Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011955.1 Corchorus capsularis cultivar CVL-1 contig11976, 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: 38373
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:28 original size:21 final size:21
Alignment explanation
Indices: 2--62 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1 A
2 AAAAGGTAATC-GATAAAAAGC
1 AAAAGGTAATCAG-TAAAAAGC
* *
23 AAAAGGCAATCAGTAAAAAGT
1 AAAAGGTAATCAGTAAAAAGC
* *
44 AAAAAGTAACCAGTAAAAA
1 AAAAGGTAATCAGTAAAAA
63 AGGGAGTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.61, C:0.10, G:0.16, T:0.13
Consensus pattern (21 bp):
AAAAGGTAATCAGTAAAAAGC
Found at i:130 original size:21 final size:22
Alignment explanation
Indices: 92--144 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
82 TCAGTAATTC
*
92 AAAAAGTAAAATGGTAATCAGT
1 AAAAAGTAAAATGATAATCAGT
114 AAAAAGTAAAA-GATAATCAGT
1 AAAAAGTAAAATGATAATCAGT
135 AAAATAGTAA
1 AAAA-AGTAA
145 TCAGTAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.60, C:0.04, G:0.15, T:0.21
Consensus pattern (22 bp):
AAAAAGTAAAATGATAATCAGT
Found at i:147 original size:15 final size:14
Alignment explanation
Indices: 118--165 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
108 ATCAGTAAAA
118 AGTAAAAGATAATC
1 AGTAAAAGATAATC
*
132 AGTAAAATAGTAATC
1 AGTAAAAGA-TAATC
147 AGTAAAAGATAATC
1 AGTAAAAGATAATC
161 AGTAA
1 AGTAA
166 GAGTAAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.23
Consensus pattern (14 bp):
AGTAAAAGATAATC
Found at i:160 original size:77 final size:76
Alignment explanation
Indices: 16--165 Score: 180
Period size: 77 Copynumber: 2.0 Consensus size: 76
6 GGTAATCGAT
* *
16 AAAAAGCAAAAGGCAATCAGTAAAAAGTAAAAAGTAACCAGTAAAAAAGGGAGTAGAAAATGGTA
1 AAAAAGCAAAAGGCAATCAGTAAAAAGTAAAAAGTAACCAGTAAAAAAGGGAATAGAAAATGATA
81 ATCAGTAATTC
66 ATCAGTAATTC
* * * * *
92 AAAAAGTAAAATGGTAATCAGTAAAAAGT-AAAAGATAATCAGTAAAATA-GTAATCAGTAAAA-
1 AAAAAGCAAAA-GGCAATCAGTAAAAAGTAAAAAG-TAACCAGTAAAAAAGGGAAT-AG-AAAAT
154 GATAATCAGTAA
62 GATAATCAGTAA
166 GAGTAAAACA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
76 18 0.29
77 41 0.65
78 4 0.06
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.19
Consensus pattern (76 bp):
AAAAAGCAAAAGGCAATCAGTAAAAAGTAAAAAGTAACCAGTAAAAAAGGGAATAGAAAATGATA
ATCAGTAATTC
Found at i:165 original size:21 final size:20
Alignment explanation
Indices: 140--213 Score: 51
Period size: 21 Copynumber: 3.5 Consensus size: 20
130 TCAGTAAAAT
140 AGTAATCAGTAAAAGATAATC
1 AGTAA-CAGTAAAAGATAATC
* *
161 AGTAAGAGTAAAACAGTAATC
1 AGTAACAGTAAAAGA-TAATC
* * *
182 GGTAAGAGCAAAAGCGATAAT-
1 AGTAACAGTAAAA--GATAATC
203 AGTAATCAGTA
1 AGTAA-CAGTA
214 GAGAGTAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
20 8 0.20
21 25 0.61
22 7 0.17
23 1 0.02
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.20
Consensus pattern (20 bp):
AGTAACAGTAAAAGATAATC
Found at i:354 original size:29 final size:28
Alignment explanation
Indices: 292--356 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
282 AGTGGTAATA
* *
292 AATAAAAGAGAGTAAGAAGAGAGTAATT
1 AATAAAAGAGAGTAAGAAAAGAGTAAAT
**
320 GGTAAAA-AGAGTAAGAAAAGAGTAAAAAT
1 AATAAAAGAGAGTAAGAAAAGAGT--AAAT
349 AATAAAAG
1 AATAAAAG
357 TAGCAAAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
27 15 0.54
28 5 0.18
29 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (28 bp):
AATAAAAGAGAGTAAGAAAAGAGTAAAT
Found at i:2435 original size:20 final size:21
Alignment explanation
Indices: 2410--2462 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
2400 ACTAGCGCTG
*
2410 GGCG-CCCATGTGGTTTGCTT
1 GGCGACCCATGTGGTTTGCAT
*
2430 GGCGCCCCATGTGGTTTGCAT
1 GGCGACCCATGTGGTTTGCAT
*
2451 CGCGACCCATGT
1 GGCGACCCATGT
2463 ACTCCAGTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.09, C:0.30, G:0.32, T:0.28
Consensus pattern (21 bp):
GGCGACCCATGTGGTTTGCAT
Found at i:11910 original size:6 final size:6
Alignment explanation
Indices: 11899--11990 Score: 51
Period size: 6 Copynumber: 13.3 Consensus size: 6
11889 GGCTGTGAAG
11899 AATTGA AATTGAA ACATTGA AATTG- AATTCGAA GAATTGA AATTGAA
1 AATTGA AATTG-A A-ATTGA AATTGA AATT-G-A -AATTGA AATTG-A
*
11946 ACATGGAA GAATTGA AATTGA AGCATTGA CATATTGA AATTGA AA
