Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 176 of 228
Found at i:52661176 original size:132 final size:133
Alignment explanation
Indices: 52660938--52661183 Score: 424
Period size: 132 Copynumber: 1.9 Consensus size: 133
52660928 TTCTTTCGTT
* *
52660938 TGCTCCACTGTAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTTCAGAGAG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTCAGAGAG
*
52661003 ATAAGATCTGTGGTTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTGTAGCTTTTTTT
66 ATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTGTAGCTTTTTTT
52661068 GTC
131 GTC
*
52661071 TGCTCTACTGCAACTTCAGGGAGATAAGAC-GAGATGCGATCTGCTCTACTGCAAC-TTCAGAGA
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTG-GATGCGATCTGCTCTACTGCAACTTTCAGAGA
*
52661134 GATAAGATCTGTGATTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGG
65 GATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGG
52661184 GCTAGTAACT
Statistics
Matches: 107, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
132 57 0.53
133 50 0.47
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (133 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTCAGAGAG
ATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTGTAGCTTTTTTT
GTC
Found at i:52661551 original size:46 final size:46
Alignment explanation
Indices: 52661492--52662637 Score: 1601
Period size: 46 Copynumber: 24.8 Consensus size: 46
52661482 CTATCGGTAT
*
52661492 AGGAAGATAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
*
52661538 AGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* * * *
52661584 AGGAAGACAAAATCTGTTATATCTTTGATCTACTTCGCTGCCAAATAC
1 AGGAAGACAAGATCTG--CTATCTTCGATCTACTCCGCTGCCAAATAC
* *
52661632 AGGAAGACAAGATCTGCTATATCTTCGATCTAATCCGCTGCCAAATAT
1 AGGAAGACAAGATCTGC--TATCTTCGATCTACTCCGCTGCCAAATAC
* * * *
52661680 AGGAAGACAATATTTGCTATCTTTGATCTACTCCGCTGCCAAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* * * *
52661726 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACTACCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* *
52661772 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* *
52661818 AGGAAGACAAGATCTGCTATCTTCGATCTAATCCGCTGCCAAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
** * * *
52661864 AATAAGACAATATTTGCTATCTTTGATCTACTCCGCTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* * *
52661910 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* * *
52661956 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
52662002 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* * * * * *
52662048 AGGAAGACAAGATCTACTATTTTCGGTCTACTTCACTGCTAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* * *
52662094 AGGAAGACAAGATCTACTATCTTCAATCTACTCCGCTGCCAAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* * *
52662140 AGGAAAACAAGATCTGCTATCTTCGATCGACTCCACTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* * * *
52662186 AAGAAGACAAGATCTGAC-ATCTTCGATCTATTTCACTGCCAAATAC
1 AGGAAGACAAGATCTG-CTATCTTCGATCTACTCCGCTGCCAAATAC
* * * * *
52662232 AGGAAGATAAGATCTGCTATCTTTGATCTACTTCACTGCCAAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
52662278 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* * * *
52662324 AGGAAGACAAGATCTGCTATTTTCGGTCTACTTCGCTGCTAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* * *
52662370 AAGAAGACAAGATCTGCTATCTTCAATCTACTCCGCTGCCAAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* * *
52662416 AGGAAGACAAGATCTACTATCTTCGATCGACTCCACTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* * * *
52662462 AGGAACACAAGATCTGCCATCTTCGATCTACTTCACTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
*
52662508 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* *
52662554 AGGAAGACAAGATCTACTATCTTCGATCTACTCCACTGCCAAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
* *
52662600 AGGAAGACAAGATCTGCTATCTTTGATCTATTCCGCTG
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTG
52662638 TAATTTCTAA
Statistics
Matches: 985, Mismatches: 109, Indels: 12
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.00
46 900 0.91
47 1 0.00
48 83 0.08
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (46 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAATAC
Found at i:52663679 original size:108 final size:106
Alignment explanation
Indices: 52663508--52663826 Score: 356
Period size: 97 Copynumber: 3.1 Consensus size: 106
52663498 GAAAAATGCT
* * * * * * *
52663508 TGAAAAAGATTACCAAAATGGACAAGAAAG-AATTTTATTGAGAATAAGGCTCAAAATAAATAAA
1 TGAAAAAGATTATCACAATGGATAA-AATGAAATTTTATTGAGAACAAAGCTCAAAATGAATAAA
*
52663572 TTAATCAAGATATCAAATTTTGTTCAAATACGAACTGAATAAGA
65 TTAATCAAGATAGCAAATTTTG-TCAAATACGAA-TGAATAAGA
* * * * *
52663616 TGAAAAATATTATTACAATGGATAAGATGAAATTTTATTGAAAACAAAGCTCGAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATAAAT
52663681 TAATCAAGATAGCAAATTTTG-C---T---AA-G-ATAAGA
66 TAATCAAGATAGCAAATTTTGTCAAATACGAATGAATAAGA
* *
52663713 TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAGCACAGCTCAAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATAAAT
*
52663778 TAATTAAGATAGCAAATTTTG-CTAATATACGAAATGAATAAGA
66 TAATCAAGATAGCAAATTTTGTC-AA-ATACG-AATGAATAAGA
52663821 T-AAAAA
1 TGAAAAA
52663827 CAGGTGCCCC
Statistics
Matches: 178, Mismatches: 21, Indels: 25
0.79 0.09 0.11
Matches are distributed among these distances:
97 85 0.48
98 1 0.01
100 2 0.01
102 1 0.01
103 1 0.01
106 3 0.02
107 8 0.04
108 77 0.43
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.27
Consensus pattern (106 bp):
TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATAAAT
TAATCAAGATAGCAAATTTTGTCAAATACGAATGAATAAGA
Found at i:52664110 original size:5 final size:5
Alignment explanation
Indices: 52664091--52664146 Score: 64
Period size: 5 Copynumber: 11.8 Consensus size: 5
52664081 GGCCTCTCCT
* * *
52664091 TTTTC TTTT- TCTTC TTTTC TTTTC TTTTT TTTTC TTTTC -TTT- TTTCC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
52664138 TTTTC TTTT
1 TTTTC TTTT
52664147 TTCTGTTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
4 8 0.19
5 34 0.81
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:52664112 original size:20 final size:20
Alignment explanation
Indices: 52664089--52664162 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
52664079 TTGGCCTCTC
52664089 CTTTTTCTTTTTCTTCTTTT
1 CTTTTTCTTTTTCTTCTTTT
*
52664109 C-TTTTCTTTTTTTTTCTTTT
1 CTTTTTC-TTTTTCTTCTTTT
*
52664129 CTTTTTTCCTTTTCTT-TTTT
1 C-TTTTTCTTTTTCTTCTTTT
52664149 CTGTTCTTCTTTTT
1 CT-TT-TTCTTTTT
52664163 TTTTTTGGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
19 6 0.13
20 21 0.47
21 13 0.29
22 5 0.11
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (20 bp):
CTTTTTCTTTTTCTTCTTTT
Found at i:52664128 original size:28 final size:29
Alignment explanation
Indices: 52664090--52664167 Score: 97
Period size: 28 Copynumber: 2.6 Consensus size: 29
52664080 TGGCCTCTCC
52664090 TTTTTCTTTTTCTTCTTTT-CTTTTCTTTT
1 TTTTTCTTTTTCTT-TTTTCCTTTTCTTTT
52664119 TTTTTC-TTTTCTTTTTTCCTTTTCTTTT
1 TTTTTCTTTTTCTTTTTTCCTTTTCTTTT
*
52664147 TTCTGTTCTTCTTTTTTTTTT
1 TT-T-TTCTT-TTTCTTTTTT
52664168 TGGACATTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
27 4 0.09
28 19 0.44
29 7 0.16
30 3 0.07
31 1 0.02
32 9 0.21
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.82
Consensus pattern (29 bp):
TTTTTCTTTTTCTTTTTTCCTTTTCTTTT
Found at i:52668937 original size:10 final size:10
Alignment explanation
Indices: 52668922--52668956 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
52668912 ATATGTATTA
52668922 AAATATATAT
1 AAATATATAT
52668932 AAATATATAT
1 AAATATATAT
*
52668942 AAAAATATAT
1 AAATATATAT
52668952 AAATA
1 AAATA
52668957 CACATACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATATATAT
Found at i:52668937 original size:22 final size:21
Alignment explanation
Indices: 52668902--52668975 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 21
52668892 GGGTATTTAG
* * *
52668902 ATATATGTAGATATGTATTAAA
1 ATATATATAAATATATA-TAAA
52668924 ATATATATAAATATATATAAA
1 ATATATATAAATATATATAAA
* *
52668945 A-ATATATAAATACACATACAA
1 ATATATATAAATATATATA-AA
*
52668966 ATATAAATAA
1 ATATATATAA
52668976 GTTACAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 15 0.34
21 8 0.18
22 21 0.48
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (21 bp):
ATATATATAAATATATATAAA
Found at i:52668939 original size:12 final size:12
Alignment explanation
Indices: 52668902--52668952 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
52668892 GGGTATTTAG
* *
52668902 ATATATGTAGAT
1 ATATATATAAAT
*
52668914 ATGTAT-TAAA-
1 ATATATATAAAT
52668924 ATATATATAAAT
1 ATATATATAAAT
*
52668936 ATATATAAAAAT
1 ATATATATAAAT
52668948 ATATA
1 ATATA
52668953 AATACACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 5 0.15
11 7 0.21
12 21 0.64
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:52668951 original size:20 final size:20
Alignment explanation
Indices: 52668920--52668970 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
52668910 AGATATGTAT
* *
52668920 TAAAATATATATAAATATATA
1 TAAAA-ATATATAAATACACA
52668941 TAAAAATATATAAATACACA
1 TAAAAATATATAAATACACA
*
52668961 TACAAATATA
1 TAAAAATATA
52668971 AATAAGTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAATATATAAATACACA
Found at i:52674271 original size:41 final size:41
Alignment explanation
Indices: 52674214--52674494 Score: 264
Period size: 41 Copynumber: 6.9 Consensus size: 41
52674204 ATTTTTAAAC
* *
52674214 CTTTAGTGGCGTTTTTATTTGAGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * *
52674255 CTTTAGCAGCGTTTTTAACTGAGCGCCGCTAAT-C-C-AAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * *
52674293 GGCATTTATCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
1 --C-TTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * * * *
52674337 CTTTAGTGGCGTTTTTATCTGAGCGCCACTAGTTCTTTGG-C
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGC-TCGGAT
* * * *
52674378 CTTTAGCAGCGTTTATCTCTAAGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * **
52674419 CTTTAGTGGCGTTTTTATCTGAGCGCCACTAATTCTCGGGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * *
