Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 87 of 136
Found at i:28871607 original size:20 final size:20
Alignment explanation
Indices: 28871572--28871609 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28871562 CAGAAATCTC
**
28871572 TCTTTTCTCTTTTTTCTTTT
1 TCTTTTCTCTACTTTCTTTT
28871592 TCTTTTCTCTACTTTCTT
1 TCTTTTCTCTACTTTCTT
28871610 CTTATCTCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (20 bp):
TCTTTTCTCTACTTTCTTTT
Found at i:28875193 original size:43 final size:43
Alignment explanation
Indices: 28875140--28875243 Score: 163
Period size: 46 Copynumber: 2.3 Consensus size: 43
28875130 TCAATATTTA
* *
28875140 GCACTGAGTGTGCGAGTATAGAATAGTTATGGCTATATGATTG
1 GCACTAAGTGTGCGAGTATAGAATAGTTACGGCTATATGATTG
28875183 GCACTAAGTGTTGTGCGAGTATAGAATAGTTACGGCTATATGATTG
1 GCACTAA--G-TGTGCGAGTATAGAATAGTTACGGCTATATGATTG
28875229 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
28875244 AATTAAATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
43 13 0.23
44 1 0.02
45 1 0.02
46 41 0.73
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.31
Consensus pattern (43 bp):
GCACTAAGTGTGCGAGTATAGAATAGTTACGGCTATATGATTG
Found at i:28875203 original size:46 final size:46
Alignment explanation
Indices: 28875148--28875239 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
28875138 TAGCACTGAG
*
28875148 TGTGCGAGTATAGAATAGTTATGGCTATATGATTGGCACTAAGTGT
1 TGTGCGAGTATAGAATAGTTACGGCTATATGATTGGCACTAAGTGT
28875194 TGTGCGAGTATAGAATAGTTACGGCTATATGATTGGCACTAAGTGT
1 TGTGCGAGTATAGAATAGTTACGGCTATATGATTGGCACTAAGTGT
28875240 GCGAAATTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34
Consensus pattern (46 bp):
TGTGCGAGTATAGAATAGTTACGGCTATATGATTGGCACTAAGTGT
Found at i:28875276 original size:41 final size:41
Alignment explanation
Indices: 28875229--28875361 Score: 205
Period size: 41 Copynumber: 3.3 Consensus size: 41
28875219 TATATGATTG
* *
28875229 GCACTAAGTGTGCGAAATTAAATAATGATGTTGAATAATGA
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
*
28875270 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
* * *
28875311 GCACTAAGTGTGCGAAACCAAATAATTATGTT-AATAACGG
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
28875351 GCACTAAGTGT
1 GCACTAAGTGT
28875362 NNNNNNNNNN
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 18 0.21
41 67 0.79
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (41 bp):
GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
Found at i:28878541 original size:17 final size:17
Alignment explanation
Indices: 28878519--28878552 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28878509 ATGTGGCATG
*
28878519 TACCTAGGTAATGTATA
1 TACCTAAGTAATGTATA
*
28878536 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
28878553 GGGGTTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:28886853 original size:15 final size:15
Alignment explanation
Indices: 28886833--28886862 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28886823 ATATTTCATC
28886833 TTTTTATGCTATAAA
1 TTTTTATGCTATAAA
28886848 TTTTTATGCTATAAA
1 TTTTTATGCTATAAA
28886863 AATGATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
TTTTTATGCTATAAA
Found at i:28889983 original size:73 final size:73
Alignment explanation
Indices: 28889862--28890010 Score: 174
Period size: 73 Copynumber: 2.0 Consensus size: 73
28889852 CCACTTGTCC
* * * * * * ** *
28889862 TTGGACAAGGGGTTCTCTCAAAGGGTGCCTAGTAAGGGGTTGTCTTGGTGGGTTGTGAAGGGTGG
1 TTGGACAAGGGGTACTCTCAAAGAGTGCCCAGTAAGGGATTATCTTGGTGGGTAGCAAAAGGTGG
28889927 CATAACAA
66 CATAACAA
* * *
28889935 TTGGACGAGGGGTACTCTCGAAA-AGTGCCCAGTAAGGGATTATTTTGGTGGGTAGCAAAAGGTT
1 TTGGACAAGGGGTACTCTC-AAAGAGTGCCCAGTAAGGGATTATCTTGGTGGGTAGCAAAAGGTG
28889999 GCATAACAA
65 GCATAACAA
28890008 TTG
1 TTG
28890011 CCTCATTTAG
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
73 60 0.95
74 3 0.05
ACGTcount: A:0.26, C:0.13, G:0.35, T:0.27
Consensus pattern (73 bp):
TTGGACAAGGGGTACTCTCAAAGAGTGCCCAGTAAGGGATTATCTTGGTGGGTAGCAAAAGGTGG
CATAACAA
Found at i:28892301 original size:25 final size:25
Alignment explanation
Indices: 28892273--28892349 Score: 59
Period size: 24 Copynumber: 3.1 Consensus size: 25
28892263 TGAGCTTTCT
28892273 GTTATTAAGCTCGGATAAGCTTCCC
1 GTTATTAAGCTCGGATAAGCTTCCC
* ** * *
28892298 GTTA-CAAGCTCACATGAGCTTCCT
1 GTTATTAAGCTCGGATAAGCTTCCC
** *
28892322 GTTATTTGGCTTGGA-AGAGCTTCCC
1 GTTATTAAGCTCGGATA-AGCTTCCC
28892347 GTT
1 GTT
28892350 TAAATGCTCA
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
24 19 0.51
25 18 0.49
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (25 bp):
GTTATTAAGCTCGGATAAGCTTCCC
Found at i:28892307 original size:49 final size:49
Alignment explanation
Indices: 28892262--28892365 Score: 124
Period size: 49 Copynumber: 2.1 Consensus size: 49
28892252 TTAAGCTCTT
*
28892262 ATGAGCTTTCTGTTATTAAGCTCGGATA-AGCTTCCCGTTACAAGCTCAC
1 ATGAGCTTCCTGTTATTAAGCTCGGA-AGAGCTTCCCGTTACAAGCTCAC
** *
28892311 ATGAGCTTCCTGTTATTTGGCTTGGAAGAGCTTCCCGTTTA-AATGCTCA-
1 ATGAGCTTCCTGTTATTAAGCTCGGAAGAGCTTCCCG-TTACAA-GCTCAC
28892360 ATGAGC
1 ATGAGC
28892366 ATTCTTGAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
48 1 0.02
49 39 0.81
50 8 0.17
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (49 bp):
ATGAGCTTCCTGTTATTAAGCTCGGAAGAGCTTCCCGTTACAAGCTCAC
Found at i:28894217 original size:79 final size:78
Alignment explanation
Indices: 28894113--28894294 Score: 262
Period size: 76 Copynumber: 2.3 Consensus size: 78
28894103 TAGCAACCCC
* * *
28894113 TTGGGAGAATCAGCACTTAGCAACCCCCTTTTGCACATTC-AAAAATATGGTGGAATCAGCACTT
1 TTGGG-GAATCAGCACTTAGCAACCCCCTTTT-CACATCCGAAAAA-ACGGTGGAATAAGCACTT
28894177 AGCAACCACCAATGAT
63 AGCAACCACCAATGAT
* *
28894193 TTGGGGAATCAGCACTTAGCAA--CCCTTTTCATATCCGAAGAAACGGTGGAATAAGCACTTAGC
1 TTGGGGAATCAGCACTTAGCAACCCCCTTTTCACATCCGAAAAAACGGTGGAATAAGCACTTAGC
*
28894256 AACCACCGATGAT
66 AACCACCAATGAT
28894269 TTGGGGAATCAGCACTTAGCAACCCC
1 TTGGGGAATCAGCACTTAGCAACCCC
28894295 TTGGGGGAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
76 58 0.62
77 11 0.12
78 2 0.02
79 17 0.18
80 5 0.05
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (78 bp):
TTGGGGAATCAGCACTTAGCAACCCCCTTTTCACATCCGAAAAAACGGTGGAATAAGCACTTAGC
AACCACCAATGAT
Found at i:28894801 original size:21 final size:21
Alignment explanation
Indices: 28894776--28894819 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28894766 TAGCTTATTT
28894776 AACATTCACATTTAATAAAAA
1 AACATTCACATTTAATAAAAA
28894797 AACATTCACATTTAATAAAAA
1 AACATTCACATTTAATAAAAA
28894818 AA
1 AA
28894820 TCATCGACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (21 bp):
AACATTCACATTTAATAAAAA
Found at i:28898106 original size:14 final size:14
Alignment explanation
Indices: 28898087--28898113 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28898077 TAAAAAGAAT
28898087 ACTCGACATTGCCG
1 ACTCGACATTGCCG
28898101 ACTCGACATTGCC
1 ACTCGACATTGCC
28898114 TTCTCTTGCT
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:0.37, G:0.19, T:0.22
Consensus pattern (14 bp):
ACTCGACATTGCCG
Found at i:28909272 original size:2 final size:2
Alignment explanation
Indices: 28909265--28909327 Score: 80
Period size: 2 Copynumber: 33.5 Consensus size: 2
28909255 GAAATAAATA
*
28909265 AT AT AT AT -T AT AC AT A- AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
28909304 AT AC AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28909328 CATAATNNNN
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
1 4 0.08
2 49 0.92
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:28909309 original size:30 final size:31
Alignment explanation
Indices: 28909267--28909327 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
28909257 AATAAATAAT
28909267 ATATATTATACATAATATATATATATATATA
1 ATATATTATACATAATATATATATATATATA
28909298 ATATA-TATACATAATATATATATATATATA
1 ATATATTATACATAATATATATATATATATA
28909328 CATAATNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATATTATACATAATATATATATATATATA
Found at i:28911522 original size:89 final size:89
Alignment explanation
Indices: 28911365--28911623 Score: 446
Period size: 89 Copynumber: 2.9 Consensus size: 89
28911355 TGCACTTTGG
* *
28911365 CCCCCTAAAAATAATAAAAAAATTCATTTAATCCATTAAAAATTATAAAAAAATATAGGCTATTC
1 CCCCCTAAAAATAAT-AAAAATTTGATTTAATCCATTAAAAATTAT--AAAAATATAGGCTATTC
28911430 AAATGGTGAAATTACAATTTAATTTCA
63 AAATGGTGAAATTACAATTTAATTTCA
*
28911457 CCCCCTAAAAATAATAAATATTTGATTTAATCCATTAAAAATTATAAAAATATAGGCTATTCAAA
1 CCCCCTAAAAATAATAAAAATTTGATTTAATCCATTAAAAATTATAAAAATATAGGCTATTCAAA
28911522 TGGTGAAATTACAATTTAATTTCA
66 TGGTGAAATTACAATTTAATTTCA
* *
28911546 CCCCCTAAAAATAATAAAAATTTGATTTAATCCATTGAAAATTATAAAAATATAGGCCATTCAAA
1 CCCCCTAAAAATAATAAAAATTTGATTTAATCCATTAAAAATTATAAAAATATAGGCTATTCAAA
28911611 TGGTGAAATTACA
66 TGGTGAAATTACA
28911624 TTTTTACTAT
Statistics
Matches: 161, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
89 119 0.74
91 27 0.17
92 15 0.09
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (89 bp):
CCCCCTAAAAATAATAAAAATTTGATTTAATCCATTAAAAATTATAAAAATATAGGCTATTCAAA
TGGTGAAATTACAATTTAATTTCA
Found at i:28913145 original size:21 final size:21
Alignment explanation
Indices: 28913119--28913190 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
28913109 ACAAATGCTA
28913119 AACGGAAACCCATAAGGGTTG
1 AACGGAAACCCATAAGGGTTG
* * * *
28913140 AACGGAAGCTCATAAGAGCTG
1 AACGGAAACCCATAAGGGTTG
* * *
28913161 AACTGAAACCCATTAGGGTTA
1 AACGGAAACCCATAAGGGTTG
*
28913182 AACGAAAAC
1 AACGGAAAC
28913191 TATATGAGTT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (21 bp):
AACGGAAACCCATAAGGGTTG
Found at i:28913790 original size:42 final size:42
Alignment explanation
Indices: 28913743--28913924 Score: 165
Period size: 42 Copynumber: 4.3 Consensus size: 42
28913733 TTTTTTTCGA
* *
28913743 AAACGCCGCTATAGATTAAGACGTTTAGTGGCGC-TTTCCCAC
1 AAACGCCGCTATAGA-TAAGACCTTTAGCGGCGCTTTTCCCAC
* * **
28913785 AAACGCCGCTATAGATCAGGACCTTTAGCGGTGC--AACCACAC
1 AAACGCCGCTATAGAT-AAGACCTTTAGCGGCGCTTTTCC-CAC
* * *
28913827 AAAACGCTGCTATAGATAAAGACCTTTAACGGCACTTTTTCCCAC
