTCATCC
1 CGTGTCACATATTCTCATCATGG
* *
24467909 CGTGTCATATATTC-CCTCCATGG
1 CGTGTCACATATTCTCAT-CATGG
*
24467932 TGTGTCACATATT-TCATCCATGG
1 CGTGTCACATATTCTCAT-CATGG
* * *
24467955 CATGTCAAATATTC-CTTCCATGG
1 CGTGTCACATATTCTCAT-CATGG
* * **
24467978 CATCTCACATATT-TTTTCCATGG
1 CGTGTCACATATTCTCAT-CATGG
24468001 CGTGTCACATATTCTCATCATGG
1 CGTGTCACATATTCTCATCATGG
* *
24468024 CATGTCACATATTCTCACCATGG
1 CGTGTCACATATTCTCATCATGG
24468047 CGTGT
1 CGTGT
24468052 TATGTGGGAC
Statistics
Matches: 222, Mismatches: 50, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
22 6 0.03
23 211 0.95
24 5 0.02
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (23 bp):
CGTGTCACATATTCTCATCATGG
Found at i:24467825 original size:46 final size:46
Alignment explanation
Indices: 24467750--24468051 Score: 274
Period size: 46 Copynumber: 6.6 Consensus size: 46
24467740 ATTTATGACG
*
24467750 TGTCACATATTCTCATCATGGTGTGTCACATATTCCTTCCATGGCA
1 TGTCACATATTCTCATCATGGAGTGTCACATATTCCTTCCATGGCA
* *
24467796 TGTCACATATTCTCATCATGGAGTTTCACATATTCCTTCCATGGCG
1 TGTCACATATTCTCATCATGGAGTGTCACATATTCCTTCCATGGCA
* * * * *
24467842 TGTCGCATATTCTCACCATGAAGTCTCACATATT--TTCACCATGACA
1 TGTCACATATTCTCATCATGGAGTGTCACATATTCCTT--CCATGGCA
* * * *** * * **
24467888 TCTCACATATTCCCTTCATCCCGTGTCATATATTCCCTCCATGGTG
1 TGTCACATATTCTCATCATGGAGTGTCACATATTCCTTCCATGGCA
*
24467934 TGTCACATATT-TCATCCATGGCA-TGTCAAATATTCCTTCCATGGCA
1 TGTCACATATTCTCAT-CATGG-AGTGTCACATATTCCTTCCATGGCA
* ** * *
24467980 TCTCACATATT-TTTTCCATGGCGTGTCACATATTCTCAT-CATGGCA
1 TGTCACATATTCTCAT-CATGGAGTGTCACATATTC-CTTCCATGGCA
* *
24468026 TGTCACATATTCTCACCATGGCGTGT
1 TGTCACATATTCTCATCATGGAGTGT
24468052 TATGTGGGAC
Statistics
Matches: 204, Mismatches: 43, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
44 2 0.01
45 2 0.01
46 196 0.96
47 3 0.01
48 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.36
Consensus pattern (46 bp):
TGTCACATATTCTCATCATGGAGTGTCACATATTCCTTCCATGGCA
Found at i:24467871 original size:69 final size:69
Alignment explanation
Indices: 24467750--24468051 Score: 285
Period size: 69 Copynumber: 4.4 Consensus size: 69
24467740 ATTTATGACG
* *
24467750 TGTCACATATTCTCAT-CATGGTGTGTCACATATTC-CTTCCATGGCA-TGTCACATATTCTCAT
1 TGTCACATATTC-CTTCCATGGCGTGTCACATATTCTC-TCCATGG-AGTGTCACATATTCTCAT
24467812 CATGG-A
63 CATGGCA
* * * * * * *
24467818 GTTTCACATATTCCTTCCATGGCGTGTCGCATATTCTCACCATGAAGTCTCACATATTTTCACCA
1 -TGTCACATATTCCTTCCATGGCGTGTCACATATTCTCTCCATGGAGTGTCACATATTCTCATCA
*
24467883 TGACA
65 TGGCA
* ** * * *
24467888 TCTCACATATTCCCTT-CATCCCGTGTCATATATTCCCTCCATGGTGTGTCACATATT-TCATCC
1 TGTCACATATT-CCTTCCATGGCGTGTCACATATTCTCTCCATGGAGTGTCACATATTCTCAT-C
24467951 ATGGCA
64 ATGGCA
* * * * * *
24467957 TGTCAAATATTCCTTCCATGGCATCTCACATATTTTTTCCATGGCGTGTCACATATTCTCATCAT
1 TGTCACATATTCCTTCCATGGCGTGTCACATATTCTCTCCATGGAGTGTCACATATTCTCATCAT
24468022 GGCA
66 GGCA
*
24468026 TGTCACATATT-CTCACCATGGCGTGT
1 TGTCACATATTCCT-TCCATGGCGTGT
24468052 TATGTGGGAC
Statistics
Matches: 187, Mismatches: 37, Indels: 18
0.77 0.15 0.07
Matches are distributed among these distances:
68 12 0.06
69 165 0.88
70 10 0.05
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.36
Consensus pattern (69 bp):
TGTCACATATTCCTTCCATGGCGTGTCACATATTCTCTCCATGGAGTGTCACATATTCTCATCAT
GGCA
Found at i:24471871 original size:14 final size:15
Alignment explanation
Indices: 24471839--24471868 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24471829 ACTTATGATG
24471839 AGTTGTTTTAATTTA
1 AGTTGTTTTAATTTA
*
24471854 AGTTGTTTTATTTTA
1 AGTTGTTTTAATTTA
24471869 GTTTTAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.63
Consensus pattern (15 bp):
AGTTGTTTTAATTTA
Found at i:24474837 original size:2 final size:2
Alignment explanation
Indices: 24474824--24475014 Score: 373
Period size: 2 Copynumber: 95.5 Consensus size: 2
24474814 ATGTGGAAAG
*
24474824 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
24474866 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
24474908 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
24474950 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
24474992 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
24475015 AAAATGTCCA
Statistics
Matches: 187, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
2 187 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:24477391 original size:80 final size:82
Alignment explanation
Indices: 24477294--24477496 Score: 205
Period size: 80 Copynumber: 2.5 Consensus size: 82
24477284 AAAGATCTTA
* * * * * * * *
24477294 AACATAAACGTAGATAACTAAAAACAAATATCCATACAACGATATAAACTTAAATAACTATACAT
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAACAACAACATAAACTTAAATAACCAAACAC
*
24477359 AAACATCC-AA-ATAAC
66 AAACATCCAAACACAAC
* * * *
24477374 AACATAAACTTAAATAACTAAACACAAAGATCTAAACAAATAACATAAACTTAAATAACCAAACA
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAAC-AACAACATAAACTTAAATAACCAAACA
** *
24477439 CCTATATCCAAACGACAAC
65 CAAACATCCAAAC-ACAAC
* *
24477458 AATATAAACTTAAATAACT-AAAATAAATATCCAAACAAC
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAACAAC
24477497 TAGTTATAAT
Statistics
Matches: 97, Mismatches: 22, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
80 31 0.32
81 27 0.28
82 4 0.04
83 13 0.13
84 22 0.23
ACGTcount: A:0.58, C:0.20, G:0.02, T:0.20
Consensus pattern (82 bp):
AACATAAACTTAAATAACTAAAAACAAATATCCAAACAACAACATAAACTTAAATAACCAAACAC
AAACATCCAAACACAAC
Found at i:24477431 original size:15 final size:14
Alignment explanation
Indices: 24477378--24477437 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
24477368 AATAACAACA
24477378 TAAACTTAAATAAC
1 TAAACTTAAATAAC
** * *
24477392 TAAACACAAAGATC
1 TAAACTTAAATAAC
24477406 TAAAC--AAATAAC
1 TAAACTTAAATAAC
24477418 ATAAACTTAAATAAC
1 -TAAACTTAAATAAC
*
24477433 CAAAC
1 TAAAC
24477438 ACCTATATCC
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
12 5 0.14
13 5 0.14
14 19 0.53
15 7 0.19
ACGTcount: A:0.60, C:0.18, G:0.02, T:0.20
Consensus pattern (14 bp):
TAAACTTAAATAAC
Found at i:24477431 original size:41 final size:41
Alignment explanation
Indices: 24477294--24477495 Score: 185
Period size: 40 Copynumber: 5.0 Consensus size: 41
24477284 AAAGATCTTA
* * * * *
24477294 AACATAAACGTAGATAACTAAAAACAAATATCCATAC-AAC
1 AACATAAACTTAAATAACTAAACACAAACATCCAAACAAAC
* * * * *
24477334 GATATAAACTTAAATAACTATACATAAACATCCAAA-TAAC
1 AACATAAACTTAAATAACTAAACACAAACATCCAAACAAAC
* * *
24477374 AACATAAACTTAAATAACTAAACACAAAGATCTAAACAAAT
1 AACATAAACTTAAATAACTAAACACAAACATCCAAACAAAC
* ** *
24477415 AACATAAACTTAAATAACCAAACACCTATATCCAAACGACAAC
1 AACATAAACTTAAATAACTAAACACAAACATCCAAAC-A-AAC
* * *
24477458 AATATAAACTTAAATAACTAAA-ATAAATATCCAAACAA
1 AACATAAACTTAAATAACTAAACACAAACATCCAAACAA
24477496 CTAGTTATAA
Statistics