1 A-ATTG-A -AATTGA AATTGA A--ATTGA -A-ATTGA AATTGA AA
11991 CATTGATATT
Statistics
Matches: 71, Mismatches: 3, Indels: 24
0.72 0.03 0.24
Matches are distributed among these distances:
5 4 0.06
6 29 0.41
7 9 0.13
8 23 0.32
9 6 0.08
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.28
Consensus pattern (6 bp):
AATTGA
Found at i:11917 original size:14 final size:14
Alignment explanation
Indices: 11900--11996 Score: 54
Period size: 14 Copynumber: 6.4 Consensus size: 14
11890 GCTGTGAAGA
11900 ATTGAAATTGAAAC
1 ATTGAAATTGAAAC
*
11914 ATTGAAATTGAATTCGAAGA
1 ATTGAAATTG-A----AA-C
11934 ATTGAAATTGAAAC
1 ATTGAAATTGAAAC
*
11948 ATGGAAGAATTG-AA-
1 ATTG-A-AATTGAAAC
* *
11962 ATTGAAGCATTGACAT
1 ATTGAA--ATTGAAAC
11978 ATTGAAATTGAAAC
1 ATTGAAATTGAAAC
11992 ATTGA
1 ATTGA
11997 TATTTGGAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 24
0.67 0.07 0.25
Matches are distributed among these distances:
12 1 0.02
13 1 0.02
14 31 0.48
15 7 0.11
16 11 0.17
19 3 0.05
20 10 0.16
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (14 bp):
ATTGAAATTGAAAC
Found at i:11957 original size:22 final size:22
Alignment explanation
Indices: 11929--11993 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
11919 AATTGAATTC
11929 GAAGAATTGAAATTGAAACATG
1 GAAGAATTGAAATTGAAACATG
* *
11951 GAAGAATTGAAATTGAAGCATT
1 GAAGAATTGAAATTGAAACATG
*
11973 GACA-TATTGAAATTGAAACAT
1 GA-AGAATTGAAATTGAAACAT
11994 TGATATTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 37 0.97
23 1 0.03
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (22 bp):
GAAGAATTGAAATTGAAACATG
Found at i:12022 original size:14 final size:15
Alignment explanation
Indices: 12000--12041 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
11990 ACATTGATAT
12000 TTGGAATTTGAAGAA
1 TTGGAATTTGAAGAA
*
12015 TTGG-ATTTGAAGCA
1 TTGGAATTTGAAGAA
*
12029 TTGAAATATTGAA
1 TTGGAAT-TTGAA
12042 ATTGAAGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 12 0.52
15 6 0.26
16 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (15 bp):
TTGGAATTTGAAGAA
Found at i:12120 original size:14 final size:14
Alignment explanation
Indices: 12103--12136 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12093 CATTTGGAAT
12103 TTGAAGAATTGAAA
1 TTGAAGAATTGAAA
* *
12117 TTGAAGTATTGAAG
1 TTGAAGAATTGAAA
12131 TTGAAG
1 TTGAAG
12137 CGTTCGAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.32
Consensus pattern (14 bp):
TTGAAGAATTGAAA
Found at i:12178 original size:29 final size:29
Alignment explanation
Indices: 12146--12204 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
12136 GCGTTCGAAG
* *
12146 AATTGAAATTGAGGCATTAAAGAATTGAA
1 AATTGAAATTGAAGCATCAAAGAATTGAA
* *
12175 AATTGAAATTGAAGCGTCAAAGATTTGAA
1 AATTGAAATTGAAGCATCAAAGAATTGAA
12204 A
1 A
12205 TGGAGGTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.27
Consensus pattern (29 bp):
AATTGAAATTGAAGCATCAAAGAATTGAA
Found at i:12239 original size:24 final size:24
Alignment explanation
Indices: 12212--12258 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12202 AAATGGAGGT
*
12212 ATTGAATAATTGAGGAATTGAAGC
1 ATTGAATAATTGAAGAATTGAAGC
*
12236 ATTGAATGATTGAAGAATTGAAG
1 ATTGAATAATTGAAGAATTGAAG
12259 AAAGACCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.26, T:0.30
Consensus pattern (24 bp):
ATTGAATAATTGAAGAATTGAAGC
Found at i:12260 original size:8 final size:8
Alignment explanation
Indices: 12103--12260 Score: 61
Period size: 8 Copynumber: 21.0 Consensus size: 8
12093 CATTTGGAAT
12103 TTGAAGAA
1 TTGAAGAA
12111 TTG-A-AA
1 TTGAAGAA
*
12117 TTGAAGTA
1 TTGAAGAA
12125 TTGAAG--
1 TTGAAGAA
**
12131 TTGAAGCG
1 TTGAAGAA
12139 TTCGAAGAA
1 TT-GAAGAA
12148 TTG-A-AA
1 TTGAAGAA
* *
12154 TTGAGGCA
1 TTGAAGAA
*
12162 TTAAAGAA
1 TTGAAGAA
12170 TTGAA-AA
1 TTGAAGAA
12177 TTG-A-AA
1 TTGAAGAA
**
12183 TTGAAGCG
1 TTGAAGAA
** *
12191 TCAAAGAT
1 TTGAAGAA
12199 TTG-A-AA
1 TTGAAGAA
* * *
12205 TGGAGGTA
1 TTGAAGAA
*
12213 TTGAATAA
1 TTGAAGAA
*
12221 TTGAGGAA
1 TTGAAGAA
*
12229 TTGAAGCA
1 TTGAAGAA
12237 TTGAATG-A
1 TTGAA-GAA
12245 TTGAAGAA
1 TTGAAGAA
12253 TTGAAGAA
1 TTGAAGAA
12261 AGACCACCCT
Statistics
Matches: 108, Mismatches: 29, Indels: 26
0.66 0.18 0.16
Matches are distributed among these distances:
6 25 0.23
7 11 0.10
8 65 0.60
9 7 0.06
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.28
Consensus pattern (8 bp):
TTGAAGAA
Found at i:12400 original size:22 final size:22
Alignment explanation
Indices: 12318--12416 Score: 92
Period size: 22 Copynumber: 4.5 Consensus size: 22
12308 ACCCTGGGTA
* * * *
12318 ATTGAAGTACTGAAGTTGAATC
1 ATTGAAGAATTGAAATTGAAGC
* *
12340 ATTGAAGAATTGCAATTGAAAC
1 ATTGAAGAATTGAAATTGAAGC
12362 ATTGAAGAATTGAAATTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
* * *
12384 ATTAGAA-ATTTGGAATTGAGGC
1 ATT-GAAGAATTGAAATTGAAGC
*
12406 ATTGAATAATT
1 ATTGAAGAATT
12417 AGGGAATGGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
21 3 0.05
22 58 0.91
23 3 0.05
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.31
Consensus pattern (22 bp):
ATTGAAGAATTGAAATTGAAGC
Found at i:12525 original size:8 final size:8
Alignment explanation
Indices: 12512--12601 Score: 69
Period size: 8 Copynumber: 11.2 Consensus size: 8
12502 TCATTGAAGT
12512 GAATTGAA
1 GAATTGAA
12520 GAATTGAA
1 GAATTGAA
**
12528 GCTTTG-A
1 GAATTGAA
12535 GTAATTGAA
1 G-AATTGAA
*
12544 AAATTGAA
1 GAATTGAA
12552 GCAA-T-AA
1 G-AATTGAA
*
12559 GTAATCGAA
1 G-AATTGAA
12568 GAATTGAA
1 GAATTGAA
*
12576 GTATTGAA
1 GAATTGAA
*
12584 TAATTGAA
1 GAATTGAA
*
12592 GAATGGAA
1 GAATTGAA
12600 GA
1 GA
12602 GTTGGATCAT
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
7 7 0.11
8 50 0.79
9 6 0.10
ACGTcount: A:0.47, C:0.03, G:0.23, T:0.27
Consensus pattern (8 bp):
GAATTGAA
Found at i:12540 original size:24 final size:24
Alignment explanation
Indices: 12513--12600 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
12503 CATTGAAGTG
12513 AATTGAAGAATTGAAGCTTTGAGT
1 AATTGAAGAATTGAAGCTTTGAGT
* ** *
12537 AATTGAAAAATTGAAGCAATAAGT
1 AATTGAAGAATTGAAGCTTTGAGT
* *
12561 AATCGAAGAATTGAAG-TATTGAAT
1 AATTGAAGAATTGAAGCT-TTGAGT
*
12585 AATTGAAGAATGGAAG
1 AATTGAAGAATTGAAG
12601 AGTTGGATCA
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.47, C:0.03, G:0.23, T:0.27
Consensus pattern (24 bp):
AATTGAAGAATTGAAGCTTTGAGT
Found at i:12572 original size:48 final size:49
Alignment explanation
Indices: 12508--12600 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 49
12498 TGGGTCATTG
* * *
12508 AAGTGAATTGAAGAATTGAAGCT-TTGAGTAATTGAAAAATTGAAGCAAT
1 AAGTGAATCGAAGAATTGAAG-TATTGAATAATTGAAAAATGGAAGCAAT
*
12557 AAGT-AATCGAAGAATTGAAGTATTGAATAATTGAAGAATGGAAG
1 AAGTGAATCGAAGAATTGAAGTATTGAATAATTGAAAAATGGAAG
12601 AGTTGGATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
47 1 0.03
48 34 0.87
49 4 0.10
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.27
Consensus pattern (49 bp):
AAGTGAATCGAAGAATTGAAGTATTGAATAATTGAAAAATGGAAGCAAT
Found at i:13615 original size:15 final size:16
Alignment explanation
Indices: 13589--13619 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
13579 TTTTCCATTC
13589 ATTTTCTCATTTTTTT
1 ATTTTCTCATTTTTTT
13605 ATTTT-TCATTTTTTT
1 ATTTTCTCATTTTTTT
13620 CTTTGCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTCTCATTTTTTT
Found at i:16344 original size:24 final size:24
Alignment explanation
Indices: 16299--16345 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
16289 AAACATTCTT
*
16299 AAAAATTCAAAGCAATCATCAATC
1 AAAAATTCAAAGCAATAATCAATC
*
16323 AAAAA-TCAAATCAATAACTCAAT
1 AAAAATTCAAAGCAATAA-TCAAT
16346 ATAAGCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.57, C:0.19, G:0.02, T:0.21
Consensus pattern (24 bp):
AAAAATTCAAAGCAATAATCAATC
Found at i:20442 original size:19 final size:20
Alignment explanation
Indices: 20405--20442 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
20395 AAACCCTCAA
* *
20405 ATTTATTTTTATCGTAAAAT
1 ATTTATTTTTATAGAAAAAT
20425 ATTT-TTTTTATAGAAAAA
1 ATTTATTTTTATAGAAAAA
20443 ACGGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
ATTTATTTTTATAGAAAAAT
Found at i:22543 original size:5 final size:6
Alignment explanation
Indices: 22516--22548 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
22506 TCACATTCAT
*
22516 TTTTTA TTTTGA TTTTGA TTTTGA -TTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
22549 TTTTTCACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (6 bp):
TTTTGA