1 -AAACGCCGCTATAGAT-AAGACCTTTAGCGGCGC-TTTTCCCAC
* **
28913872 AAACGTCGCTATAGA-ACAGACCTTTAGCGGCGCTTTTCATAC
1 AAACGCCGCTATAGATA-AGACCTTTAGCGGCGCTTTTCCCAC
28913914 AAACGCCGCTA
1 AAACGCCGCTA
28913925 AAAACATATC
Statistics
Matches: 112, Mismatches: 21, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
41 3 0.03
42 49 0.44
43 42 0.38
44 13 0.12
45 3 0.03
46 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTATAGATAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:28913832 original size:85 final size:85
Alignment explanation
Indices: 28913742--28913901 Score: 223
Period size: 85 Copynumber: 1.9 Consensus size: 85
28913732 GTTTTTTTCG
* * ** * *
28913742 AAAACGCCGCTATAGATTAAGACGTTTAGTGGCGC-TTTCCCACAAACGCCGCTATAGATCAGGA
1 AAAACGCCGCTATAGATAAAGACCTTTAACGGCACTTTTCCCACAAACGCCGCTATAGAACA-GA
28913806 CCTTTAGCGGTGCAACCACAC
65 CCTTTAGCGGTGCAACCACAC
* *
28913827 AAAACGCTGCTATAGATAAAGACCTTTAACGGCACTTTTTCCCACAAACGTCGCTATAGAACAGA
1 AAAACGCCGCTATAGATAAAGACCTTTAACGGCAC-TTTTCCCACAAACGCCGCTATAGAACAGA
28913892 CCTTTAGCGG
65 CCTTTAGCGG
28913902 CGCTTTTCAT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
85 29 0.45
86 12 0.18
87 24 0.37
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (85 bp):
AAAACGCCGCTATAGATAAAGACCTTTAACGGCACTTTTCCCACAAACGCCGCTATAGAACAGAC
CTTTAGCGGTGCAACCACAC
Found at i:28918784 original size:7 final size:7
Alignment explanation
Indices: 28918772--28918814 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
28918762 TACCTATCCA
28918772 TAACCCC
1 TAACCCC
*
28918779 TAACCCT
1 TAACCCC
* *
28918786 TAATCCT
1 TAACCCC
*
28918793 TAACCTC
1 TAACCCC
28918800 TAACCCC
1 TAACCCC
28918807 TAACCCC
1 TAACCCC
28918814 T
1 T
28918815 CTTTTACAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.28, C:0.47, G:0.00, T:0.26
Consensus pattern (7 bp):
TAACCCC
Found at i:28919037 original size:61 final size:64
Alignment explanation
Indices: 28918926--28919062 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 64
28918916 TCACAACTCT
* * *
28918926 TAACCTCTAACCCCTAACTACTAATTTAATATATAAATTTAAAAACACTAATTTATCTAAACCC
1 TAACCCCTAACCCCTAAATACTAATTTAATATATAAATTTAAAAACACTAATTAATCTAAACCC
*
28918990 TAACCCCTAACCCCTAAAT-CTTATTT-A-ATATAAA-TTAAAACACACTAATTAATCTAAACCC
1 TAACCCCTAACCCCTAAATACTAATTTAATATATAAATTTAAAA-ACACTAATTAATCTAAACCC
**
28919051 TAAAGCCTAACC
1 TAACCCCTAACC
28919063 TCACACTGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
60 6 0.09
61 36 0.55
62 1 0.02
63 6 0.09
64 17 0.26
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.30
Consensus pattern (64 bp):
TAACCCCTAACCCCTAAATACTAATTTAATATATAAATTTAAAAACACTAATTAATCTAAACCC
Found at i:28919592 original size:41 final size:41
Alignment explanation
Indices: 28919542--28919733 Score: 192
Period size: 41 Copynumber: 4.7 Consensus size: 41
28919532 ATAAAATGTT
* * * *
28919542 TTAGTGGCGCTTTTTTAAAAAAGCCTCTAAA-AGCCCGAGTA
1 TTAGCGGCGCTTTTTCAAAAAAGCCGCTAAAGA-CCCGAGCA
* * *
28919583 TTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGATCTGAGCA
1 TTAGCGGCGCTTTTTCAAAAAAGCCGCTAAAGACCCGAGCA
* * * * *
28919624 TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGACCAGGGCA
1 TTAGCGGCGCTTTTTCAAAAAAGCCGCTAAAGACCCGAGCA
* * *
28919665 TTAGCGGCGCTTTTT-AAAAAACGCCGTTAAA-ATCCCGATCT
1 TTAGCGGCGCTTTTTCAAAAAA-GCCGCTAAAGA-CCCGAGCA
*
28919706 TTAGCGGCGCTTTTTCAAAAACGCCGCT
1 TTAGCGGCGCTTTTTCAAAAAAGCCGCT
28919734 TTTTCAGAAA
Statistics
Matches: 124, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
40 6 0.05
41 112 0.90
42 6 0.05
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.26
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAAAGCCGCTAAAGACCCGAGCA
Found at i:28919685 original size:82 final size:82
Alignment explanation
Indices: 28919582--28919733 Score: 216
Period size: 82 Copynumber: 1.9 Consensus size: 82
28919572 AAGCCCGAGT
* * *
28919582 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGAT-CTGAGCATTAGCGGCGCTTCTCCAAAAAC
1 ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAA-ATCCCGAGCATTAGCGGCGCTTCTCCAAAAAC
28919646 GCCGCTAAAGACCAGGGC
65 GCCGCTAAAGACCAGGGC
* * * * *
28919664 ATTAGCGGCGCTTTTTAAAAAACGCCGTTAAAATCCCGATCTTTAGCGGCGCTTTTTCAAAAACG
1 ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAATCCCGAGCATTAGCGGCGCTTCTCCAAAAACG
28919729 CCGCT
66 CCGCT
28919734 TTTTCAGAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
81 2 0.03
82 59 0.97
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (82 bp):
ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAATCCCGAGCATTAGCGGCGCTTCTCCAAAAACG
CCGCTAAAGACCAGGGC
Found at i:28919735 original size:17 final size:18
Alignment explanation
Indices: 28919713--28919746 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
28919703 TCTTTAGCGG
28919713 CGCTTTTTCA-AAAACGC
1 CGCTTTTTCAGAAAACGC
28919730 CGCTTTTTCAGAAAACG
1 CGCTTTTTCAGAAAACG
28919747 ATGCCGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (18 bp):
CGCTTTTTCAGAAAACGC
Found at i:28926934 original size:26 final size:27
Alignment explanation
Indices: 28926882--28926935 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
28926872 TCTAACTTGA
* * *
28926882 TTTATGGATCTTTCAAAAGCACTTTAT
1 TTTATGGACCTTTCAAAACCACATTAT
28926909 TTTATGGACCTTTC-AAACCACATTAT
1 TTTATGGACCTTTCAAAACCACATTAT
28926935 T
1 T
28926936 CATGGTCTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.43
Consensus pattern (27 bp):
TTTATGGACCTTTCAAAACCACATTAT
Found at i:28927096 original size:20 final size:20
Alignment explanation
Indices: 28927071--28927110 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28927061 CGTAAAATGA
*
28927071 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
28927091 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
28927111 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:28928229 original size:11 final size:11
Alignment explanation
Indices: 28928180--28928241 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 11
28928170 GTCCAAAATT
28928180 TAATTTTTTTA
1 TAATTTTTTTA
* *
28928191 -ACTTTATTTA
1 TAATTTTTTTA
*
28928201 T-ATATTTTTA
1 TAATTTTTTTA
* *
28928211 GAA-ATTTTTA
1 TAATTTTTTTA
28928221 -AATTTTTTTA
1 TAATTTTTTTA
28928231 TAATTTTTTTA
1 TAATTTTTTTA
28928242 AAAATATAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
9 2 0.05
10 27 0.68
11 11 0.28
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:28928400 original size:18 final size:18
Alignment explanation
Indices: 28928377--28928416 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
28928367 CACAAATTTG
28928377 TTATTTCAATTATTCGAA
1 TTATTTCAATTATTCGAA
* *
28928395 TTATTTGAGTTATTCGAA
1 TTATTTCAATTATTCGAA
28928413 TTAT
1 TTAT
28928417 AAAATTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (18 bp):
TTATTTCAATTATTCGAA
Found at i:28934876 original size:3 final size:3
Alignment explanation
Indices: 28934868--28934895 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28934858 GGCTTTTTCC
28934868 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
28934896 TTGGCTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:28935236 original size:21 final size:21
Alignment explanation
Indices: 28935210--28935257 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28935200 ATTTTTTTTT
**
28935210 AAAAATCATTAAAAATCTTTA-
1 AAAAATCACAAAAAAT-TTTAG
28935231 AAAAATCACAAAAAATTTTAG
1 AAAAATCACAAAAAATTTTAG
28935252 AAAAAT
1 AAAAAT
28935258 TCCAAGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAAATCACAAAAAATTTTAG
Found at i:28936332 original size:13 final size:12
Alignment explanation
Indices: 28936316--28936345 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
28936306 AATTTTTCTT
28936316 TTTTTTTTTGGGA
1 TTTTTTTTT-GGA
28936329 TTTTTTTTTGGA
1 TTTTTTTTTGGA
28936341 TTTTT
1 TTTTT
28936346 AACTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.07, C:0.00, G:0.17, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGGA
Found at i:28943230 original size:16 final size:16
Alignment explanation
Indices: 28943211--28943246 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28943201 AATGGGGCTT
*
28943211 TAATGGAATAGAGATG
1 TAATAGAATAGAGATG
*
28943227 TAATAGAATAGAGTTG
1 TAATAGAATAGAGATG
28943243 TAAT
1 TAAT
28943247 CAGTAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (16 bp):
TAATAGAATAGAGATG
Found at i:28943500 original size:56 final size:56
Alignment explanation
Indices: 28943425--28943583 Score: 160
Period size: 56 Copynumber: 2.8 Consensus size: 56
28943415 TTTTAATAAG
* *
28943425 ATTATTATTAAAT-CTAATTTAATAAAAATATTAATAAATAATCATATT-TTAACATA
1 ATTATTATTAAATAC-AATTTAATAAAAATA-TAATAAATAATAACATTCTTAACATA
* * *
28943481 ATTATTATTAAATACAATTTTATAAAAATAATATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATACAATTTAATAAAAAT-ATA-ATAA-ATAATAACATTCTTAACATA
* * * *
28943540 ATAATTATTAAAATATAAATTAATAAAAATCATAATATATAATA
1 ATTATTATT-AAATACAATTTAATAAAAAT-ATAATAAATAATA
28943584 TTATAAATTT
Statistics
Matches: 85, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
56 28 0.33
57 6 0.07
58 13 0.15
59 18 0.21
60 20 0.24
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (56 bp):
ATTATTATTAAATACAATTTAATAAAAATATAATAAATAATAACATTCTTAACATA
Found at i:28943557 original size:39 final size:38
Alignment explanation
Indices: 28943508--28943591 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 38
28943498 TTTTATAAAA
* * * *
28943508 ATAATATATAATTTAATAACATTCTTAATATAATAATTATT
1 ATAA-ATATAAATTAATAAAAATCATAATAT-ATAA-TATT
28943549 A-AAATATAAATTAATAAAAATCATAATATATAATATT
1 ATAAATATAAATTAATAAAAATCATAATATATAATATT
28943586 ATAAAT
1 ATAAAT
28943592 TTATTTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
37 5 0.13
38 8 0.21
39 22 0.58
40 2 0.05
41 1 0.03
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (38 bp):
ATAAATATAAATTAATAAAAATCATAATATATAATATT
Found at i:28944830 original size:94 final size:94
Alignment explanation
Indices: 28944669--28944858 Score: 362
Period size: 94 Copynumber: 2.0 Consensus size: 94
28944659 GAGTGATTTT
*
28944669 GTAATGTATTCCAATCGTTCTATTAGTGGGTAACTAAGCTTTCATTCGGAAAGTCTTAGAGGTGG
