Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 41 of 120
Found at i:11098189 original size:64 final size:64
Alignment explanation
Indices: 11098082--11098349 Score: 303
Period size: 64 Copynumber: 4.2 Consensus size: 64
11098072 TGCAGGGGTC
* * * *
11098082 ACACAAGCGTGTGTCTAGGCCGTGTAACTCACTGATTATAAAATATGGATCACACAGGCCAAGA
1 ACACGAGCGTGTGTCCAGGCCGTGTAACTCACTGATTACAAAATACGGATCACACAGGCCAAGA
* * * * *
11098146 ACACGGGCGTGTGTCCAGGCTGTGTAACTCACTAATTACAAAATACAGATCACACGGGCCAAGGA
1 ACACGAGCGTGTGTCCAGGCCGTGTAACTCACTGATTACAAAATACGGATCACACAGGCCAA-GA
* ** * *
11098211 TACA-G-GAGTGTGTTTAGGCCATGTAACTCACTGATTAC-AAATACGGATCACACGGGCCAA-A
1 -ACACGAGCGTGTGTCCAGGCCGTGTAACTCACTGATTACAAAATACGGATCACACAGGCCAAGA
** * * *
11098272 GACACGAGCGTGTGTCCAGGTTGTGTAACTCACTGATTACAAAATAAGGATCACACAGGCAAAGG
1 -ACACGAGCGTGTGTCCAGGCCGTGTAACTCACTGATTACAAAATACGGATCACACAGGCCAAGA
11098337 ACAC-AGCGTGTGT
1 ACACGAGCGTGTGT
11098350 TACGCTGTGT
Statistics
Matches: 171, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
61 4 0.02
62 1 0.01
63 57 0.33
64 103 0.60
65 3 0.02
66 3 0.02
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (64 bp):
ACACGAGCGTGTGTCCAGGCCGTGTAACTCACTGATTACAAAATACGGATCACACAGGCCAAGA
Found at i:11098317 original size:127 final size:127
Alignment explanation
Indices: 11098090--11098350 Score: 366
Period size: 127 Copynumber: 2.1 Consensus size: 127
11098080 TCACACAAGC
* * * *
11098090 GTGTGTCTAGGCCGTGTAACTCACTGATTATAAAATATGGATCACACAGGCCAAGAACACGGGCG
1 GTGTGTTTAGGCCATGTAACTCACTGATTATAAAATACGGATCACACAGGCCAAGAACACGAGCG
* * *
11098155 TGTGTCCAGGCTGTGTAACTCACTAATTACAAAATACA-GATCACACGGGCCAAGGATACAGGA
66 TGTGTCCAGGCTGTGTAACTCACTAATTACAAAATA-AGGATCACACAGGCAAAGGACACA-GA
* *
11098218 GTGTGTTTAGGCCATGTAACTCACTGATTA-CAAATACGGATCACACGGGCCAA-AGACACGAGC
1 GTGTGTTTAGGCCATGTAACTCACTGATTATAAAATACGGATCACACAGGCCAAGA-ACACGAGC
* * *
11098281 GTGTGTCCAGGTTGTGTAACTCACTGATTACAAAATAAGGATCACACAGGCAAAGGACACAGC
65 GTGTGTCCAGGCTGTGTAACTCACTAATTACAAAATAAGGATCACACAGGCAAAGGACACAGA
11098344 GTGTGTT
1 GTGTGTT
11098351 ACGCTGTGTA
Statistics
Matches: 119, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
126 10 0.08
127 81 0.68
128 28 0.24
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (127 bp):
GTGTGTTTAGGCCATGTAACTCACTGATTATAAAATACGGATCACACAGGCCAAGAACACGAGCG
TGTGTCCAGGCTGTGTAACTCACTAATTACAAAATAAGGATCACACAGGCAAAGGACACAGA
Found at i:11100069 original size:23 final size:23
Alignment explanation
Indices: 11100039--11100129 Score: 146
Period size: 23 Copynumber: 4.0 Consensus size: 23
11100029 GTGTTATTAA
*
11100039 TCAGTGGTAGCTTCGGCTACGTT
1 TCAGTGGTAGCTTCGGCTACATT
*
11100062 TCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
*
11100085 ACAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
11100108 TTAGTGGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
11100130 AACAGTGTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:11100093 original size:46 final size:46
Alignment explanation
Indices: 11100040--11100136 Score: 176
Period size: 46 Copynumber: 2.1 Consensus size: 46
11100030 TGTTATTAAT
*
11100040 CAGTGGTAGCTTCGGCTACGTTTCAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
*
11100086 CAGTGGTAGCTTCGGCTACATTTTAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
11100132 CAGTG
1 CAGTG
11100137 TTGCACTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
Found at i:11107174 original size:27 final size:27
Alignment explanation
Indices: 11107144--11107223 Score: 106
Period size: 27 Copynumber: 3.0 Consensus size: 27
11107134 GGAACTGATT
*
11107144 CTTCAGAGTTCGCCATACGTACTATTC
1 CTTCAGAGTTCACCATACGTACTATTC
*
11107171 CTTCAGAGTTCATCATACGTACTATTC
1 CTTCAGAGTTCACCATACGTACTATTC
* * **
11107198 CTTTAGATTTTTCCATACGTACTATT
1 CTTCAGAGTTCACCATACGTACTATT
11107224 TGTTCAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (27 bp):
CTTCAGAGTTCACCATACGTACTATTC
Found at i:11107234 original size:27 final size:27
Alignment explanation
Indices: 11107156--11107251 Score: 77
Period size: 27 Copynumber: 3.6 Consensus size: 27
11107146 TCAGAGTTCG
* * **
11107156 CCATACGTACTATTCCTTCAGAGTTCAT
1 CCATACGTACTATTTCTTCA-AATTTTT
* * *
11107184 -CATACGTACTATTCCTTTAGATTTTT
1 CCATACGTACTATTTCTTCAAATTTTT
*
11107210 CCATACGTACTATTTGTTCAAATTTTT
1 CCATACGTACTATTTCTTCAAATTTTT
* * *
11107237 TCATACTTACCATTT
1 CCATACGTACTATTT
11107252 TTAGAGTTAG
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
26 3 0.05
27 52 0.95
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (27 bp):
CCATACGTACTATTTCTTCAAATTTTT
Found at i:11107424 original size:27 final size:28
Alignment explanation
Indices: 11107380--11107447 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
11107370 AGGCGCCATG
*
11107380 AAGGCGTTCC-TTTCCATAGATCGTCACA
1 AAGGC-TTCCATTTCCATAGATCGCCACA
* *
11107408 AAGGTTTCCATTT-CATAGATTGCCACA
1 AAGGCTTCCATTTCCATAGATCGCCACA
11107435 AAGGCTTCCATTT
1 AAGGCTTCCATTT
11107448 TATGGTGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 28 0.80
28 7 0.20
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (28 bp):
AAGGCTTCCATTTCCATAGATCGCCACA
Found at i:11110154 original size:10 final size:10
Alignment explanation
Indices: 11110139--11110164 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
11110129 TTTAATATTT
11110139 TATTTTTAAA
1 TATTTTTAAA
11110149 TATTTTTAAA
1 TATTTTTAAA
11110159 TATTTT
1 TATTTT
11110165 ATAAGTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TATTTTTAAA
Found at i:11110895 original size:2 final size:2
Alignment explanation
Indices: 11110888--11110940 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
11110878 TCCTCCCTGT
11110888 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
11110930 TA TA TC TA TA T
1 TA TA TA TA TA T
11110941 GTGCGTGAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11115367 original size:21 final size:21
Alignment explanation
Indices: 11115343--11115384 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
11115333 TTCTTAGTTA
11115343 AATTACTTAGTTAATTTTTAG
1 AATTACTTAGTTAATTTTTAG
11115364 AATTACTTAGTTAATTTTTAG
1 AATTACTTAGTTAATTTTTAG
11115385 TTTTTAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (21 bp):
AATTACTTAGTTAATTTTTAG
Found at i:11121660 original size:22 final size:24
Alignment explanation
Indices: 11121635--11121678 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
11121625 AATTTGTTCA
11121635 ACTTTAACTT-TTAT-TCAAAAAC
1 ACTTTAACTTGTTATATCAAAAAC
*
11121657 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
11121679 CATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAAAC
Found at i:11124291 original size:20 final size:20
Alignment explanation
Indices: 11124262--11124299 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11124252 GAACCAGATG
*
11124262 AAATGGTAGATAAAACTACA
1 AAATGATAGATAAAACTACA
*
11124282 AAATGATAGATCAAACTA
1 AAATGATAGATAAAACTA
11124300 TACGCCAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (20 bp):
AAATGATAGATAAAACTACA
Found at i:11128114 original size:19 final size:20
Alignment explanation
Indices: 11128084--11128126 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
11128074 GCTATAGGTA
11128084 TAATATCTGTTCCGACCAGG
1 TAATATCTGTTCCGACCAGG
* *
11128104 TAATA-CTGTTCTGACTAGG
1 TAATATCTGTTCCGACCAGG
11128123 TAAT
1 TAAT
11128127 TCGAAGATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (20 bp):
TAATATCTGTTCCGACCAGG
Found at i:11129374 original size:22 final size:22
Alignment explanation
Indices: 11129332--11129375 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11129322 CCCATGTTTC
*
11129332 TTTTAATTTATTTAATTTTGAA
1 TTTTAATTTATTTAATGTTGAA
*
11129354 TTTTAGTTTAATTTAA-GTTGAA
1 TTTTAATTT-ATTTAATGTTGAA
11129376 AATAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (22 bp):
TTTTAATTTATTTAATGTTGAA
Found at i:11130096 original size:15 final size:15
Alignment explanation
Indices: 11130076--11130116 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
11130066 CAAAACCCAT
11130076 AACACCAACCTTCAA
1 AACACCAACCTTCAA
*
11130091 AACACCAAAC--CAA
1 AACACCAACCTTCAA
*
11130104 AACACCCACCTTC
1 AACACCAACCTTC
11130117 CTCCATAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
13 11 0.52
15 10 0.48
ACGTcount: A:0.46, C:0.44, G:0.00, T:0.10
Consensus pattern (15 bp):
AACACCAACCTTCAA
Found at i:11132252 original size:40 final size:40
Alignment explanation
Indices: 11132208--11132293 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
11132198 TGCTACTTCA
*
11132208 AAAAGTCATATTTAAGGTTTGATCAGATTTTTGACTTTGT
1 AAAAGTCATATTTAAGGTTTGATCAGATTTTTGACTTCGT
*
11132248 AAAAGACATATTTAAGGTTTGATCAGATTTTTGACTTCGT
1 AAAAGTCATATTTAAGGTTTGATCAGATTTTTGACTTCGT
11132288 AAAAGT
1 AAAAGT
11132294 TTTATTTAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (40 bp):
AAAAGTCATATTTAAGGTTTGATCAGATTTTTGACTTCGT
Found at i:11138859 original size:12 final size:12
Alignment explanation
Indices: 11138829--11138861 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
11138819 TATATATTTT
11138829 AAAATT-ATATA
1 AAAATTAATATA
11138840 AAAA-TAATATA
1 AAAATTAATATA
11138851 AAAATTAATAT
1 AAAATTAATAT
11138862 GGGCGGGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:11148084 original size:18 final size:19
Alignment explanation
Indices: 11148042--11148092 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
11148032 ATTTCATTTC
*
11148042 TCATTTCATCATTTCATATT
1 TCATTTC-TCATCTCATATT
11148062 TCATTTCTCATCTCATA-T
1 TCATTTCTCATCTCATATT
11148080 TCATTTCTCATCT
1 TCATTTCTCATCT
11148093 TTGCCATCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 14 0.47
19 9 0.30
20 7 0.23
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (19 bp):
TCATTTCTCATCTCATATT
Found at i:11152791 original size:11 final size:11
Alignment explanation