52674460 CTTTAGCGGCGTTTATAGCTAAGCGCCGCTAATGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGC
52674495 ATTTACCTTT
Statistics
Matches: 187, Mismatches: 45, Indels: 16
0.75 0.18 0.06
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 5 0.03
41 171 0.91
42 5 0.03
43 1 0.01
44 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
Found at i:52674359 original size:82 final size:82
Alignment explanation
Indices: 52674213--52674516 Score: 369
Period size: 82 Copynumber: 3.7 Consensus size: 82
52674203 GATTTTTAAA
* * * * ** *
52674213 CCTTTAGTGGCGTTTTTATTTGAGCGCCGCTAATGCTCGGATCTTTAGCAGCGTTTTTAACTGAG
1 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAG
* * *
52674278 CGCCGCTAATCCAATGG
66 CGCCACTAATTCTATGG
* *
52674295 CATTTATCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAG
* *
52674360 CGCCACTAGTTCTTTGG
66 CGCCACTAATTCTATGG
* * *
52674377 CCTTTAGCAGCGTTTATCTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAG
**
52674442 CGCCACTAATTCTCGGG
66 CGCCACTAATTCTATGG
* ** *
52674459 CCTTTAGCGGCGTTTATAG-CTAAGCGCCGCTAATGCAT-TTACCTTTAGTGGCGTTTTT
1 CCTTTAGCGGCGTTT-TTGTCTAAGCGCCGCTAATGC-TCGGATCTTTAGTGGCGTTTTT
52674517 GCCGAAGCGC
Statistics
Matches: 191, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
82 190 0.99
83 1 0.01
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (82 bp):
CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAG
CGCCACTAATTCTATGG
Found at i:52674504 original size:123 final size:123
Alignment explanation
Indices: 52674303--52674533 Score: 268
Period size: 123 Copynumber: 1.9 Consensus size: 123
52674293 GGCATTTATC
* * * * * * *
52674303 GGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAGCGCCACTA
1 GGCGTTTTTATCTAAGCGCCACTAATGCTCGGACCTTTAGCGGCGTTTATAGCTAAGCGCCACTA
* * * *
52674368 GTTCTTTGGCCTTTAGCAGCGTTTAT-CTCTAAGCGCCGCTAATGCTCGGATCTTTAGT
66 ATGCTTTGACCTTTAGCAGCGTTTATGC-CGAAGCGCCGCTAATGCTCGGATCTTTAGT
* * * *
52674426 GGCGTTTTTATCTGAGCGCCACTAATTCTCGGGCCTTTAGCGGCGTTTATAGCTAAGCGCCGCTA
1 GGCGTTTTTATCTAAGCGCCACTAATGCTCGGACCTTTAGCGGCGTTTATAGCTAAGCGCCACTA
** *
52674491 ATGCATTT-ACCTTTAGTGGCGTTTTTGCCGAAGCGCCGCTAAT
66 ATGC-TTTGACCTTTAGCAGCGTTTATGCCGAAGCGCCGCTAAT
52674534 AGTAATAAAA
Statistics
Matches: 88, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
123 84 0.95
124 4 0.05
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (123 bp):
GGCGTTTTTATCTAAGCGCCACTAATGCTCGGACCTTTAGCGGCGTTTATAGCTAAGCGCCACTA
ATGCTTTGACCTTTAGCAGCGTTTATGCCGAAGCGCCGCTAATGCTCGGATCTTTAGT
Found at i:52675075 original size:15 final size:15
Alignment explanation
Indices: 52675054--52675091 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
52675044 AATAAGGTTA
52675054 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
52675069 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
52675084 ATTTAGGG
1 ATTTAGGG
52675092 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:52675916 original size:21 final size:21
Alignment explanation
Indices: 52675890--52675931 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
52675880 TAATTATTAC
*
52675890 ATAATTTATAGTATTTGAAAT
1 ATAATTTATAATATTTGAAAT
52675911 ATAATTTATAATATTTGAAAT
1 ATAATTTATAATATTTGAAAT
52675932 TTTGAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (21 bp):
ATAATTTATAATATTTGAAAT
Found at i:52676263 original size:16 final size:18
Alignment explanation
Indices: 52676237--52676276 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
52676227 TGAAAGTTAC
*
52676237 AAAATTAGCA-TCATTTA
1 AAAATTAGCATTCATTCA
52676254 AAAATT-GCATTCATTCA
1 AAAATTAGCATTCATTCA
52676271 AAAATT
1 AAAATT
52676277 TAGAGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (18 bp):
AAAATTAGCATTCATTCA
Found at i:52676862 original size:20 final size:19
Alignment explanation
Indices: 52676835--52676892 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 19
52676825 AAAAATTCTA
52676835 TTTTTATTTTTAAAATGAT
1 TTTTTATTTTTAAAATGAT
*
52676854 TTTTCTATTATTTTAATATG-T
1 TTTT-TA-T-TTTTAAAATGAT
52676875 TTTTTATAATTTTAAAAT
1 TTTTTAT--TTTTAAAAT
52676893 TCTATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 5 0.15
20 13 0.39
21 6 0.18
22 9 0.27
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTATTTTTAAAATGAT
Found at i:52676900 original size:22 final size:21
Alignment explanation
Indices: 52676810--52676919 Score: 84
Period size: 22 Copynumber: 5.2 Consensus size: 21
52676800 ACTATTTTAA
52676810 TTTTTTATAATTTTTAAAAATTC
1 TTTTTTATAA-TTTT-AAAATTC
**
52676833 TATTTTTAT--TTTTAAAATGA
1 T-TTTTTATAATTTTAAAATTC
* * *
52676853 TTTTTCTATTATTTTAATA-TG
1 TTTTT-TATAATTTTAAAATTC
52676874 TTTTTTATAATTTTAAAATTC
1 TTTTTTATAATTTTAAAATTC
* *
52676895 TATTTTTAAAATTTTTAAATT-
1 T-TTTTTATAATTTTAAAATTC
52676916 TTTT
1 TTTT
52676920 ATGATTTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
19 4 0.06
20 23 0.32
21 12 0.17
22 24 0.34
23 1 0.01
24 7 0.10
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTTATAATTTTAAAATTC
Found at i:52676930 original size:62 final size:63
Alignment explanation
Indices: 52676810--52676931 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 63
52676800 ACTATTTTAA
*
52676810 TTTTTTATAATTTTTAAAAATTCTATTTTTATTTTTAAAATGATTTTTCTATTATTTTAATATG
1 TTTTTTATAATTTTTAAAAATTCTATTTTTATTTTTAAAAT-ATTTTTATATTATTTTAATATG
52676874 TTTTTTATAA-TTTT-AAAATTCTATTTTTAAAATTTTT-AAAT-TTTTTATGATT-TTTTAA
1 TTTTTTATAATTTTTAAAAATTCTATTTTT---ATTTTTAAAATATTTTTAT-ATTATTTTAA
52676932 ATAAATATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
62 26 0.49
63 7 0.13
64 14 0.26
65 6 0.11
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (63 bp):
TTTTTTATAATTTTTAAAAATTCTATTTTTATTTTTAAAATATTTTTATATTATTTTAATATG
Found at i:52677030 original size:30 final size:30
Alignment explanation
Indices: 52676990--52677060 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
52676980 AAAAGACAAT
* *
52676990 GGCTTGATTGATTGCTT-AAATTCGATTGAG
1 GGCTTAATTGAGTGCTTGAAATT-GATTGAG
*
52677020 GGCTTAATTGAGTGCTTGAACTTGATTGAG
1 GGCTTAATTGAGTGCTTGAAATTGATTGAG
*
52677050 GGCTCAATTGA
1 GGCTTAATTGA
52677061 ATGTTGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (30 bp):
GGCTTAATTGAGTGCTTGAAATTGATTGAG
Found at i:52686482 original size:497 final size:498
Alignment explanation
Indices: 52685537--52686526 Score: 1892
Period size: 497 Copynumber: 2.0 Consensus size: 498
52685527 CCCCCAAAAT
* *
52685537 AGCCATTTCATGATCCGTGCTTATGAGTAACGGACAGTGGTCTAAAAAGGAGTGTGGCAAATGAC
1 AGCCATTTCATGATCCGTGCTTATGAGTAACAGACAGTGGTCTAAAAAAGAGTGTGGCAAATGAC
*
52685602 GGATTCAGGTATTTAGAAACAAAGTCAACCATTTATCATTTGCGACCCCTTTGTCTATCTCTCCC
66 GGATTCAGGTATTTAGAAACAAAATCAACCATTTATCATTTGCGACCCCTTTGTCTATCTCTCCC
*
52685667 TTATGTTTGTCTTCGGCAAATTCCCTCTTTCTAATGTGAACCACTCTTCTAAATATCCCACATCC
131 TTATGTTTGTCTTCGGCAAATTCCCTCTTTCCAATGTGAACCACTCTTCTAAATATCCCACATCC
*
52685732 ATTAATTGACACTCTTCAAGGACATCTTGGAAAGCCTCCATTCTTCTCTCATCCCTTGGCATACC
196 ATTAATTGACACTCTTCAAGGACATCTTGGAAAGCCTCCATTCTTCTCTCATCCATTGGCATACC
52685797 TCCAGCCTTCTCAAAGGAATACATGATTTTATTGGAGTCTCCACACACCAACCAAGGAAAATTCC
261 TCCAGCCTTCTCAAAGGAATACATGATTTTATTGGAGTCTCCACACACCAACCAAGGAAAATTCC
52685862 AATTCTACCCTAGTCTCCGAAATAAGTTCCAAGAACCATTTCTATAACTTGCAAAATGTGCTCTA
326 AATTCTACCCTAGTCTCCGAAATAAGTTCCAAGAACCATTTCTATAACTTGCAAAATGTGCTCTA
52685927 TAAAACCCAATGAATCTCTATTCCTTATCATCACTATCCTCTTTAACCAAAGCATTTAAATGATT
391 TAAAACCCAATGAATCTCTATTCCTTATCATCACTATCCTCTTTAACCAAAGCATTTAAATGATT
52685992 TTTAGAAAAGCTCCTTAGACTAACAGTAACATCTCCTTAGAAA
456 TTTAGAAAAGCTCCTTAGACTAACAGTAACATCTCCTTAGAAA
* *
52686035 AGCCCTTTCGTGATCCGTGCTTATGAGTAACAGACAGTGGTCTAAAAAAGAGTGTGGCAAATGAC
1 AGCCATTTCATGATCCGTGCTTATGAGTAACAGACAGTGGTCTAAAAAAGAGTGTGGCAAATGAC
52686100 GGATTCAGGTATTTAGAAACAAAATCAACCATTTATCATTTGCGACCCCTTTGTCTATCTCTCCC
66 GGATTCAGGTATTTAGAAACAAAATCAACCATTTATCATTTGCGACCCCTTTGTCTATCTCTCCC
52686165 TTATGTTTGTCTTCGGCAAATTCCCTCTTTCCAATGTGAACCACTCTTCTAAATATCCCACATCC
131 TTATGTTTGTCTTCGGCAAATTCCCTCTTTCCAATGTGAACCACTCTTCTAAATATCCCACATCC
*
52686230 ATTAATTGACACTCTTCAAGGACATCTTGG-AAGCCTCCATTCTTCTCTCCTCCATTGGCATACC
196 ATTAATTGACACTCTTCAAGGACATCTTGGAAAGCCTCCATTCTTCTCTCATCCATTGGCATACC
52686294 TCCAGCCTTCTCAAAGGAATACATGATTTTATTGGAGTCTCCACACACCAACCAAGGAAAATTCC
261 TCCAGCCTTCTCAAAGGAATACATGATTTTATTGGAGTCTCCACACACCAACCAAGGAAAATTCC
52686359 AATTCTACCCTAGTCTCCGAAATAAGTTCCAAGAACCATTTCTATAACTTGCAAAATGTGCTCTA
326 AATTCTACCCTAGTCTCCGAAATAAGTTCCAAGAACCATTTCTATAACTTGCAAAATGTGCTCTA
*
52686424 TAAAACCCAGTGAATCTCTATTCCTTATCATCACTATCCTCTTTAACCAAAGCATTTAAATGATT
391 TAAAACCCAATGAATCTCTATTCCTTATCATCACTATCCTCTTTAACCAAAGCATTTAAATGATT
52686489 TTTAGAAAAGCTCCTTAGACTAACAGTAACATCTCCTT
456 TTTAGAAAAGCTCCTTAGACTAACAGTAACATCTCCTT
52686527 TCCACACAAA
Statistics
Matches: 483, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
497 264 0.55
498 219 0.45
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (498 bp):
AGCCATTTCATGATCCGTGCTTATGAGTAACAGACAGTGGTCTAAAAAAGAGTGTGGCAAATGAC
GGATTCAGGTATTTAGAAACAAAATCAACCATTTATCATTTGCGACCCCTTTGTCTATCTCTCCC
TTATGTTTGTCTTCGGCAAATTCCCTCTTTCCAATGTGAACCACTCTTCTAAATATCCCACATCC
ATTAATTGACACTCTTCAAGGACATCTTGGAAAGCCTCCATTCTTCTCTCATCCATTGGCATACC
TCCAGCCTTCTCAAAGGAATACATGATTTTATTGGAGTCTCCACACACCAACCAAGGAAAATTCC
AATTCTACCCTAGTCTCCGAAATAAGTTCCAAGAACCATTTCTATAACTTGCAAAATGTGCTCTA
TAAAACCCAATGAATCTCTATTCCTTATCATCACTATCCTCTTTAACCAAAGCATTTAAATGATT
TTTAGAAAAGCTCCTTAGACTAACAGTAACATCTCCTTAGAAA
Found at i:52690101 original size:18 final size:18
Alignment explanation
Indices: 52690073--52690115 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
52690063 TTTTTAATAT
*
52690073 AATATTTAAAAGAT-AAAA
1 AATAATTAAAA-ATCAAAA
*
52690091 ATTAATTAAAAATCAAAA
1 AATAATTAAAAATCAAAA
52690109 AATAATT
1 AATAATT
52690116 TTTTAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
AATAATTAAAAATCAAAA
Found at i:52691144 original size:93 final size:95
Alignment explanation
Indices: 52691016--52691249 Score: 253
Period size: 96 Copynumber: 2.5 Consensus size: 95
52691006 TTGTATTTGA
* * * *
52691016 GTAAACTTTCAGTTTTGGTCTCTCTGTTAAACTCGAATTTAAGATTTAA-ATTT-TATATCT-A-
1 GTAAAATTTCAGTTTTGATCCCTCTATTAAACTCGAATTTAAGATTTAATATTTATAT-TCTCAC
