Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014853.1 Corchorus capsularis cultivar CVL-1 contig14874, 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: 37784
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:7599 original size:21 final size:21
Alignment explanation
Indices: 7551--7600 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
7541 TTTGGATGAG
* **
7551 ATCAAATTTTGGAGTTTGATT
1 ATCAAAATTTGGAGTTTGACC
* *
7572 ATTAAAATTTGGATTTTGACC
1 ATCAAAATTTGGAGTTTGACC
7593 ATCAAAAT
1 ATCAAAAT
7601 ATAGCAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (21 bp):
ATCAAAATTTGGAGTTTGACC
Found at i:10649 original size:44 final size:44
Alignment explanation
Indices: 10600--10689 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
10590 TTGGTACAAG
10600 AGAAATACATCTAAGGAAGAAATTAAAGGTAAGTGACAAGAAAT
1 AGAAATACATCTAAGGAAGAAATTAAAGGTAAGTGACAAGAAAT
*
10644 AGAAATACATCTAAGGAAGAAATTAAAGGTAAGTGAGAAGAAAT
1 AGAAATACATCTAAGGAAGAAATTAAAGGTAAGTGACAAGAAAT
10688 AG
1 AG
10690 GAGACCTATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.54, C:0.06, G:0.22, T:0.18
Consensus pattern (44 bp):
AGAAATACATCTAAGGAAGAAATTAAAGGTAAGTGACAAGAAAT
Found at i:10685 original size:21 final size:21
Alignment explanation
Indices: 10615--10687 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
10605 TACATCTAAG
10615 GAAGAAATTAAAGGTAAGTGA
1 GAAGAAATTAAAGGTAAGTGA
* * * *
10636 CAAGAAA-TAGAA-ATACATCTAA
1 GAAGAAATTA-AAGGTA-A-GTGA
10658 GGAAGAAATTAAAGGTAAGTGA
1 -GAAGAAATTAAAGGTAAGTGA
10680 GAAGAAAT
1 GAAGAAAT
10688 AGGAGACCTA
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
20 4 0.11
21 17 0.45
22 4 0.11
23 9 0.24
24 4 0.11
ACGTcount: A:0.55, C:0.04, G:0.23, T:0.18
Consensus pattern (21 bp):
GAAGAAATTAAAGGTAAGTGA
Found at i:11444 original size:32 final size:32
Alignment explanation
Indices: 11395--11471 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
11385 TGTGCACCCA
* *
11395 ATTG-TTTTTTTTCCTCCAGAAATATCACACC
1 ATTGTTTTTTTTTTCTCCAGAAATACCACACC
11426 ATTGTTTTTTTTTTCTCCAGAAATACCACACC
1 ATTGTTTTTTTTTTCTCCAGAAATACCACACC
11458 ATTGTTTTTTTTTT
1 ATTGTTTTTTTTTT
11472 AGCACAGCCG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
31 4 0.09
32 39 0.91
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.51
Consensus pattern (32 bp):
ATTGTTTTTTTTTTCTCCAGAAATACCACACC
Found at i:14145 original size:15 final size:14
Alignment explanation
Indices: 14127--14203 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 14
14117 AACCGACCGA
14127 ATATTAATATATATT
1 ATATT-ATATATATT
* *
14142 ATATTTTTATATTTT
1 ATA-TTATATATATT
14157 ATATTATATATATT
1 ATATTATATATATT
* * *
14171 GTATATATCTGATTTT
1 ATAT-TATAT-ATATT
14187 AGTATTTATATATATT
1 A-TA-TTATATATATT
14203 A
1 A
14204 AAAATTTTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
14 12 0.26
15 17 0.36
16 11 0.23
17 6 0.13
18 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (14 bp):
ATATTATATATATT
Found at i:17692 original size:50 final size:50
Alignment explanation
Indices: 17634--17784 Score: 266
Period size: 50 Copynumber: 3.0 Consensus size: 50
17624 GAAGTTTTAT
17634 AATAAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGATTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGATTTTCAA
*
17684 AATAAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGATTTTCAG
1 AATAAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGATTTTCAA
* * *
17734 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGATTTTCAA
17784 A
1 A
17785 GGGCATTTTA
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 96 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (50 bp):
AATAAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGATTTTCAA
Found at i:18463 original size:68 final size:69
Alignment explanation
Indices: 18324--18455 Score: 185
Period size: 68 Copynumber: 1.9 Consensus size: 69
18314 GTTCAACTTG
* ** *
18324 TTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAGGCGGCAAGGACTTTTCCACAAGCTAAA
1 TTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACAAGGACTTTTCCACAAGCCAAA
18389 CTCA
66 CTCA
* * * *
18393 TTTCCATACGAGTCAGTTTAAG-CTTGGTTCCATCCAAGCAACATGGGCTTTTCCATAAGCCAA
1 TTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACAAGGACTTTTCCACAAGCCAA
18456 GTTCATTTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
68 34 0.62
69 21 0.38
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (69 bp):
TTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACAAGGACTTTTCCACAAGCCAAA
CTCA
Found at i:18842 original size:14 final size:14
Alignment explanation
Indices: 18823--18856 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
18813 TTGTCAGTTG
*
18823 TTCAATTTCAATTC
1 TTCAATTTCAATCC
18837 TTCAATTTCAATCC
1 TTCAATTTCAATCC
18851 TTCAAT
1 TTCAAT
18857 GTTTCAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (14 bp):
TTCAATTTCAATCC
Found at i:18878 original size:30 final size:27
Alignment explanation
Indices: 18823--18897 Score: 71
Period size: 30 Copynumber: 2.6 Consensus size: 27
18813 TTGTCAGTTG
18823 TTCAA-TTTCAATTCTTCAATTTCAATCC
1 TTCAATTTTCAA-T-TTCAATTTCAATCC
*
18851 TTCAATGTTTCAATTTCAATTTGTCAATGC
1 TTCAAT-TTTCAATTTCAA-TT-TCAATCC
*
18881 TTCGATTCTTCAATTTC
1 TTCAATT-TTCAATTTC
18898 GAAGCTTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 10 0.25
29 4 0.10
30 26 0.65
ACGTcount: A:0.25, C:0.21, G:0.05, T:0.48
Consensus pattern (27 bp):
TTCAATTTTCAATTTCAATTTCAATCC
Found at i:18879 original size:22 final size:22
Alignment explanation
Indices: 18829--18870 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
18819 GTTGTTCAAT
18829 TTCAAT-TCTTCAATTTCAATCC
1 TTCAATGT-TTCAATTTCAATCC
18851 TTCAATGTTTCAATTTCAAT
1 TTCAATGTTTCAATTTCAAT
18871 TTGTCAATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.29, C:0.21, G:0.02, T:0.48
Consensus pattern (22 bp):
TTCAATGTTTCAATTTCAATCC
Found at i:18951 original size:97 final size:100
Alignment explanation
Indices: 18842--19088 Score: 242
Period size: 97 Copynumber: 2.5 Consensus size: 100
18832 AATTCTTCAA
* * * *
18842 TTTCAATCCTTCAATGTTTCAATTTCAATTTGTCAATGCTTCGATTCTTCAAT-TTCGAA-GCTT
1 TTTCAATTCTTCAATGATTCAATTTCAATTTGTCAATGCTTCAATTCCTCAATATTC-AATGCTT
18905 CAATTTACTTCAACGATCCAGGGCGGTC-TTCTT-T
65 CAATTTACTTCAACGATCCAGGGCGGTCTTTCTTAT
* * *
18939 TTTCAATTCTTCAATCATTCAATGGTTCAA---GTC-TTTCTTCAATTCCTCAATCATTCAATGC
1 TTTCAATTCTTCAATGATTCAAT--TTCAATTTGTCAATGCTTCAATTCCTCAAT-ATTCAATGC
* *