Indices: 11152777--11152802 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11152767 ATTTATCAGC
11152777 TATTATTATTT
1 TATTATTATTT
11152788 TATTATTATTT
1 TATTATTATTT
11152799 TATT
1 TATT
11152803 CCAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTATTT
Found at i:11157302 original size:22 final size:22
Alignment explanation
Indices: 11157277--11157318 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
11157267 TATTTTCTTC
11157277 CTTA-TTATTCTATTTTAATTAT
1 CTTAGTTATT-TATTTTAATTAT
11157299 CTTAGTTATTTATTTTAATT
1 CTTAGTTATTTATTTTAATT
11157319 GTTTTATCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.64
Consensus pattern (22 bp):
CTTAGTTATTTATTTTAATTAT
Found at i:11159160 original size:5 final size:5
Alignment explanation
Indices: 11159150--11159174 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11159140 CGAAAATTGA
11159150 TTAAT TTAAT TTAAT TTAAT TTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT
11159175 AAATAATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTAAT
Found at i:11164682 original size:30 final size:30
Alignment explanation
Indices: 11164624--11164711 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
11164614 TTTCTTTGCT
*
11164624 TATATA-CTAAATATAATAATAA-AAAATAA
1 TATATATCTAATTA-AATAATAATAAAATAA
* *
11164653 TA-ATATCTCATTAAAATATTAATAAAATAA
1 TATATATCTAATT-AAATAATAATAAAATAA
* *
11164683 TATTTATCTAATTAAATAATCATAAAATA
1 TATATATCTAATTAAATAATAATAAAATA
11164712 TTAAAATATC
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 3 0.06
29 13 0.27
30 24 0.50
31 8 0.17
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (30 bp):
TATATATCTAATTAAATAATAATAAAATAA
Found at i:11170903 original size:18 final size:17
Alignment explanation
Indices: 11170870--11170908 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
11170860 TTGTATAAAT
11170870 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
11170888 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
11170905 TGTG
1 TGTG
11170909 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:11171026 original size:8 final size:8
Alignment explanation
Indices: 11171013--11171041 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
11171003 CACTAGAGAC
11171013 CAGTGTTA
1 CAGTGTTA
11171021 CAGTGTTA
1 CAGTGTTA
11171029 CAGTGTTA
1 CAGTGTTA
11171037 CAGTG
1 CAGTG
11171042 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:11171155 original size:23 final size:23
Alignment explanation
Indices: 11171128--11171203 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
11171118 AGTGTTATTG
11171128 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
11171151 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
11171174 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
11171197 ATCAGTG
1 ATCAGTG
11171204 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:11192352 original size:34 final size:34
Alignment explanation
Indices: 11192307--11192420 Score: 94
Period size: 34 Copynumber: 3.4 Consensus size: 34
11192297 TAGTTGAGTT
11192307 ATGGCAACATATGAAGTCCGTTAGGACAATAAAC
1 ATGGCAACATATGAAGTCCGTTAGGACAATAAAC
* * **
11192341 ATGGCATCATAT-AA-T--G-TAAGACCATAGCTGGAC
1 ATGGCAACATATGAAGTCCGTTAGGA-CA-A--TAAAC
*
11192374 TATGGCAACATATGAAGTCCGTCAGGACAATAAAC
1 -ATGGCAACATATGAAGTCCGTTAGGACAATAAAC
*
11192409 ATGGCATCATAT
1 ATGGCAACATAT
11192421 TATGTAAGAC
Statistics
Matches: 60, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
29 4 0.07
30 3 0.05
31 1 0.02
32 1 0.02
33 5 0.08
34 33 0.55
35 5 0.08
36 1 0.02
37 1 0.02
38 3 0.05
39 3 0.05
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (34 bp):
ATGGCAACATATGAAGTCCGTTAGGACAATAAAC
Found at i:11192401 original size:68 final size:68
Alignment explanation
Indices: 11192285--11192739 Score: 502
Period size: 68 Copynumber: 6.7 Consensus size: 68
11192275 AGTCTATAAG
* * * * ** *
11192285 AGTGTAAGACTATAGTTGAGTTATGGCAACATATGAAGTCCGTTAGGACAATAAACATGGCATCA
1 AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGACAATAAACATGACATCA
11192350 TAT
66 TAT
* * * *
11192353 AATGTAAGACCATAGCTGGACTATGGCAACATATGAAGTCCGTCAGGACAATAAACATGGCATCA
1 AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGACAATAAACATGACATCA
11192418 TATT
66 TA-T
* * * * *
11192422 A-TGTAAGACCATAGTTGGGCTATGGCAACATATGAAATTCGCCAGGATAATAAACATGACACCA
1 AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGACAATAAACATGACATCA
11192486 TAT
66 TAT
* * * * **
11192489 AGTGTAAGACCATAGCTGGGCTATGGCAATATATGAAGTCCGCCAGGACCATTAATATGGTATCA
1 AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGACAATAAACATGACATCA
11192554 TAT
66 TAT
* * * * * * *
11192557 AGTGTAAGACTATAGTTGGGTTAT-GCTAGCATATGAAGTCCACCAAGATAATAAACATGACATC
1 AGTGTAAGACCATAGCTGGGCTATGGC-AACATATGAAGTCCGCCAGGACAATAAACATGACATC
*
11192621 AAAT
65 ATAT
* * *
11192625 AGTGTAAGACCATAGCTGGGCTATGGAAACATCTGAAGTCCGCTAGGACAATAAACATGACATCA
1 AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGACAATAAACATGACATCA
*
11192690 TGT
66 TAT
* * * * * **
11192693 AGT-TAAGATCATAGTTAGGCTATTGCAATATATGAAGTTTGCCAGGA
1 AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGA
11192740 TGGTAAACAT
Statistics
Matches: 321, Mismatches: 62, Indels: 9
0.82 0.16 0.02
Matches are distributed among these distances:
67 38 0.12
68 280 0.87
69 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (68 bp):
AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGACAATAAACATGACATCA
TAT
Found at i:11197603 original size:14 final size:14
Alignment explanation
Indices: 11197584--11197623 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
11197574 TTGATTGCCA
11197584 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
11197598 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
11197612 GTAAAATGTTTT
1 GTAAAATGTTTT
11197624 ACTTTTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:11197630 original size:34 final size:35
Alignment explanation
Indices: 11197592--11197658 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
11197582 CAGTAAAATG
* *
11197592 TTTTCCGTAAAATGATTT-CTGTAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
11197626 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
11197659 CTAGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:11197632 original size:20 final size:20
Alignment explanation
Indices: 11197607--11197646 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
11197597 CGTAAAATGA
*
11197607 TTTCTGTAAAATGTTTTACT
1 TTTCTGTAAAATGATTTACT
11197627 TTTCTGTAAAATGATTTACT
1 TTTCTGTAAAATGATTTACT
11197647 GGAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (20 bp):
TTTCTGTAAAATGATTTACT
Found at i:11197790 original size:48 final size:48
Alignment explanation
Indices: 11197737--11197846 Score: 202
Period size: 48 Copynumber: 2.3 Consensus size: 48
11197727 GAAAAGTTGT
11197737 TTTTACATATATTAATATATATTAATAATTTTTTATATTTTAAATTAC
1 TTTTACATATATTAATATATATTAATAATTTTTTATATTTTAAATTAC
**
11197785 TTTTACATATATTAATATATATTAATAATTTTTTATATTTTAAATTGT
1 TTTTACATATATTAATATATATTAATAATTTTTTATATTTTAAATTAC
11197833 TTTTACATATATTA
1 TTTTACATATATTA
11197847 CAATGATTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (48 bp):
TTTTACATATATTAATATATATTAATAATTTTTTATATTTTAAATTAC
Found at i:11200400 original size:12 final size:12
Alignment explanation
Indices: 11200383--11200410 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
11200373 CTAAAATAAG
11200383 ATAAAATAACAT
1 ATAAAATAACAT
11200395 ATAAAATAACAT
1 ATAAAATAACAT
11200407 ATAA
1 ATAA
11200411 CATAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (12 bp):
ATAAAATAACAT
Found at i:11202215 original size:7 final size:7
Alignment explanation
Indices: 11202205--11202244 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
11202195 TTCTTTTCGA
11202205 TTTTTAT
1 TTTTTAT
11202212 TTTTTAT
1 TTTTTAT
11202219 TTTTATAT
1 TTTT-TAT
11202227 TTTTTAT
1 TTTTTAT
*
11202234 TATTTGAT
1 T-TTTTAT
11202242 TTT
1 TTT
11202245 ATAGTATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 17 0.57
8 13 0.43
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (7 bp):
TTTTTAT
Found at i:11202231 original size:15 final size:14
Alignment explanation
Indices: 11202205--11202244 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
11202195 TTCTTTTCGA
11202205 TTTTTATTTTTTAT
1 TTTTTATTTTTTAT
11202219 TTTTATATTTTTTAT
1 TTTT-TATTTTTTAT
*
11202234 TATTTGATTTT
1 T-TTTTATTTT
11202245 ATAGTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 16 0.70
16 3 0.13
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTTTATTTTTTAT
Found at i:11202717 original size:8 final size:8
Alignment explanation
Indices: 11202704--11202739 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
11202694 AAATTAATTC
11202704 AAAAAAAT
1 AAAAAAAT
11202712 AAAAAAAT
1 AAAAAAAT
11202720 AAAGAAAAT
1 AAA-AAAAT
*
11202729 TAAAAAAT
1 AAAAAAAT
11202737 AAA
1 AAA
11202740 TTGGTTTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:11202733 original size:17 final size:17
Alignment explanation
Indices: 11202707--11202739 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11202697 TTAATTCAAA
11202707 AAAATAAAAAAATAAAG
1 AAAATAAAAAAATAAAG
*
11202724 AAAATTAAAAAATAAA
1 AAAATAAAAAAATAAA
11202740 TTGGTTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAATAAAAAAATAAAG
Found at i:11202839 original size:18 final size:18
Alignment explanation
Indices: 11202818--11202853 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11202808 ATTAGTTCTA
11202818 AAAAAGAGAAAAAAAATT
1 AAAAAGAGAAAAAAAATT
*
11202836 AAAAAGATAAAAAAAATT
1 AAAAAGAGAAAAAAAATT
11202854 TCCCTTTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (18 bp):
AAAAAGAGAAAAAAAATT
Found at i:11206168 original size:30 final size:30
Alignment explanation
Indices: 11206128--11206197 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
