Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 25 of 56
Found at i:4330482 original size:2 final size:2
Alignment explanation
Indices: 4330475--4330499 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4330465 ATACTTTTTG
4330475 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4330500 GAGAATATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4331157 original size:13 final size:13
Alignment explanation
Indices: 4331139--4331164 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4331129 CATTATTCAA
4331139 TGTATCGATACAT
1 TGTATCGATACAT
4331152 TGTATCGATACAT
1 TGTATCGATACAT
4331165 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4331248 original size:25 final size:25
Alignment explanation
Indices: 4331203--4331252 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
4331193 TTTACCCAGA
*
4331203 TGTATCGATACATTTTGCATTGTAT
1 TGTATCGATACATTCTGCATTGTAT
4331228 TGTATCGATACATTGCT-CATTGTAT
1 TGTATCGATACATT-CTGCATTGTAT
4331253 CGACATTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (25 bp):
TGTATCGATACATTCTGCATTGTAT
Found at i:4331251 original size:20 final size:20
Alignment explanation
Indices: 4331226--4331299 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
4331216 TTTGCATTGT
4331226 ATTGTATCGATACATTGCTC
1 ATTGTATCGATACATTGCTC
4331246 ATTGTATCG--ACATTGCTC
1 ATTGTATCGATACATTGCTC
*
4331264 ATTGTATCGATACATT-TTAC
1 ATTGTATCGATACATTGCT-C
*
4331284 AATGTATCGATACATT
1 ATTGTATCGATACATT
4331300 CAGGCATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
18 18 0.37
19 1 0.02
20 30 0.61
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (20 bp):
ATTGTATCGATACATTGCTC
Found at i:4331258 original size:18 final size:18
Alignment explanation
Indices: 4331226--4331273 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
4331216 TTTGCATTGT
4331226 ATTGTATCGATACATTGCTC
1 ATTGTATCG--ACATTGCTC
4331246 ATTGTATCGACATTGCTC
1 ATTGTATCGACATTGCTC
4331264 ATTGTATCGA
1 ATTGTATCGA
4331274 TACATTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 19 0.68
20 9 0.32
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (18 bp):
ATTGTATCGACATTGCTC
Found at i:4332661 original size:51 final size:50
Alignment explanation
Indices: 4332497--4332673 Score: 196
Period size: 51 Copynumber: 3.5 Consensus size: 50
4332487 ATTTTTTGAT
* * * *
4332497 TTTTCAT-CTCGGGGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAA
1 TTTTCATAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACCAA
* * * *
4332546 TTTCTCTTAATCAGGGATACTCCAACTCCGATTTTATTTCTAAAACACCCA
1 TTT-TCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAA
*
4332597 TTTTCCATTATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAA
1 TTTT-CATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAA
** *
4332648 CTTTTCACGATCGGGGTTACTCCAAC
1 -TTTTCATAATCGGGGATACTCCAAC
4332674 CCCGTTATTT
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
49 3 0.03
50 4 0.04
51 95 0.89
52 5 0.05
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.33
Consensus pattern (50 bp):
TTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAA
Found at i:4332778 original size:76 final size:75
Alignment explanation
Indices: 4332610--4332879 Score: 342
Period size: 76 Copynumber: 3.5 Consensus size: 75
4332600 TCCATTATCG
* * * * *
4332610 GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAACTTTTCACGATCGGGGTTACTCCAACC
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAA-TTTT-TC-ATCGGGGATACTCCAACC
*
4332675 CCGTTATTTCTGAA
63 CCGTTATTTCCG-A
* * *
4332689 GGGACACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGAGGATACTCCAACCCCG
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATCGGGGATACTCCAACCCCG
4332754 TTATTTCCGA
66 TTATTTCCGA
* * *
4332764 TGAGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACCGGGGATACTCCAACCCC
1 -GGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATCGGGGATACTCCAACCCC
*
4332829 GTTATTTTCGA
65 GTTATTTCCGA
* * * *
4332840 GGGATATTCTAACCTCAGTTTTATTTCTAAAACACCAATT
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATT
4332880 CTCCACAATC
Statistics
Matches: 170, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
75 35 0.21
76 97 0.57
77 1 0.01
78 4 0.02
79 33 0.19
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.32
Consensus pattern (75 bp):
GGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATCGGGGATACTCCAACCCCG
TTATTTCCGA
Found at i:4332916 original size:51 final size:51
Alignment explanation
Indices: 4332840--4332955 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
4332830 TTATTTTCGA
*
4332840 GGGATATTCTAACCTCAGTTTTA-TTTCTAAAACACCAATTCTCCACAATCG
1 GGGATATTCCAACCTCAGTTTTATTTTC-AAAACACCAATTCTCCACAATCG
* * * *
4332891 GGGATATTCCAA-CTCTGATTTTATTTTCAAAACACTAATTTTTCACAATCG
1 GGGATATTCCAACCTCAG-TTTTATTTTCAAAACACCAATTCTCCACAATCG
*
4332942 GGGATACTCCAACC
1 GGGATATTCCAACC
4332956 CCGTTATTTC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 4 0.07
51 47 0.84
52 5 0.09
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (51 bp):
GGGATATTCCAACCTCAGTTTTATTTTCAAAACACCAATTCTCCACAATCG
Found at i:4333008 original size:157 final size:156
Alignment explanation
Indices: 4332804--4333143 Score: 366
Period size: 157 Copynumber: 2.2 Consensus size: 156
4332794 AAACATCAAT
* * * * *
4332804 TTTTCACCGGGGATACTCCAACCCCGTTATTTTCGAGGGATATTCTAACCTCAGTTTTA-TTTCT
1 TTTTCA-C-GGGATACTCCAACCCTGTTATTTCCGAGGGATACTCTAACCCCAGCTTTATTTTC-
* * * **
4332868 AAAACACCAA-TTCTCCACAATCGGGGATA-TTCCAACTCTGATTTTATTT-TCAAAACACTAAT
63 AAAACACCAATTTCT-CACAATCAGGGATACTT-CAACCCCGACCTTATTTCT-AAAACACTAAT
*
4332930 TTTTCACAATCGGGGATACTCCAACCCCGTTA
125 TTTTCACAATCGGGGATACTCCAACCCCATTA
4332962 -TTTCATCGGGATACTCCAACCCTGTTATTTCCGAAGGGATACTCTAACCCCAGCTTTATTTTCA
1 TTTTCA-CGGGATACTCCAACCCTGTTATTTCCG-AGGGATACTCTAACCCCAGCTTTATTTTCA
* *** * * * *
4333026 AAATATTGATTTCTCACAATCAGGGATACTTCAACCCCGGCCTTATTTCTAAAATATTGATTTTT
64 AAACACCAATTTCTCACAATCAGGGATACTTCAACCCCGACCTTATTTCTAAAACACTAATTTTT
* *
4333091 CATAATTGGGGATACTCCAACCCCATTA
129 CACAATCGGGGATACTCCAACCCCATTA
*
4333119 TTTTCACGGAGATACTCCAATCCTG
1 TTTTCACGG-GATACTCCAACCCTG
4333144 ATTTTATTTT
Statistics
Matches: 152, Mismatches: 23, Indels: 14
0.80 0.12 0.07
Matches are distributed among these distances:
156 24 0.16
157 98 0.64
158 30 0.20
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (156 bp):
TTTTCACGGGATACTCCAACCCTGTTATTTCCGAGGGATACTCTAACCCCAGCTTTATTTTCAAA
ACACCAATTTCTCACAATCAGGGATACTTCAACCCCGACCTTATTTCTAAAACACTAATTTTTCA
CAATCGGGGATACTCCAACCCCATTA
Found at i:4333010 original size:28 final size:27
Alignment explanation
Indices: 4332942--4333012 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
4332932 TTCACAATCG
*
4332942 GGGATACTCCAACCCCGTTATTTCATC
1 GGGATACTCCAACCCCGTTATTTCATA
*
4332969 GGGATACTCCAACCCTGTTATTTCCGA-A
1 GGGATACTCCAACCCCGTTATTT-C-ATA
*
4332997 GGGATACTCTAACCCC
1 GGGATACTCCAACCCC
4333013 AGCTTTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 22 0.58
28 15 0.39
29 1 0.03
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (27 bp):
GGGATACTCCAACCCCGTTATTTCATA
Found at i:4333062 original size:51 final size:51
Alignment explanation
Indices: 4332996--4333115 Score: 145
Period size: 51 Copynumber: 2.4 Consensus size: 51
4332986 TTATTTCCGA
*
4332996 AGGGATAC-TCTAACCCCAGCTTTATTT-TCAAAATATTGATTTCTCACAATC
1 AGGGATACTTC-AACCCCAGCCTTATTTCT-AAAATATTGATTTCTCACAATC
* * * *
4333047 AGGGATACTTCAACCCCGGCCTTATTTCTAAAATATTGATTTTTCATAATT
1 AGGGATACTTCAACCCCAGCCTTATTTCTAAAATATTGATTTCTCACAATC
* *
4333098 GGGGATACTCCAACCCCA
1 AGGGATACTTCAACCCCA
4333116 TTATTTTCAC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
51 56 0.95
52 3 0.05
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (51 bp):
AGGGATACTTCAACCCCAGCCTTATTTCTAAAATATTGATTTCTCACAATC
Found at i:4333299 original size:129 final size:126
Alignment explanation
Indices: 4332966--4333301 Score: 311
Period size: 129 Copynumber: 2.6 Consensus size: 126
4332956 CCGTTATTTC
* * * * *
4332966 ATCGGGATACTCCAACCCTGTTATTTCCGAAGGGATACTCTAACCCCAGCTTTATTTTCAAAATA
1 ATCGGGATACTCCAACCC-GTTATTTTCGAGGGGATACTCCAA-CCCTGTTTTATTTTCAAAATA
* * * *
4333031 TTGATTTCTCACAATCAGGGATACTTCAACCCCGGCCTTATTTCTAAAATATTGATTTTTCATA
64 TT-ATTTCTCACAATCAGGGACACTTCAACCCCGGCCCTATTTCTAAAATATCGATTTTTCACA
* * * * **
4333095 ATTGGGGATACTCCAACCCCATTATTTTC-ACGGAGATACTCCAATCCTGATTTTATTTTTGAAA
1 A-TCGGGATACTCCAA-CCCGTTATTTTCGA-GGGGATACTCCAACCCTG-TTTTATTTTCAAAA
* * * **
4333159 CATCTATTT-TCTATAAT-GGGGACACTTCAACCCTTGCCCTATTTCT-AAATCATCGATTTTTC
62 TAT-TATTTCTC-ACAATCAGGGACACTTCAACCCCGGCCCTATTTCTAAAAT-ATCGATTTTTC
4333221 ACA
124 ACA
* *
4333224 ATCGGAGATACTCCAATCCCGTTATTTTCGAGGGGATACTCCAACCCTGTTATTATCTCCAAAAT
1 ATCGG-GATACTCCAA-CCCGTTATTTTCGAGGGGATACTCCAACCCTGTT-TTATTTTCAAAAT
4333289 ATTAAGTTTCTCA
63 ATT-A-TTTCTCA
4333302 TCGGGAGATG
Statistics
Matches: 164, Mismatches: 30, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
128 10 0.06
129 92 0.56
130 56 0.34
131 6 0.04
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (126 bp):
ATCGGGATACTCCAACCCGTTATTTTCGAGGGGATACTCCAACCCTGTTTTATTTTCAAAATATT
ATTTCTCACAATCAGGGACACTTCAACCCCGGCCCTATTTCTAAAATATCGATTTTTCACA
Found at i:4338920 original size:6 final size:6
Alignment explanation
Indices: 4338895--4338941 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
4338885 TAGTAATAAG
* *
4338895 TAAAAA TTAAAAA TTAAAAA TAAAAA -AATAA TAATAA TAAAAA TAAA
1 TAAAAA -TAAAAA -TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAA
4338942 TGCATAGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 4 0.11
6 20 0.54
7 13 0.35
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
TAAAAA
Found at i:4338939 original size:15 final size:15
Alignment explanation
Indices: 4338902--4338941 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4338892 AAGTAAAAAT