** * **
52691077 TTTTTTTTATTTTTTTCATTTCAATTATAATG
65 TCCTTTTT-TGTTTGACATTTCAATTATAATG
* * * *
52691109 GTAAAA-TTCTAGTTTTGATCCCTCTTTTAGACTCGAATTTAAAATTTAATATTTATATTTTCAC
1 GTAAAATTTC-AGTTTTGATCCCTCTATTAAACTCGAATTTAAGATTTAATATTTATATTCTCAC
52691173 GTCCTTTTTTGTTTGACATTTCAATTATAATG
65 -TCCTTTTTTGTTTGACATTTCAATTATAATG
* **
52691205 GTAAAATTTCAATTTTGATCCCTCTATTAAACTTAAATTTAAGAT
1 GTAAAATTTCAGTTTTGATCCCTCTATTAAACTCGAATTTAAGAT
52691250 GCAATCTTGT
Statistics
Matches: 116, Mismatches: 18, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
92 3 0.03
93 39 0.34
94 6 0.05
95 4 0.03
96 55 0.47
97 9 0.08
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (95 bp):
GTAAAATTTCAGTTTTGATCCCTCTATTAAACTCGAATTTAAGATTTAATATTTATATTCTCACT
CCTTTTTTGTTTGACATTTCAATTATAATG
Found at i:52692307 original size:55 final size:59
Alignment explanation
Indices: 52692241--52692354 Score: 182
Period size: 61 Copynumber: 2.0 Consensus size: 59
52692231 GATAAGACCA
52692241 TGTTGAGATTAATG-T-T-TA-TATATATATATGTATATGCCTTACAAGTAATAAAATC
1 TGTTGAGATTAATGTTATATATTATATATATATGTATATGCCTTACAAGTAATAAAATC
52692296 TGTTGAGATTAATGTTTATATATTTATATATATATGTATATGCCTTACAAGTAATAAAA
1 TGTTGAGATTAATG-TTATATA-TTATATATATATGTATATGCCTTACAAGTAATAAAA
52692355 GAGGTATGCC
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
55 14 0.26
57 1 0.02
58 1 0.02
59 2 0.04
61 35 0.66
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (59 bp):
TGTTGAGATTAATGTTATATATTATATATATATGTATATGCCTTACAAGTAATAAAATC
Found at i:52710796 original size:14 final size:14
Alignment explanation
Indices: 52710774--52710812 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
52710764 TAGTCCATTC
* *
52710774 TTATTATTATTTTA
1 TTATTATTATATCA
*
52710788 TTATCATTATATCA
1 TTATTATTATATCA
52710802 TTATTATTATA
1 TTATTATTATA
52710813 CTGTTTGCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTATTATATCA
Found at i:52718017 original size:41 final size:40
Alignment explanation
Indices: 52717972--52718172 Score: 208
Period size: 41 Copynumber: 4.9 Consensus size: 40
52717962 ACACTAGTAT
* * *
52717972 GAAGCCTGCTAGGCTCAAAGCCTGATGTAACACATCGACAC
1 GAAGCCTGCTAGGCACAAAGCCTGATATAATACA-CGACAC
* * * *
52718013 GAAGCTTGTTAGGCACAAAGCTTGATATAATACATCGACAT
1 GAAGCCTGCTAGGCACAAAGCCTGATATAATACA-CGACAC
* * *
52718054 GCAA-CCCGCTAGGCACAAAGTCTGATATAATACACCAGCAC
1 G-AAGCCTGCTAGGCACAAAGCCTGATATAATACACGA-CAC
*
52718095 GAAGCCTGCTAGGCACAACA-CCTGATATAATACACAGGCAC
1 GAAGCCTGCTAGGCACAA-AGCCTGATATAATACAC-GACAC
* * *
52718136 GAAGCCTACTAGGCACAACGTCTGATATAATACACGA
1 GAAGCCTGCTAGGCACAAAGCCTGATATAATACACGA
52718173 AATCTAAAAT
Statistics
Matches: 132, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
40 5 0.04
41 124 0.94
42 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.18
Consensus pattern (40 bp):
GAAGCCTGCTAGGCACAAAGCCTGATATAATACACGACAC
Found at i:52725847 original size:16 final size:16
Alignment explanation
Indices: 52725826--52725867 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
52725816 AATTGGGTTG
*
52725826 AGAAAATTATTTAATT
1 AGAAAATTAATTAATT
52725842 AGAAAATTAATTAATT
1 AGAAAATTAATTAATT
52725858 --AAAATTAATT
1 AGAAAATTAATT
52725868 TCATAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 10 0.40
16 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
AGAAAATTAATTAATT
Found at i:52728612 original size:21 final size:21
Alignment explanation
Indices: 52728586--52728629 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
52728576 AGGATTAGAG
**
52728586 TTGGGAACATTATGTCCGACA
1 TTGGGAACAACATGTCCGACA
*
52728607 TTGGGAACAACATGTCTGACA
1 TTGGGAACAACATGTCCGACA
52728628 TT
1 TT
52728630 TTCCAATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (21 bp):
TTGGGAACAACATGTCCGACA
Found at i:52731073 original size:13 final size:13
Alignment explanation
Indices: 52731055--52731079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52731045 AAATAGATAT
52731055 TTATTATATTATA
1 TTATTATATTATA
52731068 TTATTATATTAT
1 TTATTATATTAT
52731080 TATTGTTAAC
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATATTATA
Found at i:52731199 original size:11 final size:11
Alignment explanation
Indices: 52731173--52731207 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
52731163 CGAAACAGGG
52731173 GAAAAGAAAGAA
1 GAAAAGAAA-AA
52731185 GAAAAGAAAAA
1 GAAAAGAAAAA
52731196 GAAAAGGAAAAA
1 GAAAA-GAAAAA
52731208 CTAGGGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:52731497 original size:19 final size:20
Alignment explanation
Indices: 52731473--52731510 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52731463 GCAAGAATTT
*
52731473 TGAAA-TTAGATATTTATGA
1 TGAAATTTAGATAGTTATGA
52731492 TGAAATTTAGATAGTTATG
1 TGAAATTTAGATAGTTATG
52731511 TCCAAGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (20 bp):
TGAAATTTAGATAGTTATGA
Found at i:52732395 original size:23 final size:23
Alignment explanation
Indices: 52732368--52732422 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
52732358 GGCTTTGCCA
52732368 ATCAGGCACTTTATGTATCGTAT
1 ATCAGGCACTTTATGTATCGTAT
*
52732391 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTATCGTAT
*
52732414 TTCAGGCAC
1 ATCAGGCAC
52732423 CTCGTATGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
ATCAGGCACTTTATGTATCGTAT
Found at i:52732453 original size:21 final size:22
Alignment explanation
Indices: 52732404--52732453 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
52732394 AGGCACTTTA
*
52732404 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAAGCACCTCG
* *
52732427 TATGTCGTA-TCAAGCACCTGG
1 TGTGTCGTATTCAAGCACCTCG
52732448 TGTGTC
1 TGTGTC
52732454 ATTTCAGGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.65
23 8 0.35
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (22 bp):
TGTGTCGTATTCAAGCACCTCG
Found at i:52732464 original size:21 final size:21
Alignment explanation
Indices: 52732412--52732464 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
52732402 TATGTGTCGT
52732412 ATTTCAGGCACCTCGTATGTC
1 ATTTCAGGCACCTCGTATGTC
* * * * *
52732433 GTATCAAGCACCTGGTGTGTC
1 ATTTCAGGCACCTCGTATGTC
52732454 ATTTCAGGCAC
1 ATTTCAGGCAC
52732465 TTATGTGTCG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (21 bp):
ATTTCAGGCACCTCGTATGTC
Found at i:52732744 original size:24 final size:24
Alignment explanation
Indices: 52732717--52732762 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
52732707 GATTTGAAAT
* *
52732717 TGAAATATATGAAATGGTTATTAA
1 TGAAATACATGAAATGGATATTAA
*
52732741 TGAAATGCATGAAATGGATATT
1 TGAAATACATGAAATGGATATT
52732763 GATATAATAA
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:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (24 bp):
TGAAATACATGAAATGGATATTAA
Found at i:52733497 original size:18 final size:18
Alignment explanation
Indices: 52733455--52733498 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
52733445 AAATATTATT
52733455 ATTTTTTAAATTATAGAA
1 ATTTTTTAAATTATAGAA
* *
52733473 ATATTTTAAATGT-TATAA
1 ATTTTTTAAAT-TATAGAA
52733491 ATTTTTTA
1 ATTTTTTA
52733499 CAAAATACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTTTTTAAATTATAGAA
Found at i:52746891 original size:44 final size:44
Alignment explanation
Indices: 52746817--52746907 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
52746807 GTAGGTCAAA
52746817 TAATATTAAAGTAACCTACACTAATAAGAGTTTAAG-TGGAAAAC
1 TAATATTAAAGTAACCTACACTAATAAGAGTTTAAGCTGG-AAAC
* * *
52746861 TAATATTAAAGTAACCTATATTAATCAGAGTTTAAGCTGGAAAC
1 TAATATTAAAGTAACCTACACTAATAAGAGTTTAAGCTGGAAAC
52746905 TAA
1 TAA
52746908 AAGTAGAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 40 0.93
45 3 0.07
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (44 bp):
TAATATTAAAGTAACCTACACTAATAAGAGTTTAAGCTGGAAAC
Found at i:52748850 original size:44 final size:44
Alignment explanation
Indices: 52748800--52748885 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
52748790 TTTGTAGGTC
52748800 AAATAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGAA
1 AAATAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGAA
* *
52748844 AAATAATATTAAAGTAATCTACACTAATCAGAGTTTAAGTGG
1 AAATAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGG
52748886 GGAACTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (44 bp):
AAATAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGAA
Found at i:52753786 original size:63 final size:63
Alignment explanation
Indices: 52753687--52753812 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
52753677 TAAACGTGAC
52753687 CATGGGTCGTTCGTCTTTGAGATAAATGACTTGATTACTATTTGGTAGTAATTGACTTTTCAT
1 CATGGGTCGTTCGTCTTTGAGATAAATGACTTGATTACTATTTGGTAGTAATTGACTTTTCAT
52753750 CATGGGTCGTTCGTCTTTGAGATAAATGACTTGATTACTATTTGGTAGTAATTGACTTTTCAT
1 CATGGGTCGTTCGTCTTTGAGATAAATGACTTGATTACTATTTGGTAGTAATTGACTTTTCAT
52753813 GAAGGAAGAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.43
Consensus pattern (63 bp):
CATGGGTCGTTCGTCTTTGAGATAAATGACTTGATTACTATTTGGTAGTAATTGACTTTTCAT
Found at i:52766115 original size:36 final size:36
Alignment explanation
Indices: 52766075--52766144 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
52766065 TGTCAAGATG
* *
52766075 AATATGAGGGTGTGTTGTTCATGCCATGTGATAGCA
1 AATATGAGGGTATGTTATTCATGCCATGTGATAGCA
52766111 AATATGAGGGTATGTTATTCATGCCATGTGATAG
1 AATATGAGGGTATGTTATTCATGCCATGTGATAG
52766145 TGATTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (36 bp):
AATATGAGGGTATGTTATTCATGCCATGTGATAGCA
Found at i:52766590 original size:23 final size:23
Alignment explanation
Indices: 52766564--52766611 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
52766554 TAATGTGTGT
*
52766564 TGTAA-TATATGTTTAAATATTCA
1 TGTAATTA-ATGTGTAAATATTCA
52766587 TGTAATTAATGTGTAAATATTCA
1 TGTAATTAATGTGTAAATATTCA
52766610 TG
1 TG
52766612 AAAGTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (23 bp):
TGTAATTAATGTGTAAATATTCA
Found at i:52772314 original size:27 final size:27
Alignment explanation
Indices: 52772222--52772371 Score: 144
Period size: 27 Copynumber: 5.5 Consensus size: 27
52772212 ATATTGAGCC
* *
52772222 CGCACACTCAGTGCTATACA-A-TCAAAT
1 CGCACACTTAGTGC-A-ACATAGTCAATT
* * *
