Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_pilon, whole genome shotgun sequence
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: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 18
Found at i:2130127 original size:20 final size:20
Alignment explanation
Indices: 2130104--2130147 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2130094 ATTCTGTCAG
*
2130104 TTTTTTTATTTACTGTGAAT
1 TTTTTTTATTTACTGTCAAT
*
2130124 TTTTTTTATTTATTGTCAAT
1 TTTTTTTATTTACTGTCAAT
2130144 TTTT
1 TTTT
2130148 GCTTCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (20 bp):
TTTTTTTATTTACTGTCAAT
Found at i:2134276 original size:2 final size:2
Alignment explanation
Indices: 2134269--2134300 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2134259 TCATTTGTTA
2134269 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
2134301 TAAAGACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2139085 original size:28 final size:28
Alignment explanation
Indices: 2139052--2139207 Score: 161
Period size: 28 Copynumber: 5.5 Consensus size: 28
2139042 GTTCAAAGTC
* *
2139052 AACGGGTTTACTCGGATGAGTTGGCTCA
1 AACGGGTTGACTCGGATGAGTTGACTCA
* *
2139080 TACGGGTTGACTCGGATGAGTTGGCTCA
1 AACGGGTTGACTCGGATGAGTTGACTCA
* * *
2139108 TACGGGTT-ATCTCGAACGAGTTGACTCA
1 AACGGGTTGA-CTCGGATGAGTTGACTCA
*
2139136 AACGGGTTGACTCAGATTGAGTTGACTCA
1 AACGGGTTGACTCGGA-TGAGTTGACTCA
* * *
2139165 AACGAGTTGACTCGAACGAGTTGACTCA
1 AACGGGTTGACTCGGATGAGTTGACTCA
* *
2139193 GATCGAGTTGACTCG
1 -AACGGGTTGACTCG
2139208 ATCGAGTCAA
Statistics
Matches: 110, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
27 1 0.01
28 71 0.65
29 38 0.35
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.27
Consensus pattern (28 bp):
AACGGGTTGACTCGGATGAGTTGACTCA
Found at i:2139161 original size:15 final size:15
Alignment explanation
Indices: 2139121--2139206 Score: 115
Period size: 14 Copynumber: 5.9 Consensus size: 15
2139111 GGGTTATCTC
2139121 GAACGAGTTGACTCA
1 GAACGAGTTGACTCA
*
2139136 -AACGGGTTGACTCA
1 GAACGAGTTGACTCA
**
2139150 GATTGAGTTGACTCA
1 GAACGAGTTGACTCA
2139165 -AACGAGTTGACTC-
1 GAACGAGTTGACTCA
2139178 GAACGAGTTGACTCA
1 GAACGAGTTGACTCA
*
2139193 GATCGAGTTGACTC
1 GAACGAGTTGACTC
2139207 GATCGAGTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
14 37 0.61
15 24 0.39
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (15 bp):
GAACGAGTTGACTCA
Found at i:2139210 original size:14 final size:14
Alignment explanation
Indices: 2139118--2139214 Score: 113
Period size: 14 Copynumber: 6.8 Consensus size: 14
2139108 TACGGGTTAT
2139118 CTCGAACGAGTTGA
1 CTCGAACGAGTTGA
* *
2139132 CTCAAACGGGTTGA
1 CTCGAACGAGTTGA
**
2139146 CTCAGATTGAGTTGA
1 CTC-GAACGAGTTGA
*
2139161 CTCAAACGAGTTGA
1 CTCGAACGAGTTGA
2139175 CTCGAACGAGTTGA
1 CTCGAACGAGTTGA
*
2139189 CTCAGATCGAGTTGA
1 CTC-GAACGAGTTGA
*
2139204 CTCGATCGAGT
1 CTCGAACGAGT
2139215 CAAACAGACC
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
14 47 0.67
15 23 0.33
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.25
Consensus pattern (14 bp):
CTCGAACGAGTTGA
Found at i:2139214 original size:43 final size:43
Alignment explanation
Indices: 2139118--2139214 Score: 149
Period size: 43 Copynumber: 2.3 Consensus size: 43
2139108 TACGGGTTAT
* *
2139118 CTCGAACGAGTTGACTCAAACGGGTTGACTCAGATTGAGTTGA
1 CTCGAACGAGTTGACTCAAACGAGTTGACTCAGATCGAGTTGA
* *
2139161 CTCAAACGAGTTGACTCGAACGAGTTGACTCAGATCGAGTTGA
1 CTCGAACGAGTTGACTCAAACGAGTTGACTCAGATCGAGTTGA
*
2139204 CTCGATCGAGT
1 CTCGAACGAGT
2139215 CAAACAGACC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.25
Consensus pattern (43 bp):
CTCGAACGAGTTGACTCAAACGAGTTGACTCAGATCGAGTTGA
Found at i:2151068 original size:13 final size:13
Alignment explanation
Indices: 2151050--2151078 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2151040 TTGGATAATA
2151050 AGATAACTTCCAT
1 AGATAACTTCCAT
2151063 AGATAACTTCCAT
1 AGATAACTTCCAT
2151076 AGA
1 AGA
2151079 GCTTTGTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (13 bp):
AGATAACTTCCAT
Found at i:2151901 original size:2 final size:2
Alignment explanation
Indices: 2151888--2151931 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2151878 ATTTAACGTG
* *
2151888 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2151930 TA
1 TA
2151932 CATTGTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2152935 original size:17 final size:18
Alignment explanation
Indices: 2152914--2152965 Score: 70
Period size: 17 Copynumber: 2.8 Consensus size: 18
2152904 AATTTAACCC
2152914 TTTATTATTTTTATTTGA
1 TTTATTATTTTTATTTGA
*
2152932 -TTATTATTTTTATTTTA
1 TTTATTATTTTTATTTGA
2152949 TTTCTATTATTTTTATT
1 -TT-TATTATTTTTATT
2152966 GTTTACACGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 16 0.53
19 1 0.03
20 13 0.43
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTATTATTTTTATTTGA
Found at i:2153053 original size:8 final size:8
Alignment explanation
Indices: 2153042--2153066 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2153032 TATATATATG
2153042 TATTTTAT
1 TATTTTAT
2153050 TATTTTAT
1 TATTTTAT
2153058 TATTTTAT
1 TATTTTAT
2153066 T
1 T
2153067 TTATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:2153065 original size:13 final size:12
Alignment explanation
Indices: 2153042--2153076 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
2153032 TATATATATG
2153042 TATTTTATTATTT
1 TATTTT-TTATTT
2153055 TATTATTTTATTT
1 TATT-TTTTATTT
2153068 TATTTTTTA
1 TATTTTTTA
2153077 GTACTATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 14 0.67
14 2 0.10
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:2153133 original size:13 final size:13
Alignment explanation
Indices: 2153115--2153139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2153105 ATACATTACT
2153115 TTATTATTTATTA
1 TTATTATTTATTA
2153128 TTATTATTTATT
1 TTATTATTTATT
2153140 TATTTTACCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:2153326 original size:10 final size:10
Alignment explanation
Indices: 2153311--2153335 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2153301 AGAGTGGGTT
2153311 TTATTTTTTA
1 TTATTTTTTA
2153321 TTATTTTTTA
1 TTATTTTTTA
2153331 TTATT
1 TTATT
2153336 ATTATAGTAT
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):
TTATTTTTTA
Found at i:2153585 original size:15 final size:15
Alignment explanation
Indices: 2153565--2153625 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
2153555 ATTCACTTAC
2153565 TTATTTT-TTTATTCT
1 TTATTTTATTTATT-T
*
2153580 TTATTTCT-TTT-GTT
1 TTATTT-TATTTATTT
2153594 TTATTTTATTTGATTT
1 TTATTTTATTT-ATTT
*
2153610 TTATTTTCTTTATTT
1 TTATTTTATTTATTT
2153625 T
1 T
2153626 ATTCATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 1 0.03
14 10 0.26
15 12 0.31
16 16 0.41
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (15 bp):
TTATTTTATTTATTT
Found at i:2153615 original size:30 final size:29
Alignment explanation
Indices: 2153565--2153628 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
2153555 ATTCACTTAC
*
2153565 TTATTTTTTTATTCTTTA-TTTCTTTTGTT
1 TTATTTTTTTATTCTTTATTTTC-TTTATT
2153594 TTATTTTATTTGATT-TTTATTTTCTTTATT
1 TTATTTT-TTT-ATTCTTTATTTTCTTTATT
2153624 TTATT
1 TTATT
2153629 CATTTTTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
29 7 0.23
30 17 0.55
31 7 0.23
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (29 bp):
TTATTTTTTTATTCTTTATTTTCTTTATT
Found at i:2153627 original size:25 final size:25
Alignment explanation
Indices: 2153571--2153641 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
2153561 TTACTTATTT
* *
2153571 TTTTATTC-TTTATTTCTTTTGTTTTA
1 TTTTATTCATTT-TTACTTTT-CTTTA
*
2153597 TTTTATTTGATTTTTA-TTTTCTTTA
1 TTTTA-TTCATTTTTACTTTTCTTTA
2153622 TTTTATTCATTTTTACTTTT
1 TTTTATTCATTTTTACTTTT
2153642 TTCCTTCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 9 0.24
25 13 0.34
26 9 0.24
27 4 0.11
28 3 0.08
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (25 bp):
TTTTATTCATTTTTACTTTTCTTTA
Found at i:2158982 original size:36 final size:36
Alignment explanation
Indices: 2158942--2159101 Score: 225
Period size: 36 Copynumber: 4.5 Consensus size: 36
2158932 CTTTGAAATT
* *
2158942 GTTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
2158978 GTTTCTC--AAAACAAAGTTTTGTTTCTCTTGAGACA
1 GTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
2159013 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
2159049 GTTTCCCTTGAAACAAATTTTATCTCTCTTGAGATA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
2159085 GTTTCCCTTGAAACAAA
1 GTTTCTCTTGAAACAAA
2159102 ATCTTTGAAT
Statistics
Matches: 112, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
34 7 0.06
35 23 0.21
36 75 0.67
37 7 0.06
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:2159041 original size:21 final size:20
Alignment explanation
Indices: 2159016--2159080 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
2159006 TGAGACAGTT
2159016 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTT-TC
* *
2159037 TCTCTTGAGAC--A-GTTTC
1 TCTCTTGAAACAAATTTTTC
2159054 -C-CTTGAAACAAATTTTATC
1 TCTCTTGAAACAAATTTT-TC
2159073 TCTCTTGA
1 TCTCTTGA
2159081 GATAGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 7 0.21
16 1 0.03
17 3 0.09
18 4 0.12
19 3 0.09
20 1 0.03
21 15 0.44
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.42
Consensus pattern (20 bp):
TCTCTTGAAACAAATTTTTC
Found at i:2159201 original size:102 final size:102
Alignment explanation
Indices: 2159014--2159203 Score: 283
Period size: 102 Copynumber: 1.9 Consensus size: 102
2159004 CTTGAGACAG
* * *
2159014 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTATCTCTCTT
2159079 GAGATAGTTTCCCTTGAAACAAAATCTTTGAATCTTT
66 GAGATAGTTTCCCTTGAAACAAAATCTTTGAATCTTT
** * * *
2159116 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAAC-AAATTTTATCTCTCT
*
2159180 TGAGATAGTTTCTCTTGAAACAAA
65 TGAGATAGTTTCCCTTGAAACAAA
2159204 TTTTGTCTCT
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 38 0.49
102 40 0.51
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTATCTCTCTT
GAGATAGTTTCCCTTGAAACAAAATCTTTGAATCTTT
Found at i:2159239 original size:73 final size:72
