Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007910.1 Corchorus capsularis cultivar CVL-1 contig07931, 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: 45010
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:934 original size:35 final size:35
Alignment explanation
Indices: 884--975 Score: 123
Period size: 35 Copynumber: 2.6 Consensus size: 35
874 TTAAGAAGGC
*
884 TTTCAGGAGTTCAGAGTTGATCTCATATCAAGAAGT
1 TTTCA-GAGATCAGAGTTGATCTCATATCAAGAAGT
* *
920 TTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGT
1 TTTCAGAGATCAGAGTTGATCTCATATCAAGAAGT
*
955 TTCCA-ACGATCAGAGTTGATC
1 TTTCAGA-GATCAGAGTTGATC
976 GCATTTTCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 1 0.02
35 45 0.88
36 5 0.10
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (35 bp):
TTTCAGAGATCAGAGTTGATCTCATATCAAGAAGT
Found at i:981 original size:35 final size:35
Alignment explanation
Indices: 929--1295 Score: 495
Period size: 35 Copynumber: 10.5 Consensus size: 35
919 TTTTCAGAGG
* *
929 TCAGAGTTGATCTCA-TTTCAAGAAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGA
*
964 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
999 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * * *
1034 TCAGAGTTGATCGCATTTTCAATATTTTTC-ATGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
1068 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* *
1103 TCGGAGTTGATCGCATTTTCAGTAGTTTCCAATGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * * *
1138 TCGGAGTTGATTGCATTTTCAGTATTTTCCAATGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
1173 TCAAAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * *
1208 TCAGAGTTTATCACATTTTCAGTAGTTTCCAACAA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* *
1243 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACAA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * *
1278 TTAGAGGTGATCTCATTT
1 TCAGAGTTGATCGCATTT
1296 CAAGAAATTT
Statistics
Matches: 305, Mismatches: 25, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
34 30 0.10
35 271 0.89
36 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (35 bp):
TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
Found at i:1145 original size:139 final size:140
Alignment explanation
Indices: 929--1295 Score: 513
Period size: 139 Copynumber: 2.6 Consensus size: 140
919 TTTTCAGAGG
* * *
929 TCAGAGTTGATCTCA-TTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTC
1 TCAGAGTTGATCACATTTTC-AGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTC
*
993 CAACGATCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAATA
65 CAACGATCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAAAGTTGATCGCATTTTCAATA
* * *
1058 TTTTTC-ATGA
130 GTTTCCAACGA
* * *
1068 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGATCGGAGTTGATCGCATTTTCAGTAGTTTCC
1 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
* * * * *
1133 AATGATCGGAGTTGATTGCATTTTCAGTATTTTCCAATGATCAAAGTTGATCGCATTTTCAGTAG
66 AACGATCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAAAGTTGATCGCATTTTCAATAG
1198 TTTCCAACGA
131 TTTCCAACGA
* * *
1208 TCAGAGTTTATCACATTTTCAGTAGTTTCCAACAATCAGAGTTGATCACATTTTCAGTAGTTTCC
1 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
* * * *
1273 AACAATTAGAGGTGATCTCATTT
66 AACGATCAGAGTTGATCGCATTT
1296 CAAGAAATTT
Statistics
Matches: 199, Mismatches: 27, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
139 117 0.59
140 82 0.41
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (140 bp):
TCAGAGTTGATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
AACGATCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAAAGTTGATCGCATTTTCAATAG
TTTCCAACGA
Found at i:1184 original size:174 final size:175
Alignment explanation
Indices: 932--1324 Score: 520
Period size: 174 Copynumber: 2.3 Consensus size: 175
922 TCAGAGGTCA
*
932 GAGTTGATCTCATTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCCAAC
1 GAGTTGATCGCATTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCCAAC
* * * *
997 GATCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAATATTTT
66 GATCAAAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCACATTTTCAATAGTTT
* ** *
1062 TC-ATGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGATCG
131 CCAACAATCAGAGTTGATCACATTTTCAGTAGTTTCCAATGATCG
* * * *
1106 GAGTTGATCGCATTTTC-AGTAGTTTCCAATGATCGGAGTTGATTGCATTTTCAGTATTTTCCAA
1 GAGTTGATCGCA-TTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCCAA
* * *
1170 TGATCAAAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTTATCACATTTTCAGTAGTT
65 CGATCAAAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCACATTTTCAATAGTT
** **
1235 TCCAACAATCAGAGTTGATCACATTTTCAGTAGTTTCCAACAATTA
130 TCCAACAATCAGAGTTGATCACATTTTCAGTAGTTTCCAATGATCG
* * * ** **
1281 GAGGTGATCTCATTTCAAGAAATTTCTGATAATCAGAGTTGATC
1 GAGTTGATCGCATTTCAAGAAGTTTCCAACGATCAGAGTTGATC
1325 CAAAGGAGTT
Statistics
Matches: 187, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
174 118 0.63
175 69 0.37
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (175 bp):
GAGTTGATCGCATTTCAAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCCAAC
GATCAAAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCACATTTTCAATAGTTT
CCAACAATCAGAGTTGATCACATTTTCAGTAGTTTCCAATGATCG
Found at i:9013 original size:22 final size:22
Alignment explanation
Indices: 8959--9043 Score: 75
Period size: 22 Copynumber: 3.8 Consensus size: 22
8949 AATTCGAAGA
* *
8959 ATTGAAATTGAAGCAATGGA-AGA
1 ATTGAAATTGAAGC-ATTGACA-T
*
8982 ATCGAAATTGAAGCATTGACAT
1 ATTGAAATTGAAGCATTGACAT
*
9004 ATTGAAATTGAAACATTGACAT
1 ATTGAAATTGAAGCATTGACAT
* *
9026 -TTGGAATTTGAAGAATTG
1 ATT-GAAATTGAAGCATTG
9044 GATTTGAAGC
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 2 0.04
22 36 0.69
23 14 0.27
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.29
Consensus pattern (22 bp):
ATTGAAATTGAAGCATTGACAT
Found at i:9066 original size:8 final size:7
Alignment explanation
Indices: 9055--9117 Score: 51
Period size: 8 Copynumber: 8.7 Consensus size: 7
9045 ATTTGAAGCT
9055 TTGAAATA
1 TTGAAA-A
9063 TTG-AAA
1 TTGAAAA
9069 TTGAAACA
1 TTGAAA-A
9077 TTGAAAAA
1 TTG-AAAA
9085 TTG-AAA
1 TTGAAAA
9091 TTGAAACA
1 TTGAAA-A
*
9099 TTGAAGGA
1 TTGAA-AA
9107 TTG-AAA
1 TTGAAAA
9113 TTGAA
1 TTGAA
9118 GCATTGGCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
6 14 0.30
7 8 0.17
8 21 0.46
9 3 0.07
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.30
Consensus pattern (7 bp):
TTGAAAA
Found at i:9072 original size:22 final size:21
Alignment explanation
Indices: 9033--9150 Score: 92
Period size: 22 Copynumber: 5.4 Consensus size: 21
9023 CATTTGGAAT
* * *
9033 TTGAAGAATTGGATTTGAAGCT
1 TTGAA-AATTGAAATTGAAGCA
*
9055 TTGAAATATTGAAATTGAAACA
1 TTGAAA-ATTGAAATTGAAGCA
*
9077 TTGAAAAATTGAAATTGAAACA
1 TTG-AAAATTGAAATTGAAGCA
*
9099 TTGAAGGATTGAAATTGAAGCA
1 TTGAA-AATTGAAATTGAAGCA
** * * *
9121 TTGGCATTTGGAATTTGAAGAA
1 TTGAAAATT-GAAATTGAAGCA
9143 TTGAAAAT
1 TTGAAAAT
9151 GAAGTATTGA
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
21 5 0.06
22 69 0.90
23 3 0.04
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.32
Consensus pattern (21 bp):
TTGAAAATTGAAATTGAAGCA
Found at i:9074 original size:14 final size:14
Alignment explanation
Indices: 9055--9117 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
9045 ATTTGAAGCT
9055 TTGAAATATTG-AAA
1 TTGAAA-ATTGAAAA
9069 TTGAAACATTGAAAAA
1 TTGAAA-ATTG-AAAA
9085 TTG-AAATTGAAACA
1 TTGAAAATTGAAA-A
*
9099 TTGAAGGATTG-AAA
1 TTGAA-AATTGAAAA
9113 TTGAA
1 TTGAA
9118 GCATTGGCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
13 3 0.07
14 24 0.57
15 5 0.12
16 10 0.24
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.30
Consensus pattern (14 bp):
TTGAAAATTGAAAA
Found at i:9116 original size:36 final size:36
Alignment explanation
Indices: 9084--9231 Score: 136
Period size: 36 Copynumber: 3.9 Consensus size: 36
9074 ACATTGAAAA
*
9084 ATTGAAATTGAAACATTGAAGGATTGAAATTGAAGC
1 ATTGAAATTGAAACATTGAAGAATTGAAATTGAAGC
* * * * * *
9120 ATTGGCATTTGGAA-TTTGAAGAATTGAAAATGAAGT
1 ATT-GAAATTGAAACATTGAAGAATTGAAATTGAAGC
* **
9156 ATTGAAATTGAAGCGCTGAAGAATTGAAATTGAAGC
1 ATTGAAATTGAAACATTGAAGAATTGAAATTGAAGC
9192 ATTGAAGAATTGAAACTGAAGTTGAAGAATTGAAATTGAA
1 ATTG-A-AATTGAAAC---A-TTGAAGAATTGAAATTGAA
9232 ACTGGGGCAT