52772249 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCAACATAGTCA-ATT
** *
52772277 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAACATAGTCAATT
* * *
52772304 CGCACACTTAGTGCATCATATTCATTT
1 CGCACACTTAGTGCAACATAGTCAATT
52772331 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCAACATAGTC-AATT
52772358 CGCACACTTAGTGC
1 CGCACACTTAGTGC
52772372 TGTACAATTT
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
25 3 0.03
26 1 0.01
27 75 0.74
28 23 0.23
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCAACATAGTCAATT
Found at i:52780322 original size:27 final size:27
Alignment explanation
Indices: 52780230--52780379 Score: 144
Period size: 27 Copynumber: 5.5 Consensus size: 27
52780220 ATATTGAGCC
* *
52780230 CGCACACTCAGTGCTATACA-A-TCAAAT
1 CGCACACTTAGTGC-A-ACATAGTCAATT
* * *
52780257 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCAACATAGTCA-ATT
** *
52780285 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAACATAGTCAATT
* * *
52780312 CGCACACTTAGTGCATCATATTCATTT
1 CGCACACTTAGTGCAACATAGTCAATT
52780339 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCAACATAGTC-AATT
52780366 CGCACACTTAGTGC
1 CGCACACTTAGTGC
52780380 TGTACAATTT
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
25 3 0.03
26 1 0.01
27 75 0.74
28 23 0.23
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCAACATAGTCAATT
Found at i:52782411 original size:22 final size:20
Alignment explanation
Indices: 52782381--52782420 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
52782371 CTTTGATACC
52782381 GTTAGAGAAGGATTCAGTTTGG
1 GTTAGAGAA-GA-TCAGTTTGG
*
52782403 GTTATAGAAGATCAGTTT
1 GTTAGAGAAGATCAGTTT
52782421 TCAAAGAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 2 0.12
22 8 0.47
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (20 bp):
GTTAGAGAAGATCAGTTTGG
Found at i:52788166 original size:27 final size:27
Alignment explanation
Indices: 52788144--52788310 Score: 170
Period size: 27 Copynumber: 6.5 Consensus size: 27
52788134 AAGGGTATAA
*
52788144 CGGTCATTTTACCCTATGGGGGTATTT
1 CGGTCATTCTACCCTATGGGGGTATTT
* *
52788171 CAGTCATTCTATCCTATGGGGGTATTT
1 CGGTCATTCTACCCTATGGGGGTATTT
*
52788198 TGGTCATTCTACCCTATGGGGGTATTT
1 CGGTCATTCTACCCTATGGGGGTATTT
** * *
52788225 CGACCATTTTACCTTATGGGGGTATTT
1 CGGTCATTCTACCCTATGGGGGTATTT
* *
52788252 TGGTTATT-T----TA---GGGTATTT
1 CGGTCATTCTACCCTATGGGGGTATTT
*
52788271 CGGTCATTTTACCCTATGGGGGTATTT
1 CGGTCATTCTACCCTATGGGGGTATTT
*
52788298 CGGTCATTTTACC
1 CGGTCATTCTACC
52788311 TATTTTGGAG
Statistics
Matches: 115, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
19 14 0.12
20 1 0.01
22 2 0.02
24 2 0.02
26 1 0.01
27 95 0.83
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (27 bp):
CGGTCATTCTACCCTATGGGGGTATTT
Found at i:52788268 original size:19 final size:19
Alignment explanation
Indices: 52788244--52788281 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
52788234 TACCTTATGG
* *
52788244 GGGTATTTTGGTTATTTTA
1 GGGTATTTCGGTCATTTTA
52788263 GGGTATTTCGGTCATTTTA
1 GGGTATTTCGGTCATTTTA
52788282 CCCTATGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.05, G:0.26, T:0.53
Consensus pattern (19 bp):
GGGTATTTCGGTCATTTTA
Found at i:52788289 original size:46 final size:46
Alignment explanation
Indices: 52788217--52788308 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
52788207 TACCCTATGG
* * *
52788217 GGGTATTTCGACCATTTTACCTTATGGGGGTATTTTGGTTATTTTA
1 GGGTATTTCGACCATTTTACCCTATGGGGGTATTTCGGTCATTTTA
**
52788263 GGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTA
1 GGGTATTTCGACCATTTTACCCTATGGGGGTATTTCGGTCATTTTA
52788309 CCTATTTTGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.16, C:0.13, G:0.25, T:0.46
Consensus pattern (46 bp):
GGGTATTTCGACCATTTTACCCTATGGGGGTATTTCGGTCATTTTA
Found at i:52790603 original size:34 final size:34
Alignment explanation
Indices: 52790560--52790628 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
52790550 ATTTAAACTT
52790560 TTAATTCTTAAATAAACCCAAGATTTCTTAATCA
1 TTAATTCTTAAATAAACCCAAGATTTCTTAATCA
52790594 TTAATTCTTAAATAAACCCAAGATTTCTTAATCA
1 TTAATTCTTAAATAAACCCAAGATTTCTTAATCA
52790628 T
1 T
52790629 ACATGATTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (34 bp):
TTAATTCTTAAATAAACCCAAGATTTCTTAATCA
Found at i:52798546 original size:28 final size:28
Alignment explanation
Indices: 52798515--52798571 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
52798505 ACATGCAATG
52798515 ACAGTCTGGGCCTGAGCCCTAAGCAGTA
1 ACAGTCTGGGCCTGAGCCCTAAGCAGTA
*
52798543 ACAGTCTGGGCCTTAGCCCTAAGCAGTA
1 ACAGTCTGGGCCTGAGCCCTAAGCAGTA
52798571 A
1 A
52798572 TAGTGTAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (28 bp):
ACAGTCTGGGCCTGAGCCCTAAGCAGTA
Found at i:52799039 original size:54 final size:54
Alignment explanation
Indices: 52798956--52799135 Score: 245
Period size: 54 Copynumber: 3.3 Consensus size: 54
52798946 TTGATTCCCA
** * * *
52798956 GGGGTATAACAGTTATTTTACCCTATGGGGGTATTTCGGTCATTCTATCCTTCG
1 GGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTATCCTTCG
* * * *
52799010 GGGGTATTTCAGTCATTTTACCCTTTGGGGGCATTTTGGTTATTTTACCCTTCG
1 GGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTATCCTTCG
52799064 GGGGTATTTC-GTTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTATCCTTCG
1 GGGGTATTTCAG-TCATTTTACCCTTTGGGGGTATTTCGGTCATTTTATCCTTCG
* *
52799118 AGGGTATTTCGGTCATTT
1 GGGGTATTTCAGTCATTT
52799136 GCCCATGAAT
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 108 0.98
55 1 0.01
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.43
Consensus pattern (54 bp):
GGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTATCCTTCG
Found at i:52799128 original size:27 final size:27
Alignment explanation
Indices: 52798970--52799135 Score: 217
Period size: 27 Copynumber: 6.1 Consensus size: 27
52798960 TATAACAGTT
52798970 ATTTTACCCTAT-GGGGGTATTTCGGTC
1 ATTTTACCCT-TCGGGGGTATTTCGGTC
* * *
52798997 ATTCTATCCTTCGGGGGTATTTCAGTC
1 ATTTTACCCTTCGGGGGTATTTCGGTC
* * * *
52799024 ATTTTACCCTTTGGGGGCATTTTGGTT
1 ATTTTACCCTTCGGGGGTATTTCGGTC
*
52799051 ATTTTACCCTTCGGGGGTATTTCGTTC
1 ATTTTACCCTTCGGGGGTATTTCGGTC
*
52799078 ATTTTACCCTTTGGGGGTATTTCGGTC
1 ATTTTACCCTTCGGGGGTATTTCGGTC
* *
52799105 ATTTTATCCTTCGAGGGTATTTCGGTC
1 ATTTTACCCTTCGGGGGTATTTCGGTC
52799132 ATTT
1 ATTT
52799136 GCCCATGAAT
Statistics
Matches: 118, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
26 1 0.01
27 117 0.99
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (27 bp):
ATTTTACCCTTCGGGGGTATTTCGGTC
Found at i:52799835 original size:15 final size:15
Alignment explanation
Indices: 52799817--52799849 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52799807 GAAGAGGAAA
52799817 AGAAGAGAAAAGAAG
1 AGAAGAGAAAAGAAG
*
52799832 AGAAGAGATAAGAAG
1 AGAAGAGAAAAGAAG
52799847 AGA
1 AGA
52799850 GGATTTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (15 bp):
AGAAGAGAAAAGAAG
Found at i:52803889 original size:13 final size:13
Alignment explanation
Indices: 52803815--52803892 Score: 52
Period size: 13 Copynumber: 5.8 Consensus size: 13
52803805 TAGCCTTGCG
52803815 TCTTTCTTTCTCTT
1 TCTTTCTTT-TCTT
52803829 T-TTTCTTTCTCTT
1 TCTTTCTTT-TCTT
*
52803842 TCTTTGTTTTCGTT
1 TCTTTCTTTTC-TT
** **
52803856 TGGTT-TTGGCTT
1 TCTTTCTTTTCTT
52803868 TGGCTTTCTTTTCTT
1 T--CTTTCTTTTCTT
52803883 TCTTTCTTTT
1 TCTTTCTTTT
52803893 TATTTGTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
12 3 0.06
13 27 0.54
14 14 0.28
15 6 0.12
ACGTcount: A:0.00, C:0.19, G:0.10, T:0.71
Consensus pattern (13 bp):
TCTTTCTTTTCTT
Found at i:52805411 original size:28 final size:28
Alignment explanation
Indices: 52805379--52805434 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
52805369 TCTTTCCATG
52805379 ATGTGCATAACATTTCTCATATATTAGT
1 ATGTGCATAACATTTCTCATATATTAGT
52805407 ATGTGCATAACATTTCTCATATATTAGT
1 ATGTGCATAACATTTCTCATATATTAGT
52805435 GCACACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (28 bp):
ATGTGCATAACATTTCTCATATATTAGT
Found at i:52805443 original size:28 final size:28
Alignment explanation
Indices: 52805384--52805443 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
52805374 CCATGATGTG
****
52805384 CATAACATTTCTCATATATTAGTATGTG
1 CATAACATTTCTCATATATTAGTACACA
*
52805412 CATAACATTTCTCATATATTAGTGCACA
1 CATAACATTTCTCATATATTAGTACACA
52805440 CATA
1 CATA
52805444 TGTGCATTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (28 bp):
CATAACATTTCTCATATATTAGTACACA
Found at i:52811305 original size:24 final size:25
Alignment explanation
Indices: 52811259--52811306 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
52811249 AACTTAGGGT
52811259 CTCACGACACAATATTTAATTTAGGC
1 CTCACGACAC-ATATTTAATTTAGGC
*
52811285 CTCACGACAC-TATTTAGTTTAG
1 CTCACGACACATATTTAATTTAG
52811307 ACCCTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
26 10 0.48
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (25 bp):
CTCACGACACATATTTAATTTAGGC
Found at i:52812221 original size:5 final size:5
Alignment explanation
Indices: 52812213--52812241 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
52812203 AAAAAAAAAA
52812213 CCCCT CCCCT CCCCT CCCCT CCCCT CCCC
1 CCCCT CCCCT CCCCT CCCCT CCCCT CCCC
52812242 ACCCTGTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.83, G:0.00, T:0.17
Consensus pattern (5 bp):
CCCCT
Found at i:52814118 original size:6 final size:6
Alignment explanation
Indices: 52814107--52814139 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
52814097 AACGATCTAG
*
52814107 TTGATA TTGATA TTGATG TTGATA TTGATA TTG
1 TTGATA TTGATA TTGATA TTGATA TTGATA TTG
52814140 TGAGGATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (6 bp):
TTGATA
Found at i:52816648 original size:20 final size:20
Alignment explanation
Indices: 52816619--52816663 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
52816609 AGCACATGAA
52816619 TGGA-ACCCCAAATGCCCAC
1 TGGATACCCCAAATGCCCAC
52816638 TGGATACCCCAAATGCCCAC
1 TGGATACCCCAAATGCCCAC
52816658 TGGATA
1 TGGATA
52816664 ATCATTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.31, C:0.36, G:0.18, T:0.16
Consensus pattern (20 bp):
TGGATACCCCAAATGCCCAC
Found at i:52820426 original size:21 final size:22