11206118 TAGACTTTTT
11206128 AAAT-ATAAAATTGTACA-TTAATCTCTTAA
1 AAATGATAAAATTGTA-ATTTAATCTCTTAA
* * *
11206157 ATATGATAAAATTTTAATTTAATCTTTTAA
1 AAATGATAAAATTGTAATTTAATCTCTTAA
*
11206187 AAATTATAAAA
1 AAATGATAAAA
11206198 ATATTAACTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (30 bp):
AAATGATAAAATTGTAATTTAATCTCTTAA
Found at i:11207475 original size:26 final size:25
Alignment explanation
Indices: 11207445--11207603 Score: 105
Period size: 24 Copynumber: 6.2 Consensus size: 25
11207435 TTGTTATTAA
11207445 ATTTTAATAAGATTATTATTAAATAT
1 ATTTTAATAA-ATTATTATTAAATAT
* * *
11207471 ATTTTAAT-AATAAATAATTTAATCAT
1 ATTTTAATAAAT-TATTATTAAAT-AT
11207497 ATTTTAATATAATTATTATTAAATAT
1 ATTTTAATA-AATTATTATTAAATAT
* * *
11207523 AATTTAATAAA--AGTAATAATATAT
1 ATTTTAATAAATTATTATTAA-ATAT
* * *
11207547 AATTTAATAACATTCTTA--ATATAT
1 ATTTTAATAA-ATTATTATTAAATAT
11207571 ATTTTAATATAATT-TTATTTTAAATTAT
1 ATTTTAATA-AATTATTA--TTAAA-TAT
11207599 ATTTT
1 ATTTT
11207604 GAAACAAAAT
Statistics
Matches: 105, Mismatches: 14, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
23 9 0.09
24 31 0.30
25 14 0.13
26 28 0.27
27 12 0.11
28 11 0.10
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (25 bp):
ATTTTAATAAATTATTATTAAATAT
Found at i:11208240 original size:19 final size:20
Alignment explanation
Indices: 11208216--11208265 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
11208206 ACATAAAAAA
11208216 AATAAAATGTAATATAA-AT-
1 AATAAAAT-TAATATAACATG
11208235 AATAAAATTAATATAACATG
1 AATAAAATTAATATAACATG
11208255 AAT-AAATTAAT
1 AATAAAATTAAT
11208266 TTCAATAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.28
19 18 0.62
20 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (20 bp):
AATAAAATTAATATAACATG
Found at i:11211783 original size:196 final size:194
Alignment explanation
Indices: 11211372--11211992 Score: 753
Period size: 196 Copynumber: 3.2 Consensus size: 194
11211362 ATGACAAGAA
11211372 AAAAGTTGAGGTACCAAATTATGTCAAAAATTAAAGTATAAAGATTAAATTTCAAAATTGAGCAT
1 AAAAGTTGAGGTACCAAATTATGTCAAAAATTAAAGTATAAAGATTAAATTTCAAAATTGAGCAT
* *
11211437 ATCATAGGCACCAAATTTG-AATTTGACCAATGTTATATGTAATCTTAAAAAAGAAGTAAAAGGT
66 ATCATAGG-ACCAAATTTGAAATTTGACCATTG-T-TATGTAATCTCAAAAAAGAAGTAAAA-GT
* * * *
11211501 CGTGTATTTGGACACGTGTACATCAACATTTTAATCAAAACGAAGCATTTAG-GATGACTATGAC
127 CGTGTATTTGGACA-GTGTACGTCAACATTTTAATCAGAATGAAGTATTTAGTG-TGACTATGAC
*
11211565 ATTAT
190 ATAAT
* *
11211570 AAAAGTTGAGGTACCAAAATATGTCAAAAATTAAAGTATACAGATTAAATTTCAAAATTGAGCAT
1 AAAAGTTGAGGTACCAAATTATGTCAAAAATTAAAGTATAAAGATTAAATTTCAAAATTGAGCAT
* *
11211635 ATCATAGGACCAAATTTGAAATTTGACTATTGTTATGTAATCTCAAAAAAGAAGTAAAATGTCAT
66 ATCATAGGACCAAATTTGAAATTTGACCATTGTTATGTAATCTCAAAAAAGAAGTAAAA-GTCGT
* *
11211700 GTATTTGGACATGTGTATGTCAACATTTTAA-CTAGAATGAAGTATTTAGTGTGACTATGACGTA
130 GTATTTGGACA-GTGTACGTCAACATTTTAATC-AGAATGAAGTATTTAGTGTGACTATGACATA
11211764 AT
193 AT
* ** * * * *
11211766 AAAAGTTGAGGTACCAAATTATATCAAAACGTAAAGTATAGAGATTAAGTTTCATATTTGAGCAT
1 AAAAGTTGAGGTACCAAATTATGTCAAAAATTAAAGTATAAAGATTAAATTTCAAAATTGAGCAT
* * * * *
11211831 AAT-ATACGAACCAACA-TTAAAATTTGACCATTATTATATAATCTC---AAAGAAGTAAAAGTT
66 -ATCATA-GGACCAA-ATTTGAAATTTGACCATTGTTATGTAATCTCAAAAAAGAAGTAAAAGTC
* * *
11211891 GTATATTTGGGTACA-TGTACGTCAACATTTTAATCAGAATGAAATATTTAGAT-T-AGCAATGA
128 GTGTATTT-GG-ACAGTGTACGTCAACATTTTAATCAGAATGAAGTATTTAG-TGTGA-CTATGA
*
11211953 CATTAT
189 CATAAT
11211959 AAAAGTTGAGGTACCAAATTATGTC-AAAATTAAA
1 AAAAGTTGAGGTACCAAATTATGTCAAAAATTAAA
11211993 TCCAAAACTT
Statistics
Matches: 373, Mismatches: 39, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
192 8 0.02
193 74 0.20
194 16 0.04
195 4 0.01
196 143 0.38
197 45 0.12
198 83 0.22
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (194 bp):
AAAAGTTGAGGTACCAAATTATGTCAAAAATTAAAGTATAAAGATTAAATTTCAAAATTGAGCAT
ATCATAGGACCAAATTTGAAATTTGACCATTGTTATGTAATCTCAAAAAAGAAGTAAAAGTCGTG
TATTTGGACAGTGTACGTCAACATTTTAATCAGAATGAAGTATTTAGTGTGACTATGACATAAT
Found at i:11214432 original size:18 final size:18
Alignment explanation
Indices: 11214409--11214445 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
11214399 AAAAATTGTT
11214409 GAGAGTACCATCAAATGA
1 GAGAGTACCATCAAATGA
*
11214427 GAGAGTGCCATCAAATGA
1 GAGAGTACCATCAAATGA
11214445 G
1 G
11214446 GATACTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.27, T:0.16
Consensus pattern (18 bp):
GAGAGTACCATCAAATGA
Found at i:11224706 original size:41 final size:42
Alignment explanation
Indices: 11224627--11224725 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 42
11224617 TGCAGTTTCT
* *
11224627 CCACAGCTCGTATGAGCAACATCGTGTAGCTAACATCCTGAC
1 CCACAGCTCGTGTGAGCAACATCGTATAGCTAACATCCTGAC
* * *
11224669 CCATAGCTCGTGTGAGCAGCAT-GTATAGCTAACATCCTGAT
1 CCACAGCTCGTGTGAGCAACATCGTATAGCTAACATCCTGAC
11224710 CCACAGCTCGTGTGAG
1 CCACAGCTCGTGTGAG
11224726 AAGACCTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 32 0.63
42 19 0.37
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (42 bp):
CCACAGCTCGTGTGAGCAACATCGTATAGCTAACATCCTGAC
Found at i:11227273 original size:19 final size:20
Alignment explanation
Indices: 11227251--11227296 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
11227241 TTAATTTAAG
*
11227251 TAATTTAGTTTAATT-ACCT
1 TAATTTAGCTTAATTAACCT
* *
11227270 TAATTTCGCTTAATTAACTT
1 TAATTTAGCTTAATTAACCT
11227290 TAATTTA
1 TAATTTA
11227297 TTTTTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.52
Consensus pattern (20 bp):
TAATTTAGCTTAATTAACCT
Found at i:11235011 original size:45 final size:45
Alignment explanation
Indices: 11234936--11235107 Score: 204
Period size: 45 Copynumber: 3.8 Consensus size: 45
11234926 TACACGATGG
* * * * * *
11234936 ATCAACACATAGC-ACCACCCTTATAGTCAATGATACTCAGTGGA
1 ATCAACACACAACAACCACCTTTATAATCAATGATACCCGGTGGA
* * * * *
11234980 ATCAGCACATAGCAACCACCTTCATAATCAAT-AGCACCCGGTGGA
1 ATCAACACACAACAACCACCTTTATAATCAATGA-TACCCGGTGGA
11235025 ATCAACACACAACAACCACCTTTATAATCAATGATACCCGGTGGA
1 ATCAACACACAACAACCACCTTTATAATCAATGATACCCGGTGGA
* *
11235070 ATCAGCACACAACAACCACCTTTATAATCAATGGTACC
1 ATCAACACACAACAACCACCTTTATAATCAATGATACC
11235108 TGGTACACAT
Statistics
Matches: 111, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
44 13 0.12
45 97 0.87
46 1 0.01
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (45 bp):
ATCAACACACAACAACCACCTTTATAATCAATGATACCCGGTGGA
Found at i:11242556 original size:19 final size:19
Alignment explanation
Indices: 11242513--11242559 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
11242503 TAAAGTATAA
*
11242513 ATTTTGAAATTTTTATAAAT
1 ATTTTGAAA-TTTTAAAAAT
11242533 ATTTTGAAA-TTTAAAAATT
1 ATTTTGAAATTTTAAAAA-T
11242552 ATTTTGAA
1 ATTTTGAA
11242560 TTATTTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 9 0.36
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (19 bp):
ATTTTGAAATTTTAAAAAT
Found at i:11242939 original size:19 final size:19
Alignment explanation
Indices: 11242915--11242962 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
11242905 AAAAAATATA
11242915 TATATTTTTCATAATTTTC
1 TATATTTTTCATAATTTTC
** *
11242934 TATATTTTTTGTAATTTTT
1 TATATTTTTCATAATTTTC
11242953 TATCATTTTT
1 TAT-ATTTTT
11242963 ATATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (19 bp):
TATATTTTTCATAATTTTC
Found at i:11242942 original size:10 final size:10
Alignment explanation
Indices: 11242915--11242986 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
11242905 AAAAAATATA
11242915 TATATTTTTC
1 TATATTTTTC
*
11242925 -ATAATTTTC
1 TATATTTTTC
11242934 TATATTTTT-
1 TATATTTTTC
*
11242943 TGTAATTTTT-
1 TAT-ATTTTTC
*
11242953 TATCATTTTTA
1 TAT-ATTTTTC
*
11242964 TAT-TTTTTT
1 TATATTTTTC
*
11242973 TATAATTTTC
1 TATATTTTTC
11242983 TATA
1 TATA
11242987 GTTTCTTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
9 18 0.36
10 29 0.58
11 3 0.06
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (10 bp):
TATATTTTTC
Found at i:11242962 original size:11 final size:10
Alignment explanation
Indices: 11242913--11243001 Score: 51
Period size: 10 Copynumber: 8.8 Consensus size: 10
11242903 TTAAAAAATA
11242913 TATATATTTTT
1 TATAT-TTTTT
* * *
11242924 CATAATTTTC
1 TATATTTTTT
11242934 TATATTTTTT
1 TATATTTTTT
11242944 GTA-A-TTTTT
1 -TATATTTTTT
*
11242953 TATCATTTTTA
1 TAT-ATTTTTT
11242964 TAT-TTTTTT
1 TATATTTTTT
* *
11242973 TATAATTTTC
1 TATATTTTTT
11242983 TATAGTTTCTTT
1 TATA-TTT-TTT
11242995 TA-ATTTT
1 TATATTTT
11243002 CTATAATTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
8 2 0.03
9 14 0.24
10 24 0.41
11 15 0.25
12 4 0.07
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (10 bp):
TATATTTTTT
Found at i:11242971 original size:20 final size:22
Alignment explanation
Indices: 11242948--11243006 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 22
11242938 TTTTTTGTAA
*
11242948 TTTTTTATCATTTT-TATA-TT
1 TTTTTTATAATTTTCTATAGTT
11242968 TTTTTTATAATTTTCTATAG-T
1 TTTTTTATAATTTTCTATAGTT
*
11242989 TTCTTT-TAATTTTCTATA
1 TTTTTTATAATTTTCTATA
11243007 ATTATTTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 25 0.71
21 10 0.29
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTTATAATTTTCTATAGTT
Found at i:11243140 original size:27 final size:27
Alignment explanation
Indices: 11243074--11243147 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
11243064 AGTTTTTCTG
* *
11243074 ATTTTTTATTAATTTTTAT-ATTTATA
1 ATTTTCTATTAATTTTTATAATGTATA
*
11243100 ATTTTCTAAATAATTTTTATAATGGTAT-
1 ATTTTCT-ATTAATTTTTATAAT-GTATA
*
11243128 GTTTTCTATTAATTTTTATA
1 ATTTTCTATTAATTTTTATA
11243148 TATTTTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 6 0.15
27 23 0.57
28 8 0.20
29 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (27 bp):
ATTTTCTATTAATTTTTATAATGTATA
Found at i:11244869 original size:22 final size:21