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
35 6 0.07
36 46 0.53
37 8 0.09
38 8 0.09
42 18 0.21
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.28
Consensus pattern (36 bp):
ATTGAAATTGAAACATTGAAGAATTGAAATTGAAGC
Found at i:9118 original size:14 final size:15
Alignment explanation
Indices: 9062--9123 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 15
9052 GCTTTGAAAT
*
9062 ATTG-AAATTGAAAC
1 ATTGAAAATTGAAGC
9076 ATTGAAAAATTGAA--
1 ATTG-AAAATTGAAGC
*
9090 ATTGAAACATTGAAGG
1 ATTGAAA-ATTGAAGC
9106 ATTG-AAATTGAAGC
1 ATTGAAAATTGAAGC
9120 ATTG
1 ATTG
9124 GCATTTGGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
13 3 0.07
14 25 0.60
15 2 0.05
16 12 0.29
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.29
Consensus pattern (15 bp):
ATTGAAAATTGAAGC
Found at i:9175 original size:22 final size:22
Alignment explanation
Indices: 9150--9231 Score: 114
Period size: 22 Copynumber: 3.8 Consensus size: 22
9140 GAATTGAAAA
* *
9150 TGAAGTATTGAAATTGAAGCGC
1 TGAAGAATTGAAATTGAAGCGT
*
9172 TGAAGAATTGAAATTGAAGCAT
1 TGAAGAATTGAAATTGAAGCGT
*
9194 TGAAGAATTGAAACTGAA--GT
1 TGAAGAATTGAAATTGAAGCGT
9214 TGAAGAATTGAAATTGAA
1 TGAAGAATTGAAATTGAA
9232 ACTGGGGCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.33
22 36 0.67
ACGTcount: A:0.44, C:0.05, G:0.24, T:0.27
Consensus pattern (22 bp):
TGAAGAATTGAAATTGAAGCGT
Found at i:9189 original size:14 final size:14
Alignment explanation
Indices: 9172--9231 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
9162 ATTGAAGCGC
9172 TGAAGAATTGAAAT
1 TGAAGAATTGAAAT
*
9186 TGAAGCATTGAAGAAT
1 TGAAGAATTG-A-AAT
* *
9202 TG-A-AACTGAAGT
1 TGAAGAATTGAAAT
9214 TGAAGAATTGAAAT
1 TGAAGAATTGAAAT
9228 TGAA
1 TGAA
9232 ACTGGGGCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
12 4 0.11
13 2 0.06
14 23 0.64
15 2 0.06
16 5 0.14
ACGTcount: A:0.47, C:0.03, G:0.23, T:0.27
Consensus pattern (14 bp):
TGAAGAATTGAAAT
Found at i:9212 original size:72 final size:70
Alignment explanation
Indices: 9082--9278 Score: 186
Period size: 72 Copynumber: 2.7 Consensus size: 70
9072 AAACATTGAA
* * * **
9082 AAATTGAAATTGAAACATTGAAGGATTGAAATTGAAGCATTG--GCATTTGGAATTTGAAGAATT
1 AAATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAG-AATT-GAAACTGAAG--TT
9145 GAA-AA-TG
62 GAAGAATTG
**
9152 AAGTATTGAAATTGAAGCGCTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAACTGAAGTTGA
1 AA--ATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAACTGAAGTTGA
9217 AGAATTG
64 AGAATTG
* ** *
9224 AAATTGAAACTGGGGCATTGAATAATTGAGGAATTGAAGCATTGAAGAACTTGAA
1 AAATTGAAATTGAAGCATTGAAGAATTGA--AATTGAAGCATTGAAGAA-TTGAA
9279 GAAAGATCAC
Statistics
Matches: 105, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
70 28 0.27
71 2 0.02
72 66 0.63
73 8 0.08
74 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.24, T:0.27
Consensus pattern (70 bp):
AAATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAACTGAAGTTGAAG
AATTG
Found at i:9224 original size:8 final size:8
Alignment explanation
Indices: 9135--9281 Score: 71
Period size: 8 Copynumber: 19.0 Consensus size: 8
9125 CATTTGGAAT
9135 TTGAAGAA
1 TTGAAGAA
9143 TTGAA-AA
1 TTGAAGAA
*
9150 -TGAAGTA
1 TTGAAGAA
9157 TTG-A-AA
1 TTGAAGAA
**
9163 TTGAAGCG
1 TTGAAGAA
*
9171 CTGAAGAA
1 TTGAAGAA
9179 TTG-A-AA
1 TTGAAGAA
*
9185 TTGAAGCA
1 TTGAAGAA
9193 TTGAAGAA
1 TTGAAGAA
9201 TTGAAACTGAA
1 TTG-AA--GAA
9212 GTTGAAGAA
1 -TTGAAGAA
9221 TTG-A-AA
1 TTGAAGAA
9227 TTG-A-AA
1 TTGAAGAA
* ** *
9233 CTGGGGCA
1 TTGAAGAA
*
9241 TTGAATAA
1 TTGAAGAA
*
9249 TTGAGGAA
1 TTGAAGAA
*
9257 TTGAAGCA
1 TTGAAGAA
9265 TTGAAGAA
1 TTGAAGAA
9273 CTTGAAGAA
1 -TTGAAGAA
9282 AGATCACCCT
Statistics
Matches: 103, Mismatches: 23, Indels: 25
0.68 0.15 0.17
Matches are distributed among these distances:
6 23 0.22
7 8 0.08
8 51 0.50
9 13 0.13
11 5 0.05
12 3 0.03
ACGTcount: A:0.44, C:0.05, G:0.25, T:0.26
Consensus pattern (8 bp):
TTGAAGAA
Found at i:9279 original size:17 final size:16
Alignment explanation
Indices: 9089--9281 Score: 57
Period size: 14 Copynumber: 13.1 Consensus size: 16
9079 GAAAAATTGA
*
9089 AATTGAAACATTGAAG
1 AATTGAAGCATTGAAG
*
9105 GATTGAA--ATTGAAG
1 AATTGAAGCATTGAAG
*