Alignment explanation
Indices: 2159116--2159348 Score: 288
Period size: 73 Copynumber: 3.2 Consensus size: 72
2159106 TTGAATCTTT
* * * * *
2159116 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACTAA-TTTTGTCTCTCT
*
2159180 TGAGATAG
65 TGAGACAG
* * *
2159188 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACTAATTTCGTCTCCCTT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACTAATTTTGTCTCTCTT
2159253 GAGACAG
66 GAGACAG
* * * * * *
2159260 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTTTCTTGAAACAAATTTTGTCTCTCT
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACTAATTTTGTCTCTCT
2159325 TGAGACAG
65 TGAGACAG
* *
2159333 TTTCCCTTAAAACAAA
1 TTTCTCTTGAAACAAA
2159349 ATCTTTGAAT
Statistics
Matches: 136, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
72 34 0.25
73 102 0.75
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (72 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACTAATTTTGTCTCTCTT
GAGACAG
Found at i:2159376 original size:247 final size:244
Alignment explanation
Indices: 2158942--2159588 Score: 873
Period size: 247 Copynumber: 2.7 Consensus size: 244
2158932 CTTTGAAATT
* * ** * *
2158942 GTTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTT--CTCAAAACAAAGTTTTGTTTCTC
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AA-TTTAGTCTC-C
* * *
2159005 TTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTT
63 TTGAGACAGTTTCTCTTGAAACTAATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTT
* * * *
2159070 ATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATCTTTGAATCTTTTTTCCTTGAAACAAATTTC
128 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTC
* *
2159135 GTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATA
193 GTCTCCCTTGAGACAATTTCTTTTGGAACAAAGTTTTGTCTCACTTGAGATA
*
2159187 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACTAATTTCGTCTCCCT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AATTTAGTCT-CCT
* * *
2159252 TGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTTTCTTGAAACAAATTTT
64 TGAGACAGTTTCTCTTGAAACTAA-TTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTT
* *
2159317 GTCTCTCTTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTT
128 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTC
* *
2159382 GTCTCCCTTGAGATAGTTTCTTTTGGAACAAAGTTTTGTCTCACTTGAGATA
193 GTCTCCCTTGAGACAATTTCTTTTGGAACAAAGTTTTGTCTCACTTGAGATA
* *
2159434 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACACTTTCCCTTGAAACAA---AATCT--TTG
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAATTTAGTCTCCTTG
* * * *
2159494 A-ATCTGTTT-TCCTTGAAACTAATTTCGTCTCCCTTGAGATAG-TTTCCTTTAGAACTAAATTT
66 AGA-CAGTTTCT-CTTGAAACTAATTTTGTCTCTCTTGAGATAGTTTTCCTTGA-AAC-AAATTT
2159556 TGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
127 TGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
2159589 GTTTTGTCTC
Statistics
Matches: 360, Mismatches: 34, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
238 7 0.02
239 23 0.06
240 56 0.16
243 3 0.01
245 38 0.11
246 31 0.09
247 202 0.56
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (244 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAATTTAGTCTCCTTG
AGACAGTTTCTCTTGAAACTAATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTTGTC
TCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTC
TCCCTTGAGACAATTTCTTTTGGAACAAAGTTTTGTCTCACTTGAGATA
Found at i:2159421 original size:37 final size:36
Alignment explanation
Indices: 2159363--2159486 Score: 169
Period size: 36 Copynumber: 3.4 Consensus size: 36
2159353 TTGAATATGT
*
2159363 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGATAG
1 TTTCTCTTGAAACAAATTTTGTCTCACTTGAGATAG
* *
2159398 TTTCTTTTGGAACAAAGTTTTGTCTCACTTGAGATAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCACTTGAGATAG
* * *
2159435 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAC
1 TTTCTCTTGAAACAAATTTTGTCTCACTTGAGATAG
*
2159471 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
2159487 ATCTTTGAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
35 4 0.05
36 41 0.53
37 33 0.42
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCACTTGAGATAG
Found at i:2159467 original size:36 final size:36
Alignment explanation
Indices: 2159116--2159348 Score: 279
Period size: 36 Copynumber: 6.4 Consensus size: 36
2159106 TTGAATCTTT
* * *
2159116 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
2159151 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
2159188 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
2159224 TTTCCCTTGAAACTAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
2159260 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
2159297 TTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
2159333 TTTCCCTTAAAACAAA
1 TTTCTCTTGAAACAAA
2159349 ATCTTTGAAT
Statistics
Matches: 164, Mismatches: 31, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
35 4 0.02
36 103 0.63
37 57 0.35
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:2159524 original size:138 final size:138
Alignment explanation
Indices: 2158943--2159690 Score: 683
Period size: 138 Copynumber: 5.4 Consensus size: 138
2158933 TTTGAAATTG
** *
2158943 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTC--TCAAAACAAAGTTTTGTTTCTCT
1 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGAAACAAAGTTTTGTCTCTCT
2159006 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTA
65 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA----A
2159071 TCTCTCTTGAGATA-GT
126 --TCT-TTGA-ATATGT
* * * * *
2159087 TTCCCTTGAAACAAA----ATCT---TTGA-ATC--TTTTTTCCTTGAAACAAA-TTTCGTCTCC
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGA-CAGTTTCTT--TTGAAACAAAGTTT--TGTCT
* * * * * ** * * *
2159141 CT-TGAGACA-ATTTCT-TTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAA
61 CTCT-TGAGACAGTT-TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
* *
2159203 ATTTTGTCTCTCTTGAGACA-GT
124 A------ATCT-TTGA-ATATGT
* * * *
2159225 TTCCCTTGAAACTAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTT
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGAAACAAAGTTTTGTCTCTCTT
* * *
2159290 GAGATAGTTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAATCTTT
66 GAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTT
2159355 GAATATGT
131 GAATATGT
* * * *
2159363 TTTCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTTTTGGAACAAAGTTTTGTCTCACTT
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGAAACAAAGTTTTGTCTCTCTT
* *
2159428 GAGATAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACACTTTCCCTTGAAACAAAATCTTT
66 GAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTT
*
2159493 GAATCTGT
131 GAATATGT
* * *
2159501 TTTCCTTGAAACTAATTTCGTCTCCCTTGAGATAGTTTCCTTT-AGAACTAAA-TTTTGTCTCTC
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGA-AAC-AAAGTTTTGTCTCTC
* ** *
2159564 TTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACACCAAT
64 TTGAGACAGTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAT
2159629 CTTTGAATATG-
127 CTTTGAATATGT
* * *
2159640 TTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTC-CTTGAAAC-AAATTTCGTCTCCCTTGAGACAGTTTCTTTTGAAACA
2159691 CAAAAAATCT
Statistics
Matches: 502, Mismatches: 69, Indels: 70
0.78 0.11 0.11
Matches are distributed among these distances:
134 3 0.01
135 1 0.00
136 5 0.01
137 5 0.01
138 290 0.58
139 52 0.10
140 25 0.05
141 28 0.06
142 4 0.01
143 11 0.02
144 12 0.02
145 57 0.11
146 4 0.01
147 5 0.01
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (138 bp):
TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGAAACAAAGTTTTGTCTCTCTT
GAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTT
GAATATGT
Found at i:2159620 original size:37 final size:36
Alignment explanation
Indices: 2159501--2159623 Score: 151
Period size: 37 Copynumber: 3.4 Consensus size: 36
2159491 TTGAATCTGT
* * * *
2159501 TTTCC-TTGAAACTAATTTCGTCTCCCTTGAGATAG
1 TTTCCTTTGAAACAAATTTTGTCTCTCTTGAGACAG
2159536 TTTCCTTT-AGAACTAAATTTTGTCTCTCTTGAGACAG
1 TTTCCTTTGA-AAC-AAATTTTGTCTCTCTTGAGACAG
*
2159573 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCTTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
*
2159610 TTTCTTTTGAAACA
1 TTTCCTTTGAAACA
2159624 CCAATCTTTG
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
35 6 0.08
36 8 0.11
37 61 0.80
38 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCCTTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:2159680 original size:67 final size:68
Alignment explanation
Indices: 2159296--2159720 Score: 245
Period size: 65 Copynumber: 6.2 Consensus size: 68
2159286 TCTTGAGATA
* * * *
2159296 GTTTTTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTT-AAA-ACAAAATCTTTG-A
1 GTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAA
2159357 ATAT
66 AT-T
* * * * **
2159361 GTTT-TCCTTGAAAC-AAATTTTGTCTCCCTTGAGATAGTTTCTTTTGGAACA-AAGTTTTGTCT
1 GTTTCT-CTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACACAA----AATCT
* *
2159423 CACTTGAGATA
61 ---TTGAAATT
* * * *
2159434 GTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACACTTTCCCTTG-AA-ACAAAATCTTTG-A
1 GTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAA
2159495 ATCT
66 AT-T
* * * * * **
2159499 GTTT-TCCTTGAAAC-TAATTTCGTCTCCCTTGAGATAGTTTC-CTTTAGAACTA-AATTTTGTC
1 GTTTCT-CTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGA-AAC-ACAA-----AA
* **
2159560 TCTCTTGAGACA
58 TCT-TTGAAATT
* * * * * *
2159572 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACAC-CAATCTTTG-A
1 GTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAA
2159635 ATAT
66 AT-T
2159639 GTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAAATCTTTG
1 GTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACAC--AAAATCTTTG
2159704 AAATT
64 AAATT
2159709 GTTTCTCTTGAA
1 GTTTCTCTTGAA
2159721 GCACAAAAAA
Statistics
Matches: 276, Mismatches: 49, Indels: 65
0.71 0.13 0.17
Matches are distributed among these distances:
64 7 0.03
65 76 0.28
66 7 0.03
67 54 0.20
68 7 0.03
70 24 0.09
71 4 0.01
72 7 0.03
73 58 0.21
74 29 0.11
75 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (68 bp):
GTTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAA
ATT
Found at i:2159746 original size:34 final size:33
Alignment explanation
Indices: 2159676--2159762 Score: 120
Period size: 34 Copynumber: 2.6 Consensus size: 33
2159666 CCTTGAGACA
* * *
2159676 GTTTCTCTTGAAACACAAAAAATCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAACCTTGGAAAGT
*
2159709 GTTTCTCTTGAAGCACAAAAAAACCTTGGAAAGT
1 GTTTCTCTTGAAACAC-AAAAAACCTTGGAAAGT
*
2159743 GTTTCTCTTGAAATACAAAA
1 GTTTCTCTTGAAACACAAAA
2159763 CCTTCAAGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 19 0.40
34 28 0.60
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTGGAAAGT
Found at i:2161556 original size:17 final size:17
Alignment explanation
Indices: 2161534--2161575 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
2161524 AACCCTTTAT
2161534 TTATTATTTTTATTTGA
1 TTATTATTTTTATTTGA
*
2161551 TTATTATTTTTATTTTA
1 TTATTATTTTTATTTGA
*
2161568 TTTTTATT
1 TTATTATT
2161576 ATTTTTATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (17 bp):
TTATTATTTTTATTTGA
Found at i:2161559 original size:11 final size:10
Alignment explanation
Indices: 2161530--2161589 Score: 53
Period size: 9 Copynumber: 6.7 Consensus size: 10
2161520 ATTTAACCCT
2161530 TTATTTATTA
1 TTATTTATTA
2161540 TT-TTTATT-
1 TTATTTATTA
*
2161548 TGA-TTATTA
1 TTATTTATTA
2161557 TT-TTTATT-
1 TTATTTATTA
2161565 TTATTT-TTA
1 TTATTTATTA
2161574 TTATTT-TTA
1 TTATTTATTA
*
2161583 TTGTTTA
1 TTATTTA
2161590 CACGTTAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
8 10 0.24
9 29 0.71
10 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (10 bp):
TTATTTATTA
Found at i:2161584 original size:6 final size:6
Alignment explanation
Indices: 2161529--2161575 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
2161519 AATTTAACCC
* *
2161529 TTTATT TATTATT TTTA-T TTGATT ATTATT TTTA-T TTTATT TTTATT
1 TTTATT T-TTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
2161576 ATTTTTATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 9 0.26
6 19 0.56
7 6 0.18
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:2161802 original size:21 final size:20
Alignment explanation
Indices: 2161716--2161873 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
2161706 AAATGACCAA
**
2161716 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2161735 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2161755 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2161775 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2161796 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2161817 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2161837 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2161858 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2161874 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2161915 original size:20 final size:20
Alignment explanation
Indices: 2161840--2162109 Score: 281
Period size: 20 Copynumber: 13.5 Consensus size: 20
2161830 CGATTTTCCA
** *
2161840 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
2161860 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
* *
2161880 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2161900 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2161920 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2161940 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2161960 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
2161980 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2162000 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
2162020 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2162040 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
2162060 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2162080 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
2162100 AAATCACAAC
1 AAATCGCAAC
2162110 ACTGAAATTT
Statistics
Matches: 218, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
20 217 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:2165315 original size:33 final size:34
Alignment explanation
Indices: 2165278--2165428 Score: 153
Period size: 33 Copynumber: 4.2 Consensus size: 34
2165268 GCAACGAGAG
2165278 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACAATGAA
*
2165311 AATCGCAATGCGGAAATGAAAATCGCAATACGAAATGAA
1 AATCGCAATGC-GAAATGAAAATC-CCA-AC--AATGAA
* * * *
2165350 AATTGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCCCAACAATGAA
*
2165383 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
2165421 AATCGCAA
1 AATCGCAA
2165429 CGAGAGAATC
Statistics
Matches: 98, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
33 39 0.40
34 13 0.13
35 3 0.03
36 4 0.04
37 2 0.02
38 22 0.22
39 15 0.15
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCCCAACAATGAA
Found at i:2165347 original size:19 final size:19
Alignment explanation
Indices: 2165278--2165466 Score: 201
Period size: 19 Copynumber: 10.7 Consensus size: 19
2165268 GCAACGAGAG
2165278 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2165297 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
2165311 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
2165331 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2165350 AATTGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2165369 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2165383 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2165402 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2165421 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
2165435 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
2165454 AATCGCATTGCGA
1 AATCGCAATGCGA
2165467 TTCTCCCGTT
Statistics
Matches: 142, Mismatches: 12, Indels: 32
0.76 0.06 0.17
Matches are distributed among these distances:
14 32 0.23
15 2 0.01
16 5 0.04
17 5 0.04
18 2 0.01
19 81 0.57
20 15 0.11
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2165397 original size:52 final size:52
Alignment explanation
Indices: 2165264--2165466 Score: 263
Period size: 52 Copynumber: 3.9 Consensus size: 52
2165254 CGGAAATTAC
*
2165264 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* * *
2165311 AATCGCAATGCGGAAATGAAAATCGCAATACGAAATGAAAATTGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2165369 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
2165421 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
2165467 TTCTCCCGTT
Statistics
Matches: 136, Mismatches: 9, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
52 83 0.61
53 27 0.20
55 2 0.01
56 1 0.01
58 13 0.10
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:2165515 original size:19 final size:19
Alignment explanation
Indices: 2165475--2165572 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
2165465 GATTCTCCCG
2165475 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2165495 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2165514 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2165528 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2165547 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2165566 TTGCGAT
1 TTGCGAT
2165573 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2165569 original size:52 final size:53
Alignment explanation
Indices: 2165456--2165572 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
2165446 GAAATTAAAA
2165456 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
2165509 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
2165561 TCGCATTGCGAT
1 TCGCATTGCGAT
2165573 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:2165697 original size:14 final size:14
Alignment explanation
Indices: 2165678--2165713 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2165668 CATCAATTAC
2165678 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2165692 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2165706 AC-AATCAA
1 ACAAATCAA
2165714 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2167140 original size:21 final size:21
Alignment explanation
Indices: 2167110--2167172 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
2167100 GTGAATCGGG
2167110 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
* * **
2167131 CTCTTCAATGATGACAGTGG-C
1 CTCTTGAATGGTGGGAG-GGAC
*
2167152 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
2167173 TCTCGAGGAA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.24
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGAC
Found at i:2167654 original size:20 final size:20
Alignment explanation
Indices: 2167629--2167694 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
2167619 TAGTTTACTT
* *
2167629 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
2167649 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
2167668 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
2167687 TCGCAACG
1 TCGCAACG
2167695 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:2167712 original size:33 final size:33
Alignment explanation
Indices: 2167666--2167757 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2167656 GCGAAACCAA
*
2167666 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
2167699 AATCGCAATGCGAAATTAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2167732 AATCGCAACGCGAAATG-AAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2167758 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 9 0.17
33 45 0.83
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2167723 original size:19 final size:18
Alignment explanation
Indices: 2167699--2167762 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
2167689 GCAACGACAG
*
2167699 AATCGCAATGCGAAATTAA
1 AATCGCAACGCGAAA-TAA
*
2167718 AATCGCAA--CG-AA-AG
1 AATCGCAACGCGAAATAA
*
2167732 AATCGCAACGCGAAATGA
1 AATCGCAACGCGAAATAA
*
2167750 AATCGCAATGCGA
1 AATCGCAACGCGA
2167763 TTTTGGTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 9 0.24
16 4 0.11
17 4 0.11
18 12 0.32
19 8 0.22
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (18 bp):
AATCGCAACGCGAAATAA
Found at i:2167737 original size:14 final size:14