4338902 TAAAAATTAAAAATAA
1 TAAAAA-TAAAAATAA
*
4338918 -AAAAATAATAATAA
1 TAAAAATAAAAATAA
4338932 TAAAAATAAA
1 TAAAAATAAA
4338942 TGCATAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAAATAAAAATAA
Found at i:4338972 original size:35 final size:35
Alignment explanation
Indices: 4338931--4339203 Score: 433
Period size: 35 Copynumber: 7.9 Consensus size: 35
4338921 AATAATAATA
* * * **
4338931 ATAAAAATAAATGCATAGAATGATGGGCATAAAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
* * *
4338966 ATAAAAATAAAGGTATGGAATGATGGGCATGAAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
4339001 ATAAAAATGAAGGCATGGAATGATAGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
4339036 ATAAAAATAAAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
4339071 ATAAAAATGAAGGCATGGAATGATGGGCATGG-A-
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
4339104 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
4339139 ATAAAAATGGAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
4339174 ATAAAAATGAAGGCATGGAATGATGGGCAT
1 ATAAAAATGAAGGCATGGAATGATGGGCAT
4339204 AAAAAATGAA
Statistics
Matches: 223, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
33 32 0.14
34 2 0.01
35 189 0.85
ACGTcount: A:0.45, C:0.05, G:0.29, T:0.21
Consensus pattern (35 bp):
ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
Found at i:4339030 original size:14 final size:13
Alignment explanation
Indices: 4339006--4339035 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
4338996 GAAATATAAA
4339006 AATGAAGGCATGG
1 AATGAAGGCATGG
4339019 AATGATAGGCATGG
1 AATGA-AGGCATGG
4339033 AAT
1 AAT
4339036 ATAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (13 bp):
AATGAAGGCATGG
Found at i:4339101 original size:14 final size:14
Alignment explanation
Indices: 4339082--4339138 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4339072 TAAAAATGAA
4339082 GGCATGGAATGATG
1 GGCATGGAATGATG
*
4339096 GGCATGGAATAAAAATG
1 GGCATGGAAT---GATG
4339113 AAGGCATGGAATGATG
1 --GGCATGGAATGATG
4339129 GGCATGGAAT
1 GGCATGGAAT
4339139 ATAAAAATGG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.37, C:0.07, G:0.37, T:0.19
Consensus pattern (14 bp):
GGCATGGAATGATG
Found at i:4339153 original size:103 final size:105
Alignment explanation
Indices: 4338931--4339203 Score: 442
Period size: 103 Copynumber: 2.6 Consensus size: 105
4338921 AATAATAATA
* * ** * *
4338931 ATAAAAATAAATGCATAGAATGATGGGCATAAAATATAAAAATAAAGGTATGGAATGATGGGCAT
1 ATAAAAATAAAGGCATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCAT
4338996 GAAATATAAAAATGAAGGCATGGAATGATAGGCATGGAAT
66 GAAATATAAAAATGAAGGCATGGAATGATAGGCATGGAAT
4339036 ATAAAAATAAAGGCATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCAT
1 ATAAAAATAAAGGCATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCAT
* *
4339101 G-GA-ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
66 GAAATATAAAAATGAAGGCATGGAATGATAGGCATGGAAT
**
4339139 ATAAAAATGGAGGCATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCAT
1 ATAAAAATAAAGGCATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCAT
4339204 AAAAAATGAA
Statistics
Matches: 158, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
103 97 0.61
104 1 0.01
105 60 0.38
ACGTcount: A:0.45, C:0.05, G:0.29, T:0.21
Consensus pattern (105 bp):
ATAAAAATAAAGGCATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCAT
GAAATATAAAAATGAAGGCATGGAATGATAGGCATGGAAT
Found at i:4340736 original size:79 final size:79
Alignment explanation
Indices: 4340605--4341194 Score: 885
Period size: 79 Copynumber: 7.4 Consensus size: 79
4340595 TTTAATTTTC
* **
4340605 TCAATTTTTCACAATCAAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
4340670 TTATCTCTAAAACA
66 TTATCTCTAAAACA
*
4340684 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
4340749 TTATCTCTAAAACA
66 TTATCTCTAAAACA
* * *
4340763 TCAATTTTTTATAATCGGGGATATTCCAACCCCGTTATTTCCGAGAGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
4340828 TTATCTCTAAAACA
66 TTATCTCTAAAACA
* * * *
4340842 TCAATTTTTCATAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCTAACCTCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
4340907 TTATCTCTAAAACA
66 TTATCTCTAAAACA
* *
4340921 TCAATTTTTCATAATCGAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGAT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
4340986 TTATCTCTAAAACA
66 TTATCTCTAAAACA
* * * *
4341000 TCAATTTTTCATAATCGGGGATACTCCAACCCTGTTATTTCCGAGGAGATACTTCAACCCCGATT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
4341065 TTATTTCTAAAACA
66 TTATCTCTAAAACA
* * * *
4341079 TCAATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTC-ATGGGGATACTCCAACCCTGGC
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGA-GGGGATACTCCAACCCCGG-
** * *
4341143 CCTTATTTCTAAAGCA
64 TTTTATCTCTAAAACA
* *
4341159 TCAATTTTTTTTATAATCGGGGATACTCTAACCCCG
1 TCAA--TTTTTCATAATCGGGGATACTCCAACCCCG
4341195 ATTTTATTTT
Statistics
Matches: 464, Mismatches: 43, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
78 1 0.00
79 420 0.91
80 17 0.04
82 26 0.06
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (79 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
TTATCTCTAAAACA
Found at i:4343587 original size:38 final size:38
Alignment explanation
Indices: 4343545--4343676 Score: 151
Period size: 38 Copynumber: 3.5 Consensus size: 38
4343535 AAAAAACCAT
* * *
4343545 TATTTTAAACCGGTGACATGGTTCGAAACGAAAATTAC
1 TATTTTAAACCGGTGGCACGATTCGAAACGAAAATTAC
* *
4343583 TATTTTAGACCGGTGGCACGATTCGAAACGAAAACTAC
1 TATTTTAAACCGGTGGCACGATTCGAAACGAAAATTAC
* * * *
4343621 TATTTTTATCCGGTGGCACGATTC-AATACAAAAATCAC
1 TATTTTAAACCGGTGGCACGATTCGAA-ACGAAAATTAC
4343659 TATTCTT-AACCGGTGGCA
1 TATT-TTAAACCGGTGGCA
4343677 TAGTTTGAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
37 2 0.03
38 76 0.95
39 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (38 bp):
TATTTTAAACCGGTGGCACGATTCGAAACGAAAATTAC
Found at i:4346196 original size:23 final size:23
Alignment explanation
Indices: 4346170--4346226 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
4346160 TGGACATGTT
4346170 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
4346193 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
4346216 AAAAATGCATG
1 AAAAATGCATG
4346227 GTCAAAGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:4347181 original size:20 final size:19
Alignment explanation
Indices: 4347131--4347208 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
4347121 GGTAAAAAGA
4347131 CATAATGTATCGATACATT
1 CATAATGTATCGATACATT
* *
4347150 GCAGAATATATCGATACATT
1 -CATAATGTATCGATACATT
*
4347170 CATACATGTATCGATATATT
1 CATA-ATGTATCGATACATT
* *
4347190 AAAAAATGTATCGATACAT
1 -CATAATGTATCGATACAT
4347209 CAAGGTAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.06
20 43 0.90
21 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Found at i:4347202 original size:40 final size:39
Alignment explanation
Indices: 4347131--4347208 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
4347121 GGTAAAAAGA
** *
4347131 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTAAAAAATATATCGATACATT
* *
4347170 CATACATGTATCGATATATTAAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTAAAAAATATATCGATACAT
4347209 CAAGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTAAAAAATATATCGATACATT
Found at i:4349088 original size:2 final size:2
Alignment explanation
Indices: 4349081--4349111 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4349071 TTATAAGATT
4349081 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
4349112 TTTTGTATTA
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:4350107 original size:18 final size:18
Alignment explanation
Indices: 4350072--4350123 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
4350062 TATTTAAAAT
*
4350072 TTTAAATTATTTTAATTA
1 TTTAAATTATATTAATTA
* *
4350090 TTTAAATTCTATTGATTA
1 TTTAAATTATATTAATTA
* *
4350108 TATTTAATCATATTAA
1 T-TTAAATTATATTAA
4350124 AAATTAGATT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTAAATTATATTAATTA
Found at i:4350159 original size:3 final size:3
Alignment explanation
Indices: 4350151--4350195 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
4350141 AATCATATAG
*
4350151 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4350196 ATAAATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:4350237 original size:20 final size:20
Alignment explanation
Indices: 4350214--4350251 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4350204 TAGAATTGTA
4350214 AATAGTATT-TATTATTTATC
1 AATA-TATTATATTATTTATC
4350234 AATATATTATATTATTTA
1 AATATATTATATTATTTA
4350252 GCTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
AATATATTATATTATTTATC
Found at i:4350297 original size:23 final size:22
Alignment explanation
Indices: 4350241--4350298 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
4350231 ATCAATATAT
**
4350241 TATATTATTTAGCTTTTTTTTA
1 TATATTATTTATATTTTTTTTA
* *
4350263 TATCTTAGTTATATTTTTTTCTA
1 TATATTATTTATATTTTTTT-TA
*
4350286 TCTATTATTTATA
1 TATATTATTTATA
4350299 GACTAGGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (22 bp):
TATATTATTTATATTTTTTTTA
Found at i:4350517 original size:3 final size:3
Alignment explanation
Indices: 4350497--4350530 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
4350487 AATTTAATCA
*
4350497 TAT TA- TAT TAT CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4350531 ATATAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:4350609 original size:17 final size:18
Alignment explanation
Indices: 4350587--4350630 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
4350577 ATTATAAAAA
4350587 TATTTATATATATT-TAT
1 TATTTATATATATTATAT
4350604 TATTTATCTATATATTATAT
1 TATTTA--TATATATTATAT
4350624 TATTTAT
1 TATTTAT
4350631 CTTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.25