9119 CATTG--GCATTTG--G
1 AATTGAAGCA-TTGAAG
*
9132 AATTTGAAGAATTGAA-
1 AA-TTGAAGCATTGAAG
*
9148 AA-TGAAGTATTG-A-
1 AATTGAAGCATTGAAG
**
9161 AATTGAAGCGCTGAAG
1 AATTGAAGCATTGAAG
9177 AATTGAA--ATTGAAG
1 AATTGAAGCATTGAAG
* *
9191 CATTGAAGAATTG-A-
1 AATTGAAGCATTGAAG
*
9205 AACTGAAG--TTGAAG
1 AATTGAAGCATTGAAG
9219 AATTGAA--ATTG-A-
1 AATTGAAGCATTGAAG
* ** *
9231 AACTGGGGCATTGAAT
1 AATTGAAGCATTGAAG
* *
9247 AATTGAGGAATTGAAG
1 AATTGAAGCATTGAAG
* *
9263 CATTGAAGAACTTGAAG
1 AATTGAAGCA-TTGAAG
9280 AA
1 AA
9282 AGATCACCCT
Statistics
Matches: 132, Mismatches: 24, Indels: 41
0.67 0.12 0.21
Matches are distributed among these distances:
12 7 0.05
13 7 0.05
14 61 0.46
15 9 0.07
16 41 0.31
17 7 0.05
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.27
Consensus pattern (16 bp):
AATTGAAGCATTGAAG
Found at i:9333 original size:24 final size:24
Alignment explanation
Indices: 9305--9361 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
9295 TCAATGAAGT
*
9305 AAATTGAAGCATTGAATTATT-AA
1 AAATTGAAGCATTGAATGATTGAA
*
9328 AGAATTGAAGCATTGGATGATTGAA
1 A-AATTGAAGCATTGAATGATTGAA
9353 AAATTGAAG
1 AAATTGAAG
9362 AAAGATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 1 0.03
24 26 0.87
25 3 0.10
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.30
Consensus pattern (24 bp):
AAATTGAAGCATTGAATGATTGAA
Found at i:9373 original size:15 final size:15
Alignment explanation
Indices: 9353--9391 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
9343 GATGATTGAA
9353 AAATTGAAGAAAGAT
1 AAATTGAAGAAAGAT
9368 AAATTGAAGAAAGAT
1 AAATTGAAGAAAGAT
9383 AAATTGAAG
1 AAATTGAAG
9392 CATTGAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (15 bp):
AAATTGAAGAAAGAT
Found at i:9402 original size:13 final size:13
Alignment explanation
Indices: 9384--9425 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
9374 AAGAAAGATA
9384 AATTGAAGCATTG
1 AATTGAAGCATTG
*
9397 AATTGAAGGATTG
1 AATTGAAGCATTG
*
9410 AACTTGAAGCAATG
1 AA-TTGAAGCATTG
9424 AA
1 AA
9426 ATATTGAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (13 bp):
AATTGAAGCATTG
Found at i:9439 original size:22 final size:22
Alignment explanation
Indices: 9396--9469 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
9386 TTGAAGCATT
**
9396 GAATTGAAGGATTG-AACTTGAA
1 GAATTGAAAAATTGAAAC-TGAA
*
9418 GCAA-TGAAATATTGAAACTGAA
1 G-AATTGAAAAATTGAAACTGAA
* *
9440 GAATTGAAAAATGGAAATTGAA
1 GAATTGAAAAATTGAAACTGAA
*
9462 GTATTGAA
1 GAATTGAA
9470 GAAGCGAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.05
22 36 0.84
23 5 0.12
ACGTcount: A:0.47, C:0.04, G:0.23, T:0.26
Consensus pattern (22 bp):
GAATTGAAAAATTGAAACTGAA
Found at i:9478 original size:22 final size:22
Alignment explanation
Indices: 9413--9642 Score: 70
Period size: 22 Copynumber: 10.6 Consensus size: 22
9403 AGGATTGAAC
* *
9413 TTGAAGCAA-TGAAATATTGAAA
1 TTGAAG-AATTGAAAAATGGAAA
*
9435 CTGAAGAATTGAAAAATGGAAA
1 TTGAAGAATTGAAAAATGGAAA
* *
9457 TTGAAGTATTGAAGAA-GCGAAA
1 TTGAAGAATTGAAAAATG-GAAA
* ** ** *
9479 TTGAAGCATTGGCATTTGGAAT
1 TTGAAGAATTGAAAAATGGAAA
** *
9501 TTG-A-AATTGAAGCATTGAAGGA
1 TTGAAGAATTGAAAAATGGAA--A
* * *
9523 TTG-A-ATTTGAAGAATTGAAA
1 TTGAAGAATTGAAAAATGGAAA
* *
9543 TTGAA-ACATTGAAGAATTGAAA
1 TTGAAGA-ATTGAAAAATGGAAA
* * *
9565 TTGAA-ACATTGAAGGATTGG-AT
1 TTGAAGA-ATTGAA-AAATGGAAA
*
9587 TTGAAGAATTG--AAATTGAAA
1 TTGAAGAATTGAAAAATGGAAA
** *
9607 TTGAACTATTGAAGAATTGG-AA
1 TTGAAGAATTGAA-AAATGGAAA
9629 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
9643 TTGACCAACT
Statistics
Matches: 158, Mismatches: 37, Indels: 27
0.71 0.17 0.12
Matches are distributed among these distances:
19 3 0.02
20 22 0.14
21 7 0.04
22 116 0.73
23 10 0.06
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (22 bp):
TTGAAGAATTGAAAAATGGAAA
Found at i:9518 original size:36 final size:36
Alignment explanation
Indices: 9478--9646 Score: 105
Period size: 36 Copynumber: 4.9 Consensus size: 36
9468 AAGAAGCGAA
* * *
9478 ATTGAAGCATTGGCATTTG-GAATTTGAAATTGAAGC
1 ATTGAAGAATTGGAATTTGAGAA-TTGAAATTGAAAC
*
9514 ATTGAAGGATT-GAATTTGAAGAATTGAAATTGAAAC
1 ATTGAAGAATTGGAATTTG-AGAATTGAAATTGAAAC
* * **
9550 ATTGAAGAATT-GAAATT--GAA---ACATTGAAGG