Alignment explanation
Indices: 11244825--11244877 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
11244815 TATTTATAAA
*
11244825 TTTTTTAT-AATTTTGTATGT
1 TTTTTTATAAATTTTGTATAT
*
11244845 TTTTTTATAGAATTTTGTGTAT
1 TTTTTTATA-AATTTTGTATAT
*
11244867 TTTTATATAAA
1 TTTTTTATAAA
11244878 AAAAGCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.29
21 2 0.07
22 18 0.64
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTTTTATAAATTTTGTATAT
Found at i:11257638 original size:27 final size:26
Alignment explanation
Indices: 11257608--11257661 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
11257598 CTCTTTCGAG
*
11257608 TTAATAAATTCTCTTTGAGCTTTCTTT
1 TTAAGAAATTCTC-TTGAGCTTTCTTT
* * *
11257635 TTAAGAATTTTTCTTGAGTTTTCTTT
1 TTAAGAAATTCTCTTGAGCTTTCTTT
11257661 T
1 T
11257662 AGAATAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.59
Consensus pattern (26 bp):
TTAAGAAATTCTCTTGAGCTTTCTTT
Found at i:11258595 original size:10 final size:10
Alignment explanation
Indices: 11258577--11258612 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
11258567 ATAAGAAGTC
11258577 TAAAGAATATA
1 TAAA-AATATA
11258588 TAAAAATATA
1 TAAAAATATA
11258598 TAAAAATATA
1 TAAAAATATA
11258608 -AAAAA
1 TAAAAA
11258613 CCCCAAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 5 0.20
10 16 0.64
11 4 0.16
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (10 bp):
TAAAAATATA
Found at i:11260717 original size:20 final size:20
Alignment explanation
Indices: 11260663--11260718 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
11260653 TGAAAAAATC
** *
11260663 AAAGTATCGATACCCTTAGT
1 AAAGTATCGATACTTTTAAT
* * *
11260683 TAAGTATTGACACTTTTAAT
1 AAAGTATCGATACTTTTAAT
11260703 AAAGTATCGATACTTT
1 AAAGTATCGATACTTT
11260719 ATCAGGGTAT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (20 bp):
AAAGTATCGATACTTTTAAT
Found at i:11261600 original size:28 final size:28
Alignment explanation
Indices: 11261552--11261625 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
11261542 ATACAGAGGG
* *
11261552 CACCGAAGTGGATTAACAGAATAGAACAA
1 CACCGAAGT-GCTTATCAGAATAGAACAA
*
11261581 CACC-AATGTGCTTATCAGAATAGAGCAA
1 CACCGAA-GTGCTTATCAGAATAGAACAA
11261609 CACCGAAGTGCTTATCA
1 CACCGAAGTGCTTATCA
11261626 AAACAGAGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
28 32 0.80
29 8 0.20
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (28 bp):
CACCGAAGTGCTTATCAGAATAGAACAA
Found at i:11261633 original size:28 final size:28
Alignment explanation
Indices: 11261578--11261633 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
11261568 CAGAATAGAA
* *
11261578 CAACACCAATGTGCTTATCAGAATAGAG
1 CAACACCAATGTGCTTATCAAAACAGAG
11261606 CAACACCGAA-GTGCTTATCAAAACAGAG
1 CAACACC-AATGTGCTTATCAAAACAGAG
11261634 AGCTCATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (28 bp):
CAACACCAATGTGCTTATCAAAACAGAG
Found at i:11268113 original size:25 final size:25
Alignment explanation
Indices: 11268085--11268134 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
11268075 CTTTTACAAC
* *
11268085 ATTAGAAAACATACCCCATTTAGAG
1 ATTAGAAAACATAACACATTTAGAG
**
11268110 ATTAGAACTCATAACACATTTAGAG
1 ATTAGAAAACATAACACATTTAGAG
11268135 GATTTTGTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (25 bp):
ATTAGAAAACATAACACATTTAGAG
Found at i:11272751 original size:15 final size:17
Alignment explanation
Indices: 11272726--11272757 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11272716 AGTAACAATA
11272726 ATTAGTACAGTA-ACAG
1 ATTAGTACAGTATACAG
11272742 ATTA-TACAGTATACAG
1 ATTAGTACAGTATACAG
11272758 GTCCTACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (17 bp):
ATTAGTACAGTATACAG
Found at i:11279893 original size:17 final size:17
Alignment explanation
Indices: 11279873--11279907 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11279863 AGTTCTCGAA
11279873 AAAATATCGAAA-AAATT
1 AAAATATC-AAAGAAATT
11279890 AAAATATCAAAGAAATT
1 AAAATATCAAAGAAATT
11279907 A
1 A
11279908 TAGCATGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (17 bp):
AAAATATCAAAGAAATT
Found at i:11280081 original size:18 final size:18
Alignment explanation
Indices: 11280058--11280093 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
11280048 TTAAATACCC
11280058 AGTCTTTCCTTGCCAGAG
1 AGTCTTTCCTTGCCAGAG
11280076 AGTCTTTCCTTGCCAGAG
1 AGTCTTTCCTTGCCAGAG
11280094 CTTATCCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (18 bp):
AGTCTTTCCTTGCCAGAG
Found at i:11284226 original size:24 final size:24
Alignment explanation
Indices: 11284199--11284273 Score: 77
Period size: 23 Copynumber: 3.2 Consensus size: 24
11284189 TAGGTTGACT
11284199 ATGTGAGATATTATGGGTGGAAGC
1 ATGTGAGATATTATGGGTGGAAGC
* * *
11284223 ATGTG-GATA-GAGTAGGTTG-A-C
1 ATGTGAGATATTA-TGGGTGGAAGC
11284244 TATGTGAGATATTATGGGTGGAAGC
1 -ATGTGAGATATTATGGGTGGAAGC
11284269 ATGTG
1 ATGTG
11284274 GGGTGGATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 1 0.03
22 7 0.18
23 18 0.46
24 12 0.31
25 1 0.03
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.31
Consensus pattern (24 bp):
ATGTGAGATATTATGGGTGGAAGC
Found at i:11284244 original size:46 final size:46
Alignment explanation
Indices: 11284177--11284274 Score: 196
Period size: 46 Copynumber: 2.1 Consensus size: 46
11284167 GACATAGGTG
11284177 ATGTGGATAGAGTAGGTTGACTATGTGAGATATTATGGGTGGAAGC
1 ATGTGGATAGAGTAGGTTGACTATGTGAGATATTATGGGTGGAAGC
11284223 ATGTGGATAGAGTAGGTTGACTATGTGAGATATTATGGGTGGAAGC
1 ATGTGGATAGAGTAGGTTGACTATGTGAGATATTATGGGTGGAAGC
11284269 ATGTGG
1 ATGTGG
11284275 GGTGGATATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (46 bp):
ATGTGGATAGAGTAGGTTGACTATGTGAGATATTATGGGTGGAAGC
Found at i:11284249 original size:22 final size:23
Alignment explanation
Indices: 11284177--11284254 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 23
11284167 GACATAGGTG
11284177 ATGTG-GATAGAGTAGGTTGACT
1 ATGTGAGATAGAGTAGGTTGACT
* * *
11284199 ATGTGAGATATTA-TGGGTGGAAGC-
1 ATGTGAGATA-GAGTAGGTTG-A-CT
11284223 ATGTG-GATAGAGTAGGTTGACT
1 ATGTGAGATAGAGTAGGTTGACT
11284245 ATGTGAGATA
1 ATGTGAGATA
11284255 TTATGGGTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
21 1 0.02
22 12 0.28
23 22 0.51
24 7 0.16
25 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (23 bp):
ATGTGAGATAGAGTAGGTTGACT
Found at i:11288032 original size:24 final size:24
Alignment explanation
Indices: 11287986--11288032 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11287976 TTTTAATTAC
* *
11287986 ACCATGAGAAATTTGAATGATTTT
1 ACCATGAAAAATTTGAATAATTTT
11288010 ACCATGAAAAA-TTGTAATAATTT
1 ACCATGAAAAATTTG-AATAATTT
11288033 GATTGTGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (24 bp):
ACCATGAAAAATTTGAATAATTTT
Found at i:11297168 original size:3 final size:3
Alignment explanation
Indices: 11297162--11297206 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
11297152 TCATCATCAT
* * * *
11297162 CTC CTC CTC TTC CTC TTC CTC TTC CTC TTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
11297207 TTTTATTTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (3 bp):
CTC
Found at i:11297175 original size:6 final size:6
Alignment explanation
Indices: 11297166--11297208 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
11297156 CATCATCTCC
* *
11297166 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCC TCCTCC TCCTCT T
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT T
11297209 TTATTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (6 bp):
TCCTCT
Found at i:11297189 original size:18 final size:18
Alignment explanation
Indices: 11297162--11297208 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
11297152 TCATCATCAT
*
11297162 CTCCTCCTCTTCCTCTTC
1 CTCCTCCTCTTCCTCCTC
*
11297180 CTCTTCCTCTTCCTCCTC
1 CTCCTCCTCTTCCTCCTC
11297198 CTCCTCCTCTT
1 CTCCTCCTCTT
11297209 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (18 bp):
CTCCTCCTCTTCCTCCTC
Found at i:11303185 original size:16 final size:16
Alignment explanation
Indices: 11303164--11303200 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
11303154 TTGGTTCACT
11303164 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
11303180 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
11303196 GTAAT
1 GTAAT
11303201 AGGTAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.35, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:11303269 original size:44 final size:46
Alignment explanation
Indices: 11303180--11303270 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
11303170 GAATAGAGGC
*
11303180 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
11303226 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
11303270 G
1 G
11303271 GAATAGAGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 20 0.45
45 3 0.07
46 21 0.48
ACGTcount: A:0.26, C:0.04, G:0.31, T:0.38
Consensus pattern (46 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
Found at i:11303271 original size:39 final size:44
Alignment explanation
Indices: 11303180--11303287 Score: 145
Period size: 46 Copynumber: 2.5 Consensus size: 44
11303170 GAATAGAGGC
*
11303180 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--AT
11303226 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
*
11303266 G-AATGGAATAGAGGTGTAATAG
1 GTAATGGAATAGAGGCGTAATAG
11303288 CATAATGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
39 18 0.31
40 3 0.05
43 1 0.02
44 13 0.22
45 3 0.05
46 21 0.36
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
Found at i:11303549 original size:23 final size:22
Alignment explanation
Indices: 11303501--11303559 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 22
11303491 GAATTTACTA
*
11303501 ATAAAATCATAATATATAACACT
1 ATAAAAT-ATAATATATAACAAT
* *
11303524 ATAAAATATAATTTAATAATAAT