Matches: 130, Mismatches: 28, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
40 61 0.47
41 35 0.27
42 12 0.09
43 22 0.17
ACGTcount: A:0.58, C:0.19, G:0.02, T:0.20
Consensus pattern (41 bp):
AACATAAACTTAAATAACTAAACACAAACATCCAAACAAAC
Found at i:24477534 original size:28 final size:28
Alignment explanation
Indices: 24477502--24477559 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
24477492 ACAACTAGTT
**
24477502 ATAATATAAAGTGTATGTGTTAAAAGAC
1 ATAATATAAAAAGTATGTGTTAAAAGAC
24477530 ATAATATAAAAAGTATGTGTTAAAAGAC
1 ATAATATAAAAAGTATGTGTTAAAAGAC
24477558 AT
1 AT
24477560 TACAAGTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.31
Consensus pattern (28 bp):
ATAATATAAAAAGTATGTGTTAAAAGAC
Found at i:24477630 original size:15 final size:17
Alignment explanation
Indices: 24477610--24477642 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
24477600 ATTACAATTA
24477610 ATAA-TTTTATAA-GTT
1 ATAATTTTTATAATGTT
24477625 ATAATTTTTATAATGTT
1 ATAATTTTTATAATGTT
24477642 A
1 A
24477643 ACACAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
ATAATTTTTATAATGTT
Found at i:24478289 original size:10 final size:10
Alignment explanation
Indices: 24478275--24478308 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
24478265 AAAGGCTTAA
24478275 AAATAAAAAT
1 AAATAAAAAT
*
24478285 TAATAAAAAAT
1 AAAT-AAAAAT
24478296 AAATAAAAAT
1 AAATAAAAAT
24478306 AAA
1 AAA
24478309 AACTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:24478321 original size:17 final size:17
Alignment explanation
Indices: 24478273--24478320 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
24478263 AAAAAGGCTT
*
24478273 AAAAATAAA-AATTAATA
1 AAAAATAAATAA-AAATA
24478290 AAAAATAAATAAAAATA
1 AAAAATAAATAAAAATA
*
24478307 AAAACT-AATAAAAA
1 AAAAATAAATAAAAA
24478321 AAATGATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 8 0.29
17 18 0.64
18 2 0.07
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAAATAAATAAAAATA
Found at i:24488737 original size:20 final size:20
Alignment explanation
Indices: 24488714--24488780 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
24488704 ATTATCCTCA
24488714 AACCTTGGCCTTGCTACTTT
1 AACCTTGGCCTTGCTACTTT
* * **
24488734 AACCTTGATG-CTT-ATCCTCA
1 AACCTTG--GCCTTGCTACTTT
24488754 AACCTTGGCCTTGCTACTTT
1 AACCTTGGCCTTGCTACTTT
24488774 AACCTTG
1 AACCTTG
24488781 ATGCTGGTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 1 0.03
19 3 0.09
20 27 0.77
21 3 0.09
22 1 0.03
ACGTcount: A:0.19, C:0.30, G:0.13, T:0.37
Consensus pattern (20 bp):
AACCTTGGCCTTGCTACTTT
Found at i:24488760 original size:40 final size:40
Alignment explanation
Indices: 24488705--24488785 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
24488695 CGATTGGATA
24488705 TTATCCTCAAACCTTGGCCTTGCTACTTTAACCTTGATGC
1 TTATCCTCAAACCTTGGCCTTGCTACTTTAACCTTGATGC
24488745 TTATCCTCAAACCTTGGCCTTGCTACTTTAACCTTGATGC
1 TTATCCTCAAACCTTGGCCTTGCTACTTTAACCTTGATGC
24488785 T
1 T
24488786 GGTTTTTATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.20, C:0.30, G:0.12, T:0.38
Consensus pattern (40 bp):
TTATCCTCAAACCTTGGCCTTGCTACTTTAACCTTGATGC
Found at i:24496812 original size:19 final size:19
Alignment explanation
Indices: 24496788--24496825 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24496778 CTGCCAAACC
*
24496788 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
24496807 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
24496826 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:24500671 original size:14 final size:14
Alignment explanation
Indices: 24500651--24500693 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
24500641 AATTTTAAGA
24500651 TAAAATAATATTATTT
1 TAAAATAATATTA--T
24500667 TAATAA-AATATTAT
1 TAA-AATAATATTAT
24500681 TAAAATAATATTA
1 TAAAATAATATTA
24500694 AAATCATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.08
14 11 0.44
16 10 0.40
17 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAAATAATATTAT
Found at i:24503768 original size:28 final size:29
Alignment explanation
Indices: 24503727--24503786 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
24503717 GTCTATGGGC
*
24503727 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
24503755 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
24503785 AA
1 AA
24503787 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:24506935 original size:21 final size:21
Alignment explanation
Indices: 24506905--24506957 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
24506895 GGATATGTTC
24506905 ATGCAATTCATGACAAAGACTA
1 ATGC-ATTCATGACAAAGACTA
24506927 ATGCATTCATGACAAAGACTA
1 ATGCATTCATGACAAAGACTA
24506948 ATGCATTCAT
1 ATGCATTCAT
24506958 TCAAAATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (21 bp):
ATGCATTCATGACAAAGACTA
Found at i:24508339 original size:6 final size:5
Alignment explanation
Indices: 24508310--24508348 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
24508300 TCTGACTTGC
*
24508310 TTTAT TTTAT TTTAT TTTACT TTTAT TTT-T ATTAT TTTA
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTA
24508349 ATTATTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 3 0.10
5 22 0.73
6 5 0.17
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:24508422 original size:14 final size:12
Alignment explanation
Indices: 24508393--24508493 Score: 60
Period size: 12 Copynumber: 7.4 Consensus size: 12
24508383 AGGTTCATGT
24508393 AAAAAAATTTCA
1 AAAAAAATTTCA
24508405 AAAAAAATTTCAAGAA
1 AAAAAAATTTC----A
24508421 AAAAATATATTTCA
1 AAAAA-A-ATTTCA
*
24508435 AAAAAATTTTCATGTAA
1 AAAAAAATTTC-----A
24508452 AAAAAAATTTTTCA
1 AAAAAAA--TTTCA
*
24508466 AAAAAATTTTCA
1 AAAAAAATTTCA
24508478 AAAAAAA-TTCA
1 AAAAAAATTTCA
24508489 AAAAA
1 AAAAA
24508494 TAAAAAATTC
Statistics
Matches: 72, Mismatches: 4, Indels: 27
0.70 0.04 0.26
Matches are distributed among these distances:
11 9 0.12
12 26 0.36
13 1 0.01
14 13 0.18
16 6 0.08
17 8 0.11
18 5 0.07
19 4 0.06
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (12 bp):
AAAAAAATTTCA
Found at i:24508454 original size:31 final size:30
Alignment explanation
Indices: 24508393--24508484 Score: 125
Period size: 31 Copynumber: 3.1 Consensus size: 30
24508383 AGGTTCATGT
*
24508393 AAAAAA-ATTTCAAAAAAAATTTCAAGAAA
1 AAAAAATATTTCAAAAAAATTTTCAAGAAA
* *
24508422 AAAATATATTTCAAAAAAATTTTCATGTAAA
1 AAAAAATATTTCAAAAAAATTTTCAAG-AAA
*
24508453 AAAAAATTTTTCAAAAAAATTTTCAA-AAA
1 AAAAAATATTTCAAAAAAATTTTCAAGAAA
24508482 AAA
1 AAA
24508485 TTCAAAAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.20
30 18 0.33
31 26 0.47
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (30 bp):
AAAAAATATTTCAAAAAAATTTTCAAGAAA
Found at i:24508500 original size:17 final size:16
Alignment explanation
Indices: 24508477--24508513 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