1 GTAATGTATTCAAATCGTTCTATTAGTGGGTAACTAAGCTTTCATTCGGAAAGTCTTAGAGGTGG
28944734 AGTGATCTAGTTCTAAGTATACGAGTGAG
66 AGTGATCTAGTTCTAAGTATACGAGTGAG
*
28944763 GTAATGTATTCAAATCGTTCTATTAGTGGGTAACTAAGCTTTCATTTGGAAAGTCTTAGAGGTGG
1 GTAATGTATTCAAATCGTTCTATTAGTGGGTAACTAAGCTTTCATTCGGAAAGTCTTAGAGGTGG
28944828 AGTGATCTAGTTCTAAGTATACGAGTGAG
66 AGTGATCTAGTTCTAAGTATACGAGTGAG
28944857 GT
1 GT
28944859 TACAATTTAA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.35
Consensus pattern (94 bp):
GTAATGTATTCAAATCGTTCTATTAGTGGGTAACTAAGCTTTCATTCGGAAAGTCTTAGAGGTGG
AGTGATCTAGTTCTAAGTATACGAGTGAG
Found at i:28948998 original size:93 final size:93
Alignment explanation
Indices: 28948839--28949020 Score: 355
Period size: 93 Copynumber: 2.0 Consensus size: 93
28948829 TTAACTCACA
*
28948839 TACAACTTATTATAATTCATCTTTGGTGATCTTATAAAAGCTTTTCTATTTTAAATAATTTGAAA
1 TACAACTTATTATAATTCATCCTTGGTGATCTTATAAAAGCTTTTCTATTTTAAATAATTTGAAA
28948904 TAAATTATGTATATGCAATCATAAACAT
66 TAAATTATGTATATGCAATCATAAACAT
28948932 TACAACTTATTATAATTCATCCTTGGTGATCTTATAAAAGCTTTTCTATTTTAAATAATTTGAAA
1 TACAACTTATTATAATTCATCCTTGGTGATCTTATAAAAGCTTTTCTATTTTAAATAATTTGAAA
28948997 TAAATTATGTATATGCAATCATAA
66 TAAATTATGTATATGCAATCATAA
28949021 TAAATATGAA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (93 bp):
TACAACTTATTATAATTCATCCTTGGTGATCTTATAAAAGCTTTTCTATTTTAAATAATTTGAAA
TAAATTATGTATATGCAATCATAAACAT
Found at i:28965270 original size:19 final size:19
Alignment explanation
Indices: 28965222--28965308 Score: 99
Period size: 19 Copynumber: 4.6 Consensus size: 19
28965212 TCAACAAAAA
28965222 TTATAAAAAAGTTCAAAATAT
1 TTAT-AAAAA-TTCAAAATAT
* *
28965243 TTTTCAAAATTCAAAATAT
1 TTATAAAAATTCAAAATAT
28965262 TTATAAAAATT-ATAAA-A-
1 TTATAAAAATTCA-AAATAT
*
28965279 TTATATAAATTCAAAATAT
1 TTATAAAAATTCAAAATAT
28965298 TTATAAAAATT
1 TTATAAAAATT
28965309 ATAAAAATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
17 13 0.23
18 4 0.07
19 32 0.57
20 4 0.07
21 3 0.05
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (19 bp):
TTATAAAAATTCAAAATAT
Found at i:28965294 original size:36 final size:37
Alignment explanation
Indices: 28965249--28965321 Score: 139
Period size: 36 Copynumber: 2.0 Consensus size: 37
28965239 ATATTTTTCA
28965249 AAATTCAAAATATTTATAAAAATTAT-AAAATTATAT
1 AAATTCAAAATATTTATAAAAATTATAAAAATTATAT
28965285 AAATTCAAAATATTTATAAAAATTATAAAAATTATAT
1 AAATTCAAAATATTTATAAAAATTATAAAAATTATAT
28965322 TTTTTTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 26 0.72
37 10 0.28
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (37 bp):
AAATTCAAAATATTTATAAAAATTATAAAAATTATAT
Found at i:28965341 original size:9 final size:9
Alignment explanation
Indices: 28965262--28965320 Score: 68
Period size: 9 Copynumber: 6.6 Consensus size: 9
28965252 TTCAAAATAT
28965262 TTATAAAAA
1 TTATAAAAA
28965271 TTAT-AAAA
1 TTATAAAAA
*
28965279 TTATATAAA
1 TTATAAAAA
*
28965288 TTCA-AAATAT
1 TT-ATAAA-AA
28965298 TTATAAAAA
1 TTATAAAAA
28965307 TTATAAAAA
1 TTATAAAAA
28965316 TTATA
1 TTATA
28965321 TTTTTTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 8 0.19
9 27 0.64
10 7 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (9 bp):
TTATAAAAA
Found at i:28965342 original size:36 final size:36
Alignment explanation
Indices: 28965249--28965343 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 36
28965239 ATATTTTTCA
28965249 AAATTCAAAATATT-TATAAAAATTATAAAATTATAT
1 AAATTCAAAATATTATA-AAAAATTATAAAATTATAT
28965285 AAATTCAAAATATT-TATAAAAATTATAAAAATTATAT
1 AAATTCAAAATATTATA-AAAAATTAT-AAAATTATAT
*** *
28965322 TTTTTTAAAA-ATTATAAAAAAT
1 AAATTCAAAATATTATAAAAAAT
28965344 AAAAAAAGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
36 35 0.66
37 18 0.34
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (36 bp):
AAATTCAAAATATTATAAAAAATTATAAAATTATAT
Found at i:28967703 original size:22 final size:22
Alignment explanation
Indices: 28967678--28967734 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
28967668 TGCACTAATG
28967678 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* ** *
28967700 AACAAAGAGCACGGATGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
*
28967722 AATAGAGAGCACT
1 AACAGAGAGCACT
28967735 GTCATGCTAG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:28968981 original size:29 final size:29
Alignment explanation
Indices: 28968936--28968994 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
28968926 AACTAGTGGT
*
28968936 ATCATCACTTTCGGTTATCAATCTTTCTA
1 ATCATCACTTTCAGTTATCAATCTTTCTA
28968965 ATCATCACTTTCAGTTATCAATCTTTCTA
1 ATCATCACTTTCAGTTATCAATCTTTCTA
28968994 A
1 A
28968995 GCTCGAATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (29 bp):
ATCATCACTTTCAGTTATCAATCTTTCTA
Found at i:28972654 original size:328 final size:328
Alignment explanation
Indices: 28972057--28972714 Score: 1181
Period size: 328 Copynumber: 2.0 Consensus size: 328
28972047 CTAGCATGAA
28972057 ATCCATAGGACTTGCTCAACACTAATAAAGACTAAGATAAGTAAGCTTATCCCTGATTAGTTACT
1 ATCCATAGGACTTGCTCAACACTAATAAAGACTAAGATAAGTAAGCTTATCCCTGATTAGTTACT
*
28972122 AAGCTTTTTAAGCTCACACATTAGTTGTTTAACACGTGTAGGTTTGGACTTACATAGAAGTCATG
66 AAGCTTTTTAAGCTCACACATTAGTTGTTTAACACGTGTAGGTTTGGACTTACATAGAAGTCATA
**
28972187 ATGTTGGCTTAGGAGCATCACATCATCCATCGAGCTTCTAAGGTTGTAATTCAAGTATTTAAATA
131 ATGTTGGCTTAGGAGCATCACATCATCCATCGAGCTTCTAAGGTTGTAATTCAAACATTTAAATA
*
28972252 CCATTTGTATTGGATTATTGGCATATATACAAAAACTTAGATTACTTGAGCAATTGTAAAGTTAG
196 CCATTTGTATTGGACTATTGGCATATATACAAAAACTTAGATTACTTGAGCAATTGTAAAGTTAG
* *
28972317 ATGATGAACTTGAGCTTCTTTTGTGTTTCTATTAAAAAATATATGTATATTTTGTTTTGGACGTG
261 ATGATGAACTTGAGCCTCTTTTGTGTTTCTATTAAAAAATATATGTATATTTTATTTTGGACGTG
*
28972382 TTC
326 CTC
* *
28972385 ATCCATAGGACTTGCTCAACACTAATAAAGACTAAGATAAGTAAGTTTATCCCTGATTAGTTATT
1 ATCCATAGGACTTGCTCAACACTAATAAAGACTAAGATAAGTAAGCTTATCCCTGATTAGTTACT
*
28972450 GAGCTTTTTAAGCTCACACATTAGTTGTTTAACACGTGTAGGTTTGGACTTACATAGAAGTCATA
66 AAGCTTTTTAAGCTCACACATTAGTTGTTTAACACGTGTAGGTTTGGACTTACATAGAAGTCATA
* * *
28972515 ATGTTGGCTTGGGAGCATCATATCATCCATCGAGCTTCTAAGGTTGTAATTCAAACGTTTAAATA
131 ATGTTGGCTTAGGAGCATCACATCATCCATCGAGCTTCTAAGGTTGTAATTCAAACATTTAAATA
*
28972580 CCATTTGTATTGGACTATTGGCATATATACAAAAACTTAGATTTCTTGAGCAATTGTAAAGTTAG
196 CCATTTGTATTGGACTATTGGCATATATACAAAAACTTAGATTACTTGAGCAATTGTAAAGTTAG
*
28972645 ATGATGAACTTGAGCCTCTTTTGTGTTTCTCTTAAAAAATATATGTATATTTTATTTTGGACGTG
261 ATGATGAACTTGAGCCTCTTTTGTGTTTCTATTAAAAAATATATGTATATTTTATTTTGGACGTG
28972710 CTC
326 CTC
28972713 AT
1 AT
28972715 GCCAAGTTTT
Statistics
Matches: 315, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
328 315 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (328 bp):
ATCCATAGGACTTGCTCAACACTAATAAAGACTAAGATAAGTAAGCTTATCCCTGATTAGTTACT
AAGCTTTTTAAGCTCACACATTAGTTGTTTAACACGTGTAGGTTTGGACTTACATAGAAGTCATA
ATGTTGGCTTAGGAGCATCACATCATCCATCGAGCTTCTAAGGTTGTAATTCAAACATTTAAATA
CCATTTGTATTGGACTATTGGCATATATACAAAAACTTAGATTACTTGAGCAATTGTAAAGTTAG
ATGATGAACTTGAGCCTCTTTTGTGTTTCTATTAAAAAATATATGTATATTTTATTTTGGACGTG
CTC
Found at i:28984452 original size:5 final size:5
Alignment explanation
Indices: 28984442--28984466 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28984432 AATGCCCCAT
28984442 CAAAA CAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA
28984467 GAAAGCTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:28985512 original size:18 final size:19
Alignment explanation
Indices: 28985473--28985513 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28985463 AAATTACAAA
* *
28985473 AAAATTTAAAATAATTTTT
1 AAAATTCAAAATAATTTAT
28985492 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
28985510 AAAA
1 AAAA
28985514 ACATCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:28985514 original size:19 final size:19
Alignment explanation
Indices: 28985472--28985537 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
28985462 AAAATTACAA
*
28985472 AAAAATTTAAAATAATTTT
1 AAAAATTCAAAATAATTTT
*
28985491 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
*
28985510 AAAAACATCAAAATTTATATTTT
1 AAAAA-TTCAAAA--TA-ATTTT
28985533 AAAAA
1 AAAAA
28985538 AATTATAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.11
19 16 0.43
20 6 0.16
22 1 0.03
23 6 0.16
24 4 0.11
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:28985556 original size:19 final size:19
Alignment explanation
Indices: 28985529--28985565 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28985519 AAAATTTATA
28985529 TTTTAAAAAAATTATAAAC
1 TTTTAAAAAAATTATAAAC
* *
28985548 TTTTTAAAAAATTCTAAA
1 TTTTAAAAAAATTATAAA
28985566 AAATATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTTAAAAAAATTATAAAC
Found at i:28985588 original size:38 final size:40
Alignment explanation
Indices: 28985535--28985609 Score: 111
Period size: 38 Copynumber: 1.9 Consensus size: 40
28985525 TATATTTTAA
*
28985535 AAAAATTATAAACTTTTTAAAAA-ATTCTAAAA-AATATAT
1 AAAAATTAGAAAC-TTTTAAAAATATTCTAAAATAATATAT
28985574 AAAAATT-GAAACTTTTAAAAATATTCTAAAATAATA
1 AAAAATTAGAAACTTTTAAAAATATTCTAAAATAATA
28985610 ATTTTGGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
37 9 0.27
38 13 0.39
39 11 0.33
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (40 bp):
AAAAATTAGAAACTTTTAAAAATATTCTAAAATAATATAT
Found at i:28996412 original size:114 final size:112
Alignment explanation
Indices: 28996213--28996579 Score: 545
Period size: 114 Copynumber: 3.2 Consensus size: 112
28996203 GAAATAAGAA
** * * *
28996213 TTAGCGGCGTTTTCCAGAAAGCGCCGTAAAAAACCTAAGCCCAACGACGCCGTTTACCGAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
* * *
28996278 CGGGGATTTTGTGGCGTTTTTAAAAAAGCGCCGCTAATTCTCAGGGCT
66 CGGGG-TTTAGTGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
28996326 TTAGCGGCGATTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAATGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCG-AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
28996391 TCGTGGGTTTAGCGGTGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCT
65 TCG-GGGTTTAGTGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