1 ATAAAATATAATAT-ATAACAAT
* *
11303547 ATATAATTTAATA
1 ATAAAATATAATA
11303560 AAATTCTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAAAATATAATATATAACAAT
Found at i:11303550 original size:18 final size:18
Alignment explanation
Indices: 11303430--11303560 Score: 79
Period size: 18 Copynumber: 7.1 Consensus size: 18
11303420 CATAATTATT
*
11303430 ATAAAATATAATTTAATA
1 ATAATATATAATTTAATA
*
11303448 AAAATATATAATTTAATA
1 ATAATATATAATTTAATA
* *
11303466 A-AAT-TGTTAA-TAAATA
1 ATAATAT-ATAATTTAATA
* ** *
11303482 TTCTTATATGAATTTACTA
1 ATAATATAT-AATTTAATA
* *
11303501 ATAAAATCATAATATATAACA
1 ATAATAT-ATAAT-T-TAATA
*
11303522 CTATAAAATATAATTTAATA
1 --ATAATATATAATTTAATA
11303542 ATAATATATAATTTAATA
1 ATAATATATAATTTAATA
11303560 A
1 A
11303561 AATTCTTATT
Statistics
Matches: 85, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
16 6 0.07
17 8 0.09
18 38 0.45
19 10 0.12
20 7 0.08
21 4 0.05
22 5 0.06
23 7 0.08
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (18 bp):
ATAATATATAATTTAATA
Found at i:11303644 original size:33 final size:33
Alignment explanation
Indices: 11303607--11303671 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
11303597 TATATAATAA
*
11303607 TATAAAATATAATTTAAATAATTATTATTAAAT
1 TATAAAATATAATCTAAATAATTATTATTAAAT
** ** *
11303640 TATAATTTATAATCTACTTTATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
11303672 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (33 bp):
TATAAAATATAATCTAAATAATTATTATTAAAT
Found at i:11308665 original size:35 final size:35
Alignment explanation
Indices: 11308624--11308696 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
11308614 TACATAATTA
11308624 ACTAAATTACATAGTATTTACTACAAATTATTTAT
1 ACTAAATTACATAGTATTTACTACAAATTATTTAT
* * **
11308659 ACTAAATTATATAGTATTTATTATTAATTATTTAT
1 ACTAAATTACATAGTATTTACTACAAATTATTTAT
11308694 ACT
1 ACT
11308697 TGGTAAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (35 bp):
ACTAAATTACATAGTATTTACTACAAATTATTTAT
Found at i:11314110 original size:3 final size:3
Alignment explanation
Indices: 11314102--11314214 Score: 201
Period size: 3 Copynumber: 37.7 Consensus size: 3
11314092 GAAGAGAGTC
11314102 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
11314150 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
11314197 AGTG AAG AAG AAG AAG AA
1 A-AG AAG AAG AAG AAG AA
11314215 AGTGAAAATG
Statistics
Matches: 106, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
2 1 0.01
3 104 0.98
4 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:11317589 original size:9 final size:9
Alignment explanation
Indices: 11317564--11317736 Score: 75
Period size: 9 Copynumber: 18.0 Consensus size: 9
11317554 GGATATAAGC
11317564 TTATAAAAA
1 TTATAAAAA
*
11317573 GTATTAAAAA
1 TTA-TAAAAA
*
11317583 TTATAAATA
1 TTATAAAAA
11317592 TTATAAAAA
1 TTATAAAAA
*
11317601 TCTA-ATAAA
1 T-TATAAAAA
*
11317610 TTGTAAAAGAA
1 TTAT-AAA-AA
11317621 TTAT-AAAA
1 TTATAAAAA
11317629 TTAATACAATATA
1 TT-ATA-AA-A-A
*
11317642 TT-TAAAAT
1 TTATAAAAA
11317650 TGTATAAAAA
1 T-TATAAAAA
*
11317660 TGTATTAAAAT
1 T-TA-TAAAAA
11317671 TCTATAAAAA
1 T-TATAAAAA
*
11317681 TCATAAAAA
1 TTATAAAAA
* *
11317690 GTATTAAAA
1 TTATAAAAA
*
11317699 GTACT-AAAA
1 TTA-TAAAAA
*
11317708 TTGATATAAAC
1 TT-ATA-AAAA
*
11317719 TTATAACAA
1 TTATAAAAA
11317728 TTATAAAAA
1 TTATAAAAA
11317737 ATTTAATTGG
Statistics
Matches: 125, Mismatches: 22, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
8 6 0.05
9 59 0.47
10 34 0.27
11 22 0.18
12 1 0.01
13 3 0.02
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:11318956 original size:24 final size:24
Alignment explanation
Indices: 11318929--11318999 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
11318919 CCTCCAAAAC
11318929 AATATGTGAACAAATCGCCAGAAT
1 AATATGTGAACAAATCGCCAGAAT
** *
11318953 AATATGCAAACAAATCGCTAGAAT
1 AATATGTGAACAAATCGCCAGAAT
*
11318977 AAAATGTGAACAAATCGCCAGAA
1 AATATGTGAACAAATCGCCAGAA
11319000 CTCCAGTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.18
Consensus pattern (24 bp):
AATATGTGAACAAATCGCCAGAAT
Found at i:11322157 original size:26 final size:26
Alignment explanation
Indices: 11322128--11322209 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
11322118 TATTAGATTT
11322128 TTTTATATTTTTATAATATTTATAAG
1 TTTTATATTTTTATAATATTTATAAG
* *
11322154 TTTTA-ACTTTTTTATAA-GTTTATATG
1 TTTTATA--TTTTTATAATATTTATAAG
* *
11322180 CTTTTAATATTTTT-T-ATTTTTATAAT
1 -TTTT-ATATTTTTATAATATTTATAAG
11322206 TTTT
1 TTTT
11322210 TTCTGATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
25 6 0.13
26 19 0.42
27 18 0.40
28 1 0.02
29 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (26 bp):
TTTTATATTTTTATAATATTTATAAG
Found at i:11322207 original size:9 final size:9
Alignment explanation
Indices: 11322127--11322209 Score: 50
Period size: 9 Copynumber: 9.6 Consensus size: 9
11322117 TTATTAGATT
11322127 TTTTTAT-A
1 TTTTTATAA
11322135 TTTTTATAA
1 TTTTTATAA
*
11322144 TATTTATAA
1 TTTTTATAA
* *
11322153 GTTTTA-ACT
1 TTTTTATA-A
11322162 TTTTTATAA
1 TTTTTATAA
* **
11322171 GTTTATATGC
1 -TTTTTATAA
*
11322181 TTTTAAT-A
1 TTTTTATAA
11322189 TTTTT-T-A
1 TTTTTATAA
11322196 TTTTTATAA
1 TTTTTATAA
11322205 TTTTT
1 TTTTT
11322210 TTCTGATTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
7 7 0.12
8 13 0.23
9 29 0.52
10 7 0.12
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:11322210 original size:18 final size:20
Alignment explanation
Indices: 11322184--11322221 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
11322174 TATATGCTTT
11322184 TAATATTTTT-T-ATTTTTA
1 TAATATTTTTCTGATTTTTA
*
11322202 TAATTTTTTTCTGATTTTTA
1 TAATATTTTTCTGATTTTTA
11322222 ATCATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (20 bp):
TAATATTTTTCTGATTTTTA
Found at i:11324382 original size:38 final size:40
Alignment explanation
Indices: 11324312--11324397 Score: 131
Period size: 38 Copynumber: 2.2 Consensus size: 40
11324302 TTAAAAATAT
* * *
11324312 TTATATTAAAAACATTACCATAAATATAATAAATGTTTTA
1 TTATATTAAAAACATCACAATAAATATAATAAATATTTTA
11324352 TTATATTAAAAACA-CA-AATAAATATAATAAATATTTTA
1 TTATATTAAAAACATCACAATAAATATAATAAATATTTTA
11324390 TTATATTA
1 TTATATTA
11324398 CATACAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 28 0.65
39 1 0.02
40 14 0.33
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (40 bp):
TTATATTAAAAACATCACAATAAATATAATAAATATTTTA
Found at i:11328132 original size:102 final size:102
Alignment explanation
Indices: 11327956--11328230 Score: 356
Period size: 102 Copynumber: 2.7 Consensus size: 102
11327946 TTCACCTTCA
* * * * * * *
11327956 CCTTCACCTTCGTCTACTTCCGGATCCATCGTGTTGCCATGGCCACCATACTCCGCTCCAGCGTT
1 CCTTCATCTTCGTCTATTTCAGGCTCCATCGTGTTGCCATGGCCACCATCCTCTGCTCCTGCGTT
* *
11328021 AATATAGTTATAAAGCTCGATTCCGATGAGAT-AAGCT
66 AATATAGTTATAAAGCGCCATTCCGATGAGATCAA-CT
* * * * * *
11328058 CCTTCATCTTCCTCTATTTCAGGCTCCCTCGTGTTTCCATGGCCGCCATCCTCTACACCTGCGTT
1 CCTTCATCTTCGTCTATTTCAGGCTCCATCGTGTTGCCATGGCCACCATCCTCTGCTCCTGCGTT
*
11328123 AATATAGTTATAAAGCGCCATTCCGATGAGCTCAACT
66 AATATAGTTATAAAGCGCCATTCCGATGAGATCAACT
**
11328160 CCTTCATCTTCGTCTATTTCAGGCTCTGTCGTGTTGCCATGGCCACCATCCTCTGCTCCAT-CGT
1 CCTTCATCTTCGTCTATTTCAGGCTCCATCGTGTTGCCATGGCCACCATCCTCTGCTCC-TGCGT
11328224 TAATATA
65 TAATATA
11328231 ATTTGGGATG
Statistics
Matches: 148, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
102 145 0.98
103 3 0.02
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (102 bp):
CCTTCATCTTCGTCTATTTCAGGCTCCATCGTGTTGCCATGGCCACCATCCTCTGCTCCTGCGTT
AATATAGTTATAAAGCGCCATTCCGATGAGATCAACT
Found at i:11329286 original size:19 final size:17
Alignment explanation
Indices: 11329264--11329306 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
11329254 CCAAATCCTT
11329264 TTTTGTTCATTTTTATTTA
1 TTTTGTTCA-TTTT-TTTA
*
11329283 TTTTATTCATTTTTTTA
1 TTTTGTTCATTTTTTTA
11329300 TTTTGTT
1 TTTTGTT
11329307 TTTGTGCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 10 0.45
18 4 0.18
19 8 0.36
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (17 bp):
TTTTGTTCATTTTTTTA
Found at i:11329981 original size:3 final size:3
Alignment explanation
Indices: 11329975--11330107 Score: 98
Period size: 3 Copynumber: 44.7 Consensus size: 3
11329965 TTAGTAGCAA
* * * * *
11329975 TAT TAT T-T ATAT TAT TAA TAG TAT TAT TAT TAT TAT TAA TGT CAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
11330020 CAT TAC TA- TAG TAT TAT TACT T-T TAT TACT T-T TAT TACT T-T TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TA-T TAT TAT TA-T TAT TAT
*
11330064 TACT T-T TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
11330108 CTACTACTAT
Statistics
Matches: 106, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
2 11 0.10
3 86 0.81
4 9 0.08
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:11329981 original size:24 final size:24
Alignment explanation
Indices: 11329953--11330014 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 24
11329943 TATTTTATCG
*
11329953 TTATTTTTATTATTAGTAGCAATA
1 TTATTTTTATTATTAATAGCAATA
*
11329977 TTATTTATATTATTAATAG---TA
1 TTATTTTTATTATTAATAGCAATA
*
11329998 TTATTATTATTATTAAT
1 TTATTTTTATTATTAAT
11330015 GTCATCATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.50
24 17 0.50
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (24 bp):
TTATTTTTATTATTAATAGCAATA
Found at i:11330451 original size:2 final size:2
Alignment explanation
Indices: 11330444--11330479 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
11330434 TTTTACGCAC
* *
11330444 AT AT AT AT GT GT 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
11330480 TATTTTCTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11335998 original size:35 final size:35
Alignment explanation
Indices: 11335959--11336074 Score: 90