18 1 0.04
19 8 0.33
20 9 0.38
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTATATATATTATAT
Found at i:4350643 original size:20 final size:20
Alignment explanation
Indices: 4350593--4350632 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4350583 AAAATATTTA
4350593 TATATATT-TATTATTTATC
1 TATATATTATATTATTTATC
4350612 TATATATTATATTATTTATC
1 TATATATTATATTATTTATC
4350632 T
1 T
4350633 TTTTTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATATTATATTATTTATC
Found at i:4350673 original size:21 final size:22
Alignment explanation
Indices: 4350623--4350673 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
4350613 ATATATTATA
*
4350623 TTATTTATCTTTTTTTTATATC
1 TTATTTATATTTTTTTTATATC
*
4350645 TTAGTTATATTTTTTTCTAT-TC
1 TTATTTATATTTTTTT-TATATC
4350667 -TATTTAT
1 TTATTTAT
4350674 TATAGTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.24
22 16 0.64
23 3 0.12
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.71
Consensus pattern (22 bp):
TTATTTATATTTTTTTTATATC
Found at i:4350686 original size:21 final size:21
Alignment explanation
Indices: 4350662--4350727 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
4350652 TATTTTTTTC
4350662 TATTCTATT-TAT-TATAGTATT
1 TATTCTATTATATGT-TA-TATT
*
4350683 TATTATATTATATGTTATATT
1 TATTCTATTATATGTTATATT
* *
4350704 TATTCTATTAGTATATTCTATT
1 TATTCTATTA-TATGTTATATT
4350726 TA
1 TA
4350728 GTATATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 21 0.55
22 16 0.42
23 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (21 bp):
TATTCTATTATATGTTATATT
Found at i:4350691 original size:17 final size:17
Alignment explanation
Indices: 4350662--4350743 Score: 60
Period size: 17 Copynumber: 4.5 Consensus size: 17
4350652 TATTTTTTTC
4350662 TATTCTATTTATTATAG
1 TATTCTATTTATTATAG
4350679 TATT-TATTATATTATATG
1 TATTCTATT-TATTATA-G
*
4350697 TTATATTTATTCTATTAGTA-
1 -TAT-TCTATT-TATTA-TAG
* *
4350717 TATTCTATTTAGTATATT
1 TATTCTATTTATTATA-G
4350735 TATTCTATT
1 TATTCTATT
4350744 AGTATAATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
16 6 0.11
17 15 0.28
18 15 0.28
19 6 0.11
20 1 0.02
21 9 0.17
22 2 0.04
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (17 bp):
TATTCTATTTATTATAG
Found at i:4350720 original size:13 final size:13
Alignment explanation
Indices: 4350704--4350776 Score: 56
Period size: 13 Copynumber: 5.2 Consensus size: 13
4350694 ATGTTATATT
4350704 TATTCTATTAGTA
1 TATTCTATTAGTA
4350717 TATTCTATTTAGTATA
1 TATTCTA-TTAG--TA
4350733 TTTATTCTATTAGTA
1 --TATTCTATTAGTA
* *
4350748 TAATATATTTAGTA
1 TATTCTA-TTAGTA
* *
4350762 TAATATATTAGTA
1 TATTCTATTAGTA
4350775 TA
1 TA
4350777 ATATTACCCT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
13 20 0.38
14 17 0.33
15 2 0.04
16 2 0.04
17 4 0.08
18 7 0.13
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (13 bp):
TATTCTATTAGTA
Found at i:4350736 original size:31 final size:31
Alignment explanation
Indices: 4350698--4350763 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
4350688 TATTATATGT
* *
4350698 TATATTTATTCTATTAGTATATTCTATTTAG
1 TATATTTATTCTATTAGTATAATATATTTAG
4350729 TATATTTATTCTATTAGTATAATATATTTAG
1 TATATTTATTCTATTAGTATAATATATTTAG
4350760 TATA
1 TATA
4350764 ATATATTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.56
Consensus pattern (31 bp):
TATATTTATTCTATTAGTATAATATATTTAG
Found at i:4350747 original size:17 final size:17
Alignment explanation
Indices: 4350698--4350749 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
4350688 TATTATATGT
4350698 TATATTTATTCTATTAG
1 TATATTTATTCTATTAG
4350715 --TA--TATTCTATTTAG
1 TATATTTATTCTA-TTAG
4350729 TATATTTATTCTATTAG
1 TATATTTATTCTATTAG
4350746 TATA
1 TATA
4350750 ATATATTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 7 0.23
14 4 0.13
15 2 0.07
16 2 0.07
17 8 0.27
18 7 0.23
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (17 bp):
TATATTTATTCTATTAG
Found at i:4350756 original size:18 final size:18
Alignment explanation
Indices: 4350715--4350756 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
4350705 ATTCTATTAG
4350715 TATATTCTATTTAGTATA
1 TATATTCTATTTAGTATA
*
4350733 TTTATTCTA-TTAGTATAA
1 TATATTCTATTTAGTAT-A
4350751 TATATT
1 TATATT
4350757 TAGTATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (18 bp):
TATATTCTATTTAGTATA
Found at i:4350776 original size:22 final size:22
Alignment explanation
Indices: 4350711--4350776 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
4350701 ATTTATTCTA
*
4350711 TTAGTATATTCTATTTAGTATAT
1 TTAGTATATTATA-TTAGTATAT
* * *
4350734 TTATTCTATTAGTA-TAATATAT
1 TTAGTATATTA-TATTAGTATAT
*
4350756 TTAGTATAATATATTAGTATA
1 TTAGTATATTATATTAGTATA
4350777 ATATTACCCT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
21 2 0.06
22 21 0.64
23 8 0.24
24 2 0.06
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (22 bp):
TTAGTATATTATATTAGTATAT
Found at i:4350777 original size:13 final size:13
Alignment explanation
Indices: 4350740--4350780 Score: 73
Period size: 13 Copynumber: 3.1 Consensus size: 13
4350730 ATATTTATTC
4350740 TATTAGTATAATA
1 TATTAGTATAATA
4350753 TATTTAGTATAATA
1 TA-TTAGTATAATA
4350767 TATTAGTATAATA
1 TATTAGTATAATA
4350780 T
1 T
4350781 TACCCTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 14 0.52
14 13 0.48
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (13 bp):
TATTAGTATAATA
Found at i:4350861 original size:16 final size:17
Alignment explanation
Indices: 4350825--4350881 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
4350815 TACATTTAAA
* *
4350825 ATTTAAATTATATATAT
1 ATTTAAATTAGATATAG
4350842 ATTTAAA-TAGATATAG
1 ATTTAAATTAGATATAG
*
4350858 ATTTAATTTA-ATAGATAG
1 ATTTAAATTAGAT--ATAG
4350876 ATTTAA
1 ATTTAA
4350882 TATAGATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 15 0.44
17 9 0.26
18 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
ATTTAAATTAGATATAG
Found at i:4350870 original size:20 final size:19
Alignment explanation
Indices: 4350842--4350882 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 19
4350832 TTATATATAT
4350842 ATTTAAATAGATATAGATTTA
1 ATTTAAATAG--ATAGATTTA
4350863 ATTT-AATAGATAGATTTA
1 ATTTAAATAGATAGATTTA
4350881 AT
1 AT
4350883 ATAGATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 11 0.55
20 5 0.25
21 4 0.20
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (19 bp):
ATTTAAATAGATAGATTTA
Found at i:4353690 original size:17 final size:17
Alignment explanation
Indices: 4353668--4353700 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4353658 GATTATGAGA
4353668 GAAGCATAGATGGATGC
1 GAAGCATAGATGGATGC
4353685 GAAGCATAGATGGATG
1 GAAGCATAGATGGATG
4353701 TGATTATGAT
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:0.36, C:0.09, G:0.36, T:0.18
Consensus pattern (17 bp):
GAAGCATAGATGGATGC
Found at i:4359797 original size:10 final size:10
Alignment explanation
Indices: 4359784--4359808 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4359774 ATATAAAATT
4359784 TTTATTTTTA
1 TTTATTTTTA
4359794 TTTATTTTTA
1 TTTATTTTTA
4359804 TTTAT
1 TTTAT
4359809 ACTTCCTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:4359866 original size:22 final size:20
Alignment explanation
Indices: 4359843--4359901 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 20
4359833 TTTTTATAAT
4359843 TTTATTCAAAAATAAAATATA
1 TTTATT-AAAAATAAAATATA
*
4359864 TTTA--ATAAATAAAATATA
1 TTTATTAAAAATAAAATATA
4359882 TTTATTAAATGAATAAAATA
1 TTTATTAAA--AATAAAATA
4359902 AAATATTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 17 0.53
20 2 0.06
21 4 0.12
22 9 0.28
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TTTATTAAAAATAAAATATA
Found at i:4359875 original size:18 final size:18
Alignment explanation
Indices: 4359852--4359891 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
4359842 TTTTATTCAA
4359852 AAATAAAATATATTTAAT
1 AAATAAAATATATTTAAT
*
4359870 AAATAAAATATATTTATT
1 AAATAAAATATATTTAAT
4359888 AAAT
1 AAAT
4359892 GAATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATAAAATATATTTAAT
Found at i:4361532 original size:16 final size:17
Alignment explanation
Indices: 4361511--4361542 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4361501 TATTAAATAA
4361511 ATATTTTTAT-ATTAAT
1 ATATTTTTATAATTAAT
4361527 ATATTTTTATAATTAA
1 ATATTTTTATAATTAA
4361543 ATTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTTTTATAATTAAT
Found at i:4362537 original size:29 final size:30
Alignment explanation
Indices: 4362462--4362539 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
4362452 TTTTTAAGTC
*
4362462 TTTA-TAAAAAATATACTTACTCTTTAACG
1 TTTAGTAAAAAATATATTTACTCTTTAACG
4362491 TTT-G--AAAAATATTCATTTACT-TTTGAA-G
1 TTTAGTAAAAAATA-T-ATTTACTCTTT-AACG
4362519 TTTAGTAAAAAATATATTTAC
1 TTTAGTAAAAAATATATTTAC
4362540 CGTTCAAACT
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
27 7 0.17
28 8 0.20
29 18 0.44
30 1 0.02
31 7 0.17
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (30 bp):
TTTAGTAAAAAATATATTTACTCTTTAACG
Found at i:4362610 original size:15 final size:15
Alignment explanation
Indices: 4362587--4362628 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
4362577 AAGATAAATA
4362587 TATATTTTTTAATTTT
1 TATA-TTTTTAATTTT
4362603 TA-ATTTTTATATTTT
1 TATATTTTTA-ATTTT
4362618 TATTATTTTTA
1 TA-TATTTTTA
4362629 CTCAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.26
15 8 0.35
16 2 0.09
17 7 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TATATTTTTAATTTT
Found at i:4362618 original size:9 final size:8
Alignment explanation
Indices: 4362587--4362628 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
4362577 AAGATAAATA
4362587 TATATTTT
1 TATATTTT
4362595 T-TAATTTT
1 TAT-ATTTT
4362603 TA-ATTTT
1 TATATTTT
4362610 TATATTTT
1 TATATTTT
4362618 TATTATTTT
1 TA-TATTTT
4362627 TA
1 TA