Found at i:22925 original size:12 final size:13
Alignment explanation
Indices: 22892--22929 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
22882 TTTTTTTTAA
22892 TTTGAAAATCATT
1 TTTGAAAATCATT
22905 TTTGAAAAAT-ATT
1 TTTG-AAAATCATT
22918 TTTGAAAATCAT
1 TTTGAAAATCAT
22930 GACTCTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.22
13 13 0.57
14 5 0.22
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (13 bp):
TTTGAAAATCATT
Found at i:22941 original size:33 final size:33
Alignment explanation
Indices: 22904--22968 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
22894 TGAAAATCAT
*
22904 TTTTGAAAAATATTTTTGAAAATCATGACTCTC
1 TTTTGAAAAATATTTTTGAAAACCATGACTCTC
22937 TTTTGAAAAATATTTTTGAAAACCATGACTCT
1 TTTTGAAAAATATTTTTGAAAACCATGACTCT
22969 ACTATTCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (33 bp):
TTTTGAAAAATATTTTTGAAAACCATGACTCTC
Found at i:30153 original size:18 final size:18
Alignment explanation
Indices: 30130--30167 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
30120 GATGTGGCAA
30130 GGGGGACCATCCAAGCTT
1 GGGGGACCATCCAAGCTT
30148 GGGGGACCATCCAAGCTT
1 GGGGGACCATCCAAGCTT
30166 GG
1 GG
30168 TCCCCCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (18 bp):
GGGGGACCATCCAAGCTT
Found at i:31925 original size:41 final size:41
Alignment explanation
Indices: 31868--31971 Score: 172
Period size: 41 Copynumber: 2.5 Consensus size: 41
31858 AAGTAAAGTC
* *
31868 TTAATCCAGGGCGATTAAGAAGGTCAAACATAGTTAAGGTT
1 TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
31909 TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
1 TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
* *
31950 TTAATCCAAGGTGATTAAGAAA
1 TTAATCCAGGGCGATTAAGAAA
31972 AGAGTAGTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.26
Consensus pattern (41 bp):
TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
Found at i:32028 original size:37 final size:36
Alignment explanation
Indices: 31980--32572 Score: 483
Period size: 37 Copynumber: 16.0 Consensus size: 36
31970 AAAGAGTAGT
* *
31980 TAAAGAACTTAATTCATGGAAATTAAGTAAAAGCAA
1 TAAAGAACTTAATTCAGGGAAATTAAGTAAAAGCAG
* *
32016 TCAAAGAACTTAATTCAGGGTAATTAAGTAAGAGCAG
1 T-AAAGAACTTAATTCAGGGAAATTAAGTAAAAGCAG
** *
32053 TTAAAGAACTTAATTCAGGTTAATTAAGTAAGAGCAAG
1 -TAAAGAACTTAATTCAGGGAAATTAAGTAAAAGC-AG
* *
32091 TTAAGAACTTAATTCAGGGCAATTAAGTAAAAGCAGG
1 TAAAGAACTTAATTCAGGGAAATTAAGTAAAAGCA-G
* *
32128 TTAAGAACTTAATTCAGGGCAATTAAGTAAAAGCAGG
1 TAAAGAACTTAATTCAGGGAAATTAAGTAAAAGCA-G
* *
32165 TAAAGAACTTAATTCAGGGTAGTTAAGTAAAGGAGCAG
1 TAAAGAACTTAATTCAGGGAAATTAAGTAAA--AGCAG
* *
32203 TTAAGAACTTAATTCAGGGCAATTAAGTAAAAGCAGG
1 TAAAGAACTTAATTCAGGGAAATTAAGTAAAAGCA-G
* *
32240 TAAAAAACTTAATTCA-GGACAATTAAGTAAAAACAG
1 TAAAGAACTTAATTCAGGGA-AATTAAGTAAAAGCAG
* * *
32276 TCAAA-ATCTTAACTCAGGGCAATTAAG-AAAAGTAAACATAG
1 T-AAAGAACTTAATTCAGGGAAATTAAGTAAAAG----C--AG
* *
32317 TAAGTCAAAATCTTAATTCAAGGAAA-TAAGGTAAAAGCAG
1 TAA---AGAA-CTTAATTCAGGGAAATTAA-GTAAAAGCAG
* * *
32357 TCAAAGGAGCTTAATTCAGGAAAATTAAGTAAACA-CGG
1 T-AAA-GAACTTAATTCAGGGAAATTAAGTAAA-AGCAG
* * *
32395 TCAAAGAACTTAATTAAGGGTAATTAAGTAAAGAACAG
1 T-AAAGAACTTAATTCAGGGAAATTAAGTAAA-AGCAG
*
32433 TTAAGAACTTAATTCA-GGACAA-T---T-AAA-CAG
1 TAAAGAACTTAATTCAGGGA-AATTAAGTAAAAGCAG
* *
32463 TTAAGAACTTAATTCA-GGACAAATAAGTAAAAGCAG
1 TAAAGAACTTAATTCAGGGA-AATTAAGTAAAAGCAG
* * * *
32499 TTAAGAACTTAATTCAGGGTAATTAAGAAAAAGCAAT
1 TAAAGAACTTAATTCAGGGAAATTAAGTAAAAGC-AG
* * * *
32536 TGAAGGACTTAATTCAGGGTAATTAAGTAAAAACAG
1 TAAAGAACTTAATTCAGGGAAATTAAGTAAAAGCAG
32572 T
1 T
32573 TAAAAGGTAA
Statistics
Matches: 470, Mismatches: 50, Indels: 74
0.79 0.08 0.12
Matches are distributed among these distances:
30 25 0.05
31 2 0.00
32 2 0.00
33 1 0.00
34 1 0.00
35 7 0.01
36 62 0.13
37 265 0.56
38 61 0.13
39 10 0.02
40 5 0.01
41 5 0.01
42 1 0.00
43 1 0.00
44 4 0.01
45 13 0.03
46 5 0.01
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (36 bp):
TAAAGAACTTAATTCAGGGAAATTAAGTAAAAGCAG
Found at i:32268 original size:223 final size:220
Alignment explanation
Indices: 31963--32575 Score: 658
Period size: 223 Copynumber: 2.8 Consensus size: 220
31953 ATCCAAGGTG
* * * * *
31963 ATTAAGAAAAGAGTAGTTAAAGAACTTAATTCATGGAAATTAAGTAAAAGCAATCAAAGAACTTA