Period size: 41 Copynumber: 3.1 Consensus size: 35
11335949 TATAAAAATC
11335959 AATTTTTATATATTATTTTGATTTTTTAAATTTTA
1 AATTTTTATATATTATTTTGATTTTTTAAATTTTA
* * * *
11335994 AATTTATATATTTTAGAATTTTTTTAGTTTTTTTAAA-TTTG
1 AATTT-T-TA---TA-TATTATTTT-GATTTTTTAAATTTTA
* *
11336035 AATTATTTATATATTATATATGATTTTTTACATTTTA
1 AATT-TTTATATATTAT-TTTGATTTTTTAAATTTTA
11336072 AAT
1 AAT
11336075 CAATATAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
35 5 0.08
36 14 0.23
37 12 0.20
40 4 0.07
41 15 0.25
42 11 0.18
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (35 bp):
AATTTTTATATATTATTTTGATTTTTTAAATTTTA
Found at i:11346481 original size:18 final size:17
Alignment explanation
Indices: 11346455--11346488 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11346445 CAACCTTAAC
11346455 ATTACATTTTTCAACATA
1 ATTACA-TTTTCAACATA
*
11346473 ATTATATTTTCAACAT
1 ATTACATTTTCAACAT
11346489 GTAACAGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTACATTTTCAACATA
Found at i:11352524 original size:38 final size:38
Alignment explanation
Indices: 11352482--11352555 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
11352472 AATCCTGAAC
11352482 GTAGGCTAGAAATGCCTCACACCCTTTCCGAACTAAAT
1 GTAGGCTAGAAATGCCTCACACCCTTTCCGAACTAAAT
* *
11352520 GTAGGCTAGAAATGCCTCACACCTTTTCTGAACTAA
1 GTAGGCTAGAAATGCCTCACACCCTTTCCGAACTAA
11352556 CTTCTTAGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (38 bp):
GTAGGCTAGAAATGCCTCACACCCTTTCCGAACTAAAT
Found at i:11354428 original size:20 final size:20
Alignment explanation
Indices: 11354403--11354449 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
11354393 AAGAACCGTA
*
11354403 AAAGATTGATTAATCAAATG
1 AAAGATTGATTAATCAAACG
11354423 AAAGATTGATTAATCAAACG
1 AAAGATTGATTAATCAAACG
11354443 AAAGATT
1 AAAGATT
11354450 AGCGTCGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (20 bp):
AAAGATTGATTAATCAAACG
Found at i:11355478 original size:18 final size:18
Alignment explanation
Indices: 11355438--11355478 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
11355428 AATAAAATTA
*
11355438 AAAAAAACAAAAAAATGG
1 AAAAAAACAAAAAAATAG
* *
11355456 GAAAAAATAAAAAAATAG
1 AAAAAAACAAAAAAATAG
11355474 AAAAA
1 AAAAA
11355479 TTTAGGAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAAAAACAAAAAAATAG
Found at i:11357312 original size:4 final size:4
Alignment explanation
Indices: 11357303--11357336 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
11357293 TTAGATCACC
11357303 ATTA ATTA ATTA ATTA ATTA ATTA ATTA TATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA -ATTA A
11357337 ATTTCATAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:11357470 original size:16 final size:18
Alignment explanation
Indices: 11357435--11357472 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
11357425 ATATATTTGG
*
11357435 ATTTGATAATTTGTATTT
1 ATTTGATAATTTGAATTT
11357453 ATTTGAT-ATTT-AATTT
1 ATTTGATAATTTGAATTT
11357469 ATTT
1 ATTT
11357473 TTAGATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 4 0.21
18 7 0.37
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (18 bp):
ATTTGATAATTTGAATTT
Found at i:11359467 original size:22 final size:23
Alignment explanation
Indices: 11359436--11359484 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
11359426 ATAGGTGAAG
*
11359436 TAAATAAAAATA-ATAATAATAAA
1 TAAATAAAAA-ACAGAATAATAAA
*
11359459 TAAAT-AAAAACAGAATCATAAA
1 TAAATAAAAAACAGAATAATAAA
11359481 TAAA
1 TAAA
11359485 ACTGTCTGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 17 0.74
23 5 0.22
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (23 bp):
TAAATAAAAAACAGAATAATAAA
Found at i:11361048 original size:44 final size:41
Alignment explanation
Indices: 11361000--11361158 Score: 122
Period size: 44 Copynumber: 3.7 Consensus size: 41
11360990 GTTTTAATCC
* *
11361000 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT-GT-GATTCA-TCT
* * * *
11361044 GCTCCACTGCAATTTAAGGGAGATAAGACTG-GATGTGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGTGAT-TCATCT
* * * * * * *
11361085 ACTCTACTGCAACTTCAGAGAGATAAGTTTTGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAG-ATTGT-G-ATTCATCT
*
11361129 GCTCCACTGCAACTTCAGGGAGATAGGATT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT
11361159 CGCCATTGCG
Statistics
Matches: 89, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
41 27 0.30
42 4 0.04
43 3 0.03
44 54 0.61
45 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTGTGATTCATCT
Found at i:11361268 original size:50 final size:50
Alignment explanation
Indices: 11361196--11362025 Score: 312
Period size: 50 Copynumber: 16.7 Consensus size: 50
11361186 AGGGAACACA
* * * * *
11361196 ATTCGCAGTCGTAGCTTTAATCTATTCCACTGCACTGCCAGGGAAGTAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAG
* * * ** * * **
11361246 ATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCAAC-GTCGGGGAAACAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGC-ACTGTCAGGGAAGTAAG
* * * *
11361296 ATTCGCCCTTGTAGCTTCAATTTGTTCCACTGCA-TCGCCATGGAAGTAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACT-GTCAGGGAAGTAAG
* ** * * ** * * * * *
11361346 ATTTGCCGTTACAGCTTCAATTTTTTAAATTGCAATATCGGGGAAGCAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAG
* * * * *
11361396 ATTCACCGTTGTAGCTTTC-ATATGCTCCACTGTACTGTCAGGGAAGTTAG
1 ATTCGCCGTTGTAGC-TTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAG
* * ** * * * * *
11361446 ATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAA
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAG
* * * * *
11361496 ATTCGCCGTTGTAGCTTTAATCTGCTCCACTGTACTGCCAGGGAAGTGAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAG
* * * ** * * * *
11361546 ATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAA-CAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAG
* * ** * *
11361595 ATTCACCGTTGTAGCTTCAATCTGTTCCACCGCA-TCACTAAGAAAGTAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGTC-AGGGAAGTAAG
* * ** ** * * * *
11361645 ATTCACCATTGCGGCTTCAATCT-TTTAATTGCAATGTCGGGGAA-CAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAG
* * * * ** * * * *
11361693 ATTCACCATTGTAGCTTCAATCTGATCCATTGCA-TCACCATGAAAATAAA
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACT-GTCAGGGAAGTAAG
** * ** * * * * *
11361743 ATTCGCCGTTCCAGCTTCAATCTTTTAAATTGTAATATCAGGGAAGCAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAG
* * * * * * *
11361793 ATTCGCTGTCGTAGCTTTAATCTGCTCCACT-CTACTGCCAGGGGAGTGAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGC-ACTGTCAGGGAAGTAAG
* * * * * ** * * * *
11361843 ATTTGCCGTTATGGCTTCAATATTTTAAATTGCAATATCAGGGAAGCAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAG
*** * * * * * * * *
11361893 ATTTATCGTCGTAGTTTTAATCTGCTCCATTGTACTGCCAGGGAAGTGAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAG
* * * ** * * * *
11361943 ATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAA-CAAG
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAG
* * * *
11361992 ATTCGCTGTTGTAGCTTTAATCTGATCTACTGCA
1 ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCA
11362026 TCGCCAGGAA
Statistics
Matches: 538, Mismatches: 227, Indels: 31
0.68 0.29 0.04
Matches are distributed among these distances:
48 27 0.05
49 84 0.16
50 419 0.78
51 8 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (50 bp):
ATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGTCAGGGAAGTAAG
Found at i:11361327 original size:100 final size:100
Alignment explanation
Indices: 11361174--11362033 Score: 812
Period size: 100 Copynumber: 8.7 Consensus size: 100
11361164 TTGCGGCTTC
* * * * * **
11361174 AATTGCAATGTCAGGG-AACACA-ATTCGCAGTCGTAGCTTTAATCTATTCCACTGCACTGCCAG
1 AATTGCAATGTCGGGGAAACA-AGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACTGCCAG
*
11361237 GGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTT
65 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTT
* * * * * *
11361273 AATTGCAACGTCGGGGAAACAAGATTCGCCCTTGTAGCTTCAATTTGTTCCACTGCA-TCGCCAT
1 AATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACT-GCCAG
* ***
11361337 GGAAGTAAGATTTGCCGTTACAGCTTCAAT-TTTTT
65 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTT
* * * * *
11361372 AAATTGCAATATCGGGGAAGCAAGATTCACCGTTGTAGCTTTC-ATATGCTCCACTGTACTGTCA
1 -AATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGC-TTCAATCTGCTCCACTGCACTGCCA
*
11361436 GGGAAGTTAGATTCGCCGTTGTGGCTTCAATCTTTTT
64 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTT
* * * * *
11361473 AATTGCAATGTCGGGGAAGCAAAATTCGCCGTTGTAGCTTTAATCTGCTCCACTGTACTGCCAGG
1 AATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACTGCCAGG
* *
11361538 GAAGTGAGATTCACCGTTGTGGCTTCAATCTTTTT
66 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTT
* *
11361573 AATTGCAATGTCGGGG-AACAAGATTCACCGTTGTAGCTTCAATCTGTTCCACCGCA-T-CACTA
1 AATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACTGC-C-A
* * * * *
11361635 AGAAAGTAAGATTCACCATTGCGGCTTCAATC-TTTT
64 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTT
* * * * *
11361671 AATTGCAATGTCGGGG-AACAAGATTCACCATTGTAGCTTCAATCTGATCCATTGCA-TCACCAT
1 AATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACT-GCCAG
* * * *** *
11361734 GAAAATAAAATTCGCCGTTCCAGCTTCAATCTTTTA
65 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTT
* * * * * * * *
11361770 AATTGTAATATCAGGGAAGCAAGATTCGCTGTCGTAGCTTTAATCTGCTCCACT-CTACTGCCAG
1 AATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGC-ACTGCCAG
* * * * * *
11361834 GGGAGTGAGATTTGCCGTTATGGCTTCAATATTTTA
65 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTT
* * * * * * * * * *
11361870 AATTGCAATATCAGGGAAGCAAGATTTATCGTCGTAGTTTTAATCTGCTCCATTGTACTGCCAGG
1 AATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACTGCCAGG
* *
11361935 GAAGTGAGATTCACCGTTGTGGCTTCAATCTTTTT