24508467 AAAAATTTTC
24508477 AAAAAAAATTCAAAAA
1 AAAAAAAATTCAAAAA
*
24508493 ATAAAAAATTCAAAAA
1 AAAAAAAATTCAAAAA
24508509 AAAAA
1 AAAAA
24508514 TGTTAAGCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAAAAATTCAAAAA
Found at i:24516815 original size:3 final size:3
Alignment explanation
Indices: 24516807--24516852 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
24516797 CACACCATCC
*
24516807 CAT CAT CAT CAT CAT CAT GCA- CAT CAT C-C CAT CAT CAT CAT C-T
1 CAT CAT CAT CAT CAT CAT -CAT CAT CAT CAT CAT CAT CAT CAT CAT
24516850 CAT
1 CAT
24516853 ATGCAACGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 5 0.14
3 30 0.81
4 2 0.05
ACGTcount: A:0.30, C:0.37, G:0.02, T:0.30
Consensus pattern (3 bp):
CAT
Found at i:24516826 original size:29 final size:29
Alignment explanation
Indices: 24516784--24516852 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
24516774 ACCATATACC
*
24516784 CATCATCAACATGCACACCATCCCATCAT
1 CATCATCATCATGCACACCATCCCATCAT
*
24516813 CATCATCATCATGCACATCATCCCATCAT
1 CATCATCATCATGCACACCATCCCATCAT
24516842 CATCATC-TCAT
1 CATCATCATCAT
24516853 ATGCAACGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 4 0.11
29 34 0.89
ACGTcount: A:0.32, C:0.39, G:0.03, T:0.26
Consensus pattern (29 bp):
CATCATCATCATGCACACCATCCCATCAT
Found at i:24517049 original size:86 final size:86
Alignment explanation
Indices: 24516904--24517069 Score: 287
Period size: 86 Copynumber: 1.9 Consensus size: 86
24516894 ATGAAGCATC
* *
24516904 CCCCCCTTCACTCGGCAATAGGTGCACTTCACTCCAGATCACGAAGCAACGGAGCAGTCCCTTTC
1 CCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCAGATCACGAAGCAACGGAGCAGTCCCTTCC
*
24516969 CTCATCTTCTAAGCTTCCCCT
66 CTCATCTTCCAAGCTTCCCCT
*
24516990 CCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGGAGCAGTCCCTTCC
1 CCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCAGATCACGAAGCAACGGAGCAGTCCCTTCC
*
24517055 CTCCTCTTCCAAGCT
66 CTCATCTTCCAAGCT
24517070 CTTGGGCGAA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 75 1.00
ACGTcount: A:0.20, C:0.40, G:0.17, T:0.22
Consensus pattern (86 bp):
CCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCAGATCACGAAGCAACGGAGCAGTCCCTTCC
CTCATCTTCCAAGCTTCCCCT
Found at i:24517227 original size:42 final size:42
Alignment explanation
Indices: 24517169--24517418 Score: 401
Period size: 42 Copynumber: 6.0 Consensus size: 42
24517159 ACGGAGGCAA
* * *
24517169 CAACGGCTTATGTGCACTCCCACTCACACATAGCCAGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* *
24517211 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGAGTTAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* *
24517253 CAACGGCTTATGTACACTCCTACTCGCACATAGCCAGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* *
24517295 CAATGGCTTATGTGCACTCCTACTCGCACATAGTCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
*
24517337 CAACGGCTTATGTGCACTCCTACTCGCACATAGTCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
*
24517379 CAATGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
24517419 CAAATCAACA
Statistics
Matches: 192, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 192 1.00
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
Found at i:24522025 original size:37 final size:37
Alignment explanation
Indices: 24521930--24522035 Score: 185
Period size: 38 Copynumber: 2.8 Consensus size: 37
24521920 ACCTAGCTCA
*
24521930 TGTGCAACCCCCACATCGTGCACAGGTAATACCGTCG
1 TGTGCATCCCCCACATCGTGCACAGGTAATACCGTCG
*
24521967 TGTGCATCCCCCCACATCGTGCACAGGTAATACCGTTG
1 TGTGCAT-CCCCCACATCGTGCACAGGTAATACCGTCG
24522005 TGTGCATCCCCCACATCGTGCACAGGTAATA
1 TGTGCATCCCCCACATCGTGCACAGGTAATA
24522036 TCATCATCCA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
37 30 0.45
38 36 0.55
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.22
Consensus pattern (37 bp):
TGTGCATCCCCCACATCGTGCACAGGTAATACCGTCG
Found at i:24522291 original size:30 final size:30
Alignment explanation
Indices: 24522255--24522326 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
24522245 CATTTTTAAG
24522255 TAAAACAAATAAAATTTCCAAATGATTCAT
1 TAAAACAAATAAAATTTCCAAATGATTCAT
24522285 TAAAACAAATAAAATTTCCAAATGATTCAT
1 TAAAACAAATAAAATTTCCAAATGATTCAT
*
24522315 TAAAACACATAA
1 TAAAACAAATAA
24522327 GCATTTTCCC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.28
Consensus pattern (30 bp):
TAAAACAAATAAAATTTCCAAATGATTCAT
Found at i:24523585 original size:18 final size:17
Alignment explanation
Indices: 24523564--24523599 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
24523554 CTTTCCTTTC
*
24523564 CTTTCTCTTTTCTTATTT
1 CTTTCCCTTTTCTT-TTT
24523582 CTTTCCCTTTTCTTTTT
1 CTTTCCCTTTTCTTTTT
24523599 C
1 C
24523600 CCGTTTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (17 bp):
CTTTCCCTTTTCTTTTT
Found at i:24527439 original size:17 final size:16
Alignment explanation
Indices: 24527405--24527457 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
24527395 TTCTCAGCTT
24527405 ATTTAGTTTATTAGTTA
1 ATTTAGTTT-TTAGTTA
*
24527422 ATTTAGTTTTTATTTTA
1 ATTTAGTTTTTA-GTTA
* *
24527439 ATTTTG-TTTTAATTA
1 ATTTAGTTTTTAGTTA
24527454 ATTT
1 ATTT
24527458 TTTGTAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 7 0.22
16 8 0.25
17 17 0.53
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (16 bp):
ATTTAGTTTTTAGTTA
Found at i:24528596 original size:13 final size:14
Alignment explanation
Indices: 24528573--24528601 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
24528563 GTTTCCCTTC
24528573 CTTTATTTGTTTTG
1 CTTTATTTGTTTTG
24528587 CTTT-TTTGTTTTG
1 CTTTATTTGTTTTG
24528600 CT
1 CT
24528602 AGGCTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.03, C:0.10, G:0.14, T:0.72
Consensus pattern (14 bp):
CTTTATTTGTTTTG
Found at i:24537383 original size:2 final size:2
Alignment explanation
Indices: 24537378--24537432 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
24537368 TATATAGAAC
*
24537378 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24537420 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
24537433 GGAAAAGATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24543099 original size:20 final size:20
Alignment explanation
Indices: 24543076--24543114 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
24543066 ACATCTATGG
24543076 ATAGATGAGC-AGATCTATCT
1 ATAGAT-AGCTAGATCTATCT
*
24543096 ATAGATAGCTAGATTTATC
1 ATAGATAGCTAGATCTATC
24543115 GATAAATGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (20 bp):
ATAGATAGCTAGATCTATCT
Found at i:24547683 original size:24 final size:24
Alignment explanation
Indices: 24547644--24547689 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
24547634 TGGTCATTAT
* *
24547644 CTATAATAATAGTTTTCAGGCTGC
1 CTATAATAACAATTTTCAGGCTGC
*
24547668 CTATAATAACAATTTTTAGGCT
1 CTATAATAACAATTTTCAGGCT