Alignment explanation
Indices: 2167685--2167741 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2167675 GCGAAATGAA
*
2167685 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
2167699 AATCGCAATGCGAAATTAA
1 AATCGCAA--CG-AA--AG
2167718 AATCGCAACGAAAG
1 AATCGCAACGAAAG
2167732 AATCGCAACG
1 AATCGCAACG
2167742 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 4 0.11
17 3 0.09
19 9 0.26
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2167780 original size:19 final size:19
Alignment explanation
Indices: 2167758--2167886 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2167748 GAAATCGCAA
2167758 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2167777 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2167791 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2167810 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2167824 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2167843 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2167862 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2167882 TGCGA
1 TGCGA
2167887 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2167800 original size:33 final size:33
Alignment explanation
Indices: 2167758--2167849 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2167748 GAAATCGCAA
2167758 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2167791 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2167824 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2167850 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2168366 original size:93 final size:93
Alignment explanation
Indices: 2167933--2168584 Score: 1240
Period size: 93 Copynumber: 7.1 Consensus size: 93
2167923 ATGGATTGCA
2167933 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2167997 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2168025 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2168088 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2168116 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2168181 TAGCAGAATTGGCAGCAACCGAA-AAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2168208 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2168273 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
* *
2168301 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTTACAGTGTTAAAGAATACATAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
2168366 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2168394 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2168459 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2168487 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
2168552 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2168580 TTACT
1 TTACT
2168585 AAGCAATCTA
Statistics
Matches: 549, Mismatches: 7, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
91 73 0.13
92 132 0.24
93 344 0.63
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2170313 original size:21 final size:21
Alignment explanation
Indices: 2170252--2170318 Score: 84
Period size: 20 Copynumber: 3.3 Consensus size: 21
2170242 AACACTGTTT
2170252 TTGCGATTTTCATTTCTCTCG
1 TTGCGATTTTCATTTCTCTCG
***
2170273 -TGCGACAGTCA-TTCTCTCG
1 TTGCGATTTTCATTTCTCTCG
*
2170292 TTGCGATTTTCATTTATCTCG
1 TTGCGATTTTCATTTCTCTCG
2170313 TTGCGA
1 TTGCGA
2170319 CTCTTCTGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 8 0.22
20 16 0.43
21 13 0.35
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (21 bp):
TTGCGATTTTCATTTCTCTCG
Found at i:2170441 original size:18 final size:18
Alignment explanation
Indices: 2170418--2170467 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
2170408 CGAGAGAATA
2170418 GCAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
*
2170436 GCAA--CGACA-G-AATC
1 GCAACGCGAAATGAAATC
*
2170450 GTAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
2170468 TAAGTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 1 0.04
16 8 0.32
17 1 0.04
18 8 0.32
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (18 bp):
GCAACGCGAAATGAAATC
Found at i:2170466 original size:32 final size:32
Alignment explanation
Indices: 2170397--2170467 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
2170387 AATACTAACT
* *
2170397 TGAAAACGCAACGAGAGAATAGCAACGCGAAA
1 TGAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2170429 TGAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAATCGCAACGACAGAATAGCAACGCGAAA
2170461 TGAAATC
1 TGAAATC
2170468 TAAGTGAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (32 bp):
TGAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2170859 original size:20 final size:20
Alignment explanation
Indices: 2170834--2170987 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
2170824 CTTTAAATAT
2170834 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2170854 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2170876 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2170895 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
2170915 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2170935 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2170955 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2170975 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2170988 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2170961 original size:40 final size:40
Alignment explanation
Indices: 2170833--2170987 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
2170823 GCTTTAAATA
*
2170833 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
2170874 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
2170914 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
2170954 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
2170988 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:2171004 original size:21 final size:21
Alignment explanation
Indices: 2170974--2171056 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
2170964 ATTTTCATAT
*
2170974 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2170995 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
2171016 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
2171037 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
2171057 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2171047 original size:42 final size:43
Alignment explanation
Indices: 2170954--2171052 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
2170944 ATTTATGTGT
* *
2170954 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
2170995 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
2171037 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
2171053 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:2171294 original size:21 final size:22
Alignment explanation
Indices: 2171266--2171349 Score: 56
Period size: 21 Copynumber: 3.9 Consensus size: 22
2171256 ATTATATATA
2171266 TATATATTACTTTATTATTTAT-
1 TATATATTA-TTTATTATTTATA
2171288 TAT-TATTATTTATTTATTT-TA
1 TATATATTATTTA-TTATTTATA
*
2171309 CCTA-ATATT-TTATATATATGTATA
1 --TATATATTATT-TAT-TATTTATA
2171333 TAT-TATTA-TTATTATTT
1 TATATATTATTTATTATTT
2171350 TTACTTATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 22
0.68 0.03 0.30
Matches are distributed among these distances:
20 9 0.18
21 14 0.28
22 13 0.26
23 12 0.24
24 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (22 bp):
TATATATTATTTATTATTTATA
Found at i:2171746 original size:26 final size:27
Alignment explanation
Indices: 2171717--2171783 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 27
2171707 GTATATACAT
2171717 TTTATTTATTCACTTATTTTTTA-TTC
1 TTTATTTATTCACTTATTTTTTATTTC
* **
2171743 TTTATTTCTTTGCTTATTTTTTATTTTC
1 TTTATTTATTCACTTATTTTTTA-TTTC
2171771 TTTATTTTATTCA
1 TTTA-TTTATTCA
2171784 TTTTTACTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 20 0.62
28 7 0.22
29 5 0.16
ACGTcount: A:0.16, C:0.10, G:0.01, T:0.72
Consensus pattern (27 bp):
TTTATTTATTCACTTATTTTTTATTTC
Found at i:2171788 original size:26 final size:25
Alignment explanation
Indices: 2171717--2171788 Score: 60
Period size: 28 Copynumber: 2.7 Consensus size: 25
2171707 GTATATACAT
2171717 TTTA-TTTATTCACTTATTTTTTATTC
1 TTTATTTTATTCA-TT-TTTTTTATTC
2171743 TTTATTTCT-TTGC-TTATTTTTTATTTTC
1 TTTATTT-TATT-CATT-TTTTTTA--TTC
2171771 TTTATTTTATTCATTTTT
1 TTTATTTTATTCATTTTT
2171789 ACTTTTTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
26 14 0.36
27 9 0.23
28 16 0.41
ACGTcount: A:0.15, C:0.10, G:0.01, T:0.74
Consensus pattern (25 bp):
TTTATTTTATTCATTTTTTTTATTC
Found at i:2176645 original size:18 final size:18
Alignment explanation
Indices: 2176622--2176686 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
2176612 TGTTTATGAG
2176622 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
2176640 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
2176658 GGAATTGGAATCTGTCAA
1 GGAATTGGAATCTGTGAA
2176676 -GAATTGGAATC
1 GGAATTGGAATC
2176687 CAATTCCATA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
17 11 0.24
18 35 0.76
ACGTcount: A:0.34, C:0.08, G:0.31, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:2177258 original size:38 final size:36
Alignment explanation
Indices: 2177213--2177330 Score: 179
Period size: 33 Copynumber: 3.3 Consensus size: 36
2177203 GTTAACCCGA
2177213 ACCCGACCCGACCCGAATATCACACTTAAAAAA---
1 ACCCGACCCGACCCGAATATCACACTTAAAAAACCG
*
2177246 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCA
1 ACCCGACCCGACCCGAATATCACACTT-AAAAAA-CCG
*
2177284 ACCCGACTCGACCCGAATATCACACTTAAAAAACCG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAACCG
2177320 ACCCGACCCGA
1 ACCCGACCCGA
2177331 ACAAAATAAA
Statistics
Matches: 77, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
33 27 0.35
34 6 0.08
36 12 0.16
37 6 0.08
38 26 0.34
ACGTcount: A:0.40, C:0.39, G:0.10, T:0.11
Consensus pattern (36 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAACCG
Found at i:2180106 original size:20 final size:21
Alignment explanation
Indices: 2180083--2180121 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2180073 TTGAACCCTA