4362629 CTCAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 8 0.27
8 14 0.47
9 8 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TATATTTT
Found at i:4362873 original size:8 final size:8
Alignment explanation
Indices: 4362860--4362891 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
4362850 TGGTTTAAGA
4362860 AAAAAAAG
1 AAAAAAAG
4362868 AAAAAAAG
1 AAAAAAAG
4362876 AAAAAAAG
1 AAAAAAAG
4362884 AAATAAAA
1 AAA-AAAA
4362892 AATATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:4365028 original size:8 final size:8
Alignment explanation
Indices: 4365015--4365053 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
4365005 CCAAACAAGC
4365015 AAAAATAA
1 AAAAATAA
*
4365023 AGAAATAA
1 AAAAATAA
4365031 AAAAATAAA
1 AAAAAT-AA
4365040 ATAAAATAA
1 A-AAAATAA
4365049 AAAAA
1 AAAAA
4365054 GATGGTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 16 0.59
9 6 0.22
10 5 0.19
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:4365041 original size:13 final size:13
Alignment explanation
Indices: 4365016--4365053 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
4365006 CAAACAAGCA
*
4365016 AAAATAAAGAAAT
1 AAAATAAAAAAAT
4365029 AAAA-AAATAAAAT
1 AAAATAAA-AAAAT
4365042 AAAATAAAAAAA
1 AAAATAAAAAAA
4365054 GATGGTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 3 0.14
13 16 0.73
14 3 0.14
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:4368787 original size:60 final size:60
Alignment explanation
Indices: 4368658--4368890 Score: 163
Period size: 60 Copynumber: 3.9 Consensus size: 60
4368648 TGCTCATATA
* ** ***
4368658 TAGTCATT-TTTAGGTTTTCT-ATTTCAT-TTAGCCTATTTCATTGAGTCTTGATTTTGC-C
1 TAGTCATTGTTTAGGTTTT-TGGTTTCATCCAAGCC-ATTTCATTGAGTCTTGATTCCACTC
* * * * * *
4368716 TAATTCGTTGTTTAGATTTTTGGTTTCATCCTAGTCATTTCGTTGAGTCTTGATTCCACT-
1 T-AGTCATTGTTTAGGTTTTTGGTTTCATCCAAGCCATTTCATTGAGTCTTGATTCCACTC
* * * * * * *
4368776 TGAGTCATTGTTTAGGTTTCTAGTTTCGA-CCAAGCCATTTTATTGATTCTTGGTTTCGCTC
1 T-AGTCATTGTTTAGGTTTTTGGTTTC-ATCCAAGCCATTTCATTGAGTCTTGATTCCACTC
* * * * *
4368837 TAGTCATTGTTTAGGTTTTTGGTTACATCCAAACCTTTTTATCGAGTCTTGATT
1 TAGTCATTGTTTAGGTTTTTGGTTTCATCCAAGCCATTTCATTGAGTCTTGATT
4368891 TTGCTCAAGT
Statistics
Matches: 135, Mismatches: 32, Indels: 14
0.75 0.18 0.08
Matches are distributed among these distances:
58 1 0.01
59 7 0.05
60 121 0.90
61 6 0.04
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.49
Consensus pattern (60 bp):
TAGTCATTGTTTAGGTTTTTGGTTTCATCCAAGCCATTTCATTGAGTCTTGATTCCACTC
Found at i:4368902 original size:60 final size:60
Alignment explanation
Indices: 4368760--4368914 Score: 152
Period size: 60 Copynumber: 2.6 Consensus size: 60
4368750 TCATTTCGTT
* * ** * * *
4368760 GAGTCTTGATTCCACTTGAGTCATTGTTTAGGTTTCTAGTTTCGACCAAGCCATTTTATT
1 GAGTCTTGATTTCGCTCAAGTCATTGTTTAGGTTTCTAGTTACGACCAAACCATTTTATC
* * * * * *
4368820 GATTCTTGGTTTCGCTCTAGTCATTGTTTAGGTTTTTGGTTAC-ATCCAAACCTTTTTATC
1 GAGTCTTGATTTCGCTCAAGTCATTGTTTAGGTTTCTAGTTACGA-CCAAACCATTTTATC
*
4368880 GAGTCTTGATTTTGCTCAAGTCATT-TTGTAGGTTT
1 GAGTCTTGATTTCGCTCAAGTCATTGTT-TAGGTTT
4368915 ATAATGCCAT
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
59 3 0.04
60 74 0.96
ACGTcount: A:0.18, C:0.17, G:0.19, T:0.46
Consensus pattern (60 bp):
GAGTCTTGATTTCGCTCAAGTCATTGTTTAGGTTTCTAGTTACGACCAAACCATTTTATC
Found at i:4369000 original size:59 final size:59
Alignment explanation
Indices: 4368937--4369099 Score: 175
Period size: 59 Copynumber: 2.8 Consensus size: 59
4368927 TTTAACAGTA
* *
4368937 TTTTGGTTTTGTCTAAGTTATTTTTAGATTTCTAGTTTTGTCTAGACCATTTTTTTGAG
1 TTTTGGTTTTGTCTAAGTCATTTTTAGATTTCTAGTTTTGTCTAGACCATTTTTGTGAG
* * * * * * * * **
4368996 TTTTGGTTTTGTCTAAGTCAGTTTCAGGTTTCTGGTCTCGTCCATACTGTTTTTGTGAG
1 TTTTGGTTTTGTCTAAGTCATTTTTAGATTTCTAGTTTTGTCTAGACCATTTTTGTGAG
* * *
4369055 TTTTGATTTTGT-TCAAGTCATTTTTAGATTTTTAATTTTGTCTAG
1 TTTTGGTTTTGTCT-AAGTCATTTTTAGATTTCTAGTTTTGTCTAG
4369100 GTAATTCCAT
Statistics
Matches: 80, Mismatches: 23, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
58 1 0.01
59 79 0.99
ACGTcount: A:0.16, C:0.10, G:0.18, T:0.55
Consensus pattern (59 bp):
TTTTGGTTTTGTCTAAGTCATTTTTAGATTTCTAGTTTTGTCTAGACCATTTTTGTGAG
Found at i:4381541 original size:19 final size:20
Alignment explanation
Indices: 4381519--4381557 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4381509 AAATTAATTA
4381519 AAAAATATAA-AAAAT-AAGG
1 AAAAATA-AATAAAATGAAGG
4381538 AAAAATAAATAAAATGAAGG
1 AAAAATAAATAAAATGAAGG
4381558 TATTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 12 0.67
20 4 0.22
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (20 bp):
AAAAATAAATAAAATGAAGG
Found at i:4381810 original size:21 final size:20
Alignment explanation
Indices: 4381748--4381818 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
4381738 TATTTTAATC
* *
4381748 AATTTTATTATCATTAAAAT
1 AATTTTATTATAATGAAAAT
* *
4381768 -ATTTTA-AATAATGAGAATT
1 AATTTTATTATAATGA-AAAT
4381787 AATTTTATTATAAATGAAAAT
1 AATTTTATTAT-AATGAAAAT
4381808 AATTTTATTAT
1 AATTTTATTAT
4381819 TTCATCTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
18 5 0.12
19 9 0.22
20 6 0.15
21 16 0.39
22 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (20 bp):
AATTTTATTATAATGAAAAT
Found at i:4383730 original size:20 final size:20
Alignment explanation
Indices: 4383680--4383730 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
4383670 TTTTACCCAG
* *
4383680 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATCA
* * *
4383700 ATATATTGATACATGTATGA
1 ATGTATCGATACATGTATCA
4383720 ATGTATCGATA
1 ATGTATCGATA
4383731 TATTCTTCAC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:4383814 original size:20 final size:19
Alignment explanation
Indices: 4383774--4383835 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
4383764 TACCCAGATA
* *
4383774 TATCAATACATTTTTAATG
1 TATCAATACATTATGAATG
4383793 TATCAATACATGTATGAATG
1 TATCAATACAT-TATGAATG
* *
4383813 TATCGATACATTCATCAATG
1 TATCAATACATT-ATGAATG
4383833 TAT
1 TAT
4383836 TGATACATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 12 0.32
20 25 0.68
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (19 bp):
TATCAATACATTATGAATG
Found at i:4383841 original size:90 final size:91
Alignment explanation
Indices: 4383669--4383871 Score: 300
Period size: 90 Copynumber: 2.2 Consensus size: 91
4383659 AAAAGTCACA
* ** *
4383669 TTTTTACCCAGATGTATCGATACATTTTTCAATATATTGATACATGTATGAATGTATCGATATAT
1 TTTTTACCCAGATGTATCAATACATTTTTCAATATATCAATACATGTATGAATGTATCGATACAT
* * * *
4383734 TCTTCACTGTGTCGATACATTCTGTC
66 TCATCAATGTATCGATACATTCTATC
* *
4383760 TTTTTACCCAGATATATCAATACATTTTT-AATGTATCAATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCAATACATTTTTCAATATATCAATACATGTATGAATGTATCGATACAT
*
4383824 TCATCAATGTATTGATACATTCTATC
66 TCATCAATGTATCGATACATTCTATC
4383850 TTTTTACCCAGATGTATCAATA
1 TTTTTACCCAGATGTATCAATA
4383872 TATTGAATAA
Statistics
Matches: 100, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 73 0.73
91 27 0.27
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (91 bp):
TTTTTACCCAGATGTATCAATACATTTTTCAATATATCAATACATGTATGAATGTATCGATACAT
TCATCAATGTATCGATACATTCTATC
Found at i:4389418 original size:19 final size:18
Alignment explanation
Indices: 4389394--4389444 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
4389384 AAATATGAAA
4389394 AGAAAAACAAAAAAAAAG
1 AGAAAAACAAAAAAAAAG
* *
4389412 TGCAAAAGCAAAATAAAAAG
1 AG-AAAAACAAAA-AAAAAG
*
4389432 AGAATAACAAAAA
1 AGAAAAACAAAAA
4389445 TCCAAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 2 0.08
19 17 0.65
20 7 0.27
ACGTcount: A:0.75, C:0.08, G:0.12, T:0.06
Consensus pattern (18 bp):
AGAAAAACAAAAAAAAAG
Found at i:4389451 original size:46 final size:45
Alignment explanation
Indices: 4389355--4389456 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
4389345 CTTCAAAATG
* * *
4389355 ACAAAAAAAAGGTCAAAAGCAAAAGTATAAAATATGAAAAGAAAA
1 ACAAAAAAAAAGTCAAAAGCAAAAGTATAAAAGATGAAAACAAAA
4389400 ACAAAAAAAAAGTGCAAAAGCAAAA-TA-AAAAGA-GAATAACAAAA
1 ACAAAAAAAAAGT-CAAAAGCAAAAGTATAAAAGATGAA-AACAAAA
*
4389444 ATCCAAAAAAAAG
1 A-CAAAAAAAAAG
4389457 GACATGAATG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
43 3 0.06
44 12 0.24
45 24 0.48
46 11 0.22
ACGTcount: A:0.71, C:0.09, G:0.12, T:0.09
Consensus pattern (45 bp):
ACAAAAAAAAAGTCAAAAGCAAAAGTATAAAAGATGAAAACAAAA
Found at i:4389452 original size:45 final size:46
Alignment explanation
Indices: 4389356--4389457 Score: 122
Period size: 46 Copynumber: 2.2 Consensus size: 46
4389346 TTCAAAATGA
* *
4389356 CAAAAAAAAGGTCAAAAGCAAAAGTATAAAATATGAAAAGAAAAA-
1 CAAAAAAAAGGTCAAAAGCAAAAGTATAAAAGATGAAAACAAAAAC
*
4389401 CAAAAAAAAAGTGCAAAAGCAAAA-TA-AAAAGA-GAATAACAAAAATC
1 CAAAAAAAAGGT-CAAAAGCAAAAGTATAAAAGATGAA-AACAAAAA-C
4389447 CAAAAAAAAGG
1 CAAAAAAAAGG
4389458 ACATGAATGC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
43 3 0.06
44 12 0.24
45 13 0.27
46 21 0.43
ACGTcount: A:0.70, C:0.09, G:0.13, T:0.09
Consensus pattern (46 bp):
CAAAAAAAAGGTCAAAAGCAAAAGTATAAAAGATGAAAACAAAAAC
Found at i:4390723 original size:27 final size:27
Alignment explanation
Indices: 4390686--4391033 Score: 444
Period size: 27 Copynumber: 12.7 Consensus size: 27
4390676 TTTCTTTTCA
* * *
4390686 AAGTCCACAACTCCATGGCATCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * *
4390713 AAGTCCACAACTCTGTGGCATCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
4390740 AAAGTTCACAACTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
*
4390768 AAAGTCCACAACTCCGTGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* *
4390796 AAGTCCACAACTCTGTGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTT
** * *
4390823 AAGTCCTTAACTCCATGGCACCCATTTA
1 AAGTCCACAACTCCGTGGCACCC-TTTT
4390851 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
4390878 AAGTCCACAACTCTGTGGTACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
4390905 AAGTCCACAACTCCGTGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
4390932 AAAGTCCACCACTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* *
4390960 AAGTCCACAACTCTGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * *
4390987 AAGTCCACAACTCTGCGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
4391014 AAGTCCACAACTCCCTGGCA
1 AAGTCCACAACTCCGTGGCA
4391034 GCACCATTTT
Statistics
Matches: 285, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
27 187 0.66
28 98 0.34
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:4390750 original size:55 final size:54
Alignment explanation
Indices: 4390686--4391033 Score: 426
Period size: 55 Copynumber: 6.4 Consensus size: 54
4390676 TTTCTTTTCA
* * * * * *
4390686 AAGTCCACAACTCCATGGCATCTTTTTAAGTCCACAACTCTGTGGCATCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCATCCTTTT
*
4390740 AAAGTTCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTT
1 -AAGTCCACAACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCATCCTTTT
* ** * * *
4390796 AAGTCCACAACTCTGTGGCACCCTTTAAAGTCCTTAACTCCATGGCACCCATTTA
1 AAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCATCC-TTTT
* * * *
4390851 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGTACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCATCCTTTT
* * *
4390905 AAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACCACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCAC-CCTTTAAAGTCCACAACTCCGTGGCATCCTTTT
* * * * *
4390960 AAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGCGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCATCCTTTT
*
4391014 AAGTCCACAACTCCCTGGCA
1 AAGTCCACAACTCCGTGGCA
4391034 GCACCATTTT
Statistics
Matches: 253, Mismatches: 37, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
54 92 0.36
55 133 0.53
56 28 0.11
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (54 bp):
AAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCATCCTTTT
Found at i:4390865 original size:82 final size:82
Alignment explanation
Indices: 4390679--4391033 Score: 496
Period size: 82 Copynumber: 4.3 Consensus size: 82
4390669 AGTGGCATTT
* * * **
4390679 CTTTTCAAAGTCCACAACTCCATGGCATCTTTTTAAGTCCACAACTCTGTGGCATCTTTTTAAAG
1 CTTTT-AAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCA-CCCTTTAAAG
*
4390744 TTCACAACTCCGTGGCACC
64 TCCACAACTCCGTGGCACC
*
4390763 CTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACCCTTTAAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTAAAGTC
** *
4390828 CTTAACTCCATGGCACC
66 CACAACTCCGTGGCACC
* * *
4390845 CATTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGTACCCTTTTAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTAAAGTC
*
4390910 CACAACTCCGTGGCACT
66 CACAACTCCGTGGCACC
* * *
4390927 CTTTTAAAGTCCACCACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTAAAGTC
* * *
4390992 CACAACTCTGCGGCATC
66 CACAACTCCGTGGCACC
*
4391009 CTTTT-AAGTCCACAACTCCCTGGCA
1 CTTTTAAAGTCCACAACTCCGTGGCA
4391034 GCACCATTTT
Statistics
Matches: 245, Mismatches: 26, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
81 18 0.07
82 176 0.72
83 46 0.19
84 5 0.02
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.30
Consensus pattern (82 bp):
CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTAAAGTC
CACAACTCCGTGGCACC
Found at i:4391168 original size:32 final size:31
Alignment explanation
Indices: 4391096--4391203 Score: 141
Period size: 32 Copynumber: 3.5 Consensus size: 31
4391086 GTGGCATCCA
*
4391096 TTCAAAGCC-CACAAGTCGGTGG-CA-TCAT
1 TTCAAAGCCACACAAGTCGGTGGTAACTCAT
4391124 TTCAAAGCCCACACAAGTCGGTGGTAACTCAT
1 TTCAAAG-CCACACAAGTCGGTGGTAACTCAT
* *
4391156 TTGAAAGTCCACACAAGTCGGTGGTAACCCAT
1 TTCAAAG-CCACACAAGTCGGTGGTAACTCAT
4391188 TTCAAAGCTCACACAA
1 TTCAAAGC-CACACAA
4391204 ATTAGTGGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
28 7 0.10
29 2 0.03
30 13 0.19
31 2 0.03
32 46 0.66
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (31 bp):
TTCAAAGCCACACAAGTCGGTGGTAACTCAT
Found at i:4391239 original size:29 final size:29
Alignment explanation
Indices: 4390652--4391802 Score: 731
Period size: 28 Copynumber: 39.8 Consensus size: 29
4390642 CTGTGACCTC
* * * *
4390652 TTCAAAGTCCACGATTCAGTGGCATTTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTT
* *
4390682 TTCAAAGTCCACAACTCCA-TGGCAT-CTT
1 TTCAAAGCCCACAAGT-CAGTGGCATCCTT
* * * *
4390710 TT-TAAGTCCACAACTCTGTGGCAT-CTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* ** * * *
4390737 TTTAAAGTTCACAACTCCGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* * *
4390766 TT-AAAGTCCACAACTCCGTGGCATCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* * * *
4390794 TT--AAGTCCACAACTCTGTGGCA-CCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* ** * * *
4390820 TT-AAAGTCCTTAACTCCA-TGGCACCCAT
1 TTCAAAGCCCACAAGT-CAGTGGCATCCTT
* * * *
4390848 TT-AAAGTCCACAACTCCGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* * * * *
4390876 TT--AAGTCCACAACTCTGTGGTACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* * *
4390903 TT--AAGTCCACAACTCCGTGGCA-CTCTT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CTT
* * * * *
4390930 TT-AAAGTCCACCACTCCGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* * *
4390958 TT--AAGTCCACAACTCTGTGGCATCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* * * *
4390985 TT--AAGTCCACAACTCTGCGGCATCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* * ** *
4391012 TT--AAGTCCACAACTCCCTGGCAGCACCATT
1 TTCAAAGCCCACAAGTCAGTGGCA--TCC-TT
* *
4391042 TT-AAAGCCCACAAGTTAGTGGCAT-CAT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* *
4391069 TTC-AAGCCCACAAGTTAGTGGCATCC-A
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* *
4391096 TTCAAAGCCCACAAGTCGGTGGCAT-CAT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* * * *
4391124 TTCAAAGCCCACACAAGTCGGTGGTAACTCAT
1 TTCAAAG-CC-CACAAGTCAGTGGCATC-CTT
* * * * *
4391156 TTGAAAGTCCACACAAGTCGGTGGTAACCCAT
1 TTCAAAG-CC-CACAAGTCAGTGG-CATCCTT
* *
4391188 TTCAAAGCTCACACAAATTAGTGGCATCCTT
1 TTCAAAGC-C-CACAAGTCAGTGGCATCCTT
* *
4391219 TTCAAAGCCCACAAGTGAGTGGCATCATT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* *
4391248 CTCAAAGCTCACAAGTCAGTGGCATCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* * *
4391277 CTCAAAGCCCACACAAATCAATGGCATCCTT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCTT
*
4391308 CTCAAAGCCCACAAGTCAGTGGCAT-CTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
4391336 TCTCAAAGCCCACAAGTCAGTGGCATCCTT
1 T-TCAAAGCCCACAAGTCAGTGGCATCCTT
* * *
4391366 CTCAAAGCCCACACAAATCAATGGCAT-CTT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCTT
**
4391396 TTCAAAGCTTACAAGTCAGTGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* * * *
4391424 TTCAAAACCCACATAAATCGGTGGCA-ACTGAT
1 TTCAAAGCCCAC--AAGTCAGTGGCATCCT--T
* * *
4391456 TTGAAAGCCCACATAAGTCGGTGGCAACCTAT
1 TTCAAAGCCCAC--AAGTCAGTGGCATCCT-T
*
4391488 TTCAAAGCCCACACAAATCAGTGGCATCCTT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCTT
*
4391519 CTCAAAGCCCACAAGTCAGTGGCATCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* *
4391548 TTCAAAGCCCACACAAATCAGTGGTAT-CTT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCTT
* *
4391578 TTCAAAGTCCACAAGTCAATGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
*
4391606 TTCAAAGCCCACAAGTCAATGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
*
4391634 TTCAAAGCCCACAAGTCAATGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* *
4391662 TTCAAAGCCCACAAGTTAGTGACATCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
*
4391691 CTCAAAGCCCACAAGTCAGTGGCATCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
* * *
4391720 CTCAAAGCCCACACAAATCAGTTGCAT-CTT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCTT
*
4391750 TTCAAAGCCCACAAGTCAATGGCAT-CTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT
4391778 TTCAAAGCCCGCACAAGTCAGTGGC
1 TTCAAAG-CC-CACAAGTCAGTGGC
4391803 TTCAAAGACC
Statistics
Matches: 958, Mismatches: 115, Indels: 96
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.01
27 201 0.21
28 271 0.28
29 172 0.18
30 103 0.11
31 104 0.11
32 91 0.09
33 6 0.01
34 3 0.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (29 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTT
Found at i:4391477 original size:32 final size:32
Alignment explanation
Indices: 4391096--4391571 Score: 172
Period size: 29 Copynumber: 15.8 Consensus size: 32
4391086 GTGGCATCCA
* *
4391096 TTCAAAGCCCAC--AAGTCGGTGGC-ATC-AT
1 TTCAAAGCCCACATAAATCGGTGGCAACCTAT
* * *
4391124 TTCAAAGCCCACACAAGTCGGTGGTAA-CTCAT
1 TTCAAAGCCCACATAAATCGGTGGCAACCT-AT
* * * * * *
4391156 TTGAAAGTCCACACAAGTCGGTGGTAACCCAT
1 TTCAAAGCCCACATAAATCGGTGGCAACCTAT
* * ** *
4391188 TTCAAAGCTCACACAAATTAGTGGCATCCT-T
1 TTCAAAGCCCACATAAATCGGTGGCAACCTAT
* *
4391219 TTCAAAGCCCAC--AAGT-GAGTGGC-ATC-AT
1 TTCAAAGCCCACATAAATCG-GTGGCAACCTAT
* * * *
4391247 TCTCAAAGCTCAC--AAGTCAGTGGCATCCT-T
1 T-TCAAAGCCCACATAAATCGGTGGCAACCTAT
* * ** *
4391277 CTCAAAGCCCACACAAATCAATGGCATCCT-T
1 TTCAAAGCCCACATAAATCGGTGGCAACCTAT
* * * *
4391308 CTCAAAGCCCAC--AAGTCAGTGGC-ATCT-T
1 TTCAAAGCCCACATAAATCGGTGGCAACCTAT
* * *
4391336 TCTCAAAGCCCAC--AAGTCAGTGGCATCCT-T
1 T-TCAAAGCCCACATAAATCGGTGGCAACCTAT
* * ** *
4391366 CTCAAAGCCCACACAAATCAATGGC-ATCT-T
1 TTCAAAGCCCACATAAATCGGTGGCAACCTAT
** * * *
4391396 TTCAAAGCTTAC--AAGTCAGTGGCATCC--T
1 TTCAAAGCCCACATAAATCGGTGGCAACCTAT
*
4391424 TTCAAAACCCACATAAATCGGTGGCAA-CTGAT
1 TTCAAAGCCCACATAAATCGGTGGCAACCT-AT
* *
4391456 TTGAAAGCCCACATAAGTCGGTGGCAACCTAT
1 TTCAAAGCCCACATAAATCGGTGGCAACCTAT
* * *
4391488 TTCAAAGCCCACACAAATCAGTGGCATCCT-T
1 TTCAAAGCCCACATAAATCGGTGGCAACCTAT
* * * *
4391519 CTCAAAGCCCAC--AAGTCAGTGGCATCCT-T
1 TTCAAAGCCCACATAAATCGGTGGCAACCTAT
* *
4391548 TTCAAAGCCCACACAAATCAGTGG
1 TTCAAAGCCCACATAAATCGGTGG
4391572 TATCTTTTCA
Statistics
Matches: 358, Mismatches: 63, Indels: 51