24547690 AGCATTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (24 bp):
CTATAATAACAATTTTCAGGCTGC
Found at i:24562360 original size:16 final size:16
Alignment explanation
Indices: 24562336--24562370 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
24562326 AACAAGTTAA
24562336 AAAACAAAAAAAAAAG
1 AAAACAAAAAAAAAAG
* *
24562352 AAAAGAAAAGAAAAAG
1 AAAACAAAAAAAAAAG
24562368 AAA
1 AAA
24562371 CACCCATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAACAAAAAAAAAAG
Found at i:24566744 original size:93 final size:95
Alignment explanation
Indices: 24566590--24566770 Score: 259
Period size: 99 Copynumber: 1.9 Consensus size: 95
24566580 AAAGAAAAGC
24566590 AAAAGAAAAAGAAAAACAACCCCGACCACAGACAAAGGGAAAAGTAGCTAGACGATGAAAAAAAG
1 AAAAGAAAAAGAAAAACAACCCCGA-CACAGACAAAGGGAAAAGTAGCTAGACGATGAAAAAAAG
24566655 TTTAAGAACAAAAGAAAATA-ATAATAATACCAA
65 TTT--G-ACAAAAGAAAATATATAATAATACCAA
24566688 NAAAAGAAAAAGAAAAAC-ACCCCG-CACAG-CAAAGGGAAAA-T-GCTAG-CGATGAAAAAAAA
1 -AAAAGAAAAAGAAAAACAACCCCGACACAGACAAAGGGAAAAGTAGCTAGACGATG-AAAAAAA
24566747 GTTTGACAAAAGAAAATATATAAT
64 GTTTGACAAAAGAAAATATATAAT
24566771 CCAATAATCT
Statistics
Matches: 80, Mismatches: 0, Indels: 12
0.87 0.00 0.13
Matches are distributed among these distances:
90 13 0.16
91 6 0.08
92 5 0.06
93 16 0.20
94 1 0.01
95 11 0.14
96 5 0.06
98 6 0.08
99 17 0.21
ACGTcount: A:0.59, C:0.14, G:0.16, T:0.11
Consensus pattern (95 bp):
AAAAGAAAAAGAAAAACAACCCCGACACAGACAAAGGGAAAAGTAGCTAGACGATGAAAAAAAGT
TTGACAAAAGAAAATATATAATAATACCAA
Found at i:24570072 original size:20 final size:20
Alignment explanation
Indices: 24570047--24570087 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
24570037 AATGATTATA
*
24570047 AATTGATTAC-TTAGTGTTAC
1 AATTGATT-CTTTAGTCTTAC
24570067 AATTGATTCTTTAGTCTTAC
1 AATTGATTCTTTAGTCTTAC
24570087 A
1 A
24570088 TTCTCACAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (20 bp):
AATTGATTCTTTAGTCTTAC
Found at i:24582025 original size:21 final size:20
Alignment explanation
Indices: 24581980--24582026 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
24581970 TCATCATTAT
**
24581980 CATTTTGGAATGTATCGGTA
1 CATTTTGGAATGTATCCATA
24582000 CATTTTGGAAATGTATCCATA
1 CATTTTGG-AATGTATCCATA
*
24582021 TATTTT
1 CATTTT
24582027 AGTAAGAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.45
Consensus pattern (20 bp):
CATTTTGGAATGTATCCATA
Found at i:24582207 original size:21 final size:22
Alignment explanation
Indices: 24582173--24582222 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
24582163 TGCAAGGGAG
*
24582173 GTTT-AAAACTTATTTAAACAA
1 GTTTAAAAACTTATTCAAACAA
*
24582194 GTTTAAAAAC-TATTCAAACTA
1 GTTTAAAAACTTATTCAAACAA
*
24582215 GTTCAAAA
1 GTTTAAAA
24582223 GTCATTCAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (22 bp):
GTTTAAAAACTTATTCAAACAA
Found at i:24582308 original size:21 final size:22
Alignment explanation
Indices: 24582284--24582370 Score: 108
Period size: 21 Copynumber: 4.1 Consensus size: 22
24582274 AACCTTATTT
24582284 AAACAAGTTTAAAAACT-ATTC
1 AAACAAGTTTAAAAACTCATTC
*
24582305 AAACAAGTTCAAAAACTCATTC
1 AAACAAGTTTAAAAACTCATTC
* *
24582327 CAACAACTTTAAAAA-TCATTC
1 AAACAAGTTTAAAAACTCATTC
* *
24582348 AAACAAGTTCAAAGA-TCATTC
1 AAACAAGTTTAAAAACTCATTC
24582369 AA
1 AA
24582371 GCAATTTTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
21 41 0.72
22 16 0.28
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.25
Consensus pattern (22 bp):
AAACAAGTTTAAAAACTCATTC
Found at i:24582348 original size:43 final size:42
Alignment explanation
Indices: 24582285--24582368 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 42
24582275 ACCTTATTTA
*
24582285 AACAAGTTTAAAAACTATTCAAACAAGTTCAAAAACTCATTCC
1 AACAACTTTAAAAACTATTCAAACAAGTTCAAAAA-TCATTCC
*
24582328 AACAACTTTAAAAA-TCATTCAAACAAGTTCAAAGATCATTC
1 AACAACTTTAAAAACT-ATTCAAACAAGTTCAAAAATCATTC
24582369 AAGCAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 7 0.18
43 31 0.82
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.26
Consensus pattern (42 bp):
AACAACTTTAAAAACTATTCAAACAAGTTCAAAAATCATTCC
Found at i:24582487 original size:21 final size:21
Alignment explanation
Indices: 24582454--24582512 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
24582444 ATAAATTAAG
24582454 TTCAAAAACTCATTCAAACAAC
1 TTCAAAAA-TCATTCAAACAAC
* *
24582476 TTCAAAAATCATTGAAACAAG
1 TTCAAAAATCATTCAAACAAC
* *
24582497 TTTAAAGATCATTCAA
1 TTCAAAAATCATTCAA
24582513 GCAATTTTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 24 0.75
22 8 0.25
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (21 bp):
TTCAAAAATCATTCAAACAAC
Found at i:24594434 original size:2 final size:2
Alignment explanation
Indices: 24594419--24594463 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
24594409 CACGGCCACC
24594419 CT CT C- CT C- CT CT CT CT CT CT CT CT CT 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 CT CT
24594459 CT CT C
1 CT CT C
24594464 ATCTGTTGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:24601943 original size:2 final size:2
Alignment explanation
Indices: 24601936--24601990 Score: 101
Period size: 2 Copynumber: 27.0 Consensus size: 2
24601926 AATATCTTCA
24601936 AT AT AT AT ANT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24601979 AT AT AT AT AT AT
1 AT AT AT AT AT AT
24601991 TGTACTTGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24605273 original size:38 final size:38
Alignment explanation
Indices: 24605212--24605285 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
24605202 TTTGTGAAAC
* **
24605212 CCTCACAAAAACTCATTTTTCACATAAGGATTATTTCT
1 CCTCACAAAAACTCATTTGTCACATAAAAATTATTTCT
* *
24605250 CCTCTCAAAACCTCATTTGTCACATAAAAATTATTT
1 CCTCACAAAAACTCATTTGTCACATAAAAATTATTT
24605286 ATCTATGCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.36
Consensus pattern (38 bp):
CCTCACAAAAACTCATTTGTCACATAAAAATTATTTCT
Found at i:24606977 original size:17 final size:16
Alignment explanation
Indices: 24606949--24606981 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
24606939 CACACAACGA
24606949 TTAAATATATAAATAG
1 TTAAATATATAAATAG
24606965 TTAAATAATATAAATAG
1 TTAAAT-ATATAAATAG
24606982 AAAGAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
TTAAATATATAAATAG
Found at i:24607177 original size:18 final size:19
Alignment explanation
Indices: 24607150--24607185 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
24607140 GTAAAAGCAC
24607150 AAAGAGAAGAGAAAGAAAA
1 AAAGAGAAGAGAAAGAAAA
*
24607169 AAAGA-AAGAGGAAGAAA
1 AAAGAGAAGAGAAAGAAA
24607186 GAGGTGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (19 bp):
AAAGAGAAGAGAAAGAAAA
Found at i:24607353 original size:49 final size:48
Alignment explanation
Indices: 24607294--24607431 Score: 192
Period size: 47 Copynumber: 2.9 Consensus size: 48
24607284 TTTGAGGAAG