2180083 AAATACTTA-AAAATCAAAAC
1 AAATACTTATAAAATCAAAAC
* *
2180103 AAATATTTATACAATCAAA
1 AAATACTTATAAAATCAAA
2180122 CGTTAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATACTTATAAAATCAAAAC
Found at i:2184546 original size:29 final size:29
Alignment explanation
Indices: 2184503--2184585 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
2184493 CTCACCTAAC
2184503 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
2184533 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
**
2184562 TAAATGATGTAAGTGATGACATCA
1 TAAATGATGTAAGCAATGACATCA
2184586 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:2199830 original size:3 final size:3
Alignment explanation
Indices: 2199824--2199919 Score: 131
Period size: 3 Copynumber: 31.7 Consensus size: 3
2199814 TTCATTTAAA
2199824 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
2199869 TAT TAT TAT AAT AAT TAT TAT TAT TAT TAT TAA TAT ATAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
2199915 TAT TA
1 TAT TA
2199920 CAAAACCCAA
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.01
3 79 0.94
4 4 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2205310 original size:15 final size:15
Alignment explanation
Indices: 2205290--2205321 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2205280 TCAATACCTT
2205290 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
2205305 TTTTGCATACATTCA
1 TTTTGCATACATGCA
2205320 TT
1 TT
2205322 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:2216235 original size:15 final size:15
Alignment explanation
Indices: 2216215--2216246 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2216205 TCAATACCTT
2216215 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
2216230 TTTTGCATACATTCA
1 TTTTGCATACATGCA
2216245 TT
1 TT
2216247 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:2223593 original size:14 final size:13
Alignment explanation
Indices: 2223567--2223642 Score: 70
Period size: 12 Copynumber: 6.1 Consensus size: 13
2223557 ATACTTGAAG
*
2223567 AGAAGAAAAAG-A
1 AGAAAAAAAAGAA
2223579 AGAAAAAAAAG--
1 AGAAAAAAAAGAA
*
2223590 AGAAAAAAAGAAAA
1 AGAAAAAAA-AGAA
*
2223604 AGAGAAAAAAGAA
1 AGAAAAAAAAGAA
*
2223617 AGAAAAAAGAGAA
1 AGAAAAAAAAGAA
*
2223630 A-AGAAAAAAGAA
1 AGAAAAAAAAGAA
2223642 A
1 A
2223643 AAGGGGGTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
11 9 0.17
12 21 0.40
13 15 0.28
14 8 0.15
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAGAA
Found at i:2223603 original size:7 final size:7
Alignment explanation
Indices: 2223572--2223644 Score: 73
Period size: 7 Copynumber: 10.6 Consensus size: 7
2223562 TGAAGAGAAG
2223572 AAAAAGA
1 AAAAAGA
2223579 AGAAAA-A
1 A-AAAAGA
*
2223586 AAAGAGAA
1 AAAAAG-A
2223594 AAAAAGA
1 AAAAAGA
2223601 AAAAGAGA
1 AAAA-AGA
2223609 AAAAAG-
1 AAAAAGA
2223615 --AAAGA
1 AAAAAGA
2223620 AAAAAGA
1 AAAAAGA
*
2223627 GAAAAGA
1 AAAAAGA
2223634 AAAAAGA
1 AAAAAGA
2223641 AAAA
1 AAAA
2223645 GGGGGTCAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
4 4 0.07
6 3 0.05
7 31 0.56
8 17 0.31
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:2223611 original size:27 final size:26
Alignment explanation
Indices: 2223569--2223642 Score: 98
Period size: 25 Copynumber: 2.8 Consensus size: 26
2223559 ACTTGAAGAG
2223569 AAGAAAAAGAAGAAAAAA-AAGAGAAAAA
1 AAGAAAAAG-AGAAAAAAGAA-AG-AAAA
2223597 AAGAAAAAGAGAAAAAAGAAAGAAAA
1 AAGAAAAAGAGAAAAAAGAAAGAAAA
*
2223623 AAGAGAAA-AGAAAAAAGAAA
1 AAGAAAAAGAGAAAAAAGAAA
2223643 AAGGGGGTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 12 0.27
26 11 0.25
27 10 0.23
28 11 0.25
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (26 bp):
AAGAAAAAGAGAAAAAAGAAAGAAAA
Found at i:2223629 original size:9 final size:9
Alignment explanation
Indices: 2223569--2223631 Score: 69
Period size: 9 Copynumber: 7.0 Consensus size: 9
2223559 ACTTGAAGAG
2223569 AAGA-AAAA
1 AAGAGAAAA
*
2223577 GAAGAAAAAA
1 -AAGAGAAAA
2223587 AAGAGAAAA
1 AAGAGAAAA
2223596 AA-AG-AAA
1 AAGAGAAAA
2223603 AAGAGAAAA
1 AAGAGAAAA
2223612 AAGAAAGAAAA
1 AAG--AGAAAA
2223623 AAGAGAAAA
1 AAGAGAAAA
2223632 GAAAAAAGAA
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
7 5 0.10
8 4 0.08
9 26 0.54
10 4 0.08
11 9 0.19
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAGAGAAAA
Found at i:2223645 original size:27 final size:26
Alignment explanation
Indices: 2223569--2223645 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 26
2223559 ACTTGAAGAG
2223569 AAGA-AAAAGAAGAAAAAAAAGAGAAAA
1 AAGAGAAAAGAA-AAAAAAAA-AGAAAA
*
2223596 AA-AGAAAAAGAGAAAAAAGAAAGAAAA
1 AAGAG-AAAAGA-AAAAAAAAAAGAAAA
2223623 AAGAGAAAAGAAAAAAGAAAAAG
1 AAGAGAAAAGAAAAAA-AAAAAG
2223646 GGGGTCAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
26 6 0.14
27 21 0.49
28 15 0.35
29 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (26 bp):
AAGAGAAAAGAAAAAAAAAAAGAAAA
Found at i:2225167 original size:92 final size:92
Alignment explanation
Indices: 2225010--2225370 Score: 596
Period size: 92 Copynumber: 3.9 Consensus size: 92
2225000 GAACAAATGC
2225010 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
*
2225075 AGAATCAATCATTGAATTTGGAAGAGG
66 AGAACCAATCATTGAATTTGGAAGAGG
* *
2225102 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCATGAACCAC
1 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
* *
2225167 AGAACCAGTTATTGAATTTGGAAGAGG
66 AGAACCAATCATTGAATTTGGAAGAGG
*
2225194 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
* *
2225259 AGAACCAGTTATTGAATTTGGAAGAGG
66 AGAACCAATCATTGAATTTGGAAGAGG
* * * *
2225286 AATGTACTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGATATAAAACCA
1 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-GAACCA
2225351 CAGAACCAATCATTGGAATT
65 CAGAACCAATCATT-GAATT
2225371 AAAAGATGAA
Statistics
Matches: 254, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
92 232 0.91
93 17 0.07
94 5 0.02
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (92 bp):
AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
AGAACCAATCATTGAATTTGGAAGAGG
Found at i:2226488 original size:113 final size:112
Alignment explanation
Indices: 2226069--2226861 Score: 888
Period size: 113 Copynumber: 7.0 Consensus size: 112
2226059 TAGCAAAGAT
* * *
2226069 TCAAATCCATCAATTGATGGATTAA-CATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCA
1 TCAAATTCATC-ATTGATGGA-TAAGCTTTGCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCA
* * *
2226132 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAATAATTTGTTCAACCTTTTGT
60 TCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
2226185 TTAAATTCATCAATTGATGGATTAA-CATTGCCATGTAG--AGTTCATAATGAGAAGAACTCATC
1 TCAAATTCATC-ATTGATGGA-TAAGCTTTGCCA-G-AGAAAGTTCATAATGAGAAGAA--C-TC
2226247 ATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGC
59 ATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGC
** * * *
2226302 TTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAAAGTCCATAATAAGAAGAACTCATCTGA
1 TCAAATTCATCA-TTGATGGATAAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
2226367 AGAAGGAAGAAAAAGTTCATAATCAAAAGAATTTGTTCAACCTTTTGC
65 AGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * ****
2226415 TCAAATCCATCATTCAATAGATAAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCATT-GATGGATAAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
2226480 AGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * *
2226528 TTGAATTCATCATTTGATGGATCAGCTTTGCCAGAGAAAG-TCTATAATAAGAAGAACTCATCTG
1 TCAAATTCATCA-TTGATGGATAAGCTTTGCCAGAGAAAGTTC-ATAATGAGAAGAACTCATCTG
*
2226592 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
64 AAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * ** * ****
2226641 CCAAATCCATCACTTGATGGATCTGCTTTTCCATTTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCA-TTGATGGATAAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
2226706 AGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGT
65 AGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
2226754 TCAAATTCATCACTTAATGGATCAACCTTT-ACAGAGAAAGTTCATAATGAGAAGAACTCATCT-
1 TCAAATTCATCA-TTGATGGAT-AAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* * ** *
2226817 --GAA-GAAGAATAAGTTCATAATAAGAAGAGCTTATTCAACCTTTTG
64 AAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
2226862 AATGACTCTA
Statistics
Matches: 592, Mismatches: 72, Indels: 33
0.85 0.10 0.05
Matches are distributed among these distances:
109 37 0.06
110 3 0.01
112 4 0.01
113 336 0.57
114 56 0.09
115 3 0.01
116 105 0.18
117 47 0.08
119 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (112 bp):
TCAAATTCATCATTGATGGATAAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:2226595 original size:226 final size:224
Alignment explanation
Indices: 2226129--2226861 Score: 1014
Period size: 226 Copynumber: 3.2 Consensus size: 224
2226119 GAAGAACTCA
* * * *
2226129 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAATAATTTGTTCAACCTTTTGTTTAAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
* * *
2226194 TCAATTGATGGATTAA-CATTGCCATGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAG
66 TC-ATTGATGGA-TAAGCTTTTCCAT-TCGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAG
2226258 GAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGCTTGAATTCATCATTTGATGGA
125 GAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGCTTGAATTCATCATTTGATGGA
*
2226323 TCAGCTTTGCCAGAGAAAGTCCATAATAAGAAGAAC
189 TCAGCTTTGCCAGAGAAAGTCTATAATAAGAAGAAC
* * *
2226359 TCATCTGAAGAAGGAAGAAAAAGTTCATAATCAAAAGAATTTGTTCAACCTTTTGCTCAAATCCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
* *
2226424 TCATTCAATAGATAAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
66 TCATT-GATGGATAAGCTTTTCCA-TTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
2226489 AAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAGC
129 AAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAGC
2226554 TTTGCCAGAGAAAGTCTATAATAAGAAGAAC
194 TTTGCCAGAGAAAGTCTATAATAAGAAGAAC
*
2226585 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCCAAATCCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
** *
2226650 TCACTTGATGGATCTGCTTTTCCATTTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