0.76 0.13 0.11
Matches are distributed among these distances:
28 37 0.10
29 108 0.30
30 38 0.11
31 70 0.20
32 102 0.28
33 3 0.01
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (32 bp):
TTCAAAGCCCACATAAATCGGTGGCAACCTAT
Found at i:4392042 original size:49 final size:49
Alignment explanation
Indices: 4391901--4392071 Score: 163
Period size: 49 Copynumber: 3.6 Consensus size: 49
4391891 TTAAAGTCCG
* * * * * *
4391901 ATATCGCTAGCATTGAATCAGCATATTAG--CACCTTT--ATTAGCTCA
1 ATATCGCTAGCCTTGAATCAGCACATTGGTCCACATTTCCCTTAGCCCA
* * * * * *
4391946 ATGTCGCTGGCTTTAAATCAGCACATT-GTCCACTTTTCCCTTGGCCCA
1 ATATCGCTAGCCTTGAATCAGCACATTGGTCCACATTTCCCTTAGCCCA
4391994 ATATCGCTAGCCTTGAATCAGCACATTGGTCCACATTTCCCTTAGCCCA
1 ATATCGCTAGCCTTGAATCAGCACATTGGTCCACATTTCCCTTAGCCCA
* * **
4392043 ATGTCGCTGGCCTTGAATTGGCACATTGG
1 ATATCGCTAGCCTTGAATCAGCACATTGG
4392072 CACTCCTCTC
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
44 1 0.01
45 22 0.22
46 6 0.06
48 29 0.28
49 44 0.43
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (49 bp):
ATATCGCTAGCCTTGAATCAGCACATTGGTCCACATTTCCCTTAGCCCA
Found at i:4392819 original size:20 final size:20
Alignment explanation
Indices: 4392794--4392865 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
4392784 TACCCAAATA
*
4392794 TATCGAAACATTTTTCAATG
1 TATCGATACATTTTTCAATG
* * *
4392814 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATG
*
4392834 TATCGATACATTCTTCAATG
1 TATCGATACATTTTTCAATG
*
4392854 TGTCGATACATT
1 TATCGATACATT
4392866 CTGTTCTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (20 bp):
TATCGATACATTTTTCAATG
Found at i:4392907 original size:20 final size:20
Alignment explanation
Indices: 4392882--4392937 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
4392872 TTTTACCCAG
*
4392882 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCATCA
* *
4392902 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTCATCA
4392922 ATGTATCGATACATTC
1 ATGTATCGATACATTC
4392938 TGTCTTTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCATCA
Found at i:4392979 original size:71 final size:71
Alignment explanation
Indices: 4392811--4392965 Score: 285
Period size: 71 Copynumber: 2.2 Consensus size: 71
4392801 ACATTTTTCA
*
4392811 ATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTGTCGATACATTCTGTTCTTTT
1 ATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATCGATACATTCTGTTCTTTT
4392876 ACCCAG
66 ACCCAG
*
4392882 ATGTATCGATACATGTATGAATGTATCGATATATTCTTCAATGTATCGATACATTCTG-TCTTTT
1 ATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATCGATACATTCTGTTCTTTT
4392946 ACCCAG
66 ACCCAG
4392952 ATGTATCGATACAT
1 ATGTATCGATACAT
4392966 TGAATAATTG
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
70 26 0.32
71 56 0.68
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (71 bp):
ATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATCGATACATTCTGTTCTTTT
ACCCAG
Found at i:4396607 original size:2 final size:2
Alignment explanation
Indices: 4396600--4396626 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4396590 TAACAAAATT
4396600 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 T
4396627 TTTTGCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4397913 original size:18 final size:18
Alignment explanation
Indices: 4397892--4397956 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 18
4397882 ATTTAAAAAA
4397892 TTAATTAAATTAAAATAT
1 TTAATTAAATTAAAATAT
*
4397910 TTAATTATATTTAAAA-ATT
1 TTAATTA-AATTAAAATA-T
4397929 TTATATTAATAAATTAAAATA-
1 TTA-A-T--TAAATTAAAATAT
4397950 TTAATTA
1 TTAATTA
4397957 TTATATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 15
0.69 0.04 0.27
Matches are distributed among these distances:
17 2 0.05
18 8 0.21
19 12 0.32
20 2 0.05
21 4 0.11
22 7 0.18
23 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAATTAAATTAAAATAT
Found at i:4397923 original size:36 final size:39
Alignment explanation
Indices: 4397882--4397957 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 39
4397872 TAAAAAATCA
4397882 ATTTAAAAA-ATTA-A-T-TAAATTAAAATATTTAATTAT
1 ATTTAAAAATATTATATTATAAATTAAAATA-TTAATTAT
*
4397918 ATTTAAAAATTTTATATTAATAAATTAAAATATTAATTAT
1 ATTTAAAAATATTATATT-ATAAATTAAAATATTAATTAT
4397958 TATATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
36 9 0.26
37 3 0.09
38 1 0.03
39 1 0.03
40 8 0.24
41 12 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (39 bp):
ATTTAAAAATATTATATTATAAATTAAAATATTAATTAT
Found at i:4398317 original size:24 final size:23
Alignment explanation
Indices: 4398286--4398343 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
4398276 TTAAAGTATG
4398286 ATTTATTT-TTATTTATAAAATTA
1 ATTTATTTATT-TTTATAAAATTA
* *
4398309 ATTTAATTTATTTTTATTAAATTT
1 ATTT-ATTTATTTTTATAAAATTA
4398333 ATTT-TTTATTT
1 ATTTATTTATTT
4398344 AATTATATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 7 0.23
23 4 0.13
24 18 0.58
25 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTATTTATTTTTATAAAATTA
Found at i:4398349 original size:15 final size:16
Alignment explanation
Indices: 4398309--4398351 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
4398299 TATAAAATTA
4398309 ATTTAATT-TATTTTT
1 ATTTAATTATATTTTT
*
4398324 ATTAAATT-TATTTTTT
1 ATTTAATTATA-TTTTT
4398340 ATTTAATTATAT
1 ATTTAATTATAT
4398352 GAGTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.38
16 13 0.54
17 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTAATTATATTTTT
Found at i:4398368 original size:19 final size:20
Alignment explanation
Indices: 4398344--4398387 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4398334 TTTTTTATTT
* *
4398344 AATTA-TATGAGTTTAAAAC
1 AATTATTATGACTTTAAAAA
*
4398363 AATTATTATTACTTTAAAAA
1 AATTATTATGACTTTAAAAA
4398383 AATTA
1 AATTA
4398388 AAAAAAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (20 bp):
AATTATTATGACTTTAAAAA
Found at i:4400549 original size:14 final size:14
Alignment explanation
Indices: 4400532--4400560 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4400522 ATTTATTTGC
4400532 ATTAATGGGTTTTT
1 ATTAATGGGTTTTT
4400546 ATTAATGGGTTTTT
1 ATTAATGGGTTTTT
4400560 A
1 A
4400561 ATATGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (14 bp):
ATTAATGGGTTTTT
Found at i:4400666 original size:22 final size:22
Alignment explanation
Indices: 4400630--4400675 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4400620 ATTAATATTG
*
4400630 TTATTTAAAAATAAAATA-TAT
1 TTATTAAAAAATAAAATATTAT
4400651 TTATTAAATAAATAAAATATTAT
1 TTATTAAA-AAATAAAATATTAT
4400674 TT
1 TT
4400676 TTCTAATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 10 0.45
23 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTATTAAAAAATAAAATATTAT
Found at i:4400788 original size:2 final size:2
Alignment explanation
Indices: 4400781--4400836 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
4400771 CATATAAGTG
* * *
4400781 TA TA TA TA CA CA TA TA -A GTA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
4400823 TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA
4400837 CACATATGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
1 1 0.02
2 44 0.96
3 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:4400795 original size:20 final size:20
Alignment explanation
Indices: 4400770--4400828 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
4400760 TTTTTTATTT
4400770 ACATATAAGTGTATATATAC
1 ACATATAAGTGTATATATAC
* *
4400790 ACATATAAGTATATATATAT
1 ACATATAAGTGTATATATAC
*
4400810 ATATATATA-TGTATATATA
1 ACATATA-AGTGTATATATA
4400829 TGTATATACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (20 bp):
ACATATAAGTGTATATATAC
Found at i:4400801 original size:18 final size:19
Alignment explanation
Indices: 4400770--4400806 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
4400760 TTTTTTATTT
4400770 ACATATAAGTGTATATATAC
1 ACATATAAG-GTATATATAC
4400790 ACATATAA-GTATATATA
1 ACATATAAGGTATATATA
4400807 TATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (19 bp):
ACATATAAGGTATATATAC
Found at i:4400990 original size:14 final size:14
Alignment explanation
Indices: 4400960--4400998 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
4400950 ACAAAAACGT
4400960 AAAACAATATATTTC
1 AAAA-AATATATTTC
4400975 AAAAAATAT-TTGTC
1 AAAAAATATATT-TC
4400989 AAAAAATATA
1 AAAAAATATA
4400999 AATTAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 16 0.73
15 4 0.18
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (14 bp):
AAAAAATATATTTC
Found at i:4401296 original size:37 final size:36
Alignment explanation
Indices: 4401233--4401302 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
4401223 TAGATGATTA
*
4401233 TATTTATTTGTTTTAGTATTTTTTTATTTTGTTTACC
1 TATTTATTTGTTTTAGTATTTGTTTA-TTTGTTTACC
4401270 TATTTATTCTGTTTTA-T-TTATGTTTATTTGTTT
1 TATTTATT-TGTTTTAGTATT-TGTTTATTTGTTT
4401303 GATATCTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
36 9 0.30
37 14 0.47
38 7 0.23
ACGTcount: A:0.16, C:0.04, G:0.09, T:0.71
Consensus pattern (36 bp):
TATTTATTTGTTTTAGTATTTGTTTATTTGTTTACC
Found at i:4404089 original size:11 final size:11
Alignment explanation
Indices: 4404073--4404105 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
4404063 ACTTGACTCG
4404073 AATTAATATTT
1 AATTAATATTT
4404084 AATTAATA-TT
1 AATTAATATTT
4404094 AATT-ATATTT
1 AATTAATATTT
4404104 AA
1 AA
4404106 ATAAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 3 0.14
10 10 0.48
11 8 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTAATATTT
Found at i:4405357 original size:20 final size:22
Alignment explanation
Indices: 4405334--4405377 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
4405324 AAATCAATTT
*
4405334 ATTAA-AA-TATTTTTATTTAA
1 ATTAATAATTATTATTATTTAA
4405354 ATTAATTAATTATTATTATTTAA
1 ATTAA-TAATTATTATTATTTAA
4405377 A
1 A