1 ATTGAAGAATTGGAATTTGAGAATTGAAATTGAAAC
*
9580 ATTG--GATTTGAAGAA-TTGA-AATTGAAATTG-AAC
1 ATTGAAGAATTG--GAATTTGAGAATTGAAATTGAAAC
9613 TATTGAAGAATTGGAA-TTGAAGAATTGAAATTGA
1 -ATTGAAGAATTGGAATTTG-AGAATTGAAATTGA
9647 CCAACTGTCA
Statistics
Matches: 104, Mismatches: 13, Indels: 31
0.70 0.09 0.21
Matches are distributed among these distances:
28 4 0.04
30 13 0.12
31 5 0.05
33 4 0.04
34 15 0.14
35 7 0.07
36 53 0.51
37 3 0.03
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.31
Consensus pattern (36 bp):
ATTGAAGAATTGGAATTTGAGAATTGAAATTGAAAC
Found at i:9519 original size:8 final size:7
Alignment explanation
Indices: 9501--9646 Score: 69
Period size: 8 Copynumber: 20.6 Consensus size: 7
9491 CATTTGGAAT
9501 TTGAA-A
1 TTGAAGA
9507 TTGAAGCA
1 TTGAAG-A
9515 TTGAAGGA
1 TTGAA-GA
*
9523 TTGAA-T
1 TTGAAGA
9529 TTGAAGAA
1 TTGAAG-A
9537 TTGAA-A
1 TTGAAGA
*
9543 TTGAAACA
1 TTG-AAGA
9551 TTGAAGAA
1 TTGAAG-A
9559 TTGAA-A
1 TTGAAGA
*
9565 TTGAAACA
1 TTG-AAGA
9573 TTGAAGGA
1 TTGAA-GA
9581 TTG--GA
1 TTGAAGA
9586 TTTGAAGAA
1 -TTGAAG-A
9595 TTGAA-A
1 TTGAAGA
9601 TTGAA-A
1 TTGAAGA
*
9607 TTGAACTA
1 TTGAA-GA
9615 TTGAAGAA
1 TTGAAG-A
*
9623 TTGGA-A
1 TTGAAGA
9629 TTGAAGAA
1 TTGAAG-A
9637 TTGAA-A
1 TTGAAGA
9643 TTGA
1 TTGA
9647 CCAACTGTCA
Statistics
Matches: 113, Mismatches: 7, Indels: 40
0.71 0.04 0.25
Matches are distributed among these distances:
5 2 0.02
6 43 0.38
7 8 0.07
8 58 0.51
9 2 0.02
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.31
Consensus pattern (7 bp):
TTGAAGA
Found at i:9528 original size:28 final size:28
Alignment explanation
Indices: 9475--9591 Score: 98
Period size: 28 Copynumber: 4.1 Consensus size: 28
9465 TTGAAGAAGC
9475 GAAATTGAAGCATTG--GCATTTGGAATTT
1 GAAATTGAAGCATTGAAGCA-TT-GAATTT
*
9503 GAAATTGAAGCATTGAAGGATTGAATTT
1 GAAATTGAAGCATTGAAGCATTGAATTT
* *
9531 GAAGAATTGAA--ATTGAAACATTGAAGAATT
1 G-A-AATTGAAGCATTGAAGCATTG-A-ATTT
* * *
9561 GAAATTGAAACATTGAAGGATTGGATTT
1 GAAATTGAAGCATTGAAGCATTGAATTT
9589 GAA
1 GAA
9592 GAATTGAAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
28 45 0.62
29 5 0.07
30 23 0.32
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (28 bp):
GAAATTGAAGCATTGAAGCATTGAATTT
Found at i:9532 original size:14 final size:14
Alignment explanation
Indices: 9514--9646 Score: 114
Period size: 14 Copynumber: 9.4 Consensus size: 14
9504 AAATTGAAGC
*
9514 ATTGAAGGATTGAA
1 ATTGAAGAATTGAA
*
9528 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
9542 ATTGAA-ACATTGAAGA
1 ATTGAAGA-ATTG-A-A
9558 ATTG-A-AATTGAAA
1 ATTGAAGAATTG-AA
* *
9571 CATTGAAGGATTGGA
1 -ATTGAAGAATTGAA
*
9586 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
9600 ATTG-A-AATTGAA
1 ATTGAAGAATTGAA
*
9612 CTATTGAAGAATTGGA
1 --ATTGAAGAATTGAA
9628 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
9642 ATTGA
1 ATTGA
9647 CCAACTGTCA
Statistics
Matches: 98, Mismatches: 11, Indels: 20
0.76 0.09 0.16
Matches are distributed among these distances:
12 7 0.07
13 3 0.03
14 67 0.68
15 6 0.06
16 15 0.15
ACGTcount: A:0.44, C:0.02, G:0.23, T:0.31
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:9625 original size:58 final size:58
Alignment explanation
Indices: 9501--9619 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 58
9491 CATTTGGAAT
* *
9501 TTGAAATTGAAGCATTGAAGGATTGAATTTGAAGAATTGAAATTGAAACATTGAAGAA
1 TTGAAATTGAAACATTGAAGGATTGAATTTGAAGAATTGAAATTGAAACATTGAACAA
* *
9559 TTGAAATTGAAACATTGAAGGATTGGATTTGAAGAATTGAAATTG-AA-ATTGAACTA
1 TTGAAATTGAAACATTGAAGGATTGAATTTGAAGAATTGAAATTGAAACATTGAACAA
9615 TTGAA
1 TTGAA
9620 GAATTGGAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
56 12 0.21
57 2 0.04
58 43 0.75
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (58 bp):
TTGAAATTGAAACATTGAAGGATTGAATTTGAAGAATTGAAATTGAAACATTGAACAA
Found at i:9910 original size:52 final size:53
Alignment explanation
Indices: 9851--9958 Score: 191
Period size: 52 Copynumber: 2.1 Consensus size: 53
9841 ATGGAACCAG
*
9851 TGCTTGAACTGACTCGTATGGAAACGAGTTT-GCTTGTGGAAAAGCCCCTGAA
1 TGCTTGAACTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCCCTGAA
*
9903 TGCTTGAACTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCTCCTGAA
1 TGCTTGAACTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCCCTGAA
9956 TGC
1 TGC
9959 CTGGATGGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
52 30 0.57
53 23 0.43
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (53 bp):
TGCTTGAACTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCCCTGAA
Found at i:9991 original size:70 final size:70
Alignment explanation
Indices: 9904--10087 Score: 287
Period size: 70 Copynumber: 2.6 Consensus size: 70
9894 GCCCCTGAAT
* * **
9904 GCTTGAACTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCTCCTGAATGCCTGGATGGAA
1 GCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCCTAAATGGAA
9969 CCAAA
66 CCAAA
*
9974 GCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTAAATGGAA
1 GCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCCTAAATGGAA
* *
10039 CTAAT
66 CCAAA
* *
10044 GTTTGAACTGACTCGTATGGAAACGAGTTTGACTTGTGGAAAAG
1 GCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
10088 TGAAAGTGTT
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 105 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (70 bp):
GCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCCTAAATGGAA
CCAAA
Found at i:10979 original size:16 final size:16
Alignment explanation
Indices: 10941--10987 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
10931 ACCCTAGAGC
10941 TTCTCTTTTTCTT--TT
1 TTCTCTTTTT-TTCATT
10956 TTCTTCTTTTTTTCATT
1 TTC-TCTTTTTTTCATT
10973 TTCTCTTTTTTTCAT
1 TTCTCTTTTTTTCAT
10988 GCGCTTGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.17
16 19 0.66
17 5 0.17
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTCTTTTTTTCATT
Found at i:10981 original size:7 final size:8
Alignment explanation
Indices: 10941--10982 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
10931 ACCCTAGAGC
10941 TTCTCTTT
1 TTCTCTTT
10949 TTCT-TTT
1 TTCTCTTT
10956 TTCTTCTTT
1 TTC-TCTTT
* *
10965 TTTTCATT
1 TTCTCTTT
10973 TTCTCTTT
1 TTCTCTTT
10981 TT
1 TT
10983 TTCATGCGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 6 0.21
8 17 0.61
9 5 0.18
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (8 bp):
TTCTCTTT
Found at i:11133 original size:103 final size:103
Alignment explanation
Indices: 10986--11184 Score: 319
Period size: 105 Copynumber: 1.9 Consensus size: 103
10976 TCTTTTTTTC
**
10986 ATGCGCTTGCTTTTGAAAAACTTTTGAAACCAATTTTCTCTAAAAAC-CTTTTTTTGAGAAAAAA
1 ATGCGCTTGCCCTTGAAAAACTTTTGAAACCAATTTTCTCTAAAAACACTTTTTTTGAGAAAAAA
* *
11050 CACTTTTCTTTTGCAAAAACTATTTTTTTTATTTCACT
66 CACTTTTCTTTTGCAAAAACAATCTTTTTTATTTCACT
* *
11088 ATGCGCTTGCCCTTGAAAAACTTTTTGAAACCAATTTTCTTTAAAAACATTTTTTTTTGAGAAAA
1 ATGCGCTTGCCCTTGAAAAAC-TTTTGAAACCAATTTTCTCTAAAAACA-CTTTTTTTGAGAAAA
11153 AACACTTTTCTTTTGCAAAAACAATCTTTTTT
64 AACACTTTTCTTTTGCAAAAACAATCTTTTTT
11185 GTTTTAGGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
102 19 0.22
103 25 0.28
105 44 0.50
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (103 bp):
ATGCGCTTGCCCTTGAAAAACTTTTGAAACCAATTTTCTCTAAAAACACTTTTTTTGAGAAAAAA
CACTTTTCTTTTGCAAAAACAATCTTTTTTATTTCACT
Found at i:11172 original size:20 final size:20
Alignment explanation
Indices: 11130--11173 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
11120 AATTTTCTTT
* *
11130 AAAAACATTTTTTTTTGAGA
1 AAAAACATTTTCTTTTGACA
11150 AAAAACACTTTTCTTTTG-CA
1 AAAAACA-TTTTCTTTTGACA
11170 AAAA
1 AAAA
11174 CAATCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (20 bp):
AAAAACATTTTCTTTTGACA
Found at i:11464 original size:12 final size:12
Alignment explanation
Indices: 11447--11493 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
11437 TTGATTCACT
11447 TTTGATTTGAAC
1 TTTGATTTGAAC
*
11459 TTTGATTTAAAC
1 TTTGATTTGAAC
*
11471 TTTGATTCGAAC
1 TTTGATTTGAAC
11483 TTTGATTTGAA
1 TTTGATTTGAA
11494 TTATTTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.49
Consensus pattern (12 bp):
TTTGATTTGAAC
Found at i:11834 original size:28 final size:29
Alignment explanation
Indices: 11783--11846 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
11773 TGGAAAAACT
*
11783 AAAAACCTTTTTTGAAAATTCATTTTC-G
1 AAAAACCTTTTTTGAAAATCCATTTTCTG