28996440 TTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGTTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAG-CTT
*
28996505 TCGGGTGTTTAGTGGCGTTTTTAAGAAAGCGCCTCTAATGCTCAGGGCT
65 TCGGG-GTTTAGTGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
28996554 TTAGCGGCGTTTTTGAGAAAGCGCCG
1 TTAGCGGCGTTTTTGAGAAAGCGCCG
28996580 CTAATGCTCA
Statistics
Matches: 229, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
113 58 0.25
114 168 0.73
115 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (112 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
CGGGGTTTAGTGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:28996573 original size:41 final size:41
Alignment explanation
Indices: 28996512--28996621 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 41
28996502 TTTTCGGGTG
* * *
28996512 TTTAGTGGCGTTTTTAAGAAAGCGCCTCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
*
28996553 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCATGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* *
28996594 TTTAGCGGCGTTTTTGGGGAAGCGCCGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC
28996622 AAAAAAACCT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:28996600 original size:155 final size:155
Alignment explanation
Indices: 28996398--28996735 Score: 493
Period size: 155 Copynumber: 2.2 Consensus size: 155
28996388 CTTTCGTGGG
* * *
28996398 TTTAGCGGTGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCG
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCG
* * * * *
28996463 CCG-AAAAAAACCTAAGCCCAACGACGCCGTTT-TTTGAGTTTTTCGGGTG-TTTAGTGGCGTTT
66 CCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTT-AG-CTTTCGGG-GAATTAGCGGCGTTT
* *
28996525 TTAAGAAAGCGCCTCTAATGCTCAGGGC
128 TTAAGAAAGCGCCGCTAATGCTCAGGGA
* * *
28996553 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCATGGCTTTAGCGGCGTTTTTGGGGAAGCG
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCG
*
28996618 CCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTTAGCTTTCGGGGAATTAGCGGCGTTTTTC
66 CCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTTAGCTTTCGGGGAATTAGCGGCGTTTTTA
28996683 AGAAAGCGCCGCTAATGCTCAGGGA
131 AGAAAGCGCCGCTAATGCTCAGGGA
*
28996708 TTTAGCGGCGTTTTTGGGAAAGCGCCGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC
28996736 AAGAAAAACT
Statistics
Matches: 165, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
154 1 0.01
155 132 0.80
156 30 0.18
157 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (155 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCG
CCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTTAGCTTTCGGGGAATTAGCGGCGTTTTTA
AGAAAGCGCCGCTAATGCTCAGGGA
Found at i:28996672 original size:114 final size:113
Alignment explanation
Indices: 28996554--28996825 Score: 397
Period size: 114 Copynumber: 2.4 Consensus size: 113
28996544 GCTCAGGGCT
* * *
28996554 TTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCATGGCTTTAGCGGCGTTTTTGGGGAAGCGC
1 TTAGCGGCGTTTTT-AGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGGAAAGCGC
*
28996619 CGCAA-AAAAACCTAAGCCCAAC-GACACCGTTTCCT-TAGCTTTCGGGGAA
65 CGCAAGAAAAA-CTAAGCCAAACAG-CACCGTTTCCTGT-GCTTTCGGGGAA
28996668 TTAGCGGCGTTTTTCAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGGAAAGCGC
1 TTAGCGGCGTTTTT-AGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGGAAAGCGC
* * *
28996733 CGCAAGAAAAACTAAGCCAAACAGCGCCGTTTTCTGTGCTTTCGGGGAT
65 CGCAAGAAAAACTAAGCCAAACAGCACCGTTTCCTGTGCTTTCGGGGAA
*
28996782 TTAGCGGCGTTTTTATGAAAGCGCCGCTAATGCTTAGGGATTTA
1 TTAGCGGCGTTTTTA-GAAAGCGCCGCTAATGCTCAGGGATTTA
28996826 AAATAATTTA
Statistics
Matches: 145, Mismatches: 9, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
113 1 0.01
114 137 0.94
115 7 0.05
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (113 bp):
TTAGCGGCGTTTTTAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGGAAAGCGCC
GCAAGAAAAACTAAGCCAAACAGCACCGTTTCCTGTGCTTTCGGGGAA
Found at i:28996778 original size:269 final size:269
Alignment explanation
Indices: 28996280--28996825 Score: 760
Period size: 269 Copynumber: 2.0 Consensus size: 269
28996270 CGAGCTTTCG
* * *
28996280 GGGATTTTGTGGCGTTTTTAAAAAAGCGCCGCTAATTCTCAGGGCTTTAGCGGCGATTTTGAGAA
1 GGGATTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGATTTTGAGAA
* * * * *
28996345 AGCGCCGCAAAAAAACCTAAGCCCAATGACGCCGTTTTCTGAGCTTTCGTGGGTTTAGCGGTGTT
66 AGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTGAGCTTTCGTGGGATTAGCGGCGTT
* *
28996410 TTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACC
131 TTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACC
* * * * *
28996475 TAAGCCCAACGACGCCGTTTTTTGAGTTTTTCGGGTG-TTTAGTGGCGTTTTTAAGAAAGCGCCT
196 TAAGCCAAACGACGCCGTTTTCTGAGTCTTTCGGG-GATTTAGCGGCGTTTTTAAGAAAGCGCCG
28996539 CTAATGCTCA
260 CTAATGCTCA
* * * * * * *
28996549 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCATGGCTTTAGCGGCGTTTTTGGGGA
1 GGGATTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGATTTTGAGAA
*
28996614 AGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTTAGCTTTCG-GGGAATTAGCGGCGT
66 AGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTGAGCTTTCGTGGG-ATTAGCGGCGT
* *
28996678 TTTTCAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAGAAAA
130 TTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCGCCG-AA-AAAA
* *
28996743 A-CTAAGCCAAAC-AGCGCCGTTTTCTGTG-CTTTCGGGGATTTAGCGGCGTTTTTATGAAAGCG
193 ACCTAAGCCAAACGA-CGCCGTTTTCTGAGTCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCG
*
28996805 CCGCTAATGCTTA
257 CCGCTAATGCTCA
28996818 GGGATTTA
1 GGGATTTA
28996826 AAATAATTTA
Statistics
Matches: 243, Mismatches: 29, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
268 4 0.02
269 210 0.86
270 24 0.10
271 5 0.02
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (269 bp):
GGGATTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGATTTTGAGAA
AGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTCCTGAGCTTTCGTGGGATTAGCGGCGTT
TTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCGCCGAAAAAAACC
TAAGCCAAACGACGCCGTTTTCTGAGTCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
TAATGCTCA
Found at i:28997128 original size:15 final size:15
Alignment explanation
Indices: 28997037--28997147 Score: 77
Period size: 15 Copynumber: 7.5 Consensus size: 15
28997027 GCCGGGGTAT
*
28997037 GGATTTA-GGGTTTG
1 GGATTTAGGGGTTAG
* *
28997051 GGATTTAAGGTTTAG
1 GGATTTAGGGGTTAG
* *
28997066 GG-GTTAGGTGTTA-
1 GGATTTAGGGGTTAG
* *
28997079 TGCTTTA-GGGTTAG
1 GGATTTAGGGGTTAG
* *
28997093 AAGGATATAAGGGTTAGG
1 --GGATTTAGGGGTTA-G
28997111 GGATTTAGGGGTTAG
1 GGATTTAGGGGTTAG
28997126 GGATTTAGGGGTTAG
1 GGATTTAGGGGTTAG
*
28997141 GGTTTTA
1 GGATTTA
28997148 ACGGTTAGGT
Statistics
Matches: 75, Mismatches: 15, Indels: 13
0.73 0.15 0.13
Matches are distributed among these distances:
13 6 0.08
14 17 0.23
15 29 0.39
16 16 0.21
17 6 0.08
18 1 0.01
ACGTcount: A:0.22, C:0.01, G:0.41, T:0.37
Consensus pattern (15 bp):
GGATTTAGGGGTTAG
Found at i:28997153 original size:15 final size:15
Alignment explanation
Indices: 28997104--28997156 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
28997094 AGGATATAAG
**
28997104 GGTTAGGGGATTTAGG
1 GGTTA-GGGATTTAAC
**
28997120 GGTTAGGGATTTAGG
1 GGTTAGGGATTTAAC
*
28997135 GGTTAGGGTTTTAAC
1 GGTTAGGGATTTAAC
28997150 GGTTAGG
1 GGTTAGG
28997157 TTAGAGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 29 0.85
16 5 0.15
ACGTcount: A:0.19, C:0.02, G:0.45, T:0.34
Consensus pattern (15 bp):
GGTTAGGGATTTAAC
Found at i:28997451 original size:17 final size:17
Alignment explanation
Indices: 28997429--28997561 Score: 83
Period size: 17 Copynumber: 7.3 Consensus size: 17
28997419 GGGGTTATGC
28997429 TTTAGGGGTTAAGGGGA
1 TTTAGGGGTTAAGGGGA
*
28997446 TTTAGGGGTT-AGGGTTA
1 TTTAGGGGTTAAGGG-GA
*
28997463 TGTTTCAGGGGTTAGGGGGA
1 --TTT-AGGGGTTAAGGGGA
*
28997483 TTTAGGGGTT-AGGGTTA
1 TTTAGGGGTTAAGGG-GA
*
28997500 TGTTTCAGGGGTTAGGGGGA
1 --TTT-AGGGGTTAAGGGGA
*
28997520 TTTAGGGGTT-AGGGCTA
1 TTTAGGGGTTAAGGG-GA
*
28997537 TGTTTCAGGGGTTAGGGGGA
1 --TTT-AGGGGTTAAGGGGA
28997557 TTTAG
1 TTTAG
28997562 ATAATTTGTT
Statistics
Matches: 90, Mismatches: 11, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
16 10 0.11
17 29 0.32
18 9 0.10
19 9 0.10
20 24 0.27
21 9 0.10
ACGTcount: A:0.17, C:0.03, G:0.45, T:0.35
Consensus pattern (17 bp):
TTTAGGGGTTAAGGGGA
Found at i:28997463 original size:37 final size:37
Alignment explanation
Indices: 28997420--28997561 Score: 250
Period size: 37 Copynumber: 3.8 Consensus size: 37
28997410 TGTGGTTTAG
*
28997420 GGGTTATGCTTT-AGGGGTTAAGGGGATTTAGGGGTTA
1 GGGTTATG-TTTCAGGGGTTAGGGGGATTTAGGGGTTA
28997457 GGGTTATGTTTCAGGGGTTAGGGGGATTTAGGGGTTA
1 GGGTTATGTTTCAGGGGTTAGGGGGATTTAGGGGTTA
28997494 GGGTTATGTTTCAGGGGTTAGGGGGATTTAGGGGTTA
1 GGGTTATGTTTCAGGGGTTAGGGGGATTTAGGGGTTA
*
28997531 GGGCTATGTTTCAGGGGTTAGGGGGATTTAG
1 GGGTTATGTTTCAGGGGTTAGGGGGATTTAG
28997562 ATAATTTGTT
Statistics
Matches: 102, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
36 3 0.03
37 99 0.97
ACGTcount: A:0.17, C:0.04, G:0.45, T:0.35
Consensus pattern (37 bp):
GGGTTATGTTTCAGGGGTTAGGGGGATTTAGGGGTTA
Found at i:28997474 original size:20 final size:20
Alignment explanation
Indices: 28997416--28997554 Score: 129
Period size: 20 Copynumber: 7.3 Consensus size: 20
28997406 GTTTTGTGGT
28997416 TTAGGGGTTATGCTTT-AGGGG
1 TTAGGGG-TATG-TTTCAGGGG
28997437 TTAAGGGG-A--TTT-AGGGG
1 TT-AGGGGTATGTTTCAGGGG
*
28997454 TTAGGGTTATGTTTCAGGGG
1 TTAGGGGTATGTTTCAGGGG
*
28997474 TTAGGGGGA--TTT-AGGGG
1 TTAGGGGTATGTTTCAGGGG
*
28997491 TTAGGGTTATGTTTCAGGGG
1 TTAGGGGTATGTTTCAGGGG
*
28997511 TTAGGGGGA--TTT-AGGGG
1 TTAGGGGTATGTTTCAGGGG
*
28997528 TTAGGGCTATGTTTCAGGGG
1 TTAGGGGTATGTTTCAGGGG
28997548 TTAGGGG
1 TTAGGGG
28997555 GATTTAGATA
Statistics
Matches: 97, Mismatches: 10, Indels: 23
0.75 0.08 0.18
Matches are distributed among these distances:
16 4 0.04
17 35 0.36
18 6 0.06
19 9 0.09
20 36 0.37
21 2 0.02
22 5 0.05
ACGTcount: A:0.17, C:0.04, G:0.45, T:0.35
Consensus pattern (20 bp):