19000 TTCAATTTACTTCAATGATCCATGGCGGTCTTTCTTCAAT
63 TTCAATTTACTTCAACGATCCAGGGCGGTCTTTCTT--AT
* *
19040 TCTTCAATTATTCAATGCTTCAATTCCTCAATTAT-TCAATGCTTCAATT
1 T-TTCAATTCTTCAATGATTCAATT--TCAATT-TGTCAATGCTTCAATT
19089 TACTTTAATG
Statistics
Matches: 119, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
95 14 0.12
96 5 0.04
97 53 0.45
98 5 0.04
99 5 0.04
100 1 0.01
101 2 0.02
102 23 0.19
105 2 0.02
106 9 0.08
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (100 bp):
TTTCAATTCTTCAATGATTCAATTTCAATTTGTCAATGCTTCAATTCCTCAATATTCAATGCTTC
AATTTACTTCAACGATCCAGGGCGGTCTTTCTTAT
Found at i:18980 original size:36 final size:36
Alignment explanation
Indices: 18934--19004 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
18924 AGGGCGGTCT
* * *
18934 TCTTTTTTCAATTCTTCAATCATTCAATGGTTCAAG
1 TCTTTCTTCAATTCCTCAATCATTCAATGCTTCAAG
18970 TCTTTCTTCAATTCCTCAATCATTCAATGCTTCAA
1 TCTTTCTTCAATTCCTCAATCATTCAATGCTTCAA
19005 TTTACTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.25, C:0.24, G:0.06, T:0.45
Consensus pattern (36 bp):
TCTTTCTTCAATTCCTCAATCATTCAATGCTTCAAG
Found at i:19044 original size:8 final size:8
Alignment explanation
Indices: 19031--19233 Score: 87
Period size: 8 Copynumber: 25.0 Consensus size: 8
19021 ATGGCGGTCT
19031 TTCTTCAA
1 TTCTTCAA
19039 TTCTTCAA
1 TTCTTCAA
*
19047 TTATTCAA
1 TTCTTCAA
*
19055 TGCTTCAA
1 TTCTTCAA
*
19063 TTCCTCAA
1 TTCTTCAA
*
19071 TTATTCAA
1 TTCTTCAA
*
19079 TGCTTCAA
1 TTCTTCAA
*
19087 TTTACTTTAA
1 -TT-CTTCAA
* *
19097 TGATCTAGGGTGATCT
1 T--TCT----TCA--A
19113 TTCTTCAA
1 TTCTTCAA
19121 TTCTTCAA
1 TTCTTCAA
*
19129 TTATTCAA
1 TTCTTCAA
*
19137 TGCTTCAA
1 TTCTTCAA
*
19145 TTCCTCAA
1 TTCTTCAA
*
19153 TTATTCAA
1 TTCTTCAA
* *
19161 TGCCTCAA
1 TTCTTCAA
19169 -T-TTCAA
1 TTCTTCAA
* **
19175 ATCTTTGA
1 TTCTTCAA
**
19183 CGCTTCAA
1 TTCTTCAA
19191 -T-TTCAA
1 TTCTTCAA
19197 TT-TTCAA
1 TTCTTCAA
19204 TTCTTCAA
1 TTCTTCAA
*
19212 TGCTTCAA
1 TTCTTCAA
19220 -T-TTCAA
1 TTCTTCAA
19226 TTCTTCAA
1 TTCTTCAA
19234 ATTCCAAATG
Statistics
Matches: 143, Mismatches: 36, Indels: 32
0.68 0.17 0.15
Matches are distributed among these distances:
6 14 0.10
7 10 0.07
8 101 0.71
9 2 0.01
10 9 0.06
11 1 0.01
14 5 0.03
16 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.45
Consensus pattern (8 bp):
TTCTTCAA
Found at i:19060 original size:24 final size:24
Alignment explanation
Indices: 19033--19233 Score: 112
Period size: 24 Copynumber: 8.2 Consensus size: 24
19023 GGCGGTCTTT
19033 CTTCAATTCTTCAATTATTCAATG
1 CTTCAATTCTTCAATTATTCAATG
*
19057 CTTCAATTCCTCAATTATTCAATG
1 CTTCAATTCTTCAATTATTCAATG
* * *
19081 CTTCAATTTACTTTAATGA-TCTAGGGTG
1 CTTCAA-TT-CTTCAATTATTC-A--ATG
*
19109 ATCTTTCTTCAATTCTTCAATTATTCAATG
1 --C-TTC-A--ATTCTTCAATTATTCAATG
*
19139 CTTCAATTCCTCAATTATTCAATG
1 CTTCAATTCTTCAATTATTCAATG
* * * ** *
19163 CCTCAA-T-TTCAAATCTTTGACG
1 CTTCAATTCTTCAATTATTCAATG
*
19185 CTTCAA-T-TTCAATT-TTCAATT
1 CTTCAATTCTTCAATTATTCAATG
* *
19206 CTTCAATGCTTCAA-T-TTCAATT
1 CTTCAATTCTTCAATTATTCAATG
19228 CTTCAA
1 CTTCAA
19234 ATTCCAAATG
Statistics
Matches: 138, Mismatches: 25, Indels: 30
0.72 0.13 0.16
Matches are distributed among these distances:
21 9 0.07
22 35 0.25
23 6 0.04
24 52 0.38
25 4 0.03
26 7 0.05
27 3 0.02
28 3 0.02