Alignment explanation
Indices: 52820385--52820432 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
52820375 TAAATTTGAA
*
52820385 CATTTTAAGTTATAAGTATTTT
1 CATTTTAAGATATAAGTATTTT
*
52820407 CATTTTAA-ATATAA-TAATTT
1 CATTTTAAGATATAAGTATTTT
52820427 -ATTTTA
1 CATTTTA
52820433 TTTTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 5 0.21
21 5 0.21
22 8 0.33
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (22 bp):
CATTTTAAGATATAAGTATTTT
Found at i:52820587 original size:18 final size:20
Alignment explanation
Indices: 52820543--52820589 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
52820533 TTATTCTATG
*
52820543 ATATTATATGATTTAATGAT
1 ATATTATATGATTTAATAAT
* *
52820563 TTTTTAT-TG-TTTAATAAT
1 ATATTATATGATTTAATAAT
52820581 ATATTATAT
1 ATATTATAT
52820590 TGACAATTGA
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
18 13 0.62
19 3 0.14
20 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
ATATTATATGATTTAATAAT
Found at i:52824194 original size:79 final size:79
Alignment explanation
Indices: 52824098--52824255 Score: 262
Period size: 79 Copynumber: 2.0 Consensus size: 79
52824088 GCTAGTACGT
* * *
52824098 CTCTACGTTACTCTGTTGATGAAGAATGTGCAATATCTGAATATGTTGGATTGATGGTTACTGAT
1 CTCTACGTTACTCTGTTGATGAAGAATATACAATATCTGAATATGTTAGATTGATGGTTACTGAT
52824163 TCTAATTTATAACC
66 TCTAATTTATAACC
* *
52824177 CTCTACGTTACTCTGTTGATGAAGAATATACGATATCTGAATATGTTAGATTGATTGTTACTGAT
1 CTCTACGTTACTCTGTTGATGAAGAATATACAATATCTGAATATGTTAGATTGATGGTTACTGAT
*
52824242 TCTGATTTATAACC
66 TCTAATTTATAACC
52824256 GTGCATGTGA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (79 bp):
CTCTACGTTACTCTGTTGATGAAGAATATACAATATCTGAATATGTTAGATTGATGGTTACTGAT
TCTAATTTATAACC
Found at i:52824759 original size:25 final size:24
Alignment explanation
Indices: 52824725--52824811 Score: 111
Period size: 25 Copynumber: 3.5 Consensus size: 24
52824715 AACGTACATG
52824725 CTCTGCTCTGTTATGTTCAATTCTA
1 CTCTGCTCTGTTATGTT-AATTCTA
*
52824750 CTCTGCTCTGTTATGTTTAGTTCTA
1 CTCTGCTCTGTTATG-TTAATTCTA
** *
52824775 CTCTGCTCTACTATGTTATATTCTG
1 CTCTGCTCTGTTATGTTA-ATTCTA
52824800 CTCTGCTCTGTT
1 CTCTGCTCTGTT
52824812 CTATTCTCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
24 3 0.06
25 48 0.91
26 2 0.04
ACGTcount: A:0.13, C:0.24, G:0.14, T:0.49
Consensus pattern (24 bp):
CTCTGCTCTGTTATGTTAATTCTA
Found at i:52824801 original size:20 final size:20
Alignment explanation
Indices: 52824776--52824818 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
52824766 TTAGTTCTAC
52824776 TCTGCTCTACTATGTTATAT
1 TCTGCTCTACTATGTTATAT
* * *
52824796 TCTGCTCTGCTCTGTTCTAT
1 TCTGCTCTACTATGTTATAT
52824816 TCT
1 TCT
52824819 CTTATGTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.26, G:0.12, T:0.51
Consensus pattern (20 bp):
TCTGCTCTACTATGTTATAT
Found at i:52824809 original size:30 final size:30
Alignment explanation
Indices: 52824775--52824833 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
52824765 TTTAGTTCTA
*
52824775 CTCTGCTCTACTATGTTATATTCTGCTCTG
1 CTCTGCTCTACTATCTTATATTCTGCTCTG
* * * *
52824805 CTCTGTTCTATTCTCTTATGTTCTGCTCT
1 CTCTGCTCTACTATCTTATATTCTGCTCT
52824834 ATCCTGTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.10, C:0.27, G:0.12, T:0.51
Consensus pattern (30 bp):
CTCTGCTCTACTATCTTATATTCTGCTCTG
Found at i:52825817 original size:17 final size:16
Alignment explanation
Indices: 52825793--52825831 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
52825783 TTATGCACAC
52825793 TTTATTAATAATATAT
1 TTTATTAATAATATAT
*
52825809 TTGTATTAATAATGTAT
1 TT-TATTAATAATATAT
52825826 TTTATT
1 TTTATT
52825832 GAGTTGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTATTAATAATATAT
Found at i:52826128 original size:15 final size:15
Alignment explanation
Indices: 52826097--52826129 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
52826087 TTAGTAATAG
52826097 TTATATATTTTATTA
1 TTATATATTTTATTA
52826112 TTAT-TATTTTATGTA
1 TTATATATTTTAT-TA
52826127 TTA
1 TTA
52826130 GTAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTATATATTTTATTA
Found at i:52826970 original size:32 final size:33
Alignment explanation
Indices: 52826915--52826982 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
52826905 TTAAAGGCCC
*
52826915 AAATTTTTTTTTTACCAAATTTTAA-GAGACCTA
1 AAATTTTTTTTCTACCAAATTTTAAGGA-ACCTA
*
52826948 AAATTTTTTTTCT-CCAACTTTTAAGGAACCTA
1 AAATTTTTTTTCTACCAAATTTTAAGGAACCTA
52826980 AAA
1 AAA
52826983 CCTCATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 18 0.56
33 14 0.44
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (33 bp):
AAATTTTTTTTCTACCAAATTTTAAGGAACCTA
Found at i:52827093 original size:6 final size:6
Alignment explanation
Indices: 52827082--52827106 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
52827072 ACTTCCAACT
52827082 CTCTCC CTCTCC CTCTCC CTCTCC C
1 CTCTCC CTCTCC CTCTCC CTCTCC C
52827107 AACCGTTGCA
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:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCTCC
Found at i:52833458 original size:22 final size:23
Alignment explanation
Indices: 52833415--52833460 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
52833405 TGTCAAGTAA
*
52833415 TTTTTTGTGGTGTGTTGGCTTAG
1 TTTTTTGTGGTGTGTTGCCTTAG
52833438 TTTTTTGT-GT-TGTTCGCCTTAG
1 TTTTTTGTGGTGTGTT-GCCTTAG
52833460 T
1 T
52833461 CTTGTGTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 9 0.43
23 8 0.38
ACGTcount: A:0.04, C:0.09, G:0.28, T:0.59
Consensus pattern (23 bp):
TTTTTTGTGGTGTGTTGCCTTAG
Found at i:52833757 original size:13 final size:13
Alignment explanation
Indices: 52833732--52833765 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
52833722 TTTTCTTTCA
52833732 TTTCTTT-TTGTT
1 TTTCTTTCTTGTT
52833744 TTTCTTTCTTGTT
1 TTTCTTTCTTGTT
*
52833757 TATCTTTCT
1 TTTCTTTCT
52833766 CTTTTTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (13 bp):
TTTCTTTCTTGTT
Found at i:52834881 original size:27 final size:27
Alignment explanation
Indices: 52834809--52834941 Score: 149
Period size: 27 Copynumber: 4.9 Consensus size: 27
52834799 TTGCTGACTA
* * *
52834809 AAATACCTTCGAAGGGTAAAATGGCTG
1 AAATACCCTCGAAGGGTAAAATGACCG
* ** *
52834836 AAATACCCTCAAATTGTAAAATGACCA
1 AAATACCCTCGAAGGGTAAAATGACCG
* *
52834863 AAATACCCTCGAAGGGTAAAATAATCG
1 AAATACCCTCGAAGGGTAAAATGACCG
* *
52834890 AAATACCCCCGAAGGGTAAAATGATCG
1 AAATACCCTCGAAGGGTAAAATGACCG
* *
52834917 AAATACCTTTGAAGGGTAAAATGAC
1 AAATACCCTCGAAGGGTAAAATGAC
52834942 TGTTATACCC
Statistics
Matches: 87, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 87 1.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATGACCG
Found at i:52834950 original size:54 final size:54
Alignment explanation
Indices: 52834803--52834952 Score: 167
Period size: 54 Copynumber: 2.8 Consensus size: 54
52834793 TTCTCTTTGC
* * * **
52834803 TGACTAAAATACCTTCGAAGGGTAAAATGGCTGAAATACCCTCAAATTGTAAAA
1 TGACCAAAATACCTTCGAAGGGTAAAATGACTGAAATACCCCCAAAGGGTAAAA
* * *
52834857 TGACCAAAATACCCTCGAAGGGTAAAAT-AATCGAAATACCCCCGAAGGGTAAAA
1 TGACCAAAATACCTTCGAAGGGTAAAATGACT-GAAATACCCCCAAAGGGTAAAA
* * * **
52834911 TGATCGAAATACCTTTGAAGGGTAAAATGACTGTTATACCCC
1 TGACCAAAATACCTTCGAAGGGTAAAATGACTGAAATACCCC
52834953 TAGGAATTGA
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 76 0.96
55 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (54 bp):
TGACCAAAATACCTTCGAAGGGTAAAATGACTGAAATACCCCCAAAGGGTAAAA
Found at i:52835145 original size:26 final size:26
Alignment explanation
Indices: 52835116--52835217 Score: 105
Period size: 26 Copynumber: 3.9 Consensus size: 26
52835106 TTGCCACAAA
*
52835116 TACTGTTATTGGCAGCTTTGCTGCGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* * * *
52835142 TACTGATACTGGCAGCTCTACTGGGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* * *
52835168 TACTGTTAGTGGCAGCTTTGTTGCAT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* * *
52835194 TACTATTACTGGTAGTTTTGCTGC
1 TACTGTTACTGGCAGCTTTGCTGC
52835218 AATATTAGTG
Statistics
Matches: 59, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCGT
Found at i:52835383 original size:28 final size:28
Alignment explanation
Indices: 52835345--52835446 Score: 105
Period size: 30 Copynumber: 3.5 Consensus size: 28
52835335 ATTTTAGGCT
*
52835345 TAAGGCTCACACTGTTACTGTATTGGGC
1 TAAGGCCCACACTGTTACTGTATTGGGC
52835373 TAAGGCCCACACTCTGTTACTGTATTGGGC
1 TAAGGCCCACA--CTGTTACTGTATTGGGC
* * * *
52835403 TATGGTCCACACACTGCTATTGTATAGGGC
1 TAAGG-CC-CACACTGTTACTGTATTGGGC
* *
52835433 TCAGGCCCAGACTG
1 TAAGGCCCACACTG
52835447 ATTCTGCATG
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
28 16 0.26
29 2 0.03
30 38 0.61
31 2 0.03
32 4 0.06
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (28 bp):
TAAGGCCCACACTGTTACTGTATTGGGC
Found at i:52835392 original size:30 final size:30
Alignment explanation
Indices: 52835352--52835441 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
52835342 GCTTAAGGCT
52835352 CACACTGTTACTGTATTGGGCTAAGGCCCA
1 CACACTGTTACTGTATTGGGCTAAGGCCCA
* * *
52835382 CACTCTGTTACTGTATTGGGCTATGGTCCA
1 CACACTGTTACTGTATTGGGCTAAGGCCCA
* * * *
52835412 CACACTGCTATTGTATAGGGCTCAGGCCCA
1 CACACTGTTACTGTATTGGGCTAAGGCCCA
52835442 GACTGATTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (30 bp):
CACACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:52837992 original size:43 final size:42
Alignment explanation
Indices: 52837865--52837980 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 42
52837855 AGCTCGTACA
* *
52837865 ATGCCATCGTCCCAGACGTGGTCTTATATGTAATCACATATCG
1 ATGCCA-CGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* *
52837908 ATGCCACTATCCCAGACAG-GGTCTTACACGTAATCAAATATCG
1 ATGCCAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
52837951 ATGCCGACGTCCCAGACGTGGTCTTACACG
1 ATGCC-ACGTCCCAGACGTGGTCTTACACG
52837981 AAAATACATA
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
42 2 0.03
43 59 0.92
44 3 0.05
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (42 bp):
ATGCCACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:52838926 original size:28 final size:28
Alignment explanation