TTAGGGGTATGTTTCAGGGG
Found at i:28997921 original size:109 final size:109
Alignment explanation
Indices: 28997797--28997998 Score: 386
Period size: 109 Copynumber: 1.9 Consensus size: 109
28997787 TTACCTTTTC
28997797 CGGCGTTTTTCGTAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTTTGTT
1 CGGCGTTTTTCGTAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTTTGTT
28997862 ATGCTAAAAATCATTTATTTTATCTGCTAAAAATTATTAGTTTG
66 ATGCTAAAAATCATTTATTTTATCTGCTAAAAATTATTAGTTTG
*
28997906 CGGCGTTTTTCGTAAAAATGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTTTGTT
1 CGGCGTTTTTCGTAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTTTGTT
*
28997971 ATGCTAAAAATCCTTTATTTTATCTGCT
66 ATGCTAAAAATCATTTATTTTATCTGCT
28997999 TAAATGAAAT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 91 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.38
Consensus pattern (109 bp):
CGGCGTTTTTCGTAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTTTGTT
ATGCTAAAAATCATTTATTTTATCTGCTAAAAATTATTAGTTTG
Found at i:28999288 original size:43 final size:43
Alignment explanation
Indices: 28999240--28999395 Score: 204
Period size: 43 Copynumber: 3.6 Consensus size: 43
28999230 TCTCTAAATA
* * * *
28999240 CGCCGCTAAAGGTCTTGCTCTTTAGTGGCGTTTTCAGGTAAAG
1 CGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTTTAGGAAAAG
* * *
28999283 AGCCGCTAAAAGTCTTGTTCTTTAGCGGCGTTTTTATGAAAAG
1 CGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTTTAGGAAAAG
* * *
28999326 CGCCGTTAAAGTTCTTGTTCTTTAGCGGCGTTTTTGGGAAAAG
1 CGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTTTAGGAAAAG
* *
28999369 CGCCGCTAAAGGTCATGATCTTTAGCG
1 CGCCGCTAAAGGTCTTGTTCTTTAGCG
28999396 ACGCTTATTT
Statistics
Matches: 96, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 96 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (43 bp):
CGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTTTAGGAAAAG
Found at i:29001192 original size:7 final size:7
Alignment explanation
Indices: 29001180--29001206 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
29001170 CTTAGCTGAT
29001180 AGTTGAA
1 AGTTGAA
29001187 AGTTGAA
1 AGTTGAA
29001194 AGTTGAA
1 AGTTGAA
29001201 AGTTGA
1 AGTTGA
29001207 TATTTGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (7 bp):
AGTTGAA
Found at i:29001780 original size:15 final size:15
Alignment explanation
Indices: 29001760--29001789 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29001750 GGTGGCTCTC
29001760 TCTTTTCTAAAGATG
1 TCTTTTCTAAAGATG
29001775 TCTTTTCTAAAGATG
1 TCTTTTCTAAAGATG
29001790 GGATATTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
TCTTTTCTAAAGATG
Found at i:29007329 original size:51 final size:52
Alignment explanation
Indices: 29007196--29007331 Score: 129
Period size: 51 Copynumber: 2.7 Consensus size: 52
29007186 CTATGAAAAT
* * *
29007196 TTGATAGAATATATAAATATT--ATAGATTAAATTTGTTAAATAAGGATTAAA
1 TTGATAAAATATGTAAATATTACATAG-TTAAATTTGTTAAATAAGGACTAAA
* * *
29007247 TTGATAAAATTTGTAAATATTACA-GGATAAATTTGTTAAATCAA-GACTAAA
1 TTGATAAAATATGTAAATATTACATAGTTAAATTTGTTAAAT-AAGGACTAAA
** * *
29007298 TTGATTGAATATGTTAATTTTA-ATAGTTAAATTT
1 TTGATAAAATATGTAAATATTACATAGTTAAATTT
29007332 ATTATTATGC
Statistics
Matches: 68, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
50 1 0.01
51 63 0.93
52 3 0.04
53 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (52 bp):
TTGATAAAATATGTAAATATTACATAGTTAAATTTGTTAAATAAGGACTAAA
Found at i:29021855 original size:57 final size:57
Alignment explanation
Indices: 29021770--29021877 Score: 189
Period size: 57 Copynumber: 1.9 Consensus size: 57
29021760 AATATATAGC
*
29021770 TAAATTAACTATGGTAACAGCAATCACATGCATTTTTTCATGCATGGCCCTGCTAAT
1 TAAATTAACTATAGTAACAGCAATCACATGCATTTTTTCATGCATGGCCCTGCTAAT
**
29021827 TAAATTAACTATAGTAATGGCAATCACATGCATTTTTTCATGCATGGCCCT
1 TAAATTAACTATAGTAACAGCAATCACATGCATTTTTTCATGCATGGCCCT
29021878 AAAGAGGAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.34
Consensus pattern (57 bp):
TAAATTAACTATAGTAACAGCAATCACATGCATTTTTTCATGCATGGCCCTGCTAAT
Found at i:29036417 original size:2 final size:2
Alignment explanation
Indices: 29036410--29036439 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29036400 TGAAGTGATA
29036410 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
29036440 TGCAAGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29039857 original size:409 final size:409
Alignment explanation
Indices: 29039098--29039921 Score: 1639
Period size: 409 Copynumber: 2.0 Consensus size: 409
29039088 AATTTTGTGT
29039098 AATGCAAATCTGTTTAAGTATGAGACGATATTTGATTTGCAGAGTCCTTGTAAGAAGGGTGAAGA
1 AATGCAAATCTGTTTAAGTATGAGACGATATTTGATTTGCAGAGTCCTTGTAAGAAGGGTGAAGA
29039163 TTTTCTATATTTTAACAAGCCTAAGGAACTGGAGTTCTGCGAGCATCAGCCAGCAAACGAGACGC
66 TTTTCTATATTTTAACAAGCCTAAGGAACTGGAGTTCTGCGAGCATCAGCCAGCAAACGAGACGC
29039228 ATGCAATAGACCAGGCTGAAACAAAAATAACAAGAGCTGATAAAGAAACAGGAAAAATGGAGCCA
131 ATGCAATAGACCAGGCTGAAACAAAAATAACAAGAGCTGATAAAGAAACAGGAAAAATGGAGCCA
29039293 GCAATAGCCAACAGACCAGGAGCCAGAATTGATAGCCATATCACAGAACCCAGCTCAAAGGGCAG
196 GCAATAGCCAACAGACCAGGAGCCAGAATTGATAGCCATATCACAGAACCCAGCTCAAAGGGCAG
29039358 CCATCACGAGTAGATCCTTAAAGCGACAAATGTCAGATTTAGCCAACCGATCAACAAATTATTGT
261 CCATCACGAGTAGATCCTTAAAGCGACAAATGTCAGATTTAGCCAACCGATCAACAAATTATTGT
29039423 CTTCTCTAGGGATGAGCTAGAAGTCAATGTTAATACATGAGCATTGTCTTAGGCAGGCTTAAATC
326 CTTCTCTAGGGATGAGCTAGAAGTCAATGTTAATACATGAGCATTGTCTTAGGCAGGCTTAAATC
29039488 ATGCTTTGGATGCCAGCTG
391 ATGCTTTGGATGCCAGCTG
29039507 AATGCAAATCTGTTTAAGTATGAGACGATATTTGATTTGCAGAGTCCTTGTAAGAAGGGTGAAGA
1 AATGCAAATCTGTTTAAGTATGAGACGATATTTGATTTGCAGAGTCCTTGTAAGAAGGGTGAAGA
29039572 TTTTCTATATTTTAACAAGCCTAAGGAACTGGAGTTCTGCGAGCATCAGCCAGCAAACGAGACGC
66 TTTTCTATATTTTAACAAGCCTAAGGAACTGGAGTTCTGCGAGCATCAGCCAGCAAACGAGACGC
29039637 ATGCAATAGACCAGGCTGAAACAAAAATAACAAGAGCTGATAAAGAAACAGGAAAAATGGAGCCA
131 ATGCAATAGACCAGGCTGAAACAAAAATAACAAGAGCTGATAAAGAAACAGGAAAAATGGAGCCA
29039702 GCAATAGCCAACAGACCAGGAGCCAGAATTGATAGCCATATCACAGAACCCAGCTCAAAGGGCAG
196 GCAATAGCCAACAGACCAGGAGCCAGAATTGATAGCCATATCACAGAACCCAGCTCAAAGGGCAG
29039767 CCATCACGAGTAGATCCTTAAAGCGACAAATGTCAGATTTAGCCAACCGATCAACAAATTATTGT
261 CCATCACGAGTAGATCCTTAAAGCGACAAATGTCAGATTTAGCCAACCGATCAACAAATTATTGT
29039832 CTTCTCTAGGGATGAGCTAGAAGTCAATGTTAATACATGAGCATTGTCTTAGGCAGGCTTAAATC
326 CTTCTCTAGGGATGAGCTAGAAGTCAATGTTAATACATGAGCATTGTCTTAGGCAGGCTTAAATC
29039897 ATGCTTTGGATGCCAGCTG
391 ATGCTTTGGATGCCAGCTG
*
29039916 ATTGCA
1 AATGCA
29039922 TTGTTGTAGT
Statistics
Matches: 414, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
409 414 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (409 bp):
AATGCAAATCTGTTTAAGTATGAGACGATATTTGATTTGCAGAGTCCTTGTAAGAAGGGTGAAGA
TTTTCTATATTTTAACAAGCCTAAGGAACTGGAGTTCTGCGAGCATCAGCCAGCAAACGAGACGC
ATGCAATAGACCAGGCTGAAACAAAAATAACAAGAGCTGATAAAGAAACAGGAAAAATGGAGCCA
GCAATAGCCAACAGACCAGGAGCCAGAATTGATAGCCATATCACAGAACCCAGCTCAAAGGGCAG
CCATCACGAGTAGATCCTTAAAGCGACAAATGTCAGATTTAGCCAACCGATCAACAAATTATTGT
CTTCTCTAGGGATGAGCTAGAAGTCAATGTTAATACATGAGCATTGTCTTAGGCAGGCTTAAATC
ATGCTTTGGATGCCAGCTG
Found at i:29042850 original size:25 final size:25
Alignment explanation
Indices: 29042816--29042866 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29042806 TCAAAGCATA
29042816 CAAGGATTCTTTTAATGCTAGTCAC
1 CAAGGATTCTTTTAATGCTAGTCAC
29042841 CAAGGATTCTTTTAATGCTAGTCAC
1 CAAGGATTCTTTTAATGCTAGTCAC
29042866 C
1 C
29042867 TGCAGAACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (25 bp):
CAAGGATTCTTTTAATGCTAGTCAC
Found at i:29044142 original size:17 final size:16
Alignment explanation
Indices: 29044110--29044143 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
29044100 ATAAAAAATT
29044110 AAATTTTAAATATATA
1 AAATTTTAAATATATA
*
29044126 AAATTTATAAATTTATA
1 AAATTT-TAAATATATA
29044143 A
1 A
29044144 CATATTNNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATTTTAAATATATA
Found at i:29060745 original size:2 final size:2
Alignment explanation
Indices: 29060732--29060765 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
29060722 TAGCTATGAG
*
29060732 AT AT AC 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
29060766 TCTTTTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29061842 original size:2 final size:2
Alignment explanation
Indices: 29061835--29061860 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29061825 TTTAAAAGTA
29061835 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
29061861 GAAAAACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29070590 original size:2 final size:2
Alignment explanation
Indices: 29070583--29070608 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29070573 TCCTCCTGAA
29070583 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
29070609 TCACAGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29071356 original size:2 final size:2
Alignment explanation
Indices: 29071349--29071380 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29071339 TACAGTACTC
29071349 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
29071381 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29075273 original size:84 final size:84
Alignment explanation
Indices: 29075161--29075413 Score: 416
Period size: 84 Copynumber: 3.0 Consensus size: 84
29075151 CGCAAAAAAT
* * * *
29075161 AAAAAACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTAGCGTTTTTGGTCTAGCGCCTCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTTGTCTAGCGCCACT
29075226 AATGGTCTGTGTTTTTAGC
66 AATGGTCTGTGTTTTTAGC
* *
29075245 AAAATACAACGGCGTCGTTTAGTGGCCTTCGATGGCCTTAGTGGCGTTTTTTGTCTAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTTGTCTAGCGCCACT
29075310 AATGGTCTGTGTTTTTAGC
66 AATGGTCTGTGTTTTTAGC
* *
29075329 AAAATAAAAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGGGTTTTTTGTCTAGCGCCAC
1 AAAAT-ACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTTGTCTAGCGCCAC
*
29075394 TAATGATCTGTGTTTTTAGC
65 TAATGGTCTGTGTTTTTAGC
29075414 GGCGTTTTAA
Statistics
Matches: 158, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 84 0.53
85 74 0.47