30 3 0.02
31 3 0.02
32 8 0.06
33 4 0.03
34 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (24 bp):
CTTCAATTCTTCAATTATTCAATG
Found at i:19086 original size:82 final size:82
Alignment explanation
Indices: 18975--19171 Score: 331
Period size: 82 Copynumber: 2.4 Consensus size: 82
18965 TCAAGTCTTT
* * *
18975 CTTCAATTCCTCAATCATTCAATGCTTCAATTTACTTCAATGATCCATGGCGGTCTTTCTTCAAT
1 CTTCAATTCCTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGCGATCTTTCTTCAAT
19040 TCTTCAATTATTCAATG
66 TCTTCAATTATTCAATG
* * *
19057 CTTCAATTCCTCAATTATTCAATGCTTCAATTTACTTTAATGATCTAGGGTGATCTTTCTTCAAT
1 CTTCAATTCCTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGCGATCTTTCTTCAAT
19122 TCTTCAATTATTCAATG
66 TCTTCAATTATTCAATG
*
19139 CTTCAATTCCTCAATTATTCAATGCCTCAATTT
1 CTTCAATTCCTCAATTATTCAATGCTTCAATTT
19172 CAAATCTTTG
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 108 1.00
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.43
Consensus pattern (82 bp):
CTTCAATTCCTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGCGATCTTTCTTCAAT
TCTTCAATTATTCAATG
Found at i:19208 original size:29 final size:29
Alignment explanation
Indices: 19165--19235 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
19155 ATTCAATGCC
**
19165 TCAA-TTTCAAATCTTTGACGCTTCAATT
1 TCAATTTTCAAATCTTCAACGCTTCAATT
* *
19193 TCAATTTTCAATTCTTCAATGCTTCAATT
1 TCAATTTTCAAATCTTCAACGCTTCAATT
19222 TCAATTCTTCAAAT
1 TCAATT-TTCAAAT
19236 TCCAAATGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 4 0.11
29 26 0.72
30 6 0.17
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (29 bp):
TCAATTTTCAAATCTTCAACGCTTCAATT
Found at i:19226 original size:22 final size:21
Alignment explanation
Indices: 19185--19304 Score: 89
Period size: 22 Copynumber: 5.5 Consensus size: 21
19175 ATCTTTGACG
19185 CTTCAATTTCAATTTTCAATT
1 CTTCAATTTCAATTTTCAATT
19206 CTTCAATGCTTCAA-TTTCAATT
1 CTTCAAT--TTCAATTTTCAATT
* * * ** *
19228 CTTCAAATTCCAAATGTGGATG
1 CTTC-AATTTCAATTTTCAATT
*
19250 CTTCAATTTCAATTCTTCAATG
1 CTTCAATTTCAATT-TTCAATT
* * **
19272 CTTAAATTTCAATCCTTCAACG
1 CTTCAATTTCAAT-TTTCAATT
19294 CTTCAATTTCA
1 CTTCAATTTCA
19305 GTTCATCAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
21 19 0.24
22 52 0.66
23 8 0.10
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (21 bp):
CTTCAATTTCAATTTTCAATT
Found at i:19255 original size:44 final size:42
Alignment explanation
Indices: 19206--19347 Score: 102
Period size: 44 Copynumber: 3.4 Consensus size: 42
19196 ATTTTCAATT
19206 CTTCAATGCTTCAATTTCAATTCTTCAAATTCCAAATGTGGATG
1 CTTCAATGCTTCAATTTCAATTCTTCAAATTCCAAATGT--ATG
* * *
19250 CTTCAAT--TTCAATTCTTCAATGCTT-AAATTTC--A---ATC
1 CTTCAATGCTTCAA-T-TTCAATTCTTCAAATTCCAAATGTATG
* * *
19286 CTTCAACGCTTCAATTTCAGTTCATCAAATTCCAAATGTCAATG
1 CTTCAATGCTTCAATTTCAATTCTTCAAATTCCAAATGT--ATG
* *
19330 CTTCAATACTTCGATTTC
1 CTTCAATGCTTCAATTTC
19348 TCAATGCTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
36 15 0.20
37 7 0.09
38 5 0.07
39 1 0.01
41 1 0.01
42 5 0.07
43 7 0.09
44 33 0.45
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (42 bp):
CTTCAATGCTTCAATTTCAATTCTTCAAATTCCAAATGTATG
Found at i:19290 original size:36 final size:36
Alignment explanation