Indices: 52838872--52838928 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
52838862 TATGTTTGTT
52838872 TTTATTATAAAAACTTTATAATATATTA
1 TTTATTATAAAAACTTTATAATATATTA
* *
52838900 TTTATTATTATAACCTTTATAAT-TATTA
1 TTTATTA-TAAAAACTTTATAATATATTA
52838928 T
1 T
52838929 AAAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTATTATAAAAACTTTATAATATATTA
Found at i:52842237 original size:21 final size:21
Alignment explanation
Indices: 52842213--52842316 Score: 115
Period size: 21 Copynumber: 5.0 Consensus size: 21
52842203 TTTGGGTGGA
*
52842213 TCAGCTCTTACGGGTTTCTGT
1 TCAGCTCTTACGAGTTTCTGT
*
52842234 TCAGCTCTTATGAGTTTCTGT
1 TCAGCTCTTACGAGTTTCTGT
*
52842255 TTAGCTCTTACGAGCTTT-TGT
1 TCAGCTCTTACGAG-TTTCTGT
* *
52842276 TCAGCT-TT-CAAGCTTCTGT
1 TCAGCTCTTACGAGTTTCTGT
* *
52842295 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTACGAGTTTCTGT
52842316 T
1 T
52842317 AATGATGTAC
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
18 2 0.03
19 12 0.17
20 4 0.06
21 49 0.70
22 3 0.04
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (21 bp):
TCAGCTCTTACGAGTTTCTGT
Found at i:52842304 original size:40 final size:41
Alignment explanation
Indices: 52842213--52842316 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 41
52842203 TTTGGGTGGA
* *
52842213 TCAGCTCTTACG-GGTTTCTGTTCAGCTCTTATGAGTTTCTGT
1 TCAGCTCTTACGAGCTTT-TGTTCAGCTCTTA-GAGCTTCTGT
*
52842255 TTAGCTCTTACGAGCTTTTGTTCAGCT-TTCA-AGCTTCTGT
1 TCAGCTCTTACGAGCTTTTGTTCAGCTCTT-AGAGCTTCTGT
* *
52842295 TCAGCTCTTATGAGCTTCTGTT
1 TCAGCTCTTACGAGCTTTTGTT
52842317 AATGATGTAC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
40 27 0.50
41 2 0.04
42 21 0.39
43 4 0.07
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (41 bp):
TCAGCTCTTACGAGCTTTTGTTCAGCTCTTAGAGCTTCTGT
Found at i:52842479 original size:21 final size:20
Alignment explanation
Indices: 52842453--52842500 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
52842443 TAGAAGTTAA
*
52842453 GAATGATAGGAAATTATCAGT
1 GAATGATAGGAAATTAACA-T
* *
52842474 GAATGAAAGGGAATTAACAT
1 GAATGATAGGAAATTAACAT
52842494 GAATGAT
1 GAATGAT
52842501 TTTATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.46, C:0.04, G:0.25, T:0.25
Consensus pattern (20 bp):
GAATGATAGGAAATTAACAT
Found at i:52857141 original size:30 final size:30
Alignment explanation
Indices: 52857097--52857156 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
52857087 ACTTAACAAG
*
52857097 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAAAAACAAAATTAA
* *
52857127 CAAATGTCTTTAAAATAAAAACAAAATTAA
1 CAAATGCCTCTAAAATAAAAACAAAATTAA
52857157 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAAAAACAAAATTAA
Found at i:52859207 original size:27 final size:27
Alignment explanation
Indices: 52859186--52859464 Score: 280
Period size: 27 Copynumber: 10.3 Consensus size: 27
52859176 GGGGTATAAA
52859186 AGTCATTTTACCCTTCGAGGGTA-TTT
1 AGTCATTTTACCCTTCGAGGGTATTTT
*
52859212 CGATCATTTTATCCC-TC-AGGGGTATTTT
1 AG-TCATTTTA-CCCTTCGA-GGGTATTTT
* * *
52859240 GGTTATTTTACCCTTTCG-GGGTATTTC
1 AGTCATTTTACCC-TTCGAGGGTATTTT
* * *
52859267 GGTCATTTTACCTTTTGAGGGTATTTT
1 AGTCATTTTACCCTTCGAGGGTATTTT
* *
52859294 AGTCATTTTATCCTTCGAGGGTATTTC
1 AGTCATTTTACCCTTCGAGGGTATTTT
* *
52859321 AGTCATTTTACCCTTCGGGGGTATTTC
1 AGTCATTTTACCCTTCGAGGGTATTTT
* * *
52859348 GGTCATTTTACCCTTTGATGGTATTTT
1 AGTCATTTTACCCTTCGAGGGTATTTT
* * *
52859375 GGTCATTTTACCCTTCGGGGGTATTTC
1 AGTCATTTTACCCTTCGAGGGTATTTT
* *
52859402 AATCATTTTACCCTTC-AGGGGTATTTC
1 AGTCATTTTACCCTTCGA-GGGTATTTT
* * *
52859429 AGTAATTTTAACCTTTGAGGGTATTTT
1 AGTCATTTTACCCTTCGAGGGTATTTT
52859456 AGTCATTTT
1 AGTCATTTT
52859465 CCCATGAATC
Statistics
Matches: 210, Mismatches: 33, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
26 8 0.04
27 192 0.91
28 10 0.05
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.46
Consensus pattern (27 bp):
AGTCATTTTACCCTTCGAGGGTATTTT
Found at i:52859316 original size:81 final size:81
Alignment explanation
Indices: 52859187--52859464 Score: 364
Period size: 81 Copynumber: 3.4 Consensus size: 81
52859177 GGGTATAAAA
* * * ** *
52859187 GTCATTTTACCCTTCGAGGGTA-TTTCGATCATTTTATCCCTC-AGGGGTATTTTGGTTATTTTA
1 GTCATTTTACCCTTTGAGGGTATTTTAG-TCATTTTATCCTTCGA-GGGTATTTCAGTCATTTTA
52859250 CCCTTTC-GGGGTATTTCG
64 CCC-TTCAGGGGTATTTCG
*
52859268 GTCATTTTACCTTTTGAGGGTATTTTAGTCATTTTATCCTTCGAGGGTATTTCAGTCATTTTACC
1 GTCATTTTACCCTTTGAGGGTATTTTAGTCATTTTATCCTTCGAGGGTATTTCAGTCATTTTACC
*
52859333 CTTCGGGGGTATTTCG
66 CTTCAGGGGTATTTCG
* * * * *
52859349 GTCATTTTACCCTTTGATGGTATTTTGGTCATTTTACCCTTCGGGGGTATTTCAATCATTTTACC
1 GTCATTTTACCCTTTGAGGGTATTTTAGTCATTTTATCCTTCGAGGGTATTTCAGTCATTTTACC
*
52859414 CTTCAGGGGTATTTCA
66 CTTCAGGGGTATTTCG
* *
52859430 GTAATTTTAACCTTTGAGGGTATTTTAGTCATTTT
1 GTCATTTTACCCTTTGAGGGTATTTTAGTCATTTT
52859465 CCCATGAATC
Statistics
Matches: 175, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
80 3 0.02
81 167 0.95
82 5 0.03
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.46
Consensus pattern (81 bp):
GTCATTTTACCCTTTGAGGGTATTTTAGTCATTTTATCCTTCGAGGGTATTTCAGTCATTTTACC
CTTCAGGGGTATTTCG
Found at i:52865920 original size:22 final size:20
Alignment explanation
Indices: 52865890--52865929 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
52865880 TTCAAAAATA
52865890 ATTTAAAATAGTTTTTCAAAAG
1 ATTTAAAATA--TTTTCAAAAG
*
52865912 ATTTCAAATATTTTCAAA
1 ATTTAAAATATTTTCAAA
52865930 CCCATTCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (20 bp):
ATTTAAAATATTTTCAAAAG
Found at i:52866619 original size:28 final size:28
Alignment explanation
Indices: 52866565--52866621 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
52866555 AACAATGTAA
* * *
52866565 TGTGGGCCTTAGCCCATTTCAGTAACAG
1 TGTGGGCCTTAGCCCAATACAGAAACAG
52866593 TGTGGGCCTTAGCCCAATACAGAAACAG
1 TGTGGGCCTTAGCCCAATACAGAAACAG
52866621 T
1 T
52866622 ACAGTGCAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGAAACAG
Found at i:52866984 original size:27 final size:27
Alignment explanation
Indices: 52866954--52867460 Score: 455
Period size: 27 Copynumber: 19.0 Consensus size: 27
52866944 GTTATAACAG
** *
52866954 TCATTTTACCCTAAGGGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
52866981 TCATTTTACCCTTC-AGGGGTATTTCAA
1 TCATTTTACCCTTCGA-GGGTATTTCGA
*
52867008 TCATTTTACCCTTCGGGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
**
52867035 TCATTTTACTATTC-AGTGGTATTTC-A
1 TCATTTTACCCTTCGAG-GGTATTTCGA
* * * *
52867061 GTAATTTTACCTTTTGAGGGTATTTTGA
1 -TCATTTTACCCTTCGAGGGTATTTCGA
* * *
52867089 TCATTTTACCTTTCAAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* ** *
52867116 TTATTTTACTGTTCGGGAGGGTATTTTGA
1 TCATTTTACCCTTC--GAGGGTATTTCGA
* * * *
52867145 CCATTTTACCTTTCGAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
52867172 TCATTTTATCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* ** * *
52867199 TCATTTTATCCTTTTAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
52867226 TCATTTTACCCTTCGAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
52867253 TTATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
52867280 TCATTTTACCCTTCG-GGG------GG
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * *
52867300 TCATTTTACCCTTTGAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
52867327 TCATTTCACCCTTCGAGGGTATTTC-A
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * *
52867353 GTTATTTTACCCTTTGAGGGTATTT-TA
1 -TCATTTTACCCTTCGAGGGTATTTCGA
*
52867380 GTCATTTTACCCTTCGCGGGTATTTC-A
1 -TCATTTTACCCTTCGAGGGTATTTCGA
* *
52867407 GTCATTTTACCCTTCGAGGGTATTTTGG
1 -TCATTTTACCCTTCGAGGGTATTTCGA
*
52867435 TCATTTTACCCTTCAAGGGTATTTCG
1 TCATTTTACCCTTCGAGGGTATTTCG
52867461 GTTATTTGCC
Statistics
Matches: 400, Mismatches: 61, Indels: 38
0.80 0.12 0.08
Matches are distributed among these distances:
20 15 0.04
21 3 0.01
26 5 0.01
27 354 0.88
28 3 0.01
29 20 0.05
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.45
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCGA
Found at i:52867361 original size:155 final size:155
Alignment explanation
Indices: 52866981--52867448 Score: 480
Period size: 155 Copynumber: 3.0 Consensus size: 155
52866971 GGTATTTCGA
* *** * *
52866981 TCATTTTACCCTTC-AGGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTC-GATCATTTTA-
1 TCATTTTACCTTTCGA-GGGTATTTTGGTCATTTCACCCTTCGAGGGTATTTCAG-TCATTTTAC
* * * * * * * *
52867043 -CTATTCAGTGGTATTTCAGTAATTTTACCTTTTGAGGGTATTT-TGATCATTTTACCTTTCAAG
64 CCT-TTGAG-GGTATTTTAGTCATTTTACCCTTCGAGGGTATTTCAG-TCATTTTACCCTTCGAG
* * **
52867106 GGTATTTCGGTTATTTTACTGTTCGGGAGGG
126 GGTATTTCGATCATTTTACCCTTCGGG-GGG
* * *
52867137 TATTTTGACCATTTTACCTTTCGAGGGTATTTTGGTCATTTTATCCTTCGAGGGTATTTCGGTCA
1 -----T---CATTTTACCTTTCGAGGGTATTTTGGTCATTTCACCCTTCGAGGGTATTTCAGTCA
* * * ** *
52867202 TTTTATCCTTTTAGGGTATTTTGGTCATTTTACCCTTCGAGGGTATTTTGGTTATTTTACCCTTC
58 TTTTACCCTTTGAGGGTATTTTAGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTC
52867267 GAGGGTATTTCGATCATTTTACCCTTCGGGGGG
123 GAGGGTATTTCGATCATTTTACCCTTCGGGGGG
*
52867300 TCATTTTACCCTTT-GAGGGTATTTTGGTCATTTCACCCTTCGAGGGTATTTCAGTTATTTTACC
1 TCATTTTA-CCTTTCGAGGGTATTTTGGTCATTTCACCCTTCGAGGGTATTTCAGTCATTTTACC
*
52867364 CTTTGAGGGTATTTTAGTCATTTTACCCTTCGCGGGTATTTCAGTCATTTTACCCTTCGAGGGTA
65 CTTTGAGGGTATTTTAGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCGAGGGTA
* *
52867429 TTTTGGTCATTTTACCCTTC
130 TTTCGATCATTTTACCCTTC
52867449 AAGGGTATTT
Statistics
Matches: 265, Mismatches: 33, Indels: 24
0.82 0.10 0.07
Matches are distributed among these distances:
155 129 0.49
156 5 0.02
158 1 0.00
161 1 0.00
163 3 0.01
164 117 0.44
165 7 0.03
166 2 0.01
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.45
Consensus pattern (155 bp):
TCATTTTACCTTTCGAGGGTATTTTGGTCATTTCACCCTTCGAGGGTATTTCAGTCATTTTACCC
TTTGAGGGTATTTTAGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCGAGGGTAT
TTCGATCATTTTACCCTTCGGGGGG
Found at i:52878830 original size:24 final size:24
Alignment explanation
Indices: 52878748--52878831 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
52878738 AGAAGGAAAC
*
52878748 CCTTGGAGGTGGTTTTGGTGGAGG
1 CCTTGGAGGTGGTTTAGGTGGAGG
* * * * *
52878772 CGTCGGAGGAGGGGTTA-GTGGTGG