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.35
Consensus pattern (84 bp):
AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTTGTCTAGCGCCACT
AATGGTCTGTGTTTTTAGC
Found at i:29075471 original size:198 final size:197
Alignment explanation
Indices: 29075245--29075713 Score: 715
Period size: 198 Copynumber: 2.4 Consensus size: 197
29075235 TGTTTTTAGC
* *
29075245 AAAATACAACGGCGTCGTTTAGTGGCCTTCGATGGCCTTAGTGGCGTTTTTTGTCTAGCGCCGCT
1 AAAATACAACGGCGTCATTTAGTGGCCTTCG-TGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
*
29075310 AATGGTCTGTGTTTTTAGCAAAATAAAAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGG
65 AATGGTCTGTGTTTTTAGCAAAAT-AAAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGC
29075375 GTTTTTTGTCTAGCGCCACTAATGATCTGTGTTTTTAGCGGCGTTTT-AAAAAAAACGCCGCAAA
129 GTTTTTTGTCTAGCGCCACTAATGATCTGTGTTTTTAGCGGCGTTTTCAAAAAAAACGCCGCAAA
29075439 AAAT
194 AAAT
* *
29075443 AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCGTAGTGACGTTTTTGGTCTAGCGCCGCT
1 AAAATACAACGGCGTCATTTAGTGGCCTTC-GTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
* * *
29075508 AATGGTCTATGTTTTTAGCAAAATACAATGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCG
65 AATGGTCTGTGTTTTTAGCAAAATAAAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCG
* * * *
29075573 TTTTTTGTCTTGCGCCGCTAATGGTCTGTGTTTTTAGCGGCGTTTTCAGAAAAAACGCCGCAAAA
130 TTTTTTGTCTAGCGCCACTAATGATCTGTGTTTTTAGCGGCGTTTTCAAAAAAAACGCCGCAAAA
29075638 AAT
195 AAT
* *
29075641 AAAATACAAC-G-G-CA--TCGT----TTAGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCTA
1 AAAATACAACGGCGTCATTTAGTGGCCTTCGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCTA
29075697 ATGGTCTGTGTTTTTAG
66 ATGGTCTGTGTTTTTAG
29075714 TGGCGTTTTT
Statistics
Matches: 252, Mismatches: 17, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
188 49 0.19
189 2 0.01
193 3 0.01
195 2 0.01
196 1 0.00
197 82 0.33
198 112 0.44
199 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (197 bp):
AAAATACAACGGCGTCATTTAGTGGCCTTCGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCTA
ATGGTCTGTGTTTTTAGCAAAATAAAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGT
TTTTTGTCTAGCGCCACTAATGATCTGTGTTTTTAGCGGCGTTTTCAAAAAAAACGCCGCAAAAA
AT
Found at i:29075588 original size:84 final size:84
Alignment explanation
Indices: 29075443--29075610 Score: 273
Period size: 84 Copynumber: 2.0 Consensus size: 84
29075433 CGCAAAAAAT
29075443 AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCGTAGTGACGTTTTTGGTCTAGCGCCGCT
1 AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCGTAGTGACGTTTTTGGTCTAGCGCCGCT
29075508 AATGGTCTATGTTTTTAGC
66 AATGGTCTATGTTTTTAGC
* * * * * *
29075527 AAAATACAATGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTTGTCTTGCGCCGCT
1 AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCGTAGTGACGTTTTTGGTCTAGCGCCGCT
*
29075592 AATGGTCTGTGTTTTTAGC
66 AATGGTCTATGTTTTTAGC
29075611 GGCGTTTTCA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.36
Consensus pattern (84 bp):
AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCGTAGTGACGTTTTTGGTCTAGCGCCGCT
AATGGTCTATGTTTTTAGC
Found at i:29075806 original size:113 final size:114
Alignment explanation
Indices: 29075527--29076003 Score: 560
Period size: 113 Copynumber: 4.3 Consensus size: 114
29075517 TGTTTTTAGC
* * *
29075527 AAAATACAATGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTTGTCTTGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
*
29075592 AATGGTCTGTGTTTTTAGCGGCGTTTTCAGAAAAAACGCCGCAAAAAAT
66 AATGGTCTGTGTTTTTAGCGGCGTTTTCAGGAAAAACGCCGCAAAAAAT
*
29075641 AAAATACAACGGCATCGTTTA----------GTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
* * * *
29075696 AATGGTCTGTGTTTTTAGTGGCGTTTTTAGGAAGAACGCCGTAAAAAAT
66 AATGGTCTGTGTTTTTAGCGGCGTTTTCAGGAAAAACGCCGCAAAAAAT
* * * * * * *
29075745 AAAATATAGCGACGTCGTTTAGTGG-CTACGATGGCGTTAGTGGCTTTTTTGGTCT-GACGCCGC
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAG-CGCCGC
* * * *
29075808 TAATGGTCTGTGTTTTTAGTGGCGTTTTCAGGATAAACACAGCAAAAAAT
65 TAATGGTCTGTGTTTTTAGCGGCGTTTTCAGGAAAAACGCCGCAAAAAAT
* * *
29075858 AAAATACAATGGCGTCGTTTAGTGGCCTTCGGTGGCCCTAGTGGCGTTTTTGGTATAGCGCCGCT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
* * * *
29075923 AATGGTCT-TTTTTTTAGCGGTGTTTTCTGGAAAAACGCCACAAAAAAT
66 AATGGTCTGTGTTTTTAGCGGCGTTTTCAGGAAAAACGCCGCAAAAAAT
*
29075971 AAAAT---A---CGTCGTTTAGTGGCCTTCGATGGCCTT
1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTT
29076004 TTACCTTAAT
Statistics
Matches: 309, Mismatches: 42, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
104 93 0.30
107 25 0.08
110 1 0.00
112 1 0.00
113 130 0.42
114 58 0.19
115 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (114 bp):
AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT
AATGGTCTGTGTTTTTAGCGGCGTTTTCAGGAAAAACGCCGCAAAAAAT
Found at i:29077206 original size:340 final size:332
Alignment explanation
Indices: 29076593--29077265 Score: 1102
Period size: 340 Copynumber: 2.0 Consensus size: 332
29076583 TTAATTAAGG
* *
29076593 GTTGGCCGGGATTTAAGGTTTAGGGGTTAGGGGTTAGATGTTAGTGGTTAAGACTTAGGGATTTT
1 GTTGGCCGGGATTTAAGGTTTAGGGGTTAGGGGTTAGATGTCAGTGGTTAAGACTTAGGGATTTA
*
29076658 GTGTTTAGGGTTTCAAGGGTCGGGTTACAGTTTTGGTTTAGATTAATTTTTTTATTTATATTTTA
66 GTGTTTAGGGTTTCAAGGGTCGGGTTACAATTTTGGTTTAGATTAATTTTTTTATTTATATTTTA
** *
29076723 AATATGTTCTTATGTAATTGTAAATTATGTATAATTTAGGGTTTAATTAATTATGCCTTGAGAGA
131 AATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTTAA-TAATTATGCCTTGAGAGA
*
29076788 GAGAGATATAATAGATAGAGTACTTAAATATTTTTATCCCTTCAATGGTTAATTTAGGCGGGTTT
195 GAGAGATATAATAGATAGAGTACTTAAATATTTATATCCCTTCAATGGTTAATTTAGGCGGGTTT
29076853 AATATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTAATGCTTTTTAATGTTTAGGG
260 AATATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTAATGCTTTTTAATGTTTAGGG
29076918 AATACTAT
325 AATACTAT
*
29076926 GTTGGCCGGGATTTAAGGTTTAGGGGAGGGGTTTAGGGGTTAGATGTCAGTTGTTAAGACTTAGG
1 GTTGGCCGGGATTTAAGGTTT-----AGGGG-TTAGGGGTTAGATGTCAGTGGTTAAGACTTAGG
*
29076991 GATTTAAG-GTTTAGGGTTTCAAGGGTCTGGTTACAATTTTGGGTTTAGATTAATTTTTTTATTT
60 GATTT-AGTGTTTAGGGTTTCAAGGGTCGGGTTACAATTTT-GGTTTAGATTAATTTTTTTATTT
29077055 ATATTTTAAATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTT-A-AATTATGCCT
123 ATATTTTAAATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTTAATAATTATGCCT
*
29077118 TGAGAGAGAGATATATAATAGATAGA-TACTTTAAATATTTATATCCCTTCAATGGTTAATTTAG
188 TGAGAGAGAGAGATATAATAGATAGAGTAC-TTAAATATTTATATCCCTTCAATGGTTAATTTAG
29077182 GCGGGTTTAATAAGATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTAATGCTTTTT
252 GCGGGTTTAAT---ATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTAATGCTTTTT
*
29077247 AATGTTTAGGGAGTACTAT
314 AATGTTTAGGGAATACTAT
29077266 ATATATATGG
Statistics
Matches: 317, Mismatches: 11, Indels: 17
0.92 0.03 0.05
Matches are distributed among these distances:
333 21 0.07
336 3 0.01
337 79 0.25
338 5 0.02
339 67 0.21
340 142 0.45
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.42
Consensus pattern (332 bp):
GTTGGCCGGGATTTAAGGTTTAGGGGTTAGGGGTTAGATGTCAGTGGTTAAGACTTAGGGATTTA
GTGTTTAGGGTTTCAAGGGTCGGGTTACAATTTTGGTTTAGATTAATTTTTTTATTTATATTTTA
AATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTTAATAATTATGCCTTGAGAGAG
AGAGATATAATAGATAGAGTACTTAAATATTTATATCCCTTCAATGGTTAATTTAGGCGGGTTTA
ATATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTAATGCTTTTTAATGTTTAGGGA
ATACTAT
Found at i:29077483 original size:28 final size:28
Alignment explanation
Indices: 29077452--29077506 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
29077442 AAATGAAATA
* *
29077452 AAAACGCTAAAATTTATAAATTTTAGTT
1 AAAACACTAAAAATTATAAATTTTAGTT
*
29077480 AAAACACTAAAAATTATAATTTTTAGT
1 AAAACACTAAAAATTATAAATTTTAGT
29077507 ACAATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.38
Consensus pattern (28 bp):
AAAACACTAAAAATTATAAATTTTAGTT
Found at i:29078170 original size:28 final size:28
Alignment explanation
Indices: 29078138--29078194 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
29078128 AATAAAAAAA
*
29078138 TAAAAAT-GAAATAAAAACACTAAAATT
1 TAAAAATATAAATAAAAACACTAAAATT
* * *
29078165 TAAAAATATTAGTGAAAACACTAAAATT
1 TAAAAATATAAATAAAAACACTAAAATT
29078193 TA
1 TA
29078195 TAATTATTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.26
Consensus pattern (28 bp):
TAAAAATATAAATAAAAACACTAAAATT
Found at i:29078202 original size:28 final size:28
Alignment explanation
Indices: 29078151--29078205 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
29078141 AAATGAAATA
29078151 AAAACACTAAAATTTAAAAATATTAGTG
1 AAAACACTAAAATTTAAAAATATTAGTG
* *
29078179 AAAACACTAAAATTTATAATTATTAGT
1 AAAACACTAAAATTTAAAAATATTAGT
29078206 ACTATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAACACTAAAATTTAAAAATATTAGTG
Found at i:29078892 original size:14 final size:14
Alignment explanation
Indices: 29078873--29078902 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29078863 TAAAAGGTTT
29078873 TTTAGTTAATCATC
1 TTTAGTTAATCATC
29078887 TTTAGTTAATCATC
1 TTTAGTTAATCATC
29078901 TT
1 TT
29078903 GTTGTTCGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTAGTTAATCATC
Found at i:29079651 original size:55 final size:55
Alignment explanation
Indices: 29079590--29079705 Score: 196
Period size: 55 Copynumber: 2.1 Consensus size: 55
29079580 TTAATATAAG
*
29079590 ATATTTTTAATATATGCAATCTATATTTTTAATATACGGCATGGATATGTAACAT
1 ATATTTTTAATAGATGCAATCTATATTTTTAATATACGGCATGGATATGTAACAT
* * *
29079645 ATATTTTTAATAGATGCAATTTATATTTTTAATATATGGTATGGATATGTAACAT
1 ATATTTTTAATAGATGCAATCTATATTTTTAATATACGGCATGGATATGTAACAT
29079700 ATATTT
1 ATATTT
29079706 CAAATTTTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (55 bp):
ATATTTTTAATAGATGCAATCTATATTTTTAATATACGGCATGGATATGTAACAT
Found at i:29079893 original size:28 final size:28
Alignment explanation
Indices: 29079860--29079913 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
29079850 TCAATCATAT
*
29079860 CATAACTTATAT-ATAAACTTACATAATA
1 CATAACTTACATAAT-AACTTACATAATA
29079888 CATAACTTACATAATAACTTACATAA