*
24607294 CCATTAAAAAATATATAATAAATAATAAATTCCATAAATTTTGGAAAAGA
1 CCATT-AAAAATATATAATAAATAA-AAATTCCAAAAATTTTGGAAAAGA
* *
24607344 TCATTAAAAATATATAATAAATAAAAATTCCAAAAATTTT-GAAAAGG
1 CCATTAAAAATATATAATAAATAAAAATTCCAAAAATTTTGGAAAAGA
*
24607391 CCATTAAAAATATAT-AT-AATAAAAAATTTCAAAAATTTTGG
1 CCATTAAAAATATATAATAAAT-AAAAATTCCAAAAATTTTGG
24607432 GGAACTCTCA
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
45 3 0.04
46 19 0.23
47 21 0.26
48 15 0.19
49 19 0.23
50 4 0.05
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (48 bp):
CCATTAAAAATATATAATAAATAAAAATTCCAAAAATTTTGGAAAAGA
Found at i:24607396 original size:47 final size:47
Alignment explanation
Indices: 24607293--24607430 Score: 190
Period size: 46 Copynumber: 2.9 Consensus size: 47
24607283 TTTTGAGGAA
*
24607293 GCCATTAAAAAATATATAATAAATAATAAATTCCATAAATTTTGGAAAAG
1 GCCATT-AAAAATATATAATAAATAA-AAATTCCAAAAATTTT-GAAAAG
**
24607343 ATCATTAAAAATATATAATAAATAAAAATTCCAAAAATTTTGAAAAG
1 GCCATTAAAAATATATAATAAATAAAAATTCCAAAAATTTTGAAAAG
*
24607390 GCCATTAAAAATATAT-AT-AATAAAAAATTTCAAAAATTTTG
1 GCCATTAAAAATATATAATAAAT-AAAAATTCCAAAAATTTTG
24607431 GGGAACTCTC
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
45 3 0.04
46 20 0.25
47 20 0.25
48 15 0.19
49 19 0.23
50 4 0.05
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (47 bp):
GCCATTAAAAATATATAATAAATAAAAATTCCAAAAATTTTGAAAAG
Found at i:24610511 original size:19 final size:19
Alignment explanation
Indices: 24610487--24610531 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
24610477 CTAGTCTCAT
24610487 TTTCATAGTGAAATTCACA
1 TTTCATAGTGAAATTCACA
24610506 TTTCATAGTGAAATTCACA
1 TTTCATAGTGAAATTCACA
24610525 TTTCATA
1 TTTCATA
24610532 AACATATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (19 bp):
TTTCATAGTGAAATTCACA
Found at i:24611281 original size:65 final size:65
Alignment explanation
Indices: 24611159--24611283 Score: 160
Period size: 65 Copynumber: 1.9 Consensus size: 65
24611149 TGGAAACATA
* * * * * *
24611159 ATCATCCATCATACTAGACGTAATGACAAAGTGTGGAATGTTGCCTCATACCGTGTGAAAATGTT
1 ATCATCCATCACACTAAACGCAATCACAAAGTGTGGAATGTTACCTCACACCGTGTGAAAATGTT
* * * *
24611224 ATCATCCATCACACTAAACGCAATCACTATGTGTGGAATGTTACCTCACATCTTGTGAAA
1 ATCATCCATCACACTAAACGCAATCACAAAGTGTGGAATGTTACCTCACACCGTGTGAAA
24611284 GCTCTAGGAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
65 50 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (65 bp):
ATCATCCATCACACTAAACGCAATCACAAAGTGTGGAATGTTACCTCACACCGTGTGAAAATGTT
Found at i:24617233 original size:14 final size:14
Alignment explanation
Indices: 24617214--24617240 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24617204 TATATTATAA
24617214 AGGCACTTGGCACT
1 AGGCACTTGGCACT
24617228 AGGCACTTGGCAC
1 AGGCACTTGGCAC
24617241 AAGCAGGTGC
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:0.22, C:0.30, G:0.30, T:0.19
Consensus pattern (14 bp):
AGGCACTTGGCACT
Found at i:24620127 original size:9 final size:9
Alignment explanation
Indices: 24620113--24620152 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
24620103 TGTTGTTAGG
24620113 AAAGGTTTA
1 AAAGGTTTA
*
24620122 AAAGGTTATGG
1 AAAGGTT-T-A
24620133 AAAGGTTTA
1 AAAGGTTTA
24620142 AAAGGTTTA
1 AAAGGTTTA
24620151 AA
1 AA
24620153 GGATATGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 18 0.67
10 2 0.07
11 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (9 bp):
AAAGGTTTA
Found at i:24620136 original size:20 final size:19
Alignment explanation
Indices: 24620107--24620148 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
24620097 AATATGTGTT
24620107 GTTAGGAAAGGTTTAAAAG
1 GTTAGGAAAGGTTTAAAAG
24620126 GTTATGGAAAGGTTTAAAAG
1 GTTA-GGAAAGGTTTAAAAG
24620146 GTT
1 GTT
24620149 TAAAGGATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (19 bp):
GTTAGGAAAGGTTTAAAAG
Found at i:24621072 original size:44 final size:41
Alignment explanation
Indices: 24621018--24621170 Score: 113
Period size: 44 Copynumber: 3.7 Consensus size: 41
24621008 TGGCATTAGT
*
24621018 TGTGAGCGATGTGAAGGTGCACACGATGATGATGATATATGCCA
1 TGTGCGCGATGTG--GGTGCACAC-ATGATGATGATATATGCCA
* *
24621062 TGTGCGCGATGTGGG-GGAGCACATGATG--GCAT-TA-G--T
1 TGTGCGCGATGTGGGTGCA-CACATGATGATG-ATATATGCCA
*
24621098 TGTGCGAGATGTGGGGGTGCACACAATGATGATGATATATGCCA
1 TGTGCGCGATGT--GGGTGCACAC-ATGATGATGATATATGCCA
* * *
24621142 TGTGCACGATGTGGGGGGAGCACATGATG
1 TGTGCGCGATGTGGGTGCA-CACATGATG
24621171 GCATTAGTTG
Statistics
Matches: 86, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
36 11 0.13
38 7 0.08
39 11 0.13
40 4 0.05
41 11 0.13
42 17 0.20
43 3 0.03
44 22 0.26
ACGTcount: A:0.25, C:0.14, G:0.37, T:0.24
Consensus pattern (41 bp):
TGTGCGCGATGTGGGTGCACACATGATGATGATATATGCCA
Found at i:24621098 original size:80 final size:81
Alignment explanation
Indices: 24620964--24621205 Score: 357
Period size: 80 Copynumber: 3.0 Consensus size: 81
24620954 AGGGAGTGTG
* *
24620964 GATGATGAGAT-TGCCTATGTGCGTGATGTGGGGGGAGCACATGATGGCATTAGTTGTGAGCGAT
1 GATGATGATATATGCC-ATGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGTTGTGAGCGAT
*
24621028 GTGAAGGTGCACACGAT
65 GTGAGGGTGCACACGAT
* *
24621045 GATGATGATATATGCCATGTGCGCGATGT-GGGGGAGCACATGATGGCATTAGTTGTGCGAGATG
1 GATGATGATATATGCCATGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGTTGTGAGCGATG
* *
24621109 TGGGGGTGCACACAAT
66 TGAGGGTGCACACGAT
*
24621125 GATGATGATATATGCCATGTGCACGATGTGGGGGGAGCACATGATGGCATTAGTTGTGCA-CGAT
1 GATGATGATATATGCCATGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGTTGTG-AGCGAT
24621189 GT-AGGGGTGCACACGAT
65 GTGA-GGGTGCACACGAT
24621206 AACTCCGGCT
Statistics
Matches: 145, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
80 74 0.51
81 67 0.46
82 4 0.03
ACGTcount: A:0.24, C:0.14, G:0.37, T:0.25
Consensus pattern (81 bp):
GATGATGATATATGCCATGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGTTGTGAGCGATG
TGAGGGTGCACACGAT
Found at i:24633426 original size:30 final size:30
Alignment explanation
Indices: 24633362--24633428 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
24633352 AGGAAATTTT
** * *
24633362 AAAAAATTACATTTTTACCCCCGTAAAGTG
1 AAAAAATTACATTTTTACCCCCAAAAACTA
**
24633392 AAAAAATTACATTTTTTGCCCCAAAAACTA
1 AAAAAATTACATTTTTACCCCCAAAAACTA
24633422 AAAAAAT
1 AAAAAAT
24633429 GCCCATAGAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.28
Consensus pattern (30 bp):
AAAAAATTACATTTTTACCCCCAAAAACTA
Found at i:24636318 original size:22 final size:24
Alignment explanation
Indices: 24636280--24636344 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 24
24636270 GCACACGGGC
* *
24636280 CTCTTTCTAGTTGTTTT-TT-TTT
1 CTCTTTCTACTTCTTTTCTTCTTT
24636302 CTCTTTCTACTTCTTTTCTTCTTT
1 CTCTTTCTACTTCTTTTCTTCTTT
*
24636326 CTTTTTTCT-CTT-TTTTCTT
1 C-TCTTTCTACTTCTTTTCTT
24636345 AGCCCTCCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 15 0.41