66 TCA-TTGATGGATAAGCTTTTCCA-TTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
* * * * *
2226715 AAAAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTG-TTCAAATTCATCACTTAATGGATCAA
129 AAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT-GAATTCATCATTTGATGGATC-A
* * *
2226779 CCTTT-ACAGAGAAAGT-TCATAATGAGAAGAAC
192 GCTTTGCCAGAGAAAGTCT-ATAATAAGAAGAAC
* * ** *
2226811 TCATCT---GAA-GAAGAATAAGTTCATAATAAGAAGAGCTTATTCAACCTTTTG
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
2226862 AATGACTCTA
Statistics
Matches: 460, Mismatches: 36, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
222 37 0.08
223 3 0.01
225 3 0.01
226 262 0.57
227 57 0.12
228 1 0.00
229 6 0.01
230 90 0.20
231 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (224 bp):
TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
TCATTGATGGATAAGCTTTTCCATTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
AAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAGCTT
TGCCAGAGAAAGTCTATAATAAGAAGAAC
Found at i:2227088 original size:3 final size:3
Alignment explanation
Indices: 2227082--2227173 Score: 107
Period size: 3 Copynumber: 30.3 Consensus size: 3
2227072 TTCATTTAAA
2227082 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
2227127 AAT TA- TACT TAT TAT AAT TAT TAT TAT TAA TAT ATAT TAT TAA TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
2227173 T
1 T
2227174 GCAAAACCCA
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
2 3 0.04
3 67 0.88
4 6 0.08
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2239450 original size:20 final size:22
Alignment explanation
Indices: 2239404--2239455 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
2239394 TTCTGGGCTA
*
2239404 GGTATCGATACCCCCTTGGATG
1 GGTACCGATACCCCCTTGGATG
2239426 GGTACCGATACCCCCTT-GA-G
1 GGTACCGATACCCCCTTGGATG
2239446 GGTACCGATA
1 GGTACCGATA
2239456 TCCTCCACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 16 0.55
ACGTcount: A:0.21, C:0.29, G:0.27, T:0.23
Consensus pattern (22 bp):
GGTACCGATACCCCCTTGGATG
Found at i:2245420 original size:27 final size:24
Alignment explanation
Indices: 2245377--2245462 Score: 95
Period size: 24 Copynumber: 3.5 Consensus size: 24
2245367 AAATTGAACG
*
2245377 ACCGGTTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTTACCGGATAAAAA
2245401 ACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTT---ACCGGATAAAAA
*
2245428 ACTGG-TTTTTTATCCGGA-AAAAA
1 ACCGGTTTTTTTA-CCGGATAAAAA
2245451 ATCCGGTTTTTT
1 A-CCGGTTTTTT
2245463 AAAAAAACTG
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
23 7 0.13
24 20 0.38
25 5 0.09
26 6 0.11
27 15 0.28
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (24 bp):
ACCGGTTTTTTTACCGGATAAAAA
Found at i:2245502 original size:41 final size:41
Alignment explanation
Indices: 2245423--2245501 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
2245413 CAAACCGGAT
*
2245423 AAAAAACTGGTTTTTTATCCGGAAAAAAATCCGGTTTTTTA
1 AAAAAACTGGATTTTTATCCGGAAAAAAATCCGGTTTTTTA
2245464 AAAAAACTGGATTTTTATCC-G-AAAAAATCCGGTTTTTT
1 AAAAAACTGGATTTTTATCCGGAAAAAAATCCGGTTTTTT
2245502 TGCAAACCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
39 17 0.46
40 1 0.03
41 19 0.51
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (41 bp):
AAAAAACTGGATTTTTATCCGGAAAAAAATCCGGTTTTTTA
Found at i:2252374 original size:83 final size:83
Alignment explanation
Indices: 2252220--2252376 Score: 233
Period size: 83 Copynumber: 1.9 Consensus size: 83
2252210 TGTAAATTTG
* * * *
2252220 TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAGATATATGGT
1 TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAAATATTAAAAGAGATATAGA
2252285 TAGAGTAAATCTATCATA
66 TAGAGTAAATCTATCATA
* * * *
2252303 TTTAATATTTTAAATTTCAAATATATTATTATCTTTTTAAATTTAAATATTAAAAGAGATTTAGA
1 TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAAATATTAAAAGAGATATAGA
*
2252368 TGGAGTAAA
66 TAGAGTAAA
2252377 ACTCTCTCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 65 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (83 bp):
TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAAATATTAAAAGAGATATAGA
TAGAGTAAATCTATCATA
Found at i:2252751 original size:26 final size:27
Alignment explanation
Indices: 2252722--2252773 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
2252712 TTTATTTCCT
2252722 TTTGATTC-TCTTTTATTTATAAAGAA
1 TTTGATTCTTCTTTTATTTATAAAGAA
*
2252748 TTTGATTCTTTCTTTTGTTTATAAAG
1 TTTGATTC-TTCTTTTATTTATAAAG
2252774 GTTCCATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 8 0.35
28 15 0.65
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.58
Consensus pattern (27 bp):
TTTGATTCTTCTTTTATTTATAAAGAA
Found at i:2255676 original size:20 final size:21
Alignment explanation
Indices: 2255623--2255681 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
2255613 TGTTGAGAGT
*
2255623 GGTATCGATACCTTGAGGGATG
1 GGTATCGATACCTT-AAGGATG
*
2255645 GGTATCGGTACCTTAAGGA-G
1 GGTATCGATACCTTAAGGATG
*
2255665 GTTATCGATACCCTTAA
1 GGTATCGATA-CCTTAA
2255682 AACATCGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 9 0.28
21 10 0.31
22 13 0.41
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (21 bp):
GGTATCGATACCTTAAGGATG
Found at i:2256379 original size:21 final size:21
Alignment explanation
Indices: 2256354--2256445 Score: 71
Period size: 21 Copynumber: 4.3 Consensus size: 21
2256344 GTCGAGGGTC
* * *
2256354 TATGTGGTCCTTCGAGATAAT
1 TATGTGGTCATTCGAGACAAA
*
2256375 TATGTGGTTATTCGAGACAAA
1 TATGTGGTCATTCGAGACAAA
*
2256396 TATGTGG-CATTTCG-GTGCAAA
1 TATGTGGTCA-TTCGAG-ACAAA
* * *
2256417 TTATGTAGTCATTCGGGACAAT
1 -TATGTGGTCATTCGAGACAAA
2256439 TATGTGG
1 TATGTGG
2256446 CACTTCGGTG
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
20 2 0.04
21 38 0.68
22 13 0.23
23 3 0.05
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (21 bp):
TATGTGGTCATTCGAGACAAA
Found at i:2256421 original size:43 final size:43
Alignment explanation
Indices: 2256372--2256462 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
2256362 CCTTCGAGAT
* * *
2256372 AATTATGTGGTTATTCGAGACAAATATGTGGCATTTCGGTGCA
1 AATTATGTAGTCATTCGAGACAAATATGTGGCACTTCGGTGCA
* *
2256415 AATTATGTAGTCATTCGGGACAATTATGTGGCACTTCGGTGCA
1 AATTATGTAGTCATTCGAGACAAATATGTGGCACTTCGGTGCA
2256458 AATTA
1 AATTA
2256463 GGAGTTGTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (43 bp):
AATTATGTAGTCATTCGAGACAAATATGTGGCACTTCGGTGCA
Found at i:2256431 original size:22 final size:22
Alignment explanation
Indices: 2256392--2256462 Score: 78
Period size: 21 Copynumber: 3.3 Consensus size: 22
2256382 TTATTCGAGA
*
2256392 CAAA-TATGTGGCATTTCGGTG
1 CAAATTATGTGGCACTTCGGTG
*
2256413 CAAATTATGTAGTCA-TTCGG-G
1 CAAATTATGT-GGCACTTCGGTG
2256434 -ACAATTATGTGGCACTTCGGTG
1 CA-AATTATGTGGCACTTCGGTG
2256456 CAAATTA
1 CAAATTA
2256463 GGAGTTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
20 4 0.10
21 18 0.43
22 16 0.38
23 4 0.10
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (22 bp):
CAAATTATGTGGCACTTCGGTG
Found at i:2258399 original size:20 final size:20
Alignment explanation
Indices: 2258374--2258417 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
2258364 ACTAGTGAAG
2258374 ATTGTGATGATCCGGAAATC
1 ATTGTGATGATCCGGAAATC
2258394 ATTGTGATGATCCGGAAATC
1 ATTGTGATGATCCGGAAATC
2258414 ATTG
1 ATTG
2258418 CAGGTACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (20 bp):
ATTGTGATGATCCGGAAATC
Found at i:2262244 original size:29 final size:29
Alignment explanation
Indices: 2262210--2262273 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
2262200 TGTAAAATGG
2262210 GTTTTTAGTTGAAACTTTGATATGGAGTA
1 GTTTTTAGTTGAAACTTTGATATGGAGTA
2262239 GTTTTTAGTTGAAACTTTGATATGGAGTA
1 GTTTTTAGTTGAAACTTTGATATGGAGTA
2262268 GTTTTT
1 GTTTTT
2262274 GAAGTATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.25, C:0.03, G:0.23, T:0.48
Consensus pattern (29 bp):
GTTTTTAGTTGAAACTTTGATATGGAGTA
Found at i:2262652 original size:22 final size:20
Alignment explanation
Indices: 2262622--2262686 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 20
2262612 ATACTTGTTG
*
2262622 AGAGTGGTATCGATACCTTGAG
1 AGAG-GGTATCGATACCTT-AA
* *
2262644 GGATGGGTATCGGTACCTTAA
1 AGA-GGGTATCGATACCTTAA
2262665 AGAGGGTATCGATACCCTTAA
1 AGAGGGTATCGATA-CCTTAA
2262686 A
1 A
2262687 ACATCGAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 10 0.28
21 10 0.28
22 15 0.42
23 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (20 bp):
AGAGGGTATCGATACCTTAA
Found at i:2262729 original size:54 final size:55
Alignment explanation
Indices: 2262651--2262754 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 55
2262641 GAGGGATGGG
2262651 TATCGGTACCTTAAAGAGGGTATCGATACCCTTAAAACATCGAATGCAAAGTGTA
1 TATCGGTACCTTAAAGAGGGTATCGATACCCTTAAAACATCGAATGCAAAGTGTA
* * * ** *
2262706 TATCGGTTCCTTGAGGA-GGTATCGATACCCTTGCAACTTCGAATGCAAA
1 TATCGGTACCTTAAAGAGGGTATCGATACCCTTAAAACATCGAATGCAAA
2262755 TTCGGTATCG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 29 0.67
55 14 0.33
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (55 bp):
TATCGGTACCTTAAAGAGGGTATCGATACCCTTAAAACATCGAATGCAAAGTGTA
Found at i:2262764 original size:54 final size:54
Alignment explanation
Indices: 2262649--2262767 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 54
2262639 TTGAGGGATG
2262649 GGTATCGGTACCTTAAAGAGGGTATCGATACCCTTAAAACATCGAATGCAAAGT
1 GGTATCGGTACCTTAAAGAGGGTATCGATACCCTTAAAACATCGAATGCAAAGT
* * * * ** * *
2262703 GTATATCGGTTCCTTGAGGA-GGTATCGATACCCTTGCAACTTCGAATGCAAATT
1 G-GTATCGGTACCTTAAAGAGGGTATCGATACCCTTAAAACATCGAATGCAAAGT
2262757 CGGTATCGGTA
1 -GGTATCGGTA
2262768 TATGTGTAGG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
54 38 0.72
55 15 0.28
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (54 bp):
GGTATCGGTACCTTAAAGAGGGTATCGATACCCTTAAAACATCGAATGCAAAGT
Found at i:2262842 original size:40 final size:41
Alignment explanation
Indices: 2262758--2262849 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 41
2262748 ATGCAAATTC
* ** **
2262758 GGTATCGGTATATGTGTAGGTATTGATACCCCCTGAAGGGT
1 GGTATCGGTACATACGTAGGTACCGATACCCCCTGAAGGGT