1 CATAACTTACATAATAACTTACATAA
29079914 CTTATATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (28 bp):
CATAACTTACATAATAACTTACATAATA
Found at i:29079958 original size:12 final size:12
Alignment explanation
Indices: 29079889--29079913 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29079879 TACATAATAC
29079889 ATAACTTACATA
1 ATAACTTACATA
29079901 ATAACTTACATA
1 ATAACTTACATA
29079913 A
1 A
29079914 CTTATATAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:29080042 original size:9 final size:9
Alignment explanation
Indices: 29079995--29080191 Score: 114
Period size: 9 Copynumber: 22.6 Consensus size: 9
29079985 ACGTAAATTG
*
29079995 CATAACTCA
1 CATAACTTA
29080004 CATAA--TA
1 CATAACTTA
*
29080011 CACAACTTA
1 CATAACTTA
*
29080020 CATAACTAA
1 CATAACTTA
*
29080029 AATAACTTA
1 CATAACTTA
29080038 CATAA--TA
1 CATAACTTA
29080045 CATAACTTA
1 CATAACTTA
*
29080054 CATTAATGTTATA
1 CA-TAA--CT-TA
29080067 CATAACTTA
1 CATAACTTA
29080076 CATAACTTA
1 CATAACTTA
29080085 -ATTAA-TTA
1 CA-TAACTTA
*
29080093 -AT-ACTAAA
1 CATAACT-TA
*
29080101 CATAACTTGT
1 CATAACTT-A
*
29080111 CA-GACTTA
1 CATAACTTA
29080119 CATAACTTA
1 CATAACTTA
29080128 CATAA--TA
1 CATAACTTA
*
29080135 CACAACTTA
1 CATAACTTA
*
29080144 CACAACTTA
1 CATAACTTA
29080153 CATAA--TA
1 CATAACTTA
*
29080160 CACAACTTA
1 CATAACTTA
*
29080169 TATAACTTA
1 CATAACTTA
* *
29080178 AAAAACTTA
1 CATAACTTA
29080187 CATAA
1 CATAA
29080192 TACACAACTT
Statistics
Matches: 145, Mismatches: 24, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
6 1 0.01
7 26 0.18
8 8 0.06
9 93 0.64
10 9 0.06
12 4 0.03
13 4 0.03
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (9 bp):
CATAACTTA
Found at i:29080141 original size:16 final size:16
Alignment explanation
Indices: 29080142--29080202 Score: 77
Period size: 16 Copynumber: 3.7 Consensus size: 16
29080132 ATACACAACT
29080142 TACACAACTTACATAA
1 TACACAACTTACATAA
*
29080158 TACACAACTTATATAA
1 TACACAACTTACATAA
* *
29080174 CTTAAAAAACTTACATAA
1 --TACACAACTTACATAA
29080192 TACACAACTTA
1 TACACAACTTA
29080203 TATATAACTC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
16 24 0.65
18 13 0.35
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACAACTTACATAA
Found at i:29080142 original size:34 final size:30
Alignment explanation
Indices: 29080114--29080201 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 30
29080104 AACTTGTCAG
29080114 ACTTACATAACTTACATAATACACAAC-TT-
1 ACTTACA-AACTTACATAATACACAACTTTA
29080143 AC--AC-AACTTACATAATACACAACTTATATA
1 ACTTACAAACTTACATAATACACAAC-T-T-TA
*
29080173 ACTTAAAAAACTTACATAATACACAACTT
1 ACTT-ACAAACTTACATAATACACAACTT
29080202 ATATATAACT
Statistics
Matches: 49, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
25 19 0.39
27 2 0.04
28 1 0.02
29 3 0.06
30 2 0.04
32 1 0.02
33 2 0.04
34 19 0.39
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (30 bp):
ACTTACAAACTTACATAATACACAACTTTA
Found at i:29080144 original size:25 final size:25
Alignment explanation
Indices: 29080114--29080177 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
29080104 AACTTGTCAG
29080114 ACTTACATAACTTACATAATACACA
1 ACTTACATAACTTACATAATACACA
*
29080139 ACTTACACAACTTACATAATACACA
1 ACTTACATAACTTACATAATACACA
*
29080164 ACTTATATAACTTA
1 ACTTACATAACTTA
29080178 AAAAACTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (25 bp):
ACTTACATAACTTACATAATACACA
Found at i:29080202 original size:34 final size:34
Alignment explanation
Indices: 29080138--29080206 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
29080128 CATAATACAC
* *
29080138 AACTTACACAACTTACATAATACACAACTTATAT
1 AACTTAAAAAACTTACATAATACACAACTTATAT
29080172 AACTTAAAAAACTTACATAATACACAACTTATAT
1 AACTTAAAAAACTTACATAATACACAACTTATAT
29080206 A
1 A
29080207 TAACTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (34 bp):
AACTTAAAAAACTTACATAATACACAACTTATAT
Found at i:29086209 original size:42 final size:41
Alignment explanation
Indices: 29086124--29086238 Score: 171
Period size: 42 Copynumber: 2.8 Consensus size: 41
29086114 GCTAAAGAAC
* *
29086124 AGAAAAAACGCCGCTAAAGA-C-TGTTATTTAGCGGCGCTT
1 AGAAAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTT
*
29086163 AGAAAGAAACGCCGCTAAAGACCATGTTCTTTAGAGGGGCTT
1 AGAAA-AAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTT
29086205 AGAAAAAAACGCCGCTAAAGACCATGTTCTTTAG
1 AG-AAAAAACGCCGCTAAAGACCATGTTCTTTAG
29086239 TAAACGCCGC
Statistics
Matches: 69, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
39 5 0.07
40 15 0.22
41 1 0.01
42 45 0.65
43 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (41 bp):
AGAAAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTT
Found at i:29086253 original size:29 final size:29
Alignment explanation
Indices: 29086211--29086267 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
29086201 GCTTAGAAAA
* *
29086211 AAACGCCGCTAAAGACCATGTTCTTTAGT
1 AAACGCCGCTAAAGAACATGATCTTTAGT
29086240 AAACGCCGCTAAAGAACATGATCTTTAG
1 AAACGCCGCTAAAGAACATGATCTTTAG
29086268 CGGCGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (29 bp):
AAACGCCGCTAAAGAACATGATCTTTAGT
Found at i:29086307 original size:42 final size:42
Alignment explanation
Indices: 29086243--29086361 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
29086233 CTTTAGTAAA
*
29086243 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTCTCTAAG
* *
29086285 CGCCTCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTCTCTAAG
*
29086327 CGCCGCTAAAGAACATGGTCTTTAGCGGCATTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
29086362 GTTTGTAAAC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTCTCTAAG
Found at i:29093444 original size:24 final size:22
Alignment explanation
Indices: 29093399--29093445 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
29093389 AATGGAAAAT
* *
29093399 AAGAATAAAAAAAGAAAGTTAA
1 AAGAATAAAAAAAAAAAATTAA
29093421 AAGAATATAAAAAATAAAAATTAA
1 AAGAATA-AAAAAA-AAAAATTAA
29093445 A
1 A
29093446 TTACTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 6 0.29
24 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (22 bp):
AAGAATAAAAAAAAAAAATTAA
Found at i:29096462 original size:6 final size:6
Alignment explanation
Indices: 29096453--29096487 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
29096443 TTTCCACTTC
29096453 CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCT
1 CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCT
29096488 AACATGTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (6 bp):
CCCCTT
Found at i:29102925 original size:17 final size:18
Alignment explanation
Indices: 29102903--29102940 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29102893 TTTATATATG
*
29102903 ATATTA-ATTATTGTAAA
1 ATATTATATTATTATAAA
*
29102920 ATATTATTTTATTATAAA
1 ATATTATATTATTATAAA
29102938 ATA
1 ATA
29102941 AATTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATTATATTATTATAAA
Found at i:29107621 original size:17 final size:18
Alignment explanation
Indices: 29107585--29107622 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
29107575 TTGGGCCGTG
29107585 CACTAGTCTCTTCATAAA
1 CACTAGTCTCTTCATAAA
* *
29107603 CACTAGT-TTTTCTTAAA
1 CACTAGTCTCTTCATAAA
29107620 CAC
1 CAC
29107623 AAGCACTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (18 bp):
CACTAGTCTCTTCATAAA
Found at i:29107893 original size:40 final size:40
Alignment explanation
Indices: 29107839--29107917 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
29107829 TTTTCGTGAT
* * *
29107839 TTTTAGTTTTTATACTTTTTGAGTTTTAAAATTTTAATCA
1 TTTTAATTTTTATACTTTTCGAATTTTAAAATTTTAATCA
29107879 TTTTAATTTTTATACTTTTCGAATTTTAAAATTTTAATC
1 TTTTAATTTTTATACTTTTCGAATTTTAAAATTTTAATC
29107918 TCAATCAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.59
Consensus pattern (40 bp):
TTTTAATTTTTATACTTTTCGAATTTTAAAATTTTAATCA
Found at i:29109326 original size:92 final size:93
Alignment explanation
Indices: 29109196--29109380 Score: 336
Period size: 92 Copynumber: 2.0 Consensus size: 93
29109186 AGCAATCCTT
29109196 TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
1 TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
29109261 TGTTGATTCATCTTTTTTATATTATTTC
66 TGTTGATTCATCTTTTTTATATTATTTC
* *
29109289 TTCTTCGCCTTTTTTTAC-TTTGTTAGGATTGAGCTCTGATTAGAGATTTTTTTTTGGGTTTAAT
1 TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
*
29109353 TGTTGATTCATCTTTTTTCTATTATTTC
66 TGTTGATTCATCTTTTTTATATTATTTC
29109381 CTGGCAGCTC
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 72 0.81
93 17 0.19
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (93 bp):
TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
TGTTGATTCATCTTTTTTATATTATTTC
Found at i:29113548 original size:5 final size:5
Alignment explanation
Indices: 29113538--29113562 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29113528 TCTTGATGGC
29113538 ATGCT ATGCT ATGCT ATGCT ATGCT
1 ATGCT ATGCT ATGCT ATGCT ATGCT
29113563 TCCATGTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
ATGCT
Found at i:29114508 original size:24 final size:23
Alignment explanation
Indices: 29114480--29114528 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
29114470 GACATTACCT
29114480 AAAAAGAATTTACAAAAAAAAAAA
1 AAAAAGAATTTA-AAAAAAAAAAA
* * *
29114504 AAAAAGACTTTAAAATAAAATAA
1 AAAAAGAATTTAAAAAAAAAAAA
29114527 AA
1 AA
29114529 TAATATTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (23 bp):
AAAAAGAATTTAAAAAAAAAAAA
Found at i:29121004 original size:6 final size:6
Alignment explanation
Indices: 29120993--29121037 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
29120983 GGAAAATTTT
* * *
29120993 CCTTTC CCTTTC CCTTTC CCTTCC CCTTCC CCTTCC CCTTCC CCT
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCT
29121038 ATCCTTGACA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (6 bp):
CCTTCC
Found at i:29123517 original size:32 final size:33
Alignment explanation
Indices: 29123481--29123567 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 33
29123471 AACTTTTCCG
* * *
29123481 GAAAATATTTT-CAGGAAATCTATCAAACAGCA