23 9 0.24
24 7 0.19
25 6 0.16
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.72
Consensus pattern (24 bp):
CTCTTTCTACTTCTTTTCTTCTTT
Found at i:24639318 original size:6 final size:6
Alignment explanation
Indices: 24639307--24639355 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
24639297 GACCTTTCAA
* *
24639307 CCCAGC CCCAGC CCCAGC CCCAGC CCCAGC CCCAGT CCCAGT CCCAGC
1 CCCAGC CCCAGC CCCAGC CCCAGC CCCAGC CCCAGC CCCAGC CCCAGC
24639355 C
1 C
24639356 AGCCTCAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.16, C:0.63, G:0.16, T:0.04
Consensus pattern (6 bp):
CCCAGC
Found at i:24643857 original size:1 final size:1
Alignment explanation
Indices: 24643853--24643878 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
24643843 TATCCAAGAT
24643853 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
24643879 CTTGAANNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:24645892 original size:29 final size:29
Alignment explanation
Indices: 24645833--24645950 Score: 119
Period size: 29 Copynumber: 4.0 Consensus size: 29
24645823 ACCCACACAA
* * * *
24645833 TGCCTTTTCATGGGAGCAAGCATAAGCTTT
1 TGCCTTTTCA-AGGATCAGGCATAACCTTT
* *
24645863 TACCTTTTCATGGATCAGGCATAACCTTT
1 TGCCTTTTCAAGGATCAGGCATAACCTTT
* * ** *
24645892 TGCCTCTTCAAGGATTAGGTGTAACCTCT
1 TGCCTTTTCAAGGATCAGGCATAACCTTT
*
24645921 TGCCTTTTCAAGGATCAGGCATAACTTTT
1 TGCCTTTTCAAGGATCAGGCATAACCTTT
24645950 T
1 T
24645951 CACAACAGTG
Statistics
Matches: 70, Mismatches: 18, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
29 61 0.87
30 9 0.13
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (29 bp):
TGCCTTTTCAAGGATCAGGCATAACCTTT
Found at i:24658837 original size:21 final size:20
Alignment explanation
Indices: 24658807--24658845 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
24658797 ATGTGCCAAT
*
24658807 GTATCAAGACCTACCTTCAAA
1 GTATCAAGACAT-CCTTCAAA
*
24658828 GTATCGAGACATCCTTCA
1 GTATCAAGACATCCTTCA
24658846 TCCTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
GTATCAAGACATCCTTCAAA
Found at i:24665138 original size:13 final size:14
Alignment explanation
Indices: 24665110--24665138 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
24665100 ACATAAAATA
24665110 TACTTAAAATCAAT
1 TACTTAAAATCAAT
24665124 TACTTAAAA-CAAT
1 TACTTAAAATCAAT
24665137 TA
1 TA
24665139 AAATAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
TACTTAAAATCAAT
Found at i:24685854 original size:27 final size:27
Alignment explanation
Indices: 24685816--24685897 Score: 164
Period size: 27 Copynumber: 3.0 Consensus size: 27
24685806 ACAAATACTA
24685816 GTTACTATATCCCCAAACACTGAACAT
1 GTTACTATATCCCCAAACACTGAACAT
24685843 GTTACTATATCCCCAAACACTGAACAT
1 GTTACTATATCCCCAAACACTGAACAT
24685870 GTTACTATATCCCCAAACACTGAACAT
1 GTTACTATATCCCCAAACACTGAACAT
24685897 G
1 G
24685898 AAGTGGCACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.37, C:0.29, G:0.09, T:0.26
Consensus pattern (27 bp):
GTTACTATATCCCCAAACACTGAACAT
Found at i:24687398 original size:52 final size:53
Alignment explanation
Indices: 24687304--24687409 Score: 178
Period size: 52 Copynumber: 2.0 Consensus size: 53
24687294 GTTTGATATA
*
24687304 TACTACATGTAGGTTTTTAGAAAAAACACAGGGCTATAAGCAATCCGATAGTT
1 TACTACATGTAGGTTTTTAGAAAAAACACAGGGCTATAAGCAATCCAATAGTT
* *
24687357 TACTATATGTAGGTTTTTAG-ACAAACACAGGGCTATAAGCAATCCAATAGTT
1 TACTACATGTAGGTTTTTAGAAAAAACACAGGGCTATAAGCAATCCAATAGTT
24687409 T
1 T
24687410 TTAGTGACCA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
52 31 0.62
53 19 0.38
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (53 bp):
TACTACATGTAGGTTTTTAGAAAAAACACAGGGCTATAAGCAATCCAATAGTT
Found at i:24695149 original size:26 final size:26
Alignment explanation
Indices: 24695120--24695178 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
24695110 ATTTTTTAGT
* *
24695120 TTTCCTTTGT-TTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTTCTCTCTTCTT-C
* *
24695146 TTTCCTCTCTATTTTCTCTCTTGTTC
1 TTTCCTTTCTATTTTCTCTCTTCTTC
24695172 TTTCCTT
1 TTTCCTT
24695179 ATGGCCGGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTCTTCTTC
Found at i:24703824 original size:20 final size:20
Alignment explanation
Indices: 24703799--24703844 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
24703789 CTTCTAAACC
24703799 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
24703819 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
24703839 TCAAAT
1 TCAAAT
24703845 GGGGCCAAAA
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:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:24706678 original size:17 final size:19
Alignment explanation
Indices: 24706638--24706678 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
24706628 ACTATATTAT
*
24706638 ATATATACTAATACTTTTA
1 ATATATACTAATACTTTAA
*
24706657 GTATATA-T-ATACTTTAA
1 ATATATACTAATACTTTAA
24706674 ATATA
1 ATATA
24706679 ATAAATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 12 0.63
18 1 0.05
19 6 0.32
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATATACTAATACTTTAA
Found at i:24706757 original size:2 final size:2
Alignment explanation
Indices: 24706744--24706788 Score: 54
Period size: 2 Copynumber: 21.5 Consensus size: 2
24706734 ATTAATTGTA
* *
24706744 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT ACT TT AT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT
24706788 A
1 A
24706789 ACTTGTAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 34 0.92
3 3 0.08
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24707251 original size:19 final size:19
Alignment explanation
Indices: 24707224--24707261 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24707214 TCATTTGACT
*
24707224 TATTGGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
24707243 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
24707262 GTTGAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:24712442 original size:19 final size:19
Alignment explanation
Indices: 24712418--24712455 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24712408 CCATTTAACT
*
24712418 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
24712437 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
24712456 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:24716548 original size:16 final size:17
Alignment explanation
Indices: 24716524--24716559 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
24716514 TATTTTGTGT
24716524 TAACATTATAAAAATTA
1 TAACATTATAAAAATTA
24716541 TAAC-TTATAAAAATTA
1 TAACATTATAAAAATTA
24716557 TAA
1 TAA
24716560 TTTTTGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
TAACATTATAAAAATTA
Found at i:24716648 original size:40 final size:40
Alignment explanation
Indices: 24716565--24716700 Score: 173