1 ATTAAGTAAAGAGCAGTT-AAGAACTTAATTCAGGGCAATTAAGTAAAAGCAGT-AAAGAACTTA
** * * *
32028 ATTCAGGGTAATTAAGTAAGAGCAGTTAAAGAACTTAATTCAGGTTAATTAAGTAAGAGCAAGTT
64 ATTCAGGACAATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTAATTAAGAAAGAGCAAGTT
**
32093 AAGAACTTAATTCAGGGCAATTAAGTAAAAGCAGGTTAA-GAACTTAATTCAGGGCAATTAAGTA
129 AAGAACTTAATTCAGGG-AATTAAGTAAAAGCA-GTTAAGGAACTTAATTCAGGAAAATTAAGTA
*
32157 AA-AGCAGGT-AAAGAACTTAATTCAGGGTA
192 AACA-C-GGTCAAAGAACTTAATTAAGGGTA
* *
32186 GTTAAGTAAAGGAGCAGTTAAGAACTTAATTCAGGGCAATTAAGTAAAAGCAGGTAAAAAACTTA
1 ATTAAGTAAA-GAGCAGTTAAGAACTTAATTCAGGGCAATTAAGTAAAAGCA-GTAAAGAACTTA
* * * * * *
32251 ATTCAGGACAATTAAGTAAAAACAGTCAAA-ATCTTAACTCAGGGCAATTAAGAAAAGTAAACAT
64 ATTCAGGACAATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTAATTAAG-AAAG--AGCA-
* * * *
32315 AG-TAAGTCAAAATCTTAATTCAAGGAAATAAGGTAAAAGCAGTCAAAGGAGCTTAATTCAGGAA
125 AGTTAAG----AA-CTTAATTCAGGGAATTAA-GTAAAAGCAGT-TAAGGAACTTAATTCAGGAA
32379 AATTAAGTAAACACGGTCAAAGAACTTAATTAAGGGTA
183 AATTAAGTAAACACGGTCAAAGAACTTAATTAAGGGTA
* * *
32417 ATTAAGTAAAGAACAGTTAAGAACTTAATTCAGGACAA-T---T-AAA-CAGTTAAGAACTTAAT
1 ATTAAGTAAAGAGCAGTTAAGAACTTAATTCAGGGCAATTAAGTAAAAGCAGTAAAGAACTTAAT
* *
32476 TCAGGACAAATAAGTAAAAGCAGTT-AAGAACTTAATTCAGGGTAATTAAGAAAAAGCAA-TTGA
66 TCAGGACAATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTAATTAAGAAAGAGCAAGTT-A
* *
32539 AGGACTTAATTCAGGGTAATTAAGTAAAAACAGTTAA
130 AGAACTTAATTCAGGG-AATTAAGTAAAAGCAGTTAA
32576 AAGGTAAGGA
Statistics
Matches: 327, Mismatches: 43, Indels: 49
0.78 0.10 0.12
Matches are distributed among these distances:
214 2 0.01
215 21 0.06
216 6 0.02
219 2 0.01
220 6 0.02
222 23 0.07
223 129 0.39
224 10 0.03
225 10 0.03
226 3 0.01
229 10 0.03
230 51 0.16
231 53 0.16
232 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (220 bp):
ATTAAGTAAAGAGCAGTTAAGAACTTAATTCAGGGCAATTAAGTAAAAGCAGTAAAGAACTTAAT
TCAGGACAATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTAATTAAGAAAGAGCAAGTTAA
GAACTTAATTCAGGGAATTAAGTAAAAGCAGTTAAGGAACTTAATTCAGGAAAATTAAGTAAACA
CGGTCAAAGAACTTAATTAAGGGTA
Found at i:32462 original size:30 final size:33
Alignment explanation
Indices: 32428--32516 Score: 130
Period size: 30 Copynumber: 2.7 Consensus size: 33
32418 TTAAGTAAAG
32428 AACAGTTAAGAACTTAATTCAGGAC-AAT-T-A
1 AACAGTTAAGAACTTAATTCAGGACAAATATAA
32458 AACAGTTAAGAACTTAATTCAGGACAAATAAGTAA
1 AACAGTTAAGAACTTAATTCAGGACAAAT-A-TAA
32493 AAGCAGTTAAGAACTTAATTCAGG
1 AA-CAGTTAAGAACTTAATTCAGG
32517 GTAATTAAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
30 25 0.47
31 3 0.06
34 1 0.02
35 3 0.06
36 21 0.40
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (33 bp):
AACAGTTAAGAACTTAATTCAGGACAAATATAA
Found at i:32561 original size:103 final size:104
Alignment explanation
Indices: 32366--32553 Score: 260
Period size: 103 Copynumber: 1.8 Consensus size: 104
32356 GTCAAAGGAG
*
32366 CTTAATTCAGGAAAATTAAGTAAACACGGTCAAAGAACTTAATTAAGGGTAATTAAGTAAAGAAC
1 CTTAATTCAGGAAAATTAAGTAAACACAGTCAAAGAACTTAATTAAGGGTAATTAAGTAAAGAAC
*
32431 AGTTAAGAACTTAATTCAGGACAATTAAACAGTTAAGAA
66 AATTAAGAACTTAATTCAGGACAATTAAACAGTTAAGAA
* *
32470 CTTAATTCAGGACAAA-TAAGTAAA-AGCAGT-TAAGAACTTAATTCAGGGTAATTAAG-AAA-A
1 CTTAATTCAGGA-AAATTAAGTAAACA-CAGTCAAAGAACTTAATTAAGGGTAATTAAGTAAAGA
*
32530 AGCAATTGAAGGACTTAATTCAGG
64 A-CAATT-AAGAACTTAATTCAGG
32554 GTAATTAAGT
Statistics
Matches: 75, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
101 2 0.03
102 7 0.09
103 40 0.53
104 23 0.31
105 3 0.04
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.25
Consensus pattern (104 bp):
CTTAATTCAGGAAAATTAAGTAAACACAGTCAAAGAACTTAATTAAGGGTAATTAAGTAAAGAAC
AATTAAGAACTTAATTCAGGACAATTAAACAGTTAAGAA
Found at i:32653 original size:94 final size:94
Alignment explanation
Indices: 32541--32868 Score: 277
Period size: 94 Copynumber: 3.3 Consensus size: 94
32531 GCAATTGAAG
*
32541 GACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAAAGGTAAGGATAGACATAGACTTAATTTTA
1 GACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAAAGGTAAGGATAGACATAGAGTTAATTTTA
32606 AGGAAGGAAATTAGGTAAAGACAAGCACA
66 AGGAAGGAAATTAGGTAAAGACAAGCACA
*
32635 GACTTAATTGAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGG-AAGGAAATTAGGTA