2262799 GGTATCGGTACATACGTAGGTACCGATA-CCCCTGAAGGGT
1 GGTATCGGTACATACGTAGGTACCGATACCCCCTGAAGGGT
2262839 GGTATCGGTAC
1 GGTATCGGTAC
2262850 CCTTAGGGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 23 0.50
41 23 0.50
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (41 bp):
GGTATCGGTACATACGTAGGTACCGATACCCCCTGAAGGGT
Found at i:2262870 original size:20 final size:21
Alignment explanation
Indices: 2262817--2262870 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2262807 TACATACGTA
2262817 GGTACCGATACCCCTGAAGGGT
1 GGTACCGATA-CCCTGAAGGGT
* * *
2262839 GGTATCGGTACCCT-TAGGGT
1 GGTACCGATACCCTGAAGGGT
2262859 GGTACCGATACC
1 GGTACCGATACC
2262871 TCTAACCATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 15 0.56
21 4 0.15
22 8 0.30
ACGTcount: A:0.20, C:0.26, G:0.31, T:0.22
Consensus pattern (21 bp):
GGTACCGATACCCTGAAGGGT
Found at i:2263398 original size:21 final size:21
Alignment explanation
Indices: 2263372--2263463 Score: 71
Period size: 21 Copynumber: 4.3 Consensus size: 21
2263362 GTCAAGGGTC
* * *
2263372 TATGTGGTCCTTCGAGATAAT
1 TATGTGGTCATTCGAGACAAA
*
2263393 TATGTGGTTATTCGAGACAAA
1 TATGTGGTCATTCGAGACAAA
*
2263414 TATGTGG-CATTTCG-GTGCAAA
1 TATGTGGTCA-TTCGAG-ACAAA
* * *
2263435 TTATGTAGTCATTCGGGACAAT
1 -TATGTGGTCATTCGAGACAAA
2263457 TATGTGG
1 TATGTGG
2263464 CACTTCGGTG
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
20 2 0.04
21 38 0.68
22 13 0.23
23 3 0.05
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (21 bp):
TATGTGGTCATTCGAGACAAA
Found at i:2263439 original size:43 final size:43
Alignment explanation
Indices: 2263390--2263480 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
2263380 CCTTCGAGAT
* * *
2263390 AATTATGTGGTTATTCGAGACAAATATGTGGCATTTCGGTGCA
1 AATTATGTAGTCATTCGAGACAAATATGTGGCACTTCGGTGCA
* *
2263433 AATTATGTAGTCATTCGGGACAATTATGTGGCACTTCGGTGCA
1 AATTATGTAGTCATTCGAGACAAATATGTGGCACTTCGGTGCA
2263476 AATTA
1 AATTA
2263481 GGAGTTGTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (43 bp):
AATTATGTAGTCATTCGAGACAAATATGTGGCACTTCGGTGCA
Found at i:2263449 original size:22 final size:22
Alignment explanation
Indices: 2263410--2263480 Score: 78
Period size: 21 Copynumber: 3.3 Consensus size: 22
2263400 TTATTCGAGA
*
2263410 CAAA-TATGTGGCATTTCGGTG
1 CAAATTATGTGGCACTTCGGTG
*
2263431 CAAATTATGTAGTCA-TTCGG-G
1 CAAATTATGT-GGCACTTCGGTG
2263452 -ACAATTATGTGGCACTTCGGTG
1 CA-AATTATGTGGCACTTCGGTG
2263474 CAAATTA
1 CAAATTA
2263481 GGAGTTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
20 4 0.10
21 18 0.43
22 16 0.38
23 4 0.10
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (22 bp):
CAAATTATGTGGCACTTCGGTG
Found at i:2277479 original size:23 final size:23
Alignment explanation
Indices: 2277453--2277497 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2277443 CACCACAGCT
*
2277453 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
* *
2277476 CGTAGAATTGCACTGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2277498 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2277894 original size:14 final size:14
Alignment explanation
Indices: 2277875--2277902 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2277865 AACTTGTAAT
2277875 TCACGTATCACATA
1 TCACGTATCACATA
2277889 TCACGTATCACATA
1 TCACGTATCACATA
2277903 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:2279261 original size:21 final size:21
Alignment explanation
Indices: 2279237--2279281 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2279227 CCATGTTCGT
* *
2279237 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2279258 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2279279 TTG
1 TTG
2279282 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2282431 original size:23 final size:23
Alignment explanation
Indices: 2282405--2282449 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2282395 CACCACAGCT
*
2282405 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
2282428 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2282450 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2282712 original size:149 final size:144
Alignment explanation
Indices: 2282417--2282726 Score: 532
Period size: 149 Copynumber: 2.1 Consensus size: 144
2282407 TATAATTGCA
2282417 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTC
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTC
*
2282481 CTTAAGAATCATATACATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACA
65 CTTAAGAATCATATACATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAA
*
2282546 GAATATATATATATC
130 GAATATACATATATC
2282561 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCAC--A-TAT
2282626 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
63 TCCTTAAGAATCATATAC--ATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
2282691 CAAAGAATATACATATGTC
126 CAAAGAATATACATATATC
2282710 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
2282727 CCCTCGACTC
Statistics
Matches: 157, Mismatches: 3, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
143 1 0.01
144 56 0.36
146 1 0.01
147 21 0.13
149 78 0.50
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (144 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTCC
TTAAGAATCATATACATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAG
AATATACATATATC
Found at i:2284216 original size:21 final size:21
Alignment explanation
Indices: 2284192--2284236 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2284182 CCATGTTCGT
* *
2284192 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2284213 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2284234 TTG
1 TTG
2284237 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2287364 original size:23 final size:23
Alignment explanation
Indices: 2287338--2287382 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2287328 CACCACAGCT
*
2287338 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
2287361 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2287383 ATATAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2287620 original size:149 final size:149
Alignment explanation
Indices: 2287350--2287664 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
2287340 TATAATTGCA
* *
2287350 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATATTGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
2287414 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* *
2287479 CCATAGAATATATATATATC
130 CCAAAGAATATACATATATC
2287499 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
2287564 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
2287629 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
2287648 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
2287665 CCCTCGACTC
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:2287784 original size:14 final size:14
Alignment explanation
Indices: 2287765--2287792 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2287755 AACTTGTAAT
2287765 TCACGTATCACATA
1 TCACGTATCACATA
2287779 TCACGTATCACATA
1 TCACGTATCACATA
2287793 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:2289173 original size:21 final size:21
Alignment explanation
Indices: 2289131--2289175 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2289121 CCATGTTCGT
* * *
2289131 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTACCC
*
2289152 TTGAATGGGTACCGATTACCC
1 TTGAAGGGGTACCGATTACCC
2289173 TTG
1 TTG
2289176 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTACCC
Found at i:2290534 original size:19 final size:19
Alignment explanation
Indices: 2290510--2290556 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
2290500 TTTGAGCATG
2290510 TGATTGATATGAGGATATA
1 TGATTGATATGAGGATATA
*
2290529 TGATTGATATGAGGATATG
1 TGATTGATATGAGGATATA
2290548 TGATT-ATAT
1 TGATTGATAT
2290557 ATTATACATG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (19 bp):
TGATTGATATGAGGATATA
Found at i:2291027 original size:2 final size:2
Alignment explanation
Indices: 2291020--2291067 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2291010 ACTTAAGTGT
2291020 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
2291062 TA TA TA
1 TA TA TA
2291068 GTTACATAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2293104 original size:36 final size:36
Alignment explanation
Indices: 2292972--2293113 Score: 178
Period size: 36 Copynumber: 3.9 Consensus size: 36
2292962 AAGGGTCTAC
* * * *
2292972 GTGGTCCTTCGGGATATAATGGTCTTTCGGGACATA
1 GTGGTCCTTCAGGACATAATGGTCCTTCGGGACACA
** *
2293008 GTGGTCCTTTGGGACATAATGGTCATTCGGGACACA
1 GTGGTCCTTCAGGACATAATGGTCCTTCGGGACACA
*
2293044 GTGGTCCTTCAGGACATAATGGTCCTTCGGGATACA
1 GTGGTCCTTCAGGACATAATGGTCCTTCGGGACACA
* *
2293080 GTGGTCTTTCAGGACATAGTGGTCCTAT-GGGACA
1 GTGGTCCTTCAGGACATAATGGTCCT-TCGGGACA
2293114 AATTTTACGC
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
36 93 0.99
37 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (36 bp):
GTGGTCCTTCAGGACATAATGGTCCTTCGGGACACA
Found at i:2293113 original size:18 final size:18
Alignment explanation
Indices: 2292972--2293105 Score: 151
Period size: 18 Copynumber: 7.4 Consensus size: 18
2292962 AAGGGTCTAC
*
2292972 GTGGTCCTTCGGGATATA
1 GTGGTCCTTCGGGACATA
* *
2292990 ATGGTCTTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
2293008 GTGGTCCTTTGGGACATA
1 GTGGTCCTTCGGGACATA
* * *
2293026 ATGGTCATTCGGGACACA
1 GTGGTCCTTCGGGACATA
*
2293044 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCGGGACATA
* * *
2293062 ATGGTCCTTCGGGATACA
1 GTGGTCCTTCGGGACATA
* *
2293080 GTGGTCTTTCAGGACATA
1 GTGGTCCTTCGGGACATA
2293098 GTGGTCCT
1 GTGGTCCT
2293106 ATGGGACAAA
Statistics
Matches: 92, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 92 1.00
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:2294129 original size:32 final size:31
Alignment explanation
Indices: 2294072--2294193 Score: 147
Period size: 32 Copynumber: 3.9 Consensus size: 31
2294062 GAGTAGAGGG
*
2294072 TTACCTATGTCCTTTGGGGACATATGGACAGTA
1 TTACCTATGTCC-TTCGGGACATATGGACA-TA
*
2294105 TTATCTATGTCCTTCGGGACATATGGACATTA
1 TTACCTATGTCCTTCGGGACATATGGACA-TA