Indices: 19207--19291 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 36
19197 TTTTCAATTC
*
19207 TTCAATGCTTCAATTTCAATTCTTCAAATTCCAAAT
1 TTCAATGCTTCAATTTCAATTCTTCAAATGCCAAAT
* ** *
19243 GTGGATGCTTCAATTTCAATTCTTC-AATGCTTAAAT
1 TTCAATGCTTCAATTTCAATTCTTCAAATGC-CAAAT
*
19279 TTCAATCCTTCAA
1 TTCAATGCTTCAA
19292 CGCTTCAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
35 4 0.10
36 35 0.90
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (36 bp):
TTCAATGCTTCAATTTCAATTCTTCAAATGCCAAAT
Found at i:19313 original size:22 final size:22
Alignment explanation
Indices: 19149--19313 Score: 86
Period size: 22 Copynumber: 7.5 Consensus size: 22
19139 CTTCAATTCC
* * *
19149 TCAATTATTCAATGCCTCAATT
1 TCAATTCTTCAACGCTTCAATT
* **
19171 TCAAATCTTTGACGCTTCAATT
1 TCAATTCTTCAACGCTTCAATT
**
19193 TCAATT-TTCAATTCTTCAATGCT
1 TCAATTCTTCAACGCTTCAAT--T
**
19216 TCAA-T-TTCAATTCTTCAAATT
1 TCAATTCTTCAACGCTTC-AATT
* * * ** *
19237 CCAAAT-GTGGATGCTTCAATT
1 TCAATTCTTCAACGCTTCAATT
* *
19258 TCAATTCTTCAATGCTTAAATT
1 TCAATTCTTCAACGCTTCAATT
*
19280 TCAATCCTTCAACGCTTCAATT
1 TCAATTCTTCAACGCTTCAATT
* *
19302 TCAGTTCATCAA
1 TCAATTCTTCAA
19314 ATTCCAAATG
Statistics
Matches: 110, Mismatches: 28, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
21 22 0.20
22 80 0.73
23 8 0.07
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (22 bp):
TCAATTCTTCAACGCTTCAATT
Found at i:19351 original size:24 final size:22
Alignment explanation
Indices: 19324--19432 Score: 114
Period size: 22 Copynumber: 4.9 Consensus size: 22
19314 ATTCCAAATG
*
19324 TCAATGCTTCAATACTTCGAT-TT
1 TCAATGCTTCAAT--TTCAATATT
*
19347 CTCAATGCTTTAATTTCAATATT
1 -TCAATGCTTCAATTTCAATATT
* * *
19370 TCAATGCTTCAAATTCCGA-ATG
1 TCAATGCTTC-AATTTCAATATT
*
19392 TCAATGTTTCAATTTCAATATT
1 TCAATGCTTCAATTTCAATATT
19414 TCAATGCTTCAATTTCAAT
1 TCAATGCTTCAATTTCAAT
19433 TCTTAAAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
21 6 0.08
22 45 0.63
23 8 0.11
24 12 0.17
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.43
Consensus pattern (22 bp):
TCAATGCTTCAATTTCAATATT
Found at i:19409 original size:14 final size:14
Alignment explanation
Indices: 19404--19554 Score: 59
Period size: 14 Copynumber: 10.9 Consensus size: 14
19394 AATGTTTCAA
19404 TTTCAATATTTCAATG
1 TTTCAAT-T-TCAATG
*
19420 CTTCAATTTCAAT-
1 TTTCAATTTCAATG
* *
19433 TCTTAAAATTCAATG
1 T-TTCAATTTCAATG
* *
19448 CTTCAATTTCAACTC
1 TTTCAATTTCAA-TG
*
19463 TTT-AAATTCAA--
1 TTTCAATTTCAATG
19474 -TTC--T-TCAATG
1 TTTCAATTTCAATG
*
19484 TTTCAATTTCAATA
1 TTTCAATTTCAATG
*
19498 TCTCAATGCTTCAATG
1 TTTCAAT--TTCAATG
* *
19514 CTTCAAATTCAAT-
1 TTTCAATTTCAATG
*
19527 TCTTCAATTTCAATC
1 T-TTCAATTTCAATG
* *
19542 CTTCAAATTCAAT
1 TTTCAATTTCAAT
19555 CCTTAATGTT
Statistics
Matches: 100, Mismatches: 21, Indels: 30
0.66 0.14 0.20
Matches are distributed among these distances:
8 4 0.04
10 2 0.02
11 3 0.03
13 1 0.01
14 70 0.70
15 4 0.04
16 16 0.16
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (14 bp):
TTTCAATTTCAATG
Found at i:19419 original size:28 final size:29
Alignment explanation
Indices: 19362--19534 Score: 96
Period size: 28 Copynumber: 5.9 Consensus size: 29
19352 TGCTTTAATT
* *
19362 TCAATATTTCAATGCTTCAA-ATTCCGAATG-
1 