Period size: 40 Copynumber: 3.4 Consensus size: 40
24716555 TATAATTTTT
* * * * *
24716565 GTTATTTAAGTTTATGTTATTTGTTTGGATCTGTGTGTTTA
1 GTTATTTAAGTTTATATT-GTTGTTTGGATATTTATGTTTA
* *
24716606 GTTATTTAAGTTTATATTGTTATTTGGATATTTATGTATA
1 GTTATTTAAGTTTATATTGTTGTTTGGATATTTATGTTTA
* * *
24716646 GTTATTTAAGTTTATATTGCTGTATGGATATTTATTTTTA
1 GTTATTTAAGTTTATATTGTTGTTTGGATATTTATGTTTA
24716686 GTTATTTAAGTTTAT
1 GTTATTTAAGTTTAT
24716701 GTTTAAGATA
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
40 66 0.80
41 17 0.20
ACGTcount: A:0.24, C:0.01, G:0.17, T:0.58
Consensus pattern (40 bp):
GTTATTTAAGTTTATATTGTTGTTTGGATATTTATGTTTA
Found at i:24717201 original size:28 final size:27
Alignment explanation
Indices: 24717168--24717221 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
24717158 ATTTGGAGTA
*
24717168 TAGGGGTAAAATGGTAATTTTCTCACCC
1 TAGGGGCAAAATGGTAATTTTC-CACCC
*
24717196 TAGGGGCAAAATTGTAATTTTCCACC
1 TAGGGGCAAAATGGTAATTTTCCACC
24717222 ACCAGGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (27 bp):
TAGGGGCAAAATGGTAATTTTCCACCC
Found at i:24724989 original size:39 final size:40
Alignment explanation
Indices: 24724907--24724995 Score: 117
Period size: 39 Copynumber: 2.2 Consensus size: 40
24724897 CTGTAGCTTC
* * * * * *
24724907 TCGCTACAGTGAGAAACTTTCTGTTTTCTGGGTTGCAATT
1 TCGCTGCAGCGAGAAACATTCTGTTTTATGGGTAGAAATT
24724947 TCGCTGCAGCGAGAAACATTCTG-TTTATGGGTAGAAATT
1 TCGCTGCAGCGAGAAACATTCTGTTTTATGGGTAGAAATT
24724986 TCGCTGCAGC
1 TCGCTGCAGC
24724996 AAGATTGAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 23 0.53
40 20 0.47
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (40 bp):
TCGCTGCAGCGAGAAACATTCTGTTTTATGGGTAGAAATT
Found at i:24749446 original size:3 final size:3
Alignment explanation
Indices: 24749438--24749473 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
24749428 ATCCAATAAG
24749438 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
24749474 ATCAATGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:24750296 original size:26 final size:26
Alignment explanation
Indices: 24750267--24750347 Score: 92
Period size: 26 Copynumber: 3.1 Consensus size: 26
24750257 AATTCTAAAA
* *
24750267 ATAATTTTACCTCCAAAAGTGACTAG
1 ATAATTTTGCCTCCAAAAGTGAATAG
*
24750293 ATAATTTTGCCAT-CAAAAGTGAATGG
1 ATAATTTTGCC-TCCAAAAGTGAATAG
* * *
24750319 ATAATTTTGCCACCAGAAGTGAATGG
1 ATAATTTTGCCTCCAAAAGTGAATAG
24750345 ATA
1 ATA
24750348 CCGTAACCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 47 0.98
27 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (26 bp):
ATAATTTTGCCTCCAAAAGTGAATAG
Found at i:24750457 original size:28 final size:28
Alignment explanation
Indices: 24750392--24750457 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
24750382 TAATAAGAAA
*
24750392 TGGATGAATATTTGTAACCCATAAAAAG
1 TGGATGAATATTTGTAACCCACAAAAAG
* *
24750420 TGTATGAATACTTT-TAACCCACCAAAAG
1 TGGATGAATA-TTTGTAACCCACAAAAAG
*
24750448 TGGATAAATA
1 TGGATGAATA
24750458 ATGAAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (28 bp):
TGGATGAATATTTGTAACCCACAAAAAG
Found at i:24752812 original size:43 final size:42
Alignment explanation
Indices: 24752764--24752899 Score: 166
Period size: 43 Copynumber: 3.2 Consensus size: 42
24752754 TTGTGTGATA
* *
24752764 ATGATGACCCAGCTATGTGCGATGT-GGGAGTGCACATGAGCTG
1 ATGATGACCC-GCTATGTGCGA-GTAGGGAGTGCACATAAGCCG
*
24752807 ATGATGACCCGACTATGTGCGAGTAGGGAGTACACATAAGCCG
1 ATGATGACCCG-CTATGTGCGAGTAGGGAGTGCACATAAGCCG
* * * *
24752850 ATGATGACTCGGCTATATGCAAGTAGGGAGTGCGCATAAGCCG
1 ATGATGAC-CCGCTATGTGCGAGTAGGGAGTGCACATAAGCCG
24752893 ATGATGA
1 ATGATGA
24752900 TGACCTGGCT
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
42 3 0.04
43 77 0.94
44 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.21
Consensus pattern (42 bp):
ATGATGACCCGCTATGTGCGAGTAGGGAGTGCACATAAGCCG
Found at i:24753203 original size:22 final size:22
Alignment explanation
Indices: 24753172--24753223 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
24753162 CCAGTCCTGT
*
24753172 TTCTCACTGCAGCT-AAAAAGAA
1 TTCTCGCTGCAG-TGAAAAAGAA
* *
24753194 TTCTCGCTGCAGTGAAAATGGA
1 TTCTCGCTGCAGTGAAAAAGAA
24753216 TTCTCGCT
1 TTCTCGCT
24753224 ATAGTGAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (22 bp):
TTCTCGCTGCAGTGAAAAAGAA
Found at i:24755606 original size:13 final size:13
Alignment explanation
Indices: 24755588--24755613 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24755578 CATAATTAAG
24755588 GAGGAATTGAATT
1 GAGGAATTGAATT
24755601 GAGGAATTGAATT
1 GAGGAATTGAATT
24755614 TACTTGCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
GAGGAATTGAATT
Found at i:24765746 original size:19 final size:19
Alignment explanation
Indices: 24765719--24765767 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
24765709 CAATTGAATA
* *
24765719 AAATCCTTTTATTCTCTCT
1 AAATACTTTTACTCTCTCT
24765738 AAATACTTTTTTACTCTCTCT
1 AAATAC--TTTTACTCTCTCT
24765759 AAATACTTT
1 AAATACTTT
24765768 CTCTTATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 8 0.31
21 18 0.69
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATACTTTTACTCTCTCT
Found at i:24765755 original size:21 final size:21
Alignment explanation
Indices: 24765725--24765767 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
24765715 AATAAAATCC
*
24765725 TTTTATTCTCTCTAAATACTT
1 TTTTACTCTCTCTAAATACTT
24765746 TTTTACTCTCTCTAAATACTT
1 TTTTACTCTCTCTAAATACTT
24765767 T
1 T
24765768 CTCTTATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTACTCTCTCTAAATACTT
Found at i:24768281 original size:13 final size:12
Alignment explanation
Indices: 24768250--24768283 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
24768240 TTTATCTAAA
*
24768250 AAAAAAAAAAGC
1 AAAAAACAAAGC
24768262 AAAAAACAAAGC
1 AAAAAACAAAGC
24768274 AAGAAAACAA
1 AA-AAAACAA
24768284 GAAAATTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAGC
Found at i:24775723 original size:22 final size:23
Alignment explanation
Indices: 24775685--24775728 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
24775675 CGTGACTGAA
*
24775685 TATTTGTTGAGCATTGCGTGACC
1 TATTTGTAGAGCATTGCGTGACC
24775708 TATTTGTAG-GCATTGCGTGAC
1 TATTTGTAGAGCATTGCGTGAC
24775729 TTTAGCTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (23 bp):
TATTTGTAGAGCATTGCGTGACC
Found at i:24776330 original size:30 final size:30
Alignment explanation
Indices: 24776294--24776353 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
24776284 GGAGGTGCCT
*
24776294 TTGAGTGTGAGGGACCAATTGCACATATTC
1 TTGAGTGTGAGAGACCAATTGCACATATTC
*
24776324 TTGAGTGTGAGAGACCAGTTGCACATATTC
1 TTGAGTGTGAGAGACCAATTGCACATATTC
24776354 CAACAAGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (30 bp):
TTGAGTGTGAGAGACCAATTGCACATATTC
Found at i:24777204 original size:111 final size:111
Alignment explanation