1 GAAAATATTTTACAGCAAATCAATCAAACACCA
*
29123513 GAAAATATTTTACA-CAGATTCAATCAAACACCA
1 GAAAATATTTTACAGCA-AATCAATCAAACACCA
* *
29123546 GAAAATATTTTCCAGTAAATCA
1 GAAAATATTTTACAGCAAATCA
29123568 TTTTACAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 12 0.27
33 32 0.71
34 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCAATCAAACACCA
Found at i:29123565 original size:14 final size:15
Alignment explanation
Indices: 29123543--29123619 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
29123533 CAATCAAACA
29123543 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
29123557 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
29123572 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
29123592 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
29123606 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
29123620 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:29123584 original size:20 final size:20
Alignment explanation
Indices: 29123559--29123598 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29123549 AATATTTTCC
*
29123559 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
29123579 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
29123599 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:29123604 original size:34 final size:35
Alignment explanation
Indices: 29123547--29123613 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
29123537 CAAACACCAG
*
29123547 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
29123582 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
29123614 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:29123620 original size:14 final size:14
Alignment explanation
Indices: 29123582--29123621 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29123572 ACAGAAAAGT
*
29123582 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
29123596 AAATCATTTTACGG
1 AAAACATTTTACAG
29123610 AAAACATTTTAC
1 AAAACATTTTAC
29123622 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:29125958 original size:29 final size:30
Alignment explanation
Indices: 29125899--29125956 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29125889 TCCGAGCCTT
*
29125899 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* * *
29125929 GGGGTAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
29125957 AGAGTTAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:29126557 original size:30 final size:30
Alignment explanation
Indices: 29126522--29126579 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29126512 CCTTGACTCT
*
29126522 AACTTTTTCAAAATTACAATTTTACCCCTA
1 AACTTTTACAAAATTACAATTTTACCCCTA
* * *
29126552 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTACCCC
29126580 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTACCCCTA
Found at i:29133567 original size:17 final size:17
Alignment explanation
Indices: 29133545--29133577 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29133535 ATATTTTTTA
29133545 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
29133562 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
29133578 TATTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:29133715 original size:127 final size:127
Alignment explanation
Indices: 29133573--29133805 Score: 423
Period size: 127 Copynumber: 1.8 Consensus size: 127
29133563 TTTTAATCAA
*
29133573 ATATATATTAAATATATATTTTTTTGGTGTTGTAAAATTTAATATGGG-CTGGGCCGAGCTGGGC
1 ATATATATTAAATATATACTTTTTTGGTGTTGTAAAATTTAATATGGGCCT-GGCCGAGCTGGGC
*
29133637 TTGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCAGGGTGGGGCTCGGGCTTGGACAAAT
65 TCGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCAGGGTGGGGCTCGGGCTTGGACAAAT
29133700 ATATATATTAAATATATACTTTTTTGGTGTTGTAAAATTTAATATGGGCCTGGCCGAGCTGGGCT
1 ATATATATTAAATATATACTTTTTTGGTGTTGTAAAATTTAATATGGGCCTGGCCGAGCTGGGCT
*
29133765 CGGGTTTGGACAAATTTTTAGGCCCATATTTCGAGCAGGGT
66 CGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCAGGGT
29133806 CGAGATCGAG
Statistics
Matches: 102, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
127 100 0.98
128 2 0.02
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.36
Consensus pattern (127 bp):
ATATATATTAAATATATACTTTTTTGGTGTTGTAAAATTTAATATGGGCCTGGCCGAGCTGGGCT
CGGGCTTGGACAAATTTTTAGGCCCATATTTCGAGCAGGGTGGGGCTCGGGCTTGGACAAAT
Found at i:29136295 original size:2 final size:2
Alignment explanation
Indices: 29136290--29136320 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29136280 TAATATTTTT
29136290 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
29136321 TTTTTTACTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:29143282 original size:24 final size:23
Alignment explanation
Indices: 29143240--29143295 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
29143230 TGATTTCCTT
*
29143240 CAACGGTCAAATTTCAAATCCGAC
1 CAACGGTAAAATTTCAAAT-CGAC
* *
29143264 CAACGGTAAAATTAT-AAATGGCC
1 CAACGGTAAAATT-TCAAATCGAC
29143287 CAACGGTAA
1 CAACGGTAA
29143296 CTTTTTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.39
24 16 0.57
25 1 0.04
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (23 bp):
CAACGGTAAAATTTCAAATCGAC
Found at i:29149137 original size:24 final size:23
Alignment explanation
Indices: 29149095--29149150 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
29149085 TGATTTCCTT
*
29149095 CAACGGTCAAATTTCAAATCCGAC
1 CAACGGTAAAATTTCAAAT-CGAC
* *
29149119 CAACGGTAAAATTAT-AAATGGCC
1 CAACGGTAAAATT-TCAAATCGAC
29149142 CAACGGTAA
1 CAACGGTAA
29149151 CTTTTTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.39
24 16 0.57
25 1 0.04
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (23 bp):
CAACGGTAAAATTTCAAATCGAC
Found at i:29154997 original size:97 final size:97
Alignment explanation
Indices: 29154831--29155025 Score: 354
Period size: 97 Copynumber: 2.0 Consensus size: 97
29154821 CTTCATAAGT
29154831 TGAGTTTTGCAATTTCTCTCCACTAATGTAGTCACCATAGAAATTTGAATCAATAAGTATTTTAA
1 TGAGTTTTGCAATTTCTCTCCACTAATGTAGTCACCATAGAAATTTGAATCAATAAGTATTTTAA
* *
29154896 ATAGGTTGTAATGTAGCTTGGCTAGGGGTAGG
66 ATAGGTTGTAACGTAGCTTGGCTAAGGGTAGG
* *
29154928 TGAGTTTTGCAATTTCTCTCCACTAATGTAGTCATCATAGAAATTTGAATCAATAGGTATTTTAA
1 TGAGTTTTGCAATTTCTCTCCACTAATGTAGTCACCATAGAAATTTGAATCAATAAGTATTTTAA
29154993 ATAGGTTGTAACGTAGCTTGGCTAAGGGTAGG
66 ATAGGTTGTAACGTAGCTTGGCTAAGGGTAGG
29155025 T
1 T
29155026 AAAAGATAGA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 94 1.00
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (97 bp):
TGAGTTTTGCAATTTCTCTCCACTAATGTAGTCACCATAGAAATTTGAATCAATAAGTATTTTAA
ATAGGTTGTAACGTAGCTTGGCTAAGGGTAGG
Found at i:29176876 original size:6 final size:6
Alignment explanation
Indices: 29176867--29176891 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29176857 AAAAATAAAA
29176867 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
29176892 TGAAAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:29177362 original size:28 final size:28
Alignment explanation
Indices: 29177309--29177362 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
29177299 AAATTAAAAA
* * *
29177309 AAAAATTACTAGATTAGGCTATTTTTTC
1 AAAAATTACGAGACTAGGCTAATTTTTC
29177337 AAAAATTACGAGACTAGG-TCAATTTT
1 AAAAATTACGAGACTAGGCT-AATTTT
29177363 AGGAAAATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 1 0.05
28 21 0.95
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (28 bp):
AAAAATTACGAGACTAGGCTAATTTTTC
Found at i:29177426 original size:20 final size:19
Alignment explanation
Indices: 29177401--29177438 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
29177391 TTCGTGTCCA
29177401 TTTTTTAAAAGTTAGGGTTT
1 TTTTTTAAAAG-TAGGGTTT
*
29177421 TTTTTTTAAAGTAGGGTT
1 TTTTTTAAAAGTAGGGTT
29177439 AGGAAAGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (19 bp):
TTTTTTAAAAGTAGGGTTT
Found at i:29179628 original size:40 final size:40
Alignment explanation
Indices: 29179573--29179822 Score: 491
Period size: 40 Copynumber: 6.2 Consensus size: 40
29179563 NNNNNNNNNN
29179573 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
1 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
29179613 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
1 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
29179653 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
1 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
29179693 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
1 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
29179733 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
1 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
*
29179773 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGGTTGGGT
1 AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
29179813 AATTGGGTTG
1 AATTGGGTTG
29179823 GGTAATTGAG
Statistics
Matches: 209, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 209 1.00
ACGTcount: A:0.15, C:0.02, G:0.28, T:0.54
Consensus pattern (40 bp):
AATTGGGTTGTCTTTTAGTTTTAGTTTTATTGGATTGGGT
Found at i:29179819 original size:13 final size:13
Alignment explanation
Indices: 29179801--29179830 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
29179791 TTTTAGTTTT
29179801 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
29179814 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
29179827 ATTG
1 ATTG
29179831 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:29180956 original size:2 final size:2
Alignment explanation
Indices: 29180946--29180978 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
29180936 TACTACATTG
29180946 AT AT CAT 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
29180979 TCTATGAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29181902 original size:14 final size:15
Alignment explanation
Indices: 29181883--29181911 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29181873 AAAAGAAAAA
29181883 AATTTAATAT-TTTT
1 AATTTAATATATTTT
29181897 AATTTAATATATTTT
1 AATTTAATATATTTT
29181912 TTCATTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTAATATATTTT
Done.