4405378 AATTTAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 2 0.10
23 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAATAATTATTATTATTTAA
Found at i:4409303 original size:154 final size:155
Alignment explanation
Indices: 4409021--4409306 Score: 344
Period size: 154 Copynumber: 1.9 Consensus size: 155
4409011 GGGTTATCGA
* * * * *
4409021 GATACTTTCATATCGAAGGTATACCTTAAAGGTGTTTTACTAATTTTACCTTAAAGCTGAGTCTT
1 GATACTTTCATATCAAAAGTATACCTCAAAGGTGTTTTACTAATTTTAACTTAAAGCTAAGTCTT
* * ***
4409086 TTAGAATCATCGAGATACTTTCACGTTAAAGGTGTGCTTTAAGGATAGCTTAATCATTTCATATC
66 TAAGAATCATCGAGATACTTTCACGTCAAAGGTACACTTTAAGGATAGCTTAATCATTTCATATC
4409151 ATGTTAAGTCCATTACGGTTACCAT
131 ATGTTAAGTCCATTACGGTTACCAT
* * * *
4409176 GATACTTTCATGTCAAAAGTATACCTCAAAGGTATTTTTGC-AA-TTTAACTTAGAGCTAAGTTC
1 GATACTTTCATATCAAAAGTATACCTCAAAGGT-GTTTTACTAATTTTAACTTAAAGCTAAG-TC
* * * * * **
4409239 TTTAAG-ATCATTGAGATACTTTCATGTCAAAGGTACATTTTAGGGATAGGTTTGTCATTTCATA
64 TTTAAGAATCATCGAGATACTTTCACGTCAAAGGTACACTTTAAGGATAGCTTAATCATTTCATA
4409303 TCAT
129 TCAT
4409307 ATCGAATCTT
Statistics
Matches: 108, Mismatches: 21, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
154 65 0.60
155 38 0.35
156 5 0.05
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (155 bp):
GATACTTTCATATCAAAAGTATACCTCAAAGGTGTTTTACTAATTTTAACTTAAAGCTAAGTCTT
TAAGAATCATCGAGATACTTTCACGTCAAAGGTACACTTTAAGGATAGCTTAATCATTTCATATC
ATGTTAAGTCCATTACGGTTACCAT
Found at i:4411264 original size:60 final size:60
Alignment explanation
Indices: 4411149--4411310 Score: 213
Period size: 60 Copynumber: 2.7 Consensus size: 60
4411139 GCCTATTTCA
* * *
4411149 TTGAGCCTTGGTTTTGCCCAAGTCATTG-TTAGGTTTTTAGTTTCATCCAAGCCATTTTG
1 TTGAGTCTTGGTTTTGCCTAAGTCATTGTTTAGGTTTTTAGTTTCACCCAAGCCATTTTG
* * **
4411208 TTGAGTCTTGATTCTGCCTAAGTCATTGTTTAGGTTTTTAGTTTTGCCCATA-CCATTTTG
1 TTGAGTCTTGGTTTTGCCTAAGTCATTGTTTAGGTTTTTAGTTTCACCCA-AGCCATTTTG
*
4411268 TTGAGTCTTGGTTTTG-CTCAAGTCGTTGTTTAGGTTTTTAGTT
1 TTGAGTCTTGGTTTTGCCT-AAGTCATTGTTTAGGTTTTTAGTT
4411311 ACGTCTAAAC
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
59 26 0.29
60 63 0.70
61 1 0.01
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.48
Consensus pattern (60 bp):
TTGAGTCTTGGTTTTGCCTAAGTCATTGTTTAGGTTTTTAGTTTCACCCAAGCCATTTTG
Found at i:4411335 original size:60 final size:59
Alignment explanation
Indices: 4411143--4411364 Score: 207
Period size: 60 Copynumber: 3.7 Consensus size: 59
4411133 CGTCTAGCCT
* * *
4411143 ATTTCATTGAGCCTTGGTTTTGCCCAAGTCATTG-TTAGGTTTTTAGTTTCATCCAAGCC
1 ATTTCATTGAGTCTTGGTTTTG-CCAAGTCATTGTTTAGGTTTTTAGTTTCGTCCAAACC
** * * * * *
4411202 ATTTTGTTGAGTCTTGATTCTGCCTAAGTCATTGTTTAGGTTTTTAGTTTTGCCCATACC
1 ATTTCATTGAGTCTTGGTTTTGCC-AAGTCATTGTTTAGGTTTTTAGTTTCGTCCAAACC
** * * *
4411262 ATTTTGTTGAGTCTTGGTTTTGCTCAAGTCGTTGTTTAGGTTTTTAGTTACGTCTAAACC
1 ATTTCATTGAGTCTTGGTTTTGC-CAAGTCATTGTTTAGGTTTTTAGTTTCGTCCAAACC
* * *
4411322 CTTTCATTAAGTCTTGATTTCAT-CCAAGTCATT-TTGTAGGTTT
1 ATTTCATTGAGTCTTGGTTT--TGCCAAGTCATTGTT-TAGGTTT
4411365 ATAATGTTGT
Statistics
Matches: 133, Mismatches: 24, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
58 2 0.02
59 28 0.21
60 100 0.75
61 2 0.02
62 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.47
Consensus pattern (59 bp):
ATTTCATTGAGTCTTGGTTTTGCCAAGTCATTGTTTAGGTTTTTAGTTTCGTCCAAACC
Found at i:4411362 original size:120 final size:119
Alignment explanation
Indices: 4411149--4411364 Score: 276
Period size: 120 Copynumber: 1.8 Consensus size: 119
4411139 GCCTATTTCA
* * ** *
4411149 TTGAGCCTTGGTTTTGCCCAAGTCATTGTTAGGTTTTTAGTTTCATCCAAGCCATTTTGTTGAGT
1 TTGAGCCTTGGTTTTGCCCAAGTCATTGTTAGGTTTTTAGTTACATCCAAACCATTTCATTAAGT
4411214 CTTGATTCTGCCTAAGTCATTGTTTAGGTTTTTAGTTTTGCCCATACCATTTTG
66 CTTGATTCTGCCTAAGTCATTGTTTAGGTTTTTAGTTTTGCCCATACCATTTTG
* * * * * *
4411268 TTGAGTCTTGGTTTTGCTCAAGTCGTTGTTTAGGTTTTTAGTTACGTCTAAACCCTTTCATTAAG
1 TTGAGCCTTGGTTTTGCCCAAGTCATTG-TTAGGTTTTTAGTTACATCCAAACCATTTCATTAAG
4411333 TCTTGATTTCAT-CC-AAGTCATT-TTGTAGGTTT
65 TCTTGA-TTC-TGCCTAAGTCATTGTT-TAGGTTT
4411365 ATAATGTTGT
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
119 27 0.33
120 49 0.60
121 5 0.06
122 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.19, T:0.47
Consensus pattern (119 bp):
TTGAGCCTTGGTTTTGCCCAAGTCATTGTTAGGTTTTTAGTTACATCCAAACCATTTCATTAAGT
CTTGATTCTGCCTAAGTCATTGTTTAGGTTTTTAGTTTTGCCCATACCATTTTG
Found at i:4412486 original size:63 final size:63
Alignment explanation
Indices: 4412395--4412629 Score: 210
Period size: 63 Copynumber: 3.7 Consensus size: 63
4412385 GGTCATCTCC
* * * * *
4412395 TTGACTATTATGATTTCACCCTAGTCAATCTTTTCAATTGAAGGTTTCACCCTGGTCACCTTT
1 TTGACTATTATGGTTTCACCCTAGTCAATCATTTCGACTGAAGGTTTCACCCTGATCACCTTT
* * * *
4412458 TTGACTATTATGGTTTCA-CCTTGATCAATCATTCCGACTGAA-GTTTCAGTCTTGATCACCTTT
1 TTGACTATTATGGTTTCACCCTAG-TCAATCATTTCGACTGAAGGTTTCA-CCCTGATCACCTTT
* * ** * * **
4412521 TTTACTATTATAGTTTCGTCTTGGTCAATTTTTTCGACT-AGAGGTTTC-CTCCTGATCA-CTTC
1 TTGACTATTATGGTTTCACCCTAGTCAATCATTTCGACTGA-AGGTTTCAC-CCTGATCACCTT-
4412583 T
63 T
* * *
4412584 TTAACTATTATGGTTTCACCCTAGTCAATCATATCGATTGAAGGTT
1 TTGACTATTATGGTTTCACCCTAGTCAATCATTTCGACTGAAGGTT
4412630 CCGCTTTAGT
Statistics
Matches: 135, Mismatches: 29, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
62 14 0.10
63 112 0.83
64 9 0.07
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (63 bp):
TTGACTATTATGGTTTCACCCTAGTCAATCATTTCGACTGAAGGTTTCACCCTGATCACCTTT
Found at i:4412648 original size:63 final size:61
Alignment explanation
Indices: 4412576--4412743 Score: 167
Period size: 62 Copynumber: 2.7 Consensus size: 61
4412566 TTCCTCCTGA
* * * * * *
4412576 TCACTTCTTTAACTATTATGGTTTCACCCTAGTCAATCATATC-GATTGAAGGTTCCGCTTTAG
1 TCACCTCTTTGACTATTATGGTTT-ACCCTAATCAATCAT-TCTGACTGAA-ATTCCGCCTTAG
* * * *
4412639 TCATCTCTTTGACAATTATAGTTTTGCCCTAATCAATCATTCTGACTGAAATTCCGCCTTAG
1 TCACCTCTTTGACTATTAT-GGTTTACCCTAATCAATCATTCTGACTGAAATTCCGCCTTAG
* * *
4412701 TTACCCCTTTGACTATTATAGGTTTACCCCAATCAATCATTCT
1 TCACCTCTTTGACTATTAT-GGTTTACCCTAATCAATCATTCT
4412744 AACAAAAGAT
Statistics
Matches: 86, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
62 48 0.56
63 34 0.40
64 4 0.05
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.39
Consensus pattern (61 bp):
TCACCTCTTTGACTATTATGGTTTACCCTAATCAATCATTCTGACTGAAATTCCGCCTTAG
Found at i:4412657 original size:126 final size:126
Alignment explanation
Indices: 4412436--4412662 Score: 275
Period size: 126 Copynumber: 1.8 Consensus size: 126
4412426 TTTCAATTGA
* * *
4412436 AGGTTTCACCCTGGTCACCTTTTTGACTATTATGGTTTCACCTTGATCAATCATTCCGACTGAAG
1 AGGTTTCACCCTGATCACCTTTTTAACTATTATGGTTTCACCTAGATCAATCATTCCGACTGAAG
* * * *
4412501 TTTCAGTCTTGATCACCTTTTTTACTATTATAGTTTCGTCTTGGTCAATTTTTTCGACTAG
66 GTTCAGTCTTGATCACCTCTTTGACAATTATAGTTTCGTCTTGGTCAATTTTTTCGACTAG
*
4412562 AGGTTTC-CTCCTGATCA-CTTCTTTAACTATTATGGTTTCACCCTAG-TCAATCATAT-CGATT
1 AGGTTTCAC-CCTGATCACCTT-TTTAACTATTATGGTTTCA-CCTAGATCAATCAT-TCCGACT
* * *
4412623 GAAGGTTCCG-CTTTAGTCATCTCTTTGACAATTATAGTTT
62 GAAGGTTCAGTCTTGA-TCACCTCTTTGACAATTATAGTTT
4412663 TGCCCTAATC
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
125 8 0.09
126 72 0.85
127 5 0.06
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.43
Consensus pattern (126 bp):
AGGTTTCACCCTGATCACCTTTTTAACTATTATGGTTTCACCTAGATCAATCATTCCGACTGAAG
GTTCAGTCTTGATCACCTCTTTGACAATTATAGTTTCGTCTTGGTCAATTTTTTCGACTAG
Found at i:4412865 original size:62 final size:63
Alignment explanation
Indices: 4412793--4412913 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 63
4412783 TGATTTTGCC
* * * ** * *
4412793 CTAGTAAATCTTTT-GATTGAAGGTTTTACCTTGGTTATCTCTTTGACTATTATGGTTTCGCG
1 CTAGTAAATCTTTTAGATTGAAAGTTTCAACTTAATCATCTATTTGACTATTATGGTTTCGCG
* * *
4412855 CTAGTCAATCTTTTATATTGAAAGTTTCAACTTAATCATCTATTTTACTATTATGGTTT
1 CTAGTAAATCTTTTAGATTGAAAGTTTCAACTTAATCATCTATTTGACTATTATGGTTT
4412914 TGTCTTAATC
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
62 13 0.27
63 35 0.73
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (63 bp):
CTAGTAAATCTTTTAGATTGAAAGTTTCAACTTAATCATCTATTTGACTATTATGGTTTCGCG
Found at i:4412921 original size:32 final size:31
Alignment explanation
Indices: 4412885--4412994 Score: 107
Period size: 32 Copynumber: 3.5 Consensus size: 31
4412875 AAAGTTTCAA
*
4412885 CTTAATCATCTATTTTACTATTATGGTTTTGT
1 CTTAATCATCT-TTTTACTATTATGATTTTGT
* * *
4412917 CTTAATCAAACTTTTCAATA-TATGATTTTG-
1 CTTAATC-ATCTTTTTACTATTATGATTTTGT
* *
4412947 CTTGATCATTTTTTTTACTATTATGATTTTGT
1 CTTAATCA-TCTTTTTACTATTATGATTTTGT
*
4412979 CTTAGTCAATCTTTTT
1 CTTAATC-ATCTTTTT
4412995 GATTAAAGTT
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
29 1 0.02
30 13 0.21
31 19 0.31
32 24 0.39
33 4 0.07
ACGTcount: A:0.24, C:0.13, G:0.08, T:0.55
Consensus pattern (31 bp):
CTTAATCATCTTTTTACTATTATGATTTTGT
Found at i:4412972 original size:31 final size:32
Alignment explanation
Indices: 4412897--4412994 Score: 101
Period size: 31 Copynumber: 3.1 Consensus size: 32
4412887 TAATCATCTA
*
4412897 TTTTACTATTATGGTTTTGTCTTAATCAAACT
1 TTTTACTATTATGATTTTGTCTTAATCAAACT
* * * ***
4412929 TTTCAATA-TATGATTTTG-CTTGATCATTTT
1 TTTTACTATTATGATTTTGTCTTAATCAAACT
* *
4412959 TTTTACTATTATGATTTTGTCTTAGTCAATCT
1 TTTTACTATTATGATTTTGTCTTAATCAAACT
4412991 TTTT
1 TTTT
4412995 GATTAAAGTT
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 14 0.27
31 19 0.37
32 18 0.35
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.57
Consensus pattern (32 bp):
TTTTACTATTATGATTTTGTCTTAATCAAACT
Found at i:4413008 original size:62 final size:61
Alignment explanation
Indices: 4412856--4413054 Score: 175
Period size: 62 Copynumber: 3.2 Consensus size: 61
4412846 GGTTTCGCGC
*** *
4412856 TAGTCAATCTTTTATATTGAAAGTTTCAACTTAATCATCTATTTTACTATTATGGTTTTGTCT
1 TAGTCAATCTTTT-TATT-AAAGTTTTTGCTTAATCATCTATTTTACTATTATGATTTTGTCT
* * * * * * * * *