1 GACTTAATTCAGGGTAATTAAGT-AA--AA--ACAG--TTAA----AAGGTAAGG--A-TA-G-A
* * ** ** * * * *
32699 AAAAGCAGTTAAGAACTTAATTCAGGGTAATTAAGTAAA-AGC-AGTTGA-A
50 CATAG-AGTT-A-ATTTTAA-GGAAGGAAATTAGGTAAAGA-CAAG--CACA
* *
32748 GGACATAATTCAGGGTAATTAAGTAAAAACAGTTAAAAGGTAAGGATAGACATAGAGTTAATTTC
1 -GACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAAAGGTAAGGATAGACATAGAGTTAATTTT
32813 AAGGAAGGAAATTAGGTAAAGACAAGCACA
65 AAGGAAGGAAATTAGGTAAAGACAAGCACA
*
32843 AACTTAATTCAGGGTAATTAAGTAAA
1 GACTTAATTCAGGGTAATTAAGTAAA
32869 GTAAGACAGA
Statistics
Matches: 179, Mismatches: 27, Indels: 56
0.68 0.10 0.21
Matches are distributed among these distances:
94 47 0.26
95 17 0.09
96 7 0.04
97 3 0.02
98 4 0.02
99 8 0.04
100 1 0.01
101 6 0.03
102 1 0.01
103 4 0.02
104 8 0.04
105 4 0.02
106 1 0.01
107 6 0.03
108 1 0.01
109 8 0.04
110 3 0.02
111 3 0.02
112 8 0.04
113 17 0.09
114 22 0.12
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.24
Consensus pattern (94 bp):
GACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAAAGGTAAGGATAGACATAGAGTTAATTTTA
AGGAAGGAAATTAGGTAAAGACAAGCACA
Found at i:32686 original size:76 final size:77
Alignment explanation
Indices: 32593--32737 Score: 215
Period size: 76 Copynumber: 1.9 Consensus size: 77
32583 GGATAGACAT
* * *
32593 AGACTTAATTTTAAGGAAGGAAATTAGGTAAAGA-CAAG-CACAG-ACTTAATTGAGGGTAATTA
1 AGACTTAATTTCAAGGAAGGAAATTAGGTAAAAAGC-AGTCA-AGAACTTAATTCAGGGTAATTA
32655 AGTAAAGTAAGCAC
64 AGTAAAGTAAGCAC
*
32669 AGACTTAATTTCAAGGAAGGAAATTAGGTAAAAAGCAGTTAAGAACTTAATTCAGGGTAATTAAG
1 AGACTTAATTTCAAGGAAGGAAATTAGGTAAAAAGCAGTCAAGAACTTAATTCAGGGTAATTAAG
32734 TAAA
66 TAAA
32738 AGCAGTTGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
76 36 0.58
77 26 0.42
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (77 bp):
AGACTTAATTTCAAGGAAGGAAATTAGGTAAAAAGCAGTCAAGAACTTAATTCAGGGTAATTAAG
TAAAGTAAGCAC
Found at i:32737 original size:37 final size:37
Alignment explanation
Indices: 32690--32783 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 37
32680 CAAGGAAGGA
* *
32690 AATTAGGTAAAAAGCAGTTAAGAACTTAATTCAGGGT
1 AATTAAGTAAAAAGCAGTTAAGAACATAATTCAGGGT
*
32727 AATTAAGT-AAAAGCAGTTGAAGGACATAATTCAGGGT
1 AATTAAGTAAAAAGCAGTT-AAGAACATAATTCAGGGT
32764 AATTAAGTAAAAA-CAGTTAA
1 AATTAAGTAAAAAGCAGTTAA
32784 AAGGTAAGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
36 12 0.23
37 36 0.69
38 4 0.08
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.26
Consensus pattern (37 bp):
AATTAAGTAAAAAGCAGTTAAGAACATAATTCAGGGT
Found at i:32850 original size:41 final size:41
Alignment explanation
Indices: 32805--33154 Score: 332
Period size: 36 Copynumber: 9.1 Consensus size: 41
32795 AGACATAGAG
*
32805 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAAAC
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
* * *
32846 TTAA-TTC-A-G--GGTAATTAAGTAAAG-TAAG-ACAGAC
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
* *
32880 TTAATTTCAAGGAAGGAAATTAGATAAAGACAAGCATAGAC
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
* * * * * *
32921 TTAA-TTC----ATGGTAATTAAGTACAG-TAAGTACAGAC
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
* * * * *
32956 TTAATTTTAAAGAAGGAAGTTAGGTAAAAACAAGCATAGAC
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
* * *
32997 TTAA-TTC-AGG--GTAAA-TAAGTAAAGATAAGCACAGAC
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
33033 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
* * *
33074 TTAA-TTC-A-G--GGTAATTAAGTAAAGATAAGCACAGAC
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
33110 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
33151 TTAA
1 TTAA
33155 ATCAGGGTAA
Statistics
Matches: 242, Mismatches: 44, Indels: 46
0.73 0.13 0.14
Matches are distributed among these distances:
34 9 0.04
35 18 0.07
36 77 0.32
37 10 0.04
38 6 0.02
39 17 0.07
40 29 0.12
41 76 0.31
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (41 bp):
TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGAC
Found at i:32850 original size:208 final size:206
Alignment explanation
Indices: 32491--33173 Score: 788
Period size: 208 Copynumber: 3.2 Consensus size: 206
32481 ACAAATAAGT
* * *
32491 AAAAGCAGTTAAGAACTTAATTCAGGGTAATTAAGAAAAAGCAATTGAAGGACTTAATTCAGGGT