1 CCTTGGAGG-TGGTTTAGGTGGAGG
* *
52878796 CCATGGTGGTGGTTTAGGTGGAGG
1 CCTTGGAGGTGGTTTAGGTGGAGG
*
52878820 CTTTGGAGGTGG
1 CCTTGGAGGTGG
52878832 AAAAGGTGGT
Statistics
Matches: 42, Mismatches: 16, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
23 5 0.12
24 33 0.79
25 4 0.10
ACGTcount: A:0.11, C:0.08, G:0.52, T:0.29
Consensus pattern (24 bp):
CCTTGGAGGTGGTTTAGGTGGAGG
Found at i:52878933 original size:36 final size:36
Alignment explanation
Indices: 52878893--52878963 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
52878883 CGATCTTGGA
52878893 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
1 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
**** *
52878929 GGTGGTGCTGGTGGAGGTATAGGAGGTGGAGCTGG
1 GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGG
52878964 AGGCAGTGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.20, C:0.06, G:0.55, T:0.20
Consensus pattern (36 bp):
GGTGGAAAAGGTGGAGGCATAGGAGGTGGAGCTGGT
Found at i:52878973 original size:36 final size:36
Alignment explanation
Indices: 52878902--52878994 Score: 114
Period size: 36 Copynumber: 2.6 Consensus size: 36
52878892 AGGTGGAAAA
* * **
52878902 GGTGGAGGCATAGGAGGTGGAGCTGGTGGTGGTGCT
1 GGTGGAGGTATAGGAGGTGGAGCTGGAGGCAGTGCT
52878938 GGTGGAGGTATAGGAGGTGGAGCTGGAGGCAGTGCT
1 GGTGGAGGTATAGGAGGTGGAGCTGGAGGCAGTGCT
* * * *
52878974 AGTGGTGGTTTTGGAGGTGGA
1 GGTGGAGGTATAGGAGGTGGA
52878995 AAAGGTGGAG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.16, C:0.06, G:0.54, T:0.24
Consensus pattern (36 bp):
GGTGGAGGTATAGGAGGTGGAGCTGGAGGCAGTGCT
Found at i:52879091 original size:30 final size:30
Alignment explanation
Indices: 52879034--52879091 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
52879024 TGGTGGAAAA
*
52879034 GGTGGAGGCATAGGAGCAGGTGGTGGTGTC
1 GGTGGAGGCATAGGAGCAGGTGCTGGTGTC
* *
52879064 GGTGGTGGCATTGGAGGC-GGTGCTGGTG
1 GGTGGAGGCATAGGA-GCAGGTGCTGGTG
52879092 GTGGTTTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.12, C:0.10, G:0.55, T:0.22
Consensus pattern (30 bp):
GGTGGAGGCATAGGAGCAGGTGCTGGTGTC
Found at i:52879095 original size:114 final size:114
Alignment explanation
Indices: 52878960--52879257 Score: 551
Period size: 114 Copynumber: 2.6 Consensus size: 114
52878950 GGAGGTGGAG
* *
52878960 CTGGAGGCAGTGCTAGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
1 CTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
*
52879025 GGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGTCGGTGGTGGCA
66 GGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGCCGGTGGTGGCA
*
52879074 TTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
1 CTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
*
52879139 GGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGCCGGTGGTGGCG
66 GGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGCCGGTGGTGGCA
52879188 CTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
1 CTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
52879253 GGTGG
66 GGTGG
52879258 CGCTGGAGGC
Statistics
Matches: 178, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 178 1.00
ACGTcount: A:0.18, C:0.07, G:0.54, T:0.21
Consensus pattern (114 bp):
CTGGAGGCGGTGCTGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGGATAGGAGGTGGAGCTGGT
GGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGCCGGTGGTGGCA
Found at i:52879183 original size:12 final size:12
Alignment explanation
Indices: 52879166--52879282 Score: 56
Period size: 12 Copynumber: 9.8 Consensus size: 12
52879156 CATAGGAGCA
*
52879166 GGTGGTGGTGCC
1 GGTGGTGGTGCT
*
52879178 GGTGGTGGCGCT
1 GGTGGTGGTGCT
* *
52879190 GGAGGCGGTGCT
1 GGTGGTGGTGCT
**
52879202 GGTGGTGGTTTT
1 GGTGGTGGTGCT
* ****
52879214 GGAGGTGGAAAA
1 GGTGGTGGTGCT
* *
52879226 GGTGGAGG-GAT
1 GGTGGTGGTGCT
* *
52879237 AGGAGGTGGAGCT
1 -GGTGGTGGTGCT
*
52879250 GGTGGTGGCGCT
1 GGTGGTGGTGCT
* *
52879262 GGAGGCGGTGCT
1 GGTGGTGGTGCT
52879274 GGTGGTGGT
1 GGTGGTGGT
52879283 TTTGGAGGTG
Statistics
Matches: 75, Mismatches: 28, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
11 1 0.01
12 72 0.96
13 2 0.03
ACGTcount: A:0.10, C:0.09, G:0.57, T:0.23
Consensus pattern (12 bp):
GGTGGTGGTGCT
Found at i:52879205 original size:24 final size:24
Alignment explanation
Indices: 52879172--52879281 Score: 87
Period size: 24 Copynumber: 4.6 Consensus size: 24
52879162 AGCAGGTGGT
*
52879172 GGTGCCGGTGGTGGCGCTGGAGGC
1 GGTGCTGGTGGTGGCGCTGGAGGC
*** *
52879196 GGTGCTGGTGGTGGTTTTGGAGGT
1 GGTGCTGGTGGTGGCGCTGGAGGC
**** * * *
52879220 GGAAAAGGTGGAGG-GATAGGAGGT
1 GGTGCTGGTGGTGGCGCT-GGAGGC
*
52879244 GGAGCTGGTGGTGGCGCTGGAGGC
1 GGTGCTGGTGGTGGCGCTGGAGGC
52879268 GGTGCTGGTGGTGG
1 GGTGCTGGTGGTGG
52879282 TTTTGGAGGT
Statistics
Matches: 65, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
23 1 0.02
24 62 0.95
25 2 0.03
ACGTcount: A:0.11, C:0.10, G:0.57, T:0.22
Consensus pattern (24 bp):
GGTGCTGGTGGTGGCGCTGGAGGC
Found at i:52879301 original size:24 final size:24
Alignment explanation
Indices: 52879202--52879302 Score: 67
Period size: 24 Copynumber: 4.2 Consensus size: 24
52879192 AGGCGGTGCT
52879202 GGTGGTGGTTTTGGAGGTGGAAAA
1 GGTGGTGGTTTTGGAGGTGGAAAA
* ** * ***
52879226 GGTGGAGGGATAGGAGGTGGAGCT
1 GGTGGTGGTTTTGGAGGTGGAAAA
*** * ****
52879250 GGTGGTGGCGCTGGAGGCGGTGCT
1 GGTGGTGGTTTTGGAGGTGGAAAA
52879274 GGTGGTGGTTTTGGAGGTGGAAAA
1 GGTGGTGGTTTTGGAGGTGGAAAA
52879298 GGTGG
1 GGTGG
52879303 AGGGATAGGA
Statistics
Matches: 55, Mismatches: 22, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.16, C:0.05, G:0.55, T:0.24
Consensus pattern (24 bp):
GGTGGTGGTTTTGGAGGTGGAAAA
Found at i:52879392 original size:48 final size:48
Alignment explanation
Indices: 52879340--52879455 Score: 160
Period size: 48 Copynumber: 2.4 Consensus size: 48
52879330 TGGTGGCGCT
* *
52879340 GGAGGGGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGTGGAGGGATA
1 GGAGGTGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGCGGAGGGATA
* * * *
52879388 GGAGGTGGTGCTGGCGGTGGTTTTGGAGGTGGACAAGGCGGAGGTATA
1 GGAGGTGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGCGGAGGGATA
* *
52879436 GGAGGTGGAGTTGGTGGTGG
1 GGAGGTGGTGCTGGTGGTGG
52879456 AGGAGGTGCT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.16, C:0.05, G:0.56, T:0.22
Consensus pattern (48 bp):
GGAGGTGGTGCTGGTGGTGGCTTTGGAGGTGGAAAAGGCGGAGGGATA
Found at i:52879392 original size:78 final size:77
Alignment explanation
Indices: 52879139--52879395 Score: 389
Period size: 78 Copynumber: 3.4 Consensus size: 77
52879129 TGGAGCTGGT
* ** *
52879139 GGTGGAAAAGGTGGAGGCATAGGAGCAGGTGGTGGTGCCGGTGGTGGCGCTGGAGGCGGTGCTGG
1 GGTGGAAAAGGTGGAGGGATAGGAGGTGG-GGTGGTGCTGGTGGTGGCGCTGGAGGCGGTGCTGG
52879204 TGGTGGTTTTGGA
65 TGGTGGTTTTGGA
*
52879217 GGTGGAAAAGGTGGAGGGATAGGA-----GGTGGAGCTGGTGGTGGCGCTGGAGGCGGTGCTGGT
1 GGTGGAAAAGGTGGAGGGATAGGAGGTGGGGTGGTGCTGGTGGTGGCGCTGGAGGCGGTGCTGGT
52879277 GGTGGTTTTGGA
66 GGTGGTTTTGGA
* *
52879289 GGTGGAAAAGGTGGAGGGATAGGAGGTGGGGTTGGTGGTGGTGGTGGCGCTGGAGGGGGTGCTGG
1 GGTGGAAAAGGTGGAGGGATAGGAGGTGGGG-TGGTGCTGGTGGTGGCGCTGGAGGCGGTGCTGG
*
52879354 TGGTGGCTTTGGA
65 TGGTGGTTTTGGA
52879367 GGTGGAAAAGGTGGAGGGATAGGAGGTGG
1 GGTGGAAAAGGTGGAGGGATAGGAGGTGG
52879396 TGCTGGCGGT
Statistics
Matches: 166, Mismatches: 7, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
72 70 0.42
77 2 0.01
78 94 0.57
ACGTcount: A:0.16, C:0.07, G:0.56, T:0.21
Consensus pattern (77 bp):
GGTGGAAAAGGTGGAGGGATAGGAGGTGGGGTGGTGCTGGTGGTGGCGCTGGAGGCGGTGCTGGT
GGTGGTTTTGGA
Found at i:52879460 original size:15 final size:15
Alignment explanation
Indices: 52879450--52879504 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
52879440 GTGGAGTTGG
52879450 TGGTGGAGGAGGTGC
1 TGGTGGAGGAGGTGC
* *
52879465 TGGTGGTGGCGGTGGC
1 TGGTGGAGGAGGT-GC
* *
52879481 T-TTGGAGGTGGTGC
1 TGGTGGAGGAGGTGC
52879495 TGGTGGAGGA
1 TGGTGGAGGA
52879505 ATTGGAGGGG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
14 3 0.10
15 25 0.81
16 3 0.10
ACGTcount: A:0.09, C:0.07, G:0.58, T:0.25
Consensus pattern (15 bp):
TGGTGGAGGAGGTGC
Found at i:52879473 original size:30 final size:30
Alignment explanation
Indices: 52879439--52879509 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
52879429 AGGTATAGGA
52879439 GGTGGAGTTGG-TGGTGGAGGAGGTGCTGGT
1 GGTGGAGTTGGCT-GTGGAGGAGGTGCTGGT
* * * *
52879469 GGTGGCGGTGGCTTTGGAGGTGGTGCTGGT
1 GGTGGAGTTGGCTGTGGAGGAGGTGCTGGT
* *
52879499 GGAGGAATTGG
1 GGTGGAGTTGG
52879510 AGGGGGATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.10, C:0.06, G:0.58, T:0.27
Consensus pattern (30 bp):
GGTGGAGTTGGCTGTGGAGGAGGTGCTGGT
Found at i:52880054 original size:20 final size:18
Alignment explanation
Indices: 52880017--52880056 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
52880007 ACCTAAATAC
*
52880017 AATTATAATTTAATTTAA
1 AATTATAATTCAATTTAA
52880035 AATTATTAATTCACATTTAA
1 AATTA-TAATTCA-ATTTAA
52880055 AA
1 AA
52880057 CTAATCATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 6 0.32
20 8 0.42
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTATAATTCAATTTAA
Found at i:52882932 original size:14 final size:13
Alignment explanation
Indices: 52882899--52882939 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
52882889 GTTACATATA
52882899 ATTATAATTATTT
1 ATTATAATTATTT
52882912 ATTATAATTATGTT
1 ATTATAATTAT-TT
* *
52882926 TTTATAATTTTTT
1 ATTATAATTATTT
52882939 A
1 A
52882940 GGTAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
ATTATAATTATTT
Found at i:52885188 original size:24 final size:24
Alignment explanation
Indices: 52885139--52885197 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
52885129 TATTGATGAT
*
52885139 AAATCTAAAAATAATATTAAACTTA
1 AAAT-TAAATATAATATTAAACTTA
* *
52885164 AACA-TAAATATAATATTAGATTTA
1 AA-ATTAAATATAATATTAAACTTA
52885188 AAATTAAATA
1 AAATTAAATA
52885198 AAAATAGAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 1 0.03
24 25 0.86
25 2 0.07
26 1 0.03
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (24 bp):
AAATTAAATATAATATTAAACTTA
Found at i:52886097 original size:23 final size:23
Alignment explanation
Indices: 52886020--52886097 Score: 58