*
11811 AAAAACCTTTTCTTGAAGA-CCATTTTCTTG
1 AAAAACCTTTT-TTGAAAATCCATTTTC-TG
11841 AAAAAC
1 AAAAAC
11847 GTCTCTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 18 0.58
29 6 0.19
30 7 0.23
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (29 bp):
AAAAACCTTTTTTGAAAATCCATTTTCTG
Found at i:19083 original size:93 final size:93
Alignment explanation
Indices: 18981--19164 Score: 341
Period size: 93 Copynumber: 2.0 Consensus size: 93
18971 AATTGAAAAA
18981 TGAGATTTATTAGAGTTATTGAAAATCCTTATTTATATATATGCTGTGGAGTTTAATGTTTTTAT
1 TGAGATTTATTAGAGTTATTGAAAATCCTTATTTATATATATGCTGTGGAGTTTAATGTTTTTAT
19046 CTAGTGTGTTCAGCATTTGAAAACCAAT
66 CTAGTGTGTTCAGCATTTGAAAACCAAT
* * *
19074 TGAGATTTATTAGAGTTATTGAATATCCTTATTTATTTATATGTTGTGGAGTTTAATGTTTTTAT
1 TGAGATTTATTAGAGTTATTGAAAATCCTTATTTATATATATGCTGTGGAGTTTAATGTTTTTAT
19139 CTAGTGTGTTCAGCATTTGAAAACCA
66 CTAGTGTGTTCAGCATTTGAAAACCA
19165 GCATGCTTGA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (93 bp):
TGAGATTTATTAGAGTTATTGAAAATCCTTATTTATATATATGCTGTGGAGTTTAATGTTTTTAT
CTAGTGTGTTCAGCATTTGAAAACCAAT
Found at i:21539 original size:53 final size:53
Alignment explanation
Indices: 21376--21566 Score: 228
Period size: 53 Copynumber: 3.7 Consensus size: 53
21366 CAATTTTCAG
21376 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCGCTATTTAA
1 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCGCTATTTAA
* ** * * * * * *
21429 TTTTGACTCACTTTTTCCAAAAACGCCCTTCCCGGATGGAA--TGC-A-CTAA
1 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCGCTATTTAA
** *
21478 TTTTTACTTGCTATTAACGAAAATGCCCTTCCCGGACGGAAGGCGCTATTTAA
1 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCGCTATTTAA
* *
21531 TTTTTACTTGCTTTTTCCCAAAATGCCATTCCCGGA
1 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGA
21567 AAAAAGGGCA
Statistics
Matches: 109, Mismatches: 25, Indels: 8
0.77 0.18 0.06
Matches are distributed among these distances:
49 35 0.32
50 1 0.01
51 4 0.04
52 1 0.01
53 68 0.62
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (53 bp):
TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCGCTATTTAA
Found at i:21563 original size:102 final size:102
Alignment explanation
Indices: 21376--21566 Score: 301
Period size: 102 Copynumber: 1.9 Consensus size: 102
21366 CAATTTTCAG
**
21376 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCGCTATTTAATTTTGACTCACT
1 TTTTTACTTGCTATTAACCAAAATGCCCTTCCCGGACGGAAGGCGCTATTTAATTTTGACTCACT
*
21441 TTTTCCAAAAACGCCCTTCCCGGATGGAATGCACTAA
66 TTTTCCAAAAACGCCATTCCCGGATGGAATGCACTAA
* * **
21478 TTTTTACTTGCTATTAACGAAAATGCCCTTCCCGGACGGAAGGCGCTATTTAATTTTTACTTGCT
1 TTTTTACTTGCTATTAACCAAAATGCCCTTCCCGGACGGAAGGCGCTATTTAATTTTGACTCACT
* *
21543 TTTTCCCAAAATGCCATTCCCGGA
66 TTTTCCAAAAACGCCATTCCCGGA
21567 AAAAAGGGCA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 80 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (102 bp):
TTTTTACTTGCTATTAACCAAAATGCCCTTCCCGGACGGAAGGCGCTATTTAATTTTGACTCACT
TTTTCCAAAAACGCCATTCCCGGATGGAATGCACTAA
Found at i:24557 original size:19 final size:19
Alignment explanation
Indices: 24529--24565 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24519 GCCCATTTGG
*
24529 ATTTAAGAGATAATCAAGC
1 ATTTAAGAGAGAATCAAGC
*
24548 ATTTATGAGAGAATCAAG
1 ATTTAAGAGAGAATCAAG
24566 GAAGATTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (19 bp):
ATTTAAGAGAGAATCAAGC
Found at i:25191 original size:25 final size:25
Alignment explanation
Indices: 25161--25209 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
25151 GGATACTTAT
25161 AGTGTCCACATTAATTTAACATGTA
1 AGTGTCCACATTAATTTAACATGTA
25186 AGTGTCCACATTAATTTAACATGT
1 AGTGTCCACATTAATTTAACATGT
25210 GAAAATCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (25 bp):
AGTGTCCACATTAATTTAACATGTA
Found at i:29067 original size:2 final size:2
Alignment explanation
Indices: 29060--29090 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29050 GTGGTATTAT
29060 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
29091 TACTTATAAG
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:29423 original size:26 final size:28
Alignment explanation