66 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTT
* * * * *
11361970 AATTGCAATGTCGGGG-AACAAGATTCGCTGTTGTAGCTTTAATCTGATCTACTGCA-TCGCCAG
1 AATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACT-GCCAG
11362033 G
65 G
11362034 AAAGGTAACT
Statistics
Matches: 632, Mismatches: 111, Indels: 36
0.81 0.14 0.05
Matches are distributed among these distances:
97 1 0.00
98 86 0.14
99 137 0.22
100 398 0.63
101 10 0.02
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (100 bp):
AATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACTGCCAGG
GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTT
Found at i:11361914 original size:397 final size:399
Alignment explanation
Indices: 11361174--11362015 Score: 1163
Period size: 397 Copynumber: 2.1 Consensus size: 399
11361164 TTGCGGCTTC
* * * * *
11361174 AATTGCAATGTCAGGGAACACA-ATTCGCAGTCGTAGCTTTAATCTATTCCACTGCACTGCCAGG
1 AATTGCAATGTCGGGGAACA-AGATTCGCAGTTGTAGCTTTAATCTGTTCCACCGCACTGCCAAG
* ** * * *
11361238 GAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCAACGTCGGGGAAACAAGATTCGCC
65 AAAGTAAGATTCACCATTGCGGCTTCAATCTTTTTAATTGCAACGTCGGGGAAACAAGATTCACC
* * * * * * * * *
11361303 CTTGTAGCTTCAATTTGTTCCACTGCATCGCCATGGAAGTAAGATTTGCCGTTACAGCTTCAATT
130 ATTGTAGCTTCAATCTGATCCACTGCATCACCATGAAAATAAAATTCGCCGTTACAGCTTCAATC
* * * *
11361368 TTTTAAATTGCAATATCGGGGAAGCAAGATTCACCGTTGTAGCTTTCATATGCTCCACTGTACTG
195 TTTTAAATTGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATATGCTCCACTCTACTG
* * * * * * *
11361433 TCAGGGAAGTTAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAAAT
260 CCAGGGAAGTGAGATTCGCCGTTATGGCTTCAATATTTTAAATTGCAATATCAGGGAAGCAAAAT
* *
11361498 TCGCCGTTGTAGCTTTAATCTGCTCCACTGTACTGCCAGGGAAGTGAGATTCACCGTTGTGGCTT
325 TCACCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCAGGGAAGTGAGATTCACCGTTGTGGCTT
11361563 CAATCTTTTT
390 CAATCTTTTT
* * *
11361573 AATTGCAATGTCGGGGAACAAGATTCACCGTTGTAGCTTCAATCTGTTCCACCGCA-T-CACTAA
1 AATTGCAATGTCGGGGAACAAGATTCGCAGTTGTAGCTTTAATCTGTTCCACCGCACTGC-C-AA
*
11361636 GAAAGTAAGATTCACCATTGCGGCTTCAATC-TTTTAATTGCAATGTCGGGG-AACAAGATTCAC
64 GAAAGTAAGATTCACCATTGCGGCTTCAATCTTTTTAATTGCAACGTCGGGGAAACAAGATTCAC
* *
11361699 CATTGTAGCTTCAATCTGATCCATTGCATCACCATGAAAATAAAATTCGCCGTTCCAGCTTCAAT
129 CATTGTAGCTTCAATCTGATCCACTGCATCACCATGAAAATAAAATTCGCCGTTACAGCTTCAAT
* * * *
11361764 CTTTTAAATTGTAATATCAGGGAAGCAAGATTCGCTGTCGTAGCTTTAATCTGCTCCACTCTACT
194 CTTTTAAATTGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATATGCTCCACTCTACT
* * *
11361829 GCCAGGGGAGTGAGATTTGCCGTTATGGCTTCAATATTTTAAATTGCAATATCAGGGAAGCAAGA
259 GCCAGGGAAGTGAGATTCGCCGTTATGGCTTCAATATTTTAAATTGCAATATCAGGGAAGCAAAA
* * * *
11361894 TTTATCGTCGTAGTTTTAATCTGCTCCATTGTACTGCCAGGGAAGTGAGATTCACCGTTGTGGCT
324 TTCACCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCAGGGAAGTGAGATTCACCGTTGTGGCT
11361959 TCAATCTTTTT
389 TCAATCTTTTT
*
11361970 AATTGCAATGTCGGGGAACAAGATTCGCTGTTGTAGCTTTAATCTG
1 AATTGCAATGTCGGGGAACAAGATTCGCAGTTGTAGCTTTAATCTG
11362016 ATCTACTGCA
Statistics
Matches: 387, Mismatches: 53, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
397 291 0.75
398 22 0.06
399 74 0.19
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (399 bp):
AATTGCAATGTCGGGGAACAAGATTCGCAGTTGTAGCTTTAATCTGTTCCACCGCACTGCCAAGA
AAGTAAGATTCACCATTGCGGCTTCAATCTTTTTAATTGCAACGTCGGGGAAACAAGATTCACCA
TTGTAGCTTCAATCTGATCCACTGCATCACCATGAAAATAAAATTCGCCGTTACAGCTTCAATCT
TTTAAATTGCAATATCAGGGAAGCAAGATTCACCGTCGTAGCTTTAATATGCTCCACTCTACTGC
CAGGGAAGTGAGATTCGCCGTTATGGCTTCAATATTTTAAATTGCAATATCAGGGAAGCAAAATT
CACCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCAGGGAAGTGAGATTCACCGTTGTGGCTTC
AATCTTTTT
Found at i:11363291 original size:5 final size:5
Alignment explanation
Indices: 11363281--11363329 Score: 66
Period size: 5 Copynumber: 10.0 Consensus size: 5
11363271 TTGGCCTCTC
*
11363281 CTTTT CTTTT CTTTT -TTCAT -TTTT CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTT-TT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
11363330 TCAAGTGAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 3 0.08
5 37 0.93
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:11366473 original size:19 final size:20
Alignment explanation
Indices: 11366444--11366495 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
11366434 CACTTCGTGA
* *
11366444 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
11366463 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
11366483 AAATG-AATGCAAA
1 AAATGTAATGCAAA
11366496 AAGAGACGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:11370721 original size:3 final size:3
Alignment explanation
Indices: 11370713--11370746 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
11370703 AATATTAAGG
*
11370713 ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11370747 CATCAAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:11372168 original size:30 final size:28
Alignment explanation
Indices: 11372046--11372214 Score: 119
Period size: 30 Copynumber: 5.8 Consensus size: 28
11372036 AAAAAAACTG
*
11372046 CATTTTAACCCCTAAAATTTTCT-AATTTA
1 CATTTTAA-CCCTAAAATTTT-TAAAATTA
* *
11372075 TATTTTTACCCTTAAAATTTTTCAAAATTA
1 CATTTTAACCC-TAAAATTTTT-AAAATTA
* *
11372105 CATTTCAACACCTAAACA-TTTTGAAA-TA
1 CATTTTAAC-CCTAAA-ATTTTTAAAATTA
*
11372133 GCATTTTGACCCTTAAAATTTCTTAAAATTA
1 -CATTTTAACCC-TAAAATTT-TTAAAATTA
* * *
11372164 CATTTTGACCCCTAAACTTTCTCAAAATTA
1 CATTTT-AACCCTAAAATTT-TTAAAATTA
**
11372194 TGTTTTAACCCTAAAATTTTT
1 CATTTTAACCCTAAAATTTTT
11372215 GCTGCCACTA
Statistics
Matches: 110, Mismatches: 19, Indels: 23
0.72 0.12 0.15
Matches are distributed among these distances:
28 10 0.09
29 42 0.38
30 50 0.45
31 8 0.07
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.43
Consensus pattern (28 bp):
CATTTTAACCCTAAAATTTTTAAAATTA
Found at i:11372209 original size:59 final size:59
Alignment explanation
Indices: 11372046--11372214 Score: 168
Period size: 59 Copynumber: 2.9 Consensus size: 59
11372036 AAAAAAACTG
* * * * *
11372046 CATTTTAACCCCTAAAATTTTCTAATTTATATTTTTACCCTTAAAATTTTTCAAAATTA
1 CATTTTAACCCCTAAACTTTTCAAAATTATGTTTTAACCCTTAAAATTTTTCAAAATTA
* * * *
11372105 CATTTCAACACCTAAACATTTT-GAAA-TA-GCATTTTGACCCTTAAAATTTCTT-AAAATTA
1 CATTTTAACCCCTAAAC-TTTTCAAAATTATG--TTTTAACCCTTAAAATTT-TTCAAAATTA
*
11372164 CATTTTGACCCCTAAACTTTCTCAAAATTATGTTTTAACCC-TAAAATTTTT
1 CATTTTAACCCCTAAACTTT-TCAAAATTATGTTTTAACCCTTAAAATTTTT
11372215 GCTGCCACTA
Statistics
Matches: 90, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
58 7 0.08
59 63 0.70
60 17 0.19
61 2 0.02
62 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.43
Consensus pattern (59 bp):
CATTTTAACCCCTAAACTTTTCAAAATTATGTTTTAACCCTTAAAATTTTTCAAAATTA
Found at i:11372689 original size:15 final size:15
Alignment explanation
Indices: 11372669--11372709 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
11372659 GAAGGGAGGG
*
11372669 GAAGAAGAAGAGAAA
1 GAAGAAAAAGAGAAA
11372684 GAAGAAAAAGAGAAAA
1 GAAGAAAAAGAG-AAA
11372700 GAAAGAAAAA
1 G-AAGAAAAA
11372710 AAGAGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.48
16 4 0.17
17 8 0.35
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
GAAGAAAAAGAGAAA
Found at i:11372704 original size:11 final size:10
Alignment explanation
Indices: 11372683--11372720 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
11372673 AAGAAGAGAA
11372683 AGAAGAAAAAG
1 AGAA-AAAAAG
*
11372694 AGAAAAGAA-
1 AGAAAAAAAG
11372703 AGAAAAAAAG
1 AGAAAAAAAG
11372713 AGAAAAAA
1 AGAAAAAA
11372721 TAATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.33
10 12 0.50
11 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:11372719 original size:20 final size:20
Alignment explanation
Indices: 11372674--11372718 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
11372664 GAGGGGAAGA
*
11372674 AGAAGAGAAAGAAGAAAAAG
1 AGAAAAGAAAGAAGAAAAAG
11372694 AGAAAAGAAAGAA-AAAAAG
1 AGAAAAGAAAGAAGAAAAAG
11372713 AGAAAA
1 AGAAAA
11372719 AATAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
AGAAAAGAAAGAAGAAAAAG
Found at i:11372890 original size:14 final size:14
Alignment explanation
Indices: 11372873--11372913 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
11372863 ATAGGCCTAA
11372873 CCCAATCCAGCAGG
1 CCCAATCCAGCAGG
11372887 CCCAA--CAGCAGG
1 CCCAATCCAGCAGG
* *
11372899 CCCTATCCAGTAGG
1 CCCAATCCAGCAGG
11372913 C
1 C
11372914 AGCCCAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.48
14 12 0.52
ACGTcount: A:0.27, C:0.41, G:0.22, T:0.10
Consensus pattern (14 bp):
CCCAATCCAGCAGG
Found at i:11372989 original size:21 final size:19
Alignment explanation
Indices: 11372962--11373009 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
11372952 TCGTCCCAAC
* *
11372962 AAAAAAAGAAGGAGAAAGGA
1 AAAAAAAGAAAGA-AAAAGA
11372982 AGAAAAAAGAAAGAAAAAGA
1 A-AAAAAAGAAAGAAAAAGA
11373002 AAAAAAAG
1 AAAAAAAG
11373010 GGAGAGAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 7 0.28
21 11 0.44
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAGAAAAAGA
Found at i:11373127 original size:3 final size:3
Alignment explanation
Indices: 11373121--11373168 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
11373111 ACTAGGGTTT
*
11373121 GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA G-A GAA GAA GAAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA
11373166 GAA
1 GAA
11373169 AAAAAAGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11373175 original size:12 final size:12
Alignment explanation
Indices: 11373122--11373181 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
11373112 CTAGGGTTTG
* *
11373122 AAGAAGAAGAAG
1 AAGAAGAAAAAA
*
11373134 AAGAAGAAAAAG
1 AAGAAGAAAAAA
11373146 AAGAAGAGAAGAAGA
1 AAGAAGA-AA-AA-A
11373161 AAGAAGAAAAAA
1 AAGAAGAAAAAA
11373173 AAGAA-AAAA
1 AAGAAGAAAA