Period size: 23 Copynumber: 3.3 Consensus size: 23
52886010 AATTTATTAT
*
52886020 AAATTGAAATAATATT-GA-TGA
1 AAATTAAAATAATATTAGATTGA
52886041 TAAATCTAAAAATAATATTTA-ACTT-A
1 -AAAT-T-AAAATAATA-TTAGA-TTGA
52886067 AACA-TAAAATAATATTAGATTGA
1 AA-ATTAAAATAATATTAGATTGA
52886090 AAATTAAA
1 AAATTAAA
52886098 TAAAAAATGG
Statistics
Matches: 45, Mismatches: 1, Indels: 19
0.69 0.02 0.29
Matches are distributed among these distances:
22 10 0.22
23 18 0.40
24 9 0.20
25 5 0.11
26 2 0.04
27 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.33
Consensus pattern (23 bp):
AAATTAAAATAATATTAGATTGA
Found at i:52887331 original size:18 final size:18
Alignment explanation
Indices: 52887287--52887325 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
52887277 AAAAATGGAC
*
52887287 TTTATTTTTATCTTATTG
1 TTTAGTTTTATCTTATTG
* *
52887305 TTTAGTTTTATTTTTTTG
1 TTTAGTTTTATCTTATTG
52887323 TTT
1 TTT
52887326 GCTTTTGGGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.03, G:0.08, T:0.77
Consensus pattern (18 bp):
TTTAGTTTTATCTTATTG
Found at i:52887857 original size:44 final size:44
Alignment explanation
Indices: 52887802--52888039 Score: 126
Period size: 44 Copynumber: 5.4 Consensus size: 44
52887792 TGCTCGACTG
*
52887802 CAACTTCAGGGAGATAAGACTT-GTAACTTCAATCC-ACTCCACTA
1 CAACTTTAGGGAGATAAGA-TTAGTAACTTCAA-CCTACTCCACTA
* ** * *
52887846 CAACTTTAGGGAGATAGGATTAGTGGCTTTAACCTACTCCACTG
1 CAACTTTAGGGAGATAAGATTAGTAACTTCAACCTACTCCACTA
* * * * ** * * *
52887890 CAACTTTAGGGAGATACGATTCGCCATCTTCAGTCTGCCCCACTG
1 CAACTTTAGGGAGATAAGATTAG-TAACTTCAACCTACTCCACTA
* ** * * * *
52887935 CAACTTCAGGG-GATAAGACTT-GTGGCCTCAATCTGCCCCACTA
1 CAACTTTAGGGAGATAAGA-TTAGTAACTTCAACCTACTCCACTA
* * * * * * *
52887978 AAACTTCAAGGG-GATAAGATTGGTATCTTCAACTTGCTCCACTG
1 CAACTT-TAGGGAGATAAGATTAGTAACTTCAACCTACTCCACTA
*
52888022 CAACTTCAGGGAGATAAG
1 CAACTTTAGGGAGATAAG
52888040 GTACGCTAAC
Statistics
Matches: 152, Mismatches: 35, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
43 30 0.20
44 97 0.64
45 25 0.16
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (44 bp):
CAACTTTAGGGAGATAAGATTAGTAACTTCAACCTACTCCACTA
Found at i:52888020 original size:132 final size:133
Alignment explanation
Indices: 52887755--52888082 Score: 354
Period size: 132 Copynumber: 2.5 Consensus size: 133
52887745 TCTGTTTTAT
* * ** ** *
52887755 TGCAACTTCAAGGAAATAAGATTTGTTATCTTCAGTCTGCTCGACTGCAACTTCAGGGAGATAAG
1 TGCAACTTCAGGGAGATAAGATACGCCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
* * * * * * *
52887820 ACTTGTAACTTCAATCCACTCCACTACAACTTTAGGGAGATAGGATTAGTGGCTTTAACCTACTC
66 ACTTGTAACCTCAATCCACCCCACTAAAACTTAAGGGAGATAAGATTAGTAGCTTCAACCTACTC
52887885 CAC
131 CAC
* * * *
52887888 TGCAACTTTAGGGAGATACGATTCGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGG-GATAAG
1 TGCAACTTCAGGGAGATAAGATACGCCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
** ** * * * *
52887952 ACTTGTGGCCTCAATCTGCCCCACTAAAACTTCAAGGG-GATAAGATTGGTATCTTCAACTTGCT
66 ACTTGTAACCTCAATCCACCCCACTAAAACTT-AAGGGAGATAAGATTAGTAGCTTCAACCTACT
52888016 CCAC
130 CCAC
* * * * *
52888020 TGCAACTTCAGGGAGATAAGGTACGCTAACTTCAGTCTGCTCCACTGCAGCTTCAAGGAGATA
1 TGCAACTTCAGGGAGATAAGATACGCCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATA
52888083 GGATCATTGA
Statistics
Matches: 160, Mismatches: 33, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
132 103 0.64
133 57 0.36
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (133 bp):
TGCAACTTCAGGGAGATAAGATACGCCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
ACTTGTAACCTCAATCCACCCCACTAAAACTTAAGGGAGATAAGATTAGTAGCTTCAACCTACTC
CAC
Found at i:52890256 original size:41 final size:40
Alignment explanation
Indices: 52890157--52890258 Score: 114
Period size: 41 Copynumber: 2.5 Consensus size: 40
52890147 ATATCAGTGA
* * * *
52890157 TTATCGGGCTTCGTGCCTAGCAGGCCTTGTGCCGGTGTGAT
1 TTATCAGGCTT-GAGCCTAGCAGGCCTAGTGCCGGTGAGAT
* * *
52890198 ATATCAGGCTATAAGCCTAGCAGGCCTAGTGCCGGTGAGTTT
1 TTATCAGGCT-TGAGCCTAGCAGGCCTAGTGCCGGTGAG-AT
52890240 TTATCAGGCTTGAGCCTAG
1 TTATCAGGCTTGAGCCTAG
52890259 TAGGTTTTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
41 39 0.78
42 11 0.22
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.29
Consensus pattern (40 bp):
TTATCAGGCTTGAGCCTAGCAGGCCTAGTGCCGGTGAGAT
Found at i:52890777 original size:15 final size:15
Alignment explanation
Indices: 52890752--52890792 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
52890742 GATTAGCTAA
52890752 ATTATATAAATTTATT
1 ATTA-ATAAATTTATT
52890768 ATTAATAAATTTATT
1 ATTAATAAATTTATT
*
52890783 ATTATTAAAT
1 ATTAATAAAT
52890793 CATTTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTAATAAATTTATT
Found at i:52892659 original size:42 final size:43
Alignment explanation
Indices: 52892612--52892692 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 43
52892602 GTATAGCAAG
52892612 ATCACCACATGCCCCAATCAGAT-CAAAATTTGAGCTGCTCTA
1 ATCACCACATGCCCCAATCAGATCCAAAATTTGAGCTGCTCTA
** * * *
52892654 ATCACCTTATGTCCCATTCTGATCCAAAATTTGAGCTGC
1 ATCACCACATGCCCCAATCAGATCCAAAATTTGAGCTGC
52892693 CCTTTTCGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
42 18 0.55
43 15 0.45
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (43 bp):
ATCACCACATGCCCCAATCAGATCCAAAATTTGAGCTGCTCTA
Found at i:52893862 original size:9 final size:10
Alignment explanation
Indices: 52893844--52893884 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
52893834 TTCCTTTTCC
*
52893844 TTTTCTTTTT
1 TTTTCATTTT
52893854 TTTTC-TTTT
1 TTTTCATTTT
*
52893863 TTTTCA-TTA
1 TTTTCATTTT
52893872 TTTTCATTTT
1 TTTTCATTTT
52893882 TTT
1 TTT
52893885 GAAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 17 0.63
10 10 0.37
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTCATTTT
Found at i:52893898 original size:26 final size:27
Alignment explanation
Indices: 52893869--52893922 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
52893859 TTTTTTTTCA
52893869 TTATTTTCA-TTTTTTTGAAATATTTT
1 TTATTTTCATTTTTTTTGAAATATTTT
*
52893895 TTATTTTGATTTTTTTTGAAATATTTT
1 TTATTTTCATTTTTTTTGAAATATTTT
52893922 T
1 T
52893923 GATTGGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (27 bp):
TTATTTTCATTTTTTTTGAAATATTTT
Found at i:52893931 original size:26 final size:27
Alignment explanation
Indices: 52893878--52893932 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
52893868 ATTATTTTCA
* *
52893878 TTTTTTTGAAATATTTTTTATTTTGAT
1 TTTTTTTGAAATATTTTTGATTTGGAT
52893905 TTTTTTTGAAATATTTTTGA-TTGGAT
1 TTTTTTTGAAATATTTTTGATTTGGAT
52893931 TT
1 TT
52893933 GAACTCATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (27 bp):
TTTTTTTGAAATATTTTTGATTTGGAT
Found at i:52899161 original size:23 final size:23
Alignment explanation
Indices: 52899066--52899161 Score: 67
Period size: 23 Copynumber: 4.1 Consensus size: 23
52899056 TGTAACATAC
* *
52899066 AAAATAATAATATATTATAAATT
1 AAAATAATATTAGATTATAAATT
* *
52899089 GAAATAATATT-GATGATAAATCT
1 AAAATAATATTAGATTATAAAT-T
52899112 AAAAATAATATTTA-ACTTA-AACA-T
1 -AAAATAATA-TTAGA-TTATAA-ATT
52899136 AAAATAATATTAGATTGA-AAATT
1 AAAATAATATTAGATT-ATAAATT
52899159 AAA
1 AAA
52899162 TAAAAAATGG
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
22 14 0.24
23 27 0.47
24 9 0.16
25 5 0.09
26 3 0.05
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (23 bp):
AAAATAATATTAGATTATAAATT
Found at i:52900582 original size:8 final size:8
Alignment explanation
Indices: 52900558--52900589 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
52900548 TCAATTTTGG
52900558 ATTTCAAA
1 ATTTCAAA
52900566 A-TT-AAA
1 ATTTCAAA
52900572 ATTTCAAA
1 ATTTCAAA
52900580 ATTTCAAA
1 ATTTCAAA
52900588 AT
1 AT
52900590 CCAAGATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 4 0.18
7 4 0.18
8 14 0.64
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (8 bp):
ATTTCAAA
Found at i:52901530 original size:6 final size:7
Alignment explanation
Indices: 52901476--52901544 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
52901466 TTAATTCTCA
52901476 AAAAATTT
1 AAAAA-TT
52901484 AAAAA-T
1 AAAAATT
52901490 AATAAATT
1 AA-AAATT
*
52901498 CATAAATT
1 -AAAAATT
**
52901506 GTAAATT
1 AAAAATT
52901513 AAAAATT
1 AAAAATT
52901520 AAAAATT
1 AAAAATT
*
52901527 AAAATTT
1 AAAAATT
*
52901534 TAAAATGT
1 AAAAAT-T
52901542 AAA
1 AAA
52901545 TCCAAATTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 3 0.06
7 31 0.63
8 14 0.29
9 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (7 bp):
AAAAATT
Found at i:52902693 original size:27 final size:28
Alignment explanation
Indices: 52902657--52902709 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
52902647 CCCTTACTTT
* *
52902657 AAATATTTTAATAATTAAATTTTATTTA
1 AAATATTTTAAAAACTAAATTTTATTTA
52902685 AAATA-TTTAAAAACTAAATTTTATT
1 AAATATTTTAAAAACTAAATTTTATT
52902710 AATTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
AAATATTTTAAAAACTAAATTTTATTTA
Found at i:52905904 original size:28 final size:28
Alignment explanation
Indices: 52905873--52905929 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
52905863 GATTAATAAG
52905873 TACAAATGAGCAATACCAAACACATGAA
1 TACAAATGAGCAATACCAAACACATGAA
52905901 TACAAATGAGCAATACCAAACACATGAA
1 TACAAATGAGCAATACCAAACACATGAA
52905929 T
1 T
52905930 CCTATGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.16
Consensus pattern (28 bp):
TACAAATGAGCAATACCAAACACATGAA
Found at i:52906211 original size:24 final size:24
Alignment explanation
Indices: 52906170--52906229 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
52906160 TAAGTGAAAA
*
52906170 AATAATAATATAGT-ATAACTTTTA-
1 AATAATAATACA-TAATAAC-TTTAG
*
52906194 AGTAATAATACATAATAACTTTAG
1 AATAATAATACATAATAACTTTAG
52906218 AATAATAATACA
1 AATAATAATACA
52906230 CAATGATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (24 bp):
AATAATAATACATAATAACTTTAG
Found at i:52906339 original size:3 final size:3
Alignment explanation
Indices: 52906331--52906381 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
52906321 ATAGTACATA
52906331 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52906379 AAT
1 AAT
52906382 TAAATGGTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.