Indices: 24776988--24777493 Score: 487
Period size: 118 Copynumber: 4.4 Consensus size: 111
24776978 GGTGCATAAC
* * * *
24776988 TGACTTGTGTAATTCATGTGTTACTTT-GAGACTTTTGTTCAGTAGTTTTTTA-GGTAGTGTGTG
1 TGACTTGTGCAATTCATGTATTA-TTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGGT--TGCGTG
* * * **
24777051 ACTGGTTTTTATATATTATGTTACTTGTTGTAGCAAGAGTGGTGGCGCG
63 ACTGATTTTTATATATTACGTTACCTGTTGTAGTGAGAGTGGTGGCGCG
* * * * * *
24777100 TGACTTGTGTAATTCATGTATTATTTTGAGGCTTTTGTTTAGTAATTTTTTAGGCTTACGTGACT
1 TGACTTGTGCAATTCATGTATTATTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGGTTGCGTGACT
* * *
24777165 GATTTTTATATATTGCGTTACCTATTGTAGTGTGAGTGGTGGCGCG
66 GATTTTTATATATTACGTTACCTGTTGTAGTGAGAGTGGTGGCGCG
*
24777211 TGACTTGTGCAATTCATGTATTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGGTTGCGTGA-T
1 TGACTTGTGCAATTCATGTATTATTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGGTTGCGTGACT
* * **
24777275 CGATTTTTATATATTGCGTTACCTGTTGTTATGTATTGCGAGAGTGGTTGCAAG
66 -GATTTTTATATATTACGTTACCTGTTG-TA-G---T--GAGAGTGGTGGCGCG
* * * * *
24777329 TGACTTGTGCAATTCATATGTTGTTTAGAGGCTTTTGTTCAGTAGTATTTTAGGGTTGCGTTACT
1 TGACTTGTGCAATTCATGTATTATTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGGTTGCGTGACT
* * *
24777394 GATTTTTATATATTACGTGACCTGTTGTTATATATTGCAAGAGCGGTGGCGCG
66 GATTTTTATATATTACGTTACCTGTTG-----TAGTG--AGAGTGGTGGCGCG
*** * * * *
24777447 TGACTTGTGCAATTCGCCTCTTGTTTAGGGGCTTTTGTTCACTAGTT
1 TGACTTGTGCAATTCATGTATTATTTAGAGGCTTTTGTTCAGTAGTT
24777494 ATTAGGCATT
Statistics
Matches: 331, Mismatches: 46, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
110 1 0.00
111 130 0.39
112 46 0.14
113 3 0.01
116 2 0.01
118 146 0.44
119 1 0.00
122 2 0.01
ACGTcount: A:0.19, C:0.11, G:0.25, T:0.45
Consensus pattern (111 bp):
TGACTTGTGCAATTCATGTATTATTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGGTTGCGTGACT
GATTTTTATATATTACGTTACCTGTTGTAGTGAGAGTGGTGGCGCG
Found at i:24777397 original size:229 final size:224
Alignment explanation
Indices: 24776988--24777493 Score: 518
Period size: 229 Copynumber: 2.2 Consensus size: 224
24776978 GGTGCATAAC
* * * * *
24776988 TGACTTGTGTAATTCATGTGTTACTTT-GAGACTTTTGTTCAGTAGTTTTTTAGGTAGTGTGTGA
1 TGACTTGTGCAATTCATGTATT-GTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGTA-TGCGTGA
* * ** *
24777052 CTGGTTTTTATATATTATGTTACTTGTTGTAGCAAGAGTGGTGGCGCGTGACTTGTGTAATTCAT
64 CTGATTTTTATATATTACGTTACTTGTTGTAGCAAGAGTGGTGGCAAGTGACTTGTGCAATTCAT
* * * * *
24777117 GTATTATTTTGAGGCTTTTGTTTAGTAATTTTTTAGGCTTACGTGACTGATTTTTATATATTGCG
129 ATATTATTTAGAGGCTTTTGTTCAGTAATATTTTAGGCTTACGTGACTGATTTTTATATATTACG
* * *
24777182 TTACCTATTG-TAGTG-TGAGTGGTGGCGCG
194 TGACCTATTGTTAGTGAAGAGCGGTGGCGCG
24777211 TGACTTGTGCAATTCATGTATTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGGT-TGCGTGA-
1 TGACTTGTGCAATTCATGTATTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTA-GGTATGCGTGAC
* * *
24777274 TCGATTTTTATATATTGCGTTACCTGTTGTTATGTATTGCGAGAGTGGTTGCAAGTGACTTGTGC
65 T-GATTTTTATATATTACGTTA-C--TTG-T-TGTA--GCAAGAGTGGTGGCAAGTGACTTGTGC
* * * * * *
24777339 AATTCATATGTTGTTTAGAGGCTTTTGTTCAGTAGTATTTTAGGGTTGCGTTACTGATTTTTATA
122 AATTCATATATTATTTAGAGGCTTTTGTTCAGTAATATTTTAGGCTTACGTGACTGATTTTTATA
* *
24777404 TATTACGTGACCTGTTGTTATATATTGCAAGAGCGGTGGCGCG
187 TATTACGTGACCTATTG---T-TAGTG-AAGAGCGGTGGCGCG
*** * * *
24777447 TGACTTGTGCAATTCGCCTCTTGTTTAGGGGCTTTTGTTCACTAGTT
1 TGACTTGTGCAATTCATGTATTGTTTAGAGGCTTTTGTTCAGTAGTT
24777494 ATTAGGCATT
Statistics
Matches: 231, Mismatches: 35, Indels: 21
0.80 0.12 0.07
Matches are distributed among these distances:
221 1 0.00
222 26 0.11
223 45 0.19
224 3 0.01
225 3 0.01
226 1 0.00
227 4 0.02
229 91 0.39
234 4 0.02
236 53 0.23
ACGTcount: A:0.19, C:0.11, G:0.25, T:0.45
Consensus pattern (224 bp):
TGACTTGTGCAATTCATGTATTGTTTAGAGGCTTTTGTTCAGTAGTTTTTTAGGTATGCGTGACT
GATTTTTATATATTACGTTACTTGTTGTAGCAAGAGTGGTGGCAAGTGACTTGTGCAATTCATAT
ATTATTTAGAGGCTTTTGTTCAGTAATATTTTAGGCTTACGTGACTGATTTTTATATATTACGTG
ACCTATTGTTAGTGAAGAGCGGTGGCGCG
Found at i:24781224 original size:20 final size:20
Alignment explanation
Indices: 24781199--24781242 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
24781189 CGTATACCCA
*
24781199 TCATCATCATGCA-CACCATC
1 TCATCATCAT-CATCACCAGC
24781219 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
24781239 TCAT
1 TCAT
24781243 GCGCAATCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.30, C:0.39, G:0.05, T:0.27
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:24781316 original size:43 final size:43
Alignment explanation
Indices: 24781236--24781350 Score: 110
Period size: 43 Copynumber: 2.7 Consensus size: 43
24781226 CATCATCACC
* * * **
24781236 AGCTCATGCGCAATCCCTACTCGCACAT-GGCTAGGTCATCACTA
1 AGCTTATGCGCACTCTCTACTCGCACATAACCT-GGTCATC-CTA
*
24781280 AG-TTATGCGCACT-TCTTACTCGCACATAACCTGGTCATCCTT
1 AGCTTATGCGCACTCTC-TACTCGCACATAACCTGGTCATCCTA
* *
24781322 GGCTTATGCGCACTCTCTGCTCGCACATA
1 AGCTTATGCGCACTCTCTACTCGCACATA
24781351 GTCGAGTCAA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
42 4 0.07
43 49 0.83
44 6 0.10
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (43 bp):
AGCTTATGCGCACTCTCTACTCGCACATAACCTGGTCATCCTA
Found at i:24786321 original size:25 final size:25
Alignment explanation
Indices: 24786293--24786351 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
24786283 TATCAAATAC
24786293 TCACGCGATTCTAAATCTTAACGGT
1 TCACGCGATTCTAAATCTTAACGGT
24786318 TCACGCGATTCTAAATCTTAACGGT
1 TCACGCGATTCTAAATCTTAACGGT
24786343 TCACGCGAT
1 TCACGCGAT
24786352 CCATATTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (25 bp):
TCACGCGATTCTAAATCTTAACGGT
Found at i:24788069 original size:49 final size:49
Alignment explanation
Indices: 24787999--24788253 Score: 161
Period size: 49 Copynumber: 5.3 Consensus size: 49
24787989 CATTTATTAC
* *
24787999 TCACGCGAGTCAATATAAACTAGTGACGCGATTCCACGGAGAAGTCATG
1 TCACGCGATTCCATATAAACTAGTGACGCGATTCCACGGAGAAGTCATG
* * * * ** * *
24788048 TCACGCGCTTCCATATTAACTAGTAACGTC-ACTT-CA--TATTTACT-A-C
1 TCACGCGATTCCATATAAACTAGTGACG-CGA-TTCCACGGA-GAAGTCATG
* * * *
24788094 TCACGTGAGTCAATATAAACTAGTGACGCGATTCCACGGAGAAGTCGTG
1 TCACGCGATTCCATATAAACTAGTGACGCGATTCCACGGAGAAGTCATG
* * * * * ** * *
24788143 TCACGCTATTCCATATTAACTAGTAACGCCACTCCAC--ATTTA-TTA-C
1 TCACGCGATTCCATATAAACTAGTGACGCGATTCCACGGA-GAAGTCATG
* * * *
24788189 TCACACGAGTCAATATAAACTAGTGACGCGATTCCACGGAGAAGTCGTG
1 TCACGCGATTCCATATAAACTAGTGACGCGATTCCACGGAGAAGTCATG
24788238 TCACGCGATTCCATAT
1 TCACGCGATTCCATAT
24788254 TAACCACCGA
Statistics
Matches: 141, Mismatches: 51, Indels: 28
0.64 0.23 0.13
Matches are distributed among these distances:
45 3 0.02
46 54 0.38
47 7 0.05
48 6 0.04
49 68 0.48
50 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (49 bp):
TCACGCGATTCCATATAAACTAGTGACGCGATTCCACGGAGAAGTCATG
Done.