1 AAAAGCAG-TAAG-ACTTAATTCAGGGTAATTAAGTAAAAGCAGTTGAAGGACATAATTCAGGGT
*
32556 AATTAAGTAAAAACAGTTAAAAGGTAAGGATAGACATAGACTTAATTTTAAGGAAGGAAATTAGG
64 AATTAAGTAAAAACAGTTAAAAGGTAAGGATAGACATAGACTTAATTTCAAGGAAGGAAATTAGG
*
32621 TAAAGACAAGCACAGACTTAATTGAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGA
129 TAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGA
32686 AGGAAATTAGGTA
194 AGGAAATTAGGTA
32699 AAAAGCAGTTAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTTGAAGGACATAATTCAGGGT
1 AAAAGCAG-TAAG-ACTTAATTCAGGGTAATTAAGTAAAAGCAGTTGAAGGACATAATTCAGGGT
*
32764 AATTAAGTAAAAACAGTTAAAAGGTAAGGATAGACATAGAGTTAATTTCAAGGAAGGAAATTAGG
64 AATTAAGTAAAAACAGTTAAAAGGTAAGGATAGACATAGACTTAATTTCAAGGAAGGAAATTAGG
*
32829 TAAAGACAAGCACAAACTTAATTCAGGGTAATTAAGTAAAGTAAG-ACAGACTTAATTTCAAGGA
129 TAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGA
*
32893 AGGAAATTAGATAA
194 AGGAAATTAGGT-A
* * *
32907 AGACAAGCA-T-AGACTTAATTCATGGTAATTAAGTACAGTAAGTACAGACTTAATTTTAAAGA-
1 A-A-AAGCAGTAAGACTTAATTCAGGGTAATTAAGTA-A--AAG--CAG-------TTGAAGGAC
* ** * * * * *
32969 AGGAAGTT-A-GGTAAAAACAAGCATAGACTTAATTCAGGGTAAATAAGTAAAGATA-AGCACAG
52 A-TAA-TTCAGGGT--AATTAAG--TA-A---AA-ACA-GTTAAA-AGGTAAGGATAGA-CATAG
33031 ACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAA
103 ACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAA
33096 AGATAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
168 AG-TAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTA
* * *
33136 AAGA-CAAGCACAGACTTAAATCAGGGTAATTAAGTAAA
1 AAAAGC-AGTA-AGACTTAATTCAGGGTAATTAAGTAAA
33174 TTAGCAAAGA
Statistics
Matches: 414, Mismatches: 26, Indels: 51
0.84 0.05 0.10
Matches are distributed among these distances:
206 22 0.05
207 33 0.08
208 171 0.41
209 4 0.01
210 5 0.01
211 3 0.01
217 4 0.01
218 9 0.02
219 7 0.02
221 2 0.00
222 1 0.00
225 2 0.00
226 3 0.01
227 9 0.02
228 79 0.19
229 7 0.02
230 53 0.13
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (206 bp):
AAAAGCAGTAAGACTTAATTCAGGGTAATTAAGTAAAAGCAGTTGAAGGACATAATTCAGGGTAA
TTAAGTAAAAACAGTTAAAAGGTAAGGATAGACATAGACTTAATTTCAAGGAAGGAAATTAGGTA
AAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAG
GAAATTAGGTA
Found at i:33066 original size:77 final size:77
Alignment explanation
Indices: 32805--33193 Score: 608
Period size: 77 Copynumber: 5.1 Consensus size: 77
32795 AGACATAGAG
*
32805 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAAACTTAATTCAGGGTAATTAAGTAAAG
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAG
32870 -TAAG-ACAGAC
66 ATAAGCACAGAC
* * * *
32880 TTAATTTCAAGGAAGGAAATTAGATAAAGACAAGCATAGACTTAATTCATGGTAATTAAGTACAG
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAG
*
32945 -TAAGTACAGAC
66 ATAAGCACAGAC
* * * * * *
32956 TTAATTTTAAAGAAGGAAGTTAGGTAAAAACAAGCATAGACTTAATTCAGGGTAAATAAGTAAAG
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAG
33021 ATAAGCACAGAC
66 ATAAGCACAGAC
33033 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAG
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAG
33098 ATAAGCACAGAC
66 ATAAGCACAGAC
*
33110 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAAATCAGGGTAATTAAGT-AA-
1 TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAG
* *
33173 ATTAGCAAAGAC
66 ATAAGCACAGAC
33185 TTAATTTCA
1 TTAATTTCA
33194 CAAGAATTAA
Statistics
Matches: 289, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
75 83 0.29
76 65 0.22
77 141 0.49
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (77 bp):
TTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAG
ATAAGCACAGAC
Found at i:33332 original size:37 final size:37
Alignment explanation
Indices: 33272--33389 Score: 146
Period size: 37 Copynumber: 3.2 Consensus size: 37
33262 ACCAAATGGG
* * *
33272 ATTAAGTAAAGACAAGGGCTTAGTTCCAAGGAAGGGA
1 ATTAAGTAGAGAAAAGGACTTAGTTCCAAGGAAGGGA
* *
33309 ATTAAGTAGAGAAAAGGATTTAGTTCCAAGGAACGGA
1 ATTAAGTAGAGAAAAGGACTTAGTTCCAAGGAAGGGA
** * * *
33346 ATTAAGTAGAGTTAAGGACTTAATTTCAAGGAAGGAA
1 ATTAAGTAGAGAAAAGGACTTAGTTCCAAGGAAGGGA
33383 ATTAAGT
1 ATTAAGT
33390 CAAGTCAGAG
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.42, C:0.08, G:0.26, T:0.24
Consensus pattern (37 bp):
ATTAAGTAGAGAAAAGGACTTAGTTCCAAGGAAGGGA
Found at i:33405 original size:37 final size:37
Alignment explanation
Indices: 33272--33407 Score: 116
Period size: 37 Copynumber: 3.7 Consensus size: 37
33262 ACCAAATGGG
* * * * * *
33272 ATTAAGTAAAGACAAGGGCTTAGTTCCAAGGAAGGGA
1 ATTAAGTAGAGTCAAGGACTTAATTTCAAGGAACGGA
** * * *
33309 ATTAAGTAGAGAAAAGGATTTAGTTCCAAGGAACGGA
1 ATTAAGTAGAGTCAAGGACTTAATTTCAAGGAACGGA
*
33346 ATTAAGTAGAGTTAAGGACTTAATTTCAAGGAA-GGAA
1 ATTAAGTAGAGTCAAGGACTTAATTTCAAGGAACGG-A
33383 ATTAAGTCA-AGTCAGAGG-CTTAATT
1 ATTAAGT-AGAGTCA-AGGACTTAATT
33408 CAGGGTAATT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
36 2 0.02
37 79 0.93
38 4 0.05
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (37 bp):
ATTAAGTAGAGTCAAGGACTTAATTTCAAGGAACGGA
Found at i:33429 original size:37 final size:35
Alignment explanation
Indices: 33398--33507 Score: 166
Period size: 37 Copynumber: 3.1 Consensus size: 35
33388 GTCAAGTCAG
33398 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAA
1 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAA
33433 AGTGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
1 AG-G-CTTAATTCAGGGTAATTAAGTAGCGTCAAT-AA
* * *
33471 AGGCTTAATTCTGGGTAATTAAGTGGAGTCAATAA
1 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAA
33506 AG
1 AG
33508 AACTTAATCT
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
35 6 0.09
36 28 0.41
37 31 0.45
38 4 0.06
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (35 bp):
AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAA
Found at i:33487 original size:36 final size:36
Alignment explanation
Indices: 33398--33506 Score: 166
Period size: 36 Copynumber: 3.0 Consensus size: 36
33388 GTCAAGTCAG
33398 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAAT-AA
1 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
33433 AGTGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
1 AG-G-CTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
* * *
33471 AGGCTTAATTCTGGGTAATTAAGTGGAGTCAATAAA
1 AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
33507 GAACTTAATC
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
35 2 0.03
36 31 0.46
37 31 0.46
38 4 0.06
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (36 bp):
AGGCTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
Found at i:33541 original size:73 final size:73
Alignment explanation
Indices: 33464--33626 Score: 281
Period size: 73 Copynumber: 2.2 Consensus size: 73
33454 TAAGTAGCGT
* *
33464 CAATAAAAGGCTTAATTCTGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATT
1 CAATAAAAGGCTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCCAAAAAGAGATT
*
33529 AAGTAAAA
66 AAGCAAAA
* *
33537 CAATAAAAGGCTTAGTTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCCATAAAGAGATT
1 CAATAAAAGGCTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCCAAAAAGAGATT
33602 AAGCAAAA
66 AAGCAAAA
33610 CAATAAAAGGCTTAATT
1 CAATAAAAGGCTTAATT
33627 TATAAAAATT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 84 1.00
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (73 bp):
CAATAAAAGGCTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCCAAAAAGAGATT
AAGCAAAA
Found at i:36774 original size:28 final size:29
Alignment explanation
Indices: 36718--36774 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
36708 GAGTCATGGT
* *
36718 TTTCAAAAATGTTTTTTCAAAGTGTAGTC
1 TTTCAAAAATGTTCTTTCAAAGAGTAGTC
36747 TTTCAAAAATG-TCTTTCAAAAGAG-AGTC
1 TTTCAAAAATGTTCTTTC-AAAGAGTAGTC
36775 ATGGTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (29 bp):
TTTCAAAAATGTTCTTTCAAAGAGTAGTC
Found at i:36801 original size:48 final size:46
Alignment explanation
Indices: 36747--36850 Score: 154
Period size: 48 Copynumber: 2.2 Consensus size: 46
36737 AAGTGTAGTC
*
36747 TTTCAAAAATGTCTTTCAAAAGAGAGTCATGGTTTTCAAAATTGTATT
1 TTTCAAAAATGTCTTTCAAAAGAGAGTCATGGTTTTCAAAAATG--TT
* * *
36795 TTTCAAAAAAGTTTTTCAGAAGAGAGTCATGGTTTTCAAAAATGTT
1 TTTCAAAAATGTCTTTCAAAAGAGAGTCATGGTTTTCAAAAATGTT
36841 TTTCAAAAAT
1 TTTCAAAAAT
36851 AATTTTCGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
46 11 0.22
48 40 0.78
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (46 bp):
TTTCAAAAATGTCTTTCAAAAGAGAGTCATGGTTTTCAAAAATGTT
Done.