* * *
2294137 TTACCTATATCTTTCGAGACATATGGACA-A
1 TTACCTATGTCCTTCGGGACATATGGACATA
* *
2294167 TTACCTATGTTCTTCGGAACATATGGA
1 TTACCTATGTCCTTCGGGACATATGGA
2294194 TAGGTCCTTC
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
30 23 0.30
32 43 0.56
33 11 0.14
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (31 bp):
TTACCTATGTCCTTCGGGACATATGGACATA
Found at i:2294183 original size:62 final size:64
Alignment explanation
Indices: 2294072--2294193 Score: 167
Period size: 62 Copynumber: 1.9 Consensus size: 64
2294062 GAGTAGAGGG
* * * * *
2294072 TTACCTATGTCCTTTGGGGACATATGGACAGTATTATCTATGTCCTTCGGGACATATGGACATTA
1 TTACCTATATCCTTTCGAGACATATGGACAG-ATTACCTATGTCCTTCGGAACATATGGACATTA
*
2294137 TTACCTATAT-CTTTCGAGACATATGGACA-ATTACCTATGTTCTTCGGAACATATGGA
1 TTACCTATATCCTTTCGAGACATATGGACAGATTACCTATGTCCTTCGGAACATATGGA
2294194 TAGGTCCTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
62 25 0.49
64 17 0.33
65 9 0.18
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (64 bp):
TTACCTATATCCTTTCGAGACATATGGACAGATTACCTATGTCCTTCGGAACATATGGACATTA
Found at i:2306837 original size:65 final size:64
Alignment explanation
Indices: 2306705--2306840 Score: 193
Period size: 65 Copynumber: 2.1 Consensus size: 64
2306695 ACACCATATT
* * *
2306705 TCGAATGCATTTTGTGGACCGATGCACAACCATGTATCGATGCACTCTTGAATTTATTGAAACA
1 TCGAATGCATTTTGTGGACCGATGCACAACCATGCATCGATGCACTCATGAATTTATTAAAACA
* **
2306769 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCATGGCTCTT-TTAAAAC
1 TCGAATGCATTTTGTGGACCGATGCACA-ACCATGCATCGATGCACTCATGAAT-TTATTAAAAC
2306833 A
64 A
2306834 TCGAATG
1 TCGAATG
2306841 TAATTAGTGT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 27 0.42
65 35 0.55
66 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (64 bp):
TCGAATGCATTTTGTGGACCGATGCACAACCATGCATCGATGCACTCATGAATTTATTAAAACA
Found at i:2306851 original size:65 final size:64
Alignment explanation
Indices: 2306705--2306857 Score: 173
Period size: 65 Copynumber: 2.4 Consensus size: 64
2306695 ACACCATATT
* * * * * *
2306705 TCGAATGCATTTTGTGGACCGATGCACAACCATGTATCGATGCACTCTTGAATTTATTGAAACA
1 TCGAATGCAATTAGTGTACCGATGCACAACCATGCATCGATGCACTCATGAATTTATTAAAACA
* * **
2306769 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCATGGCTCTT-TTAAAAC
1 TCGAATGCAATTAGTGTACCGATGCACA-ACCATGCATCGATGCACTCATGAAT-TTATTAAAAC
2306833 A
64 A
* *
2306834 TCGAATGTAATTAGTGTACTGATG
1 TCGAATGCAATTAGTGTACCGATG
2306858 TACCCCTAGT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 27 0.35
65 48 0.62
66 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (64 bp):
TCGAATGCAATTAGTGTACCGATGCACAACCATGCATCGATGCACTCATGAATTTATTAAAACA
Found at i:2316738 original size:21 final size:21
Alignment explanation
Indices: 2316705--2316760 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
2316695 TTTTAGATTG
*
2316705 AGAGTATCGATACTCGTTCA-T
1 AGAGTATCAATACTCGTT-AGT
* *
2316726 CGGGTATCAATACT-GTTAGT
1 AGAGTATCAATACTCGTTAGT
2316746 AGAGTATCAATACTC
1 AGAGTATCAATACTC
2316761 AGTGTTGAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 16 0.57
21 11 0.39
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (21 bp):
AGAGTATCAATACTCGTTAGT
Found at i:2321843 original size:24 final size:24
Alignment explanation
Indices: 2321809--2321862 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2321799 TAGCTCTTCA
*
2321809 TTATTGGATAAGTTATGTTTGATC
1 TTATTGCATAAGTTATGTTTGATC
*
2321833 TTATTGCATAAGTTCTGTTTGATC
1 TTATTGCATAAGTTATGTTTGATC
2321857 TTATTG
1 TTATTG
2321863 TTTTCAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (24 bp):
TTATTGCATAAGTTATGTTTGATC
Found at i:2323109 original size:14 final size:14
Alignment explanation
Indices: 2323090--2323118 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2323080 CAAGCAGGGA
2323090 CTTCAAGCAATGGT
1 CTTCAAGCAATGGT
2323104 CTTCAAGCAATGGT
1 CTTCAAGCAATGGT
2323118 C
1 C
2323119 ATTAGTGATT
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:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (14 bp):
CTTCAAGCAATGGT
Found at i:2324731 original size:2 final size:2
Alignment explanation
Indices: 2324724--2324754 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2324714 TTTTTCATGG
2324724 TA TA TA 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 TA TA TA T
2324755 TCATTTGTTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2325057 original size:3 final size:3
Alignment explanation
Indices: 2325049--2325107 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
2325039 GGGTTCTTAT
* ** * *
2325049 TTA TTA TTA AT- TTA TTA TTA ACA CTTA TTA TTA TTG TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
2325094 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
2325108 TTAACAATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.96
4 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2328207 original size:18 final size:18
Alignment explanation
Indices: 2328186--2328229 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2328176 AGAAAAATAA
*
2328186 AAATAAAAGAGA-AGAGAT
1 AAATAAAAGAGATA-AAAT
*
2328204 AAATAAAATAGATAAAAT
1 AAATAAAAGAGATAAAAT
2328222 AAATAAAA
1 AAATAAAA
2328230 TAAAGGAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
AAATAAAAGAGATAAAAT
Found at i:2328220 original size:9 final size:9
Alignment explanation
Indices: 2328202--2328233 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2328192 AAGAGAAGAG
2328202 ATAAATAAA
1 ATAAATAAA
*
2328211 ATAGATAAA
1 ATAAATAAA
2328220 ATAAATAAA
1 ATAAATAAA
2328229 ATAAA
1 ATAAA
2328234 GGAAAGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (9 bp):
ATAAATAAA
Found at i:2329604 original size:2 final size:2
Alignment explanation
Indices: 2329575--2329630 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
2329565 GTAAATAAAC
* * *
2329575 AT AT AT AC AT -T AT A- AT TT AT AA 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
2329615 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2329631 TATTATTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2330401 original size:106 final size:106
Alignment explanation
Indices: 2330076--2331231 Score: 1725
Period size: 106 Copynumber: 11.0 Consensus size: 106
2330066 GCAAGCTACA
* * * * * * ** *
2330076 TTGTCTCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGGAATCGGGAAATTACTTG
1 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
* *
2330141 TTGACAACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTG
66 TTGACAACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* * * * *
2330182 TTGTCTCGAGTCCAATATCCTTAGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTG
1 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
* * * * *
2330241 TTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* *
2330282 TTGTCTTGG-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
1 TTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
* * *
2330346 ATTGACAGCCAGCGGTCCCTTCGTCGTGAAATTGAACTTCCG
65 ATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* * *
2330388 TTGTCTTGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTA
1 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
2330453 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* * * * * *
2330494 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTCAAATTGGCTCTAAAATTGAGAAGTTTTTTG
1 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
*
2330559 TTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
*
2330600 TTGTCTGGAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
1 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
2330665 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* * * *
2330706 TTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGGAAATTGTTTG
1 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
2330771 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* * * *
2330812 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTG
1 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
2330877 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* *
2330918 TTGTCTGGAGTCCAATATCCTTTGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
1 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
**
2330983 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAGTTTGCG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* * *
2331024 TTGTCTTGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTA
1 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
* *
2331089 TTGATAACCATCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* *
2331130 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTA
1 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
*
2331195 TTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACT
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
2331232 CTACTCTCGA
Statistics
Matches: 956, Mismatches: 85, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
99 1 0.00
100 77 0.08
101 5 0.01
102 4 0.00
104 3 0.00
105 5 0.01
106 861 0.90
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
Found at i:2331549 original size:30 final size:32
Alignment explanation
Indices: 2331513--2331574 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 32
2331503 TTTGCATTAG
2331513 GATGTTGAATC-CAAAAATGCCCC-AATATTT
1 GATGTTGAATCTCAAAAATGCCCCAAATATTT
*
2331543 GATGTTGAATCTTCAAAGATGCCCCAAATATT
1 GATGTTGAATC-TCAAAAATGCCCCAAATATT
2331575 CCTCATTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 11 0.39
32 11 0.39
33 6 0.21
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAATGCCCCAAATATTT
Found at i:2331980 original size:22 final size:22
Alignment explanation
Indices: 2331954--2332030 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
2331944 TTATGTTTGG
2331954 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2331976 TCAAAGGTTTGGCATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
*
2331998 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2332020 TCAACGGTTTG
1 TCAAAGGTTTG
2332031 ATGGGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.39
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Done.