4412919 TAATCAAACTTTTCAATATATGATTTTGCTTGATCATTTTTTTTACTATTATGATTTTGTCT
1 TAGTCAATCTTTTTATTA-AAGTTTTTGCTTAATCATCTATTTTACTATTATGATTTTGTCT
** * * * *
4412981 TAGTCAATCTTTTTGATTAAAGTTTTTGCCTTAATCATCTCCTTAACTATTATCATTTCGTCA
1 TAGTCAATCTTTTT-ATTAAAGTTTTTG-CTTAATCATCTATTTTACTATTATGATTTTGTCT
4413044 T-GTCAATCTTT
1 TAGTCAATCTTT
4413055 CTAATAGAAA
Statistics
Matches: 106, Mismatches: 27, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
61 1 0.01
62 64 0.60
63 41 0.39
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.51
Consensus pattern (61 bp):
TAGTCAATCTTTTTATTAAAGTTTTTGCTTAATCATCTATTTTACTATTATGATTTTGTCT
Found at i:4415123 original size:9 final size:9
Alignment explanation
Indices: 4415104--4415136 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
4415094 ATCATTTCAT
4415104 AAAAT-ATA
1 AAAATAATA
4415112 AAAATAATA
1 AAAATAATA
4415121 AAAATAATA
1 AAAATAATA
*
4415130 ATAATAA
1 AAAATAA
4415137 GATAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATAATA
Found at i:4424712 original size:15 final size:14
Alignment explanation
Indices: 4424654--4424712 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
4424644 TTGAAAAAAA
4424654 TTAATAAAATTATT
1 TTAATAAAATTATT
*
4424668 TTAA-AAAATTAGTA
1 TTAATAAAATTA-TT
* *
4424682 ATAA-AAAATT-TA
1 TTAATAAAATTATT
4424694 TTAATTAAAATTATT
1 TTAA-TAAAATTATT
4424709 TTAA
1 TTAA
4424713 AAATAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
12 5 0.14
13 7 0.19
14 20 0.54
15 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
TTAATAAAATTATT
Found at i:4424719 original size:17 final size:17
Alignment explanation
Indices: 4424699--4424742 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
4424689 ATTTATTAAT
* *
4424699 TAAAATTATTTTAAAAA
1 TAAAATAATTTGAAAAA
*
4424716 TAAAATAATTTGAACAA
1 TAAAATAATTTGAAAAA
*
4424733 TAAATTAATT
1 TAAAATAATT
4424743 AGTTAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAAATAATTTGAAAAA
Found at i:4424720 original size:47 final size:46
Alignment explanation
Indices: 4424669--4424761 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 46
4424659 AAAATTATTT
* *
4424669 TAAAA-AATTAGTAATAAAAAATTTATTAATTAAAATTATTTTAAAAA
1 TAAAATAATTAG-AACAAAAAATTAATTAATT-AAATTATTTTAAAAA
* * *
4424716 TAAAATAATTTGAACAATAAATTAATTAGTTAAATTATTTTAAAAA
1 TAAAATAATTAGAACAAAAAATTAATTAATTAAATTATTTTAAAAA
4424762 GTTTAGTGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
46 15 0.38
47 20 0.50
48 5 0.12
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (46 bp):
TAAAATAATTAGAACAAAAAATTAATTAATTAAATTATTTTAAAAA
Found at i:4425158 original size:24 final size:25
Alignment explanation
Indices: 4425108--4425178 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 25
4425098 TTTTATTATC
* **
4425108 ATTAAAATATTTTAAAT-AATGTGA
1 ATTAAATTATTTTAAATAAAAATGA
4425132 ATTAAATTATTTTAAATAAAAAT-A
1 ATTAAATTATTTTAAATAAAAATGA
** * *
4425156 ATTTTATTAATTTATATAAAAAT
1 ATTAAATTATTTTAAATAAAAAT
4425179 TAATATATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 36 0.92
25 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (25 bp):
ATTAAATTATTTTAAATAAAAATGA
Found at i:4430222 original size:19 final size:21
Alignment explanation
Indices: 4430187--4430225 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
4430177 TCAATTACCA
4430187 TAATAATTCCTTTGTTAAGCG
1 TAATAATTCCTTTGTTAAGCG
4430208 TAATAATT-C-TTGTTAAGC
1 TAATAATTCCTTTGTTAAGC
4430226 AGAGGTGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (21 bp):
TAATAATTCCTTTGTTAAGCG
Found at i:4436932 original size:10 final size:10
Alignment explanation
Indices: 4436919--4436955 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
4436909 TTGTATTAAA
4436919 TTATATTGAT
1 TTATATTGAT
4436929 TTATATTGAT
1 TTATATTGAT
4436939 TTATATTGAT
1 TTATATTGAT
*
4436949 TAATATT
1 TTATATT
4436956 AATACATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (10 bp):
TTATATTGAT
Found at i:4437103 original size:24 final size:21
Alignment explanation
Indices: 4437053--4437097 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
4437043 TTTTTATAAT
* *
4437053 TTTATTTAAAAATAAAATATA
1 TTTATTAAAAAATAAAAAATA
4437074 TTTATTAAATAAATAAAAAATA
1 TTTATTAAA-AAATAAAAAATA
4437096 TT
1 TT
4437098 GTTATTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTATTAAAAAATAAAAAATA
Found at i:4437138 original size:21 final size:20
Alignment explanation
Indices: 4437114--4437167 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 20
4437104 TTCAATTAAC
4437114 AATAATTTATTATATT-TTTTT
1 AATAATTT-TTAT-TTATTTTT
4437135 AAT-ATTTTTATTTATTTTT
1 AATAATTTTTATTTATTTTT
*
4437154 AAAAATTTTATATT
1 AATAATTTT-TATT
4437168 AAATATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 2 0.07
19 11 0.38
20 9 0.31
21 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
AATAATTTTTATTTATTTTT
Found at i:4437188 original size:29 final size:31
Alignment explanation
Indices: 4437145--4437205 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
4437135 AATATTTTTA
*
4437145 TTTATTTTTAAAAATTTTATA-TTAAATATT
1 TTTAATTTTAAAAATTTTATATTTAAATATT
*
4437175 TTTAATTTT-AAAATTTTATATTTATATATT
1 TTTAATTTTAAAAATTTTATATTTAAATATT
4437205 T
1 T
4437206 AAAAAGTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTAATTTTAAAAATTTTATATTTAAATATT
Found at i:4437197 original size:15 final size:15
Alignment explanation
Indices: 4437145--4437197 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
4437135 AATATTTTTA
4437145 TTTAT-TTTTAAAAAT
1 TTTATATTTT-AAAAT
4437160 TTTATA--TTAAATAT
1 TTTATATTTTAAA-AT
4437174 TTT-TAATTTTAAAAT
1 TTTAT-ATTTTAAAAT
4437189 TTTATATTT
1 TTTATATTT
4437198 ATATATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 4 0.12
14 8 0.25
15 14 0.44
16 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATATTTTAAAAT
Found at i:4441769 original size:16 final size:14
Alignment explanation
Indices: 4441741--4441786 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
4441731 CCTTATTTCC
4441741 TTTTTTTCATTTTA
1 TTTTTTTCATTTTA
4441755 TTTTTTTCAGTTTTTA
1 TTTTTTTCA--TTTTA
**
4441771 TTTTTTGAATTTTA
1 TTTTTTTCATTTTA
4441785 TT
1 TT
4441787 AATATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 16 0.57
16 12 0.43
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (14 bp):
TTTTTTTCATTTTA
Found at i:4442638 original size:20 final size:20
Alignment explanation
Indices: 4442601--4442639 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4442591 TGTTTTCAAA
*
4442601 TTTTCAATTTCAATATTTTT
1 TTTTCAATTTCAAAATTTTT
* *
4442621 TTTTCATTTTTAAAATTTT
1 TTTTCAATTTCAAAATTTT
4442640 AAAATATATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTCAATTTCAAAATTTTT
Found at i:4442842 original size:2 final size:2
Alignment explanation
Indices: 4442835--4442884 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
4442825 TTACATCCAA
4442835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4442877 AT AT AT AT
1 AT AT AT AT
4442885 TATTGATTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4443872 original size:40 final size:40
Alignment explanation
Indices: 4443819--4443894 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
4443809 TTGGGAGATA
* *
4443819 AAAAAAATAAGTTACAGATATTAATATTTGAATCTCGAAT
1 AAAAAAATAAGTTACAGATATTAAGATTCGAATCTCGAAT
4443859 AAAAAAATAAGTTACAGATATTAAGATTCGAATCTC
1 AAAAAAATAAGTTACAGATATTAAGATTCGAATCTC
4443895 AAACTTATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (40 bp):
AAAAAAATAAGTTACAGATATTAAGATTCGAATCTCGAAT
Found at i:4444610 original size:16 final size:17
Alignment explanation
Indices: 4444589--4444620 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4444579 ATATTAAAAA
4444589 ATATTTTTAT-ATTAAT
1 ATATTTTTATAATTAAT
4444605 ATATTTTTATAATTAA
1 ATATTTTTATAATTAA
4444621 ATTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTTTTATAATTAAT
Found at i:4445502 original size:18 final size:18
Alignment explanation
Indices: 4445479--4445545 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 18
4445469 AAGATTAAAT
4445479 TATTTTAATTTTGTGTTA
1 TATTTTAATTTTGTGTTA
* *
4445497 TATTTTAGATTTGATTATTTTTTA
1 TATTTTA-A--T--TT-TGTGTTA
4445521 TTATTTTAATTTTGTGTTA
1 -TATTTTAATTTTGTGTTA
4445540 TATTTT
1 TATTTT
4445546 GGATTTGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
18 13 0.34
19 6 0.16
20 2 0.05
21 1 0.03
22 1 0.03
23 2 0.05
24 6 0.16
25 7 0.18
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (18 bp):
TATTTTAATTTTGTGTTA
Found at i:4445536 original size:43 final size:43
Alignment explanation
Indices: 4445477--4445563 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
4445467 TTAAGATTAA
4445477 ATTATTTTAATTTTGTGTTATATTTTAGATTTGATTATTTTTT
1 ATTATTTTAATTTTGTGTTATATTTTAGATTTGATTATTTTTT
*
4445520 ATTATTTTAATTTTGTGTTATATTTTGGATTTGATTATTTTTT
1 ATTATTTTAATTTTGTGTTATATTTTAGATTTGATTATTTTTT
4445563 A
1 A
4445564 AAATTTGAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (43 bp):
ATTATTTTAATTTTGTGTTATATTTTAGATTTGATTATTTTTT
Found at i:4445577 original size:43 final size:43
Alignment explanation
Indices: 4445480--4445578 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
4445470 AGATTAAATT
* **
4445480 ATTTTAATTTTGTGTTATATTTTAGATTTGATTATTTTTTATT
1 ATTTGAATTTTGTGTTATATTTTAGATTTGATTATTTTTTAAA
* *
4445523 ATTTTAATTTTGTGTTATATTTTGGATTTGATTATTTTTTAAA
1 ATTTGAATTTTGTGTTATATTTTAGATTTGATTATTTTTTAAA
*
4445566 ATTTGAGTTTTGT
1 ATTTGAATTTTGT
4445579 TGATTGAACC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (43 bp):
ATTTGAATTTTGTGTTATATTTTAGATTTGATTATTTTTTAAA
Found at i:4447762 original size:11 final size:11
Alignment explanation
Indices: 4447746--4447772 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4447736 TTACAGTGAT
4447746 AATAAAATAAA
1 AATAAAATAAA
4447757 AATAAAATAAA
1 AATAAAATAAA
4447768 AATAA
1 AATAA
4447773 TAATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AATAAAATAAA
Done.