11373182 GCAACACAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
11 4 0.09
12 24 0.56
13 4 0.09
14 4 0.09
15 7 0.16
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAA
Found at i:11373329 original size:9 final size:9
Alignment explanation
Indices: 11373317--11373355 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
11373307 AGGCCAAGAA
*
11373317 AAAGAAGAG
1 AAAGAAAAG
11373326 AAAGAAAAAG
1 AAAG-AAAAG
11373336 AAAGAAAAG
1 AAAGAAAAG
11373345 AAA-AAAAG
1 AAAGAAAAG
11373353 AAA
1 AAA
11373356 AAGGCAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 8 0.29
9 12 0.43
10 8 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:11373330 original size:15 final size:15
Alignment explanation
Indices: 11373312--11373358 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
11373302 GCAGCAGGCC
11373312 AAGAAAAAGAAGAGA
1 AAGAAAAAGAAGAGA
11373327 AAGAAAAAGAA-AGAA
1 AAGAAAAAGAAGAG-A
*
11373342 AAGAAAAA-AAGAAA
1 AAGAAAAAGAAGAGA
11373356 AAG
1 AAG
11373359 GCAAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.28
15 21 0.72
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAGAGA
Found at i:11373524 original size:36 final size:35
Alignment explanation
Indices: 11373483--11373559 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
11373473 ATGACATGTC
** *
11373483 ATATTTAATATTCTTGTTTTTTTTCTAAGCATTTTTT
1 ATATTTAATATT-AGGTATTTTTT-TAAGCATTTTTT
**
11373520 -TATTTCGTATTAGGTATTTTTTTAAGCATTTTTT
1 ATATTTAATATTAGGTATTTTTTTAAGCATTTTTT
11373554 ATATTT
1 ATATTT
11373560 CGTATTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
34 12 0.35
35 13 0.38
36 9 0.26
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.64
Consensus pattern (35 bp):
ATATTTAATATTAGGTATTTTTTTAAGCATTTTTT
Found at i:11373577 original size:10 final size:10
Alignment explanation
Indices: 11373562--11373595 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
11373552 TTATATTTCG
11373562 TATTTAATTT
1 TATTTAATTT
11373572 TATTTAATTT
1 TATTTAATTT
*
11373582 CA-TTAATTT
1 TATTTAATTT
11373591 TATTT
1 TATTT
11373596 TTAATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTTAATTT
Found at i:11373578 original size:34 final size:32
Alignment explanation
Indices: 11373501--11373578 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 32
11373491 TATTCTTGTT
11373501 TTTTTTCTAAGCATTTTTTTATTTCGTATTAGGTA
1 TTTTTT-TAAGCATTTTTTTATTTCGTATTA-G-A
11373536 TTTTTTTAAGCATTTTTTATATTTCGTATTTA-A
1 TTTTTTTAAGCATTTTTT-TATTTCGTA-TTAGA
11373569 TTTTATTTAA
1 TTTT-TTTAA
11373579 TTTCATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
33 5 0.12
34 17 0.43
35 15 0.38
36 3 0.08
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.63
Consensus pattern (32 bp):
TTTTTTTAAGCATTTTTTTATTTCGTATTAGA
Found at i:11373861 original size:18 final size:18
Alignment explanation
Indices: 11373822--11373861 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11373812 GTAATTTATC
* **
11373822 AAAATTTTCGTGTTTTTT
1 AAAATTCTCGTGTTTTAA
11373840 AAAATTCTCGTGTTTTAA
1 AAAATTCTCGTGTTTTAA
11373858 AAAA
1 AAAA
11373862 ACACTTTCGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (18 bp):
AAAATTCTCGTGTTTTAA
Found at i:11376742 original size:25 final size:25
Alignment explanation
Indices: 11376708--11376759 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
11376698 TTATTATAAG
11376708 TTAGTAAGATGCGCAACAAAAGACT
1 TTAGTAAGATGCGCAACAAAAGACT
11376733 TTAGTAAGATGCGCAACAAAAGACT
1 TTAGTAAGATGCGCAACAAAAGACT
11376758 TT
1 TT
11376760 GCAGACATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (25 bp):
TTAGTAAGATGCGCAACAAAAGACT
Found at i:11381327 original size:12 final size:11
Alignment explanation
Indices: 11381306--11381348 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
11381296 TATTATGCCT
11381306 AAAAAAAAGCA
1 AAAAAAAAGCA
11381317 AAAAAAGAAGCA
1 AAAAAA-AAGCA
11381329 AAAACAAAA-CA
1 AAAA-AAAAGCA
11381340 AAAAGAAAA
1 AAAA-AAAA
11381349 ATCAATATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 16 0.55
12 11 0.38
13 2 0.07
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGCA
Found at i:11382464 original size:79 final size:76
Alignment explanation
Indices: 11382190--11384128 Score: 1660
Period size: 79 Copynumber: 24.7 Consensus size: 76
11382180 CAAAAATTAT
* *
11382190 TTTTTCAATTTCTGTTTTTTCAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGG
1 TTTTTAAATTTCTG-TTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
*
11382255 TCACATGCCGAGGTA
62 TCACACGCCGAGGTA
* * * *
11382270 TTTCTTTTAAATTTAT-ATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGA
1 --T-TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
11382333 CACATGCCGAGGTA
63 CACACGCCGAGGTA
* * * * * *
11382347 TTTTTCAATTTCTGTTTTTAAAAAAATCAACTCATATTGTGAGAGGTGAATTGAGCCTCGGATCG
1 TTTTTAAATTTCTGTTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* **
11382412 CATGTTGAGGTA
65 CACGCCGAGGTA
* * * *
11382424 TTTCTCTTAAAATTCTGTTTGTCAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGT
1 -TT-T-TTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
* *
11382489 CACATGTCGAGGTA
63 CACACGCCGAGGTA
* * * *
11382503 TTTGTTTTAAATTTATGTTTTTCAATAATAAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG-
1 --T-TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
11382567 CACACGCCGAGGTA
63 CACACGCCGAGGTA
* *
11382581 TTTTTCAATTTCTGTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--
1 TTTTTAAATTTCTGTTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
11382644 CACGCTGAGGTA
65 CACGCCGAGGTA
* * *
11382656 TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGG-CAC
1 TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
11382720 ACGCCGAGGTA
66 ACGCCGAGGTA
* * * ** * * * * **
11382731 TTTCTTTTAAATTTCTGTTTTTCAAAAAACAAAAATCAAAATCAACTCATATTTCGAGAGGGGAG
1 --T-TTTTAAATTTCTGTTTTTCAAAAATC--AACTC-ATAT-TGC-GAGA---GGTGAGTTGAG
* * * *
11382796 -TTGAGCCTCGGGCACACGCCGACGTA
55 CCT----C-GGGTCACACGCCGAGGTA
*
11382822 TTTTT-AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGGTCAC
1 TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
11382886 ATGCTGAGGTA
66 ACGCCGAGGTA
* * * *
11382897 TTTCTCTTAAAATTCTGTTTGTCAAAAATCAACTCATATTGCTAGAAGTGAGTTGA-CCTCGGGT
1 -TT-T-TTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
11382961 CACACGCTGAGGTA
63 CACACGCCGAGGTA
* *
11382975 -TTTTAAATTTCTGTTTTTGAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGTCAC
1 TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* **
11383039 ATGTTGAGGTA
66 ACGCCGAGGTA
* * * * *
11383050 TTTCTCTTAAAATTCTGTTTGTCAAAAATCAACTCATATTGCTAGAAGTGAGTTGAGCCTTGGGT
1 -TT-T-TTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
* *
11383115 CACATGCCGATGTA
63 CACACGCCGAGGTA
* *
11383129 TTTTTTTTAAATTTATGTTTTTCAATAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-
1 ---TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
11383193 CACACGCCAAGGTA
63 CACACGCCGAGGTA
* * * * *
11383207 TTTTTTAATTTCTGTTTTTAAAAAAATCAACTCATATTTCGAGAGGTGAGTTGAGGCTCGAGT--
1 TTTTTAAATTTCTGTTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
11383270 CACGCTGAGGTA
65 CACGCCGAGGTA
*
11383282 TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CAC
1 TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
11383346 ACGCCGAGATA
66 ACGCCGAGGTA
* * * * * * * * *
11383357 TTTCTTTTAGATTTCTGTTTTTCAAAAAATAAAAATCAAAATCAACT-CATATTACGAGAGGTGA
1 --T-TTTTAAATTTCTGTTTTTC-AAAAAT-CAACTC---AT--ATTGC-GA-GAGGTGAGTTGA
* * *
11383421 G-TTGAACCTCGGGCACACGCCGAGGTA
54 GCCT----C-GGGTCACACGCCGAGGTA
* *
11383448 TTTTTCAATTTCTGTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--
1 TTTTTAAATTTCTGTTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
11383511 CACGCTGAGGTA
65 CACGCCGAGGTA
* * *
11383523 TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGG-CAT
1 TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
11383587 ACGCTGAGGTA
66 ACGCCGAGGTA
* * * * ** * * ** *
11383598 TTTCTTTTAAATTTCTATTTTTCAAAAAACAAAAATCAAAATCAACTCATATTTCGATAGGTGAG
1 --T-TTTTAAATTTCTGTTTTTCAAAAATC--AACTC-ATAT-TGC-GAGAGGT-G--AGTTGAG
* * *
11383663 -TTGAGCCTCGGGCACACGCCGAGGTA
55 CCT----C-GGGTCACACGCCGAGGTA
* *
11383689 TTTTT-AATTTCTGTTTTTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCAC
1 TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
11383753 ATGCTGAGGTA
66 ACGCCGAGGTA
* * * * * *
11383764 TTTCTCTTAAAATTCTGTTTGTCAAAAATCAACTCATATTACTAGAAGTTAGTTGAGCCTCGGGT
1 -TT-T-TTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
**
11383829 CACA-GTTGAGGTA
63 CACACGCCGAGGTA
* * *
11383842 -TTTTAAATTTCTATTTTTCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCGC
1 TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
11383906 ACGCTGAAGTA
66 ACGCCGAGGTA
* * *
11383917 -TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTAGAGCCTCGGGTCGC
1 TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
11383981 ATGTCGAGGTA
66 ACGCCGAGGTA
* * *
11383992 TTCTTTTCAATTTCTGTTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTAGAGCCTCGGGT
1 -T-TTTTAAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
* *
11384057 CGCATGCCGAGGTA
63 CACACGCCGAGGTA
* * *
11384071 TTCTTTTCAATTTCTGTTTTTCAGAAAATCAACTCATAATT-CAAGAGATGAGTTGAGC
1 -T-TTTTAAATTTCTGTTTTTCA-AAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGC
11384129 TTTGAGTCGC
Statistics
Matches: 1527, Mismatches: 232, Indels: 199
0.78 0.12 0.10
Matches are distributed among these distances:
74 225 0.15
75 281 0.18
76 119 0.08
77 34 0.02
78 180 0.12
79 430 0.28
80 34 0.02
81 25 0.02
82 12 0.01
83 20 0.01
84 10 0.01
85 14 0.01
86 21 0.01
87 42 0.03
88 30 0.02
89 6 0.00
90 6 0.00
91 38 0.02
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (76 bp):
TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
ACGCCGAGGTA
Done.