Indices: 29394--29449 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
29384 TATCATACTA
29394 TTTTATTAAG-ATACTACATCAAGACTT
1 TTTTATTAAGAATACTACATCAAGACTT
* *
29421 TTTTTTTACGTAATACTACATCAAGACTT
1 TTTTATTAAG-AATACTACATCAAGACTT
29450 ATATTTCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.32
29 17 0.68
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (28 bp):
TTTTATTAAGAATACTACATCAAGACTT
Found at i:31981 original size:7 final size:7
Alignment explanation
Indices: 31969--32020 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
31959 AATTTTATTT
31969 TAATATA
1 TAATATA
31976 TAATATA
1 TAATATA
*
31983 TATTAT-
1 TAATATA
*
31989 TAATATG
1 TAATATA
31996 TAATATA
1 TAATATA
32003 TATATATGTA
1 TA-ATA--TA
32013 TAATATA
1 TAATATA
32020 T
1 T
32021 TCAAATCGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 5 0.13
7 23 0.61
8 3 0.08
9 3 0.08
10 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (7 bp):
TAATATA
Found at i:31993 original size:20 final size:19
Alignment explanation
Indices: 31964--32005 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
31954 GTAAGAATTT
31964 TATTTTAATATATAATATA
1 TATTTTAATATATAATATA
*
31983 TATTATTAATATGTAATATA
1 TATT-TTAATATATAATATA
32003 TAT
1 TAT
32006 ATATGTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATTTTAATATATAATATA
Found at i:31994 original size:13 final size:12
Alignment explanation
Indices: 31974--32020 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
31964 TATTTTAATA
31974 TATAATATATAT
1 TATAATATATAT
* *
31986 TATTAATATGTAA
1 TA-TAATATATAT
31999 TAT-ATATATAT
1 TATAATATATAT
32010 GTATAATATAT
1 -TATAATATAT
32021 TCAAATCGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
11 6 0.21
12 6 0.21
13 16 0.57
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (12 bp):
TATAATATATAT
Found at i:33428 original size:22 final size:23
Alignment explanation
Indices: 33400--33445 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
33390 ATATTTTAAT
*
33400 TGAAGAGAGTTCTTT-ACAAAAA
1 TGAAGAGACTTCTTTCACAAAAA
33422 TGAAGAGACTTCTTTGCACAAAAA
1 TGAAGAGACTTCTTT-CACAAAAA
33446 AATATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
24 7 0.33
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (23 bp):
TGAAGAGACTTCTTTCACAAAAA
Found at i:34002 original size:21 final size:21
Alignment explanation
Indices: 33959--34004 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
33949 ATGTTGTTGT
**
33959 GAATTGGAATTTTGAAAGGTG
1 GAATTGGAATTTTGAAACATG
*
33980 GAATTGGACTTTTGAAACATG
1 GAATTGGAATTTTGAAACATG
34001 GAAT
1 GAAT
34005 AGAAGAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (21 bp):
GAATTGGAATTTTGAAACATG
Found at i:35322 original size:25 final size:24
Alignment explanation
Indices: 35294--35342 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
35284 ACTTACATGA
*
35294 TGGTAAGTGCGAGTTAAATGAGGGC
1 TGGTAAGTGCAAGTTAAATG-GGGC
35319 TGGTAAGTGCAAGTTAAATGGGGC
1 TGGTAAGTGCAAGTTAAATGGGGC
35343 AATTAGCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.29, C:0.08, G:0.39, T:0.24
Consensus pattern (24 bp):
TGGTAAGTGCAAGTTAAATGGGGC
Found at i:40842 original size:6 final size:6
Alignment explanation
Indices: 40826--40862 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
40816 CAAAACAAAG
40826 TAAAT- TAAATC TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TA
40863 TGGCAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:42239 original size:19 final size:18
Alignment explanation
Indices: 42206--42241 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42196 TTGAAATAAT
42206 TCTTCAATAATCTTCAAA
1 TCTTCAATAATCTTCAAA
*
42224 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
42242 TAAGTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAA
Found at i:44633 original size:30 final size:29
Alignment explanation
Indices: 44566--44637 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
44556 ACACCGAACC
****
44566 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
44595 GCCAAATAAGCCCCTGAACTCTTAAAAAAA
1 GTCAAATAAGCCCCTGAACTATT-AAAAAA
44625 GTCAAATAAGCCC
1 GTCAAATAAGCCC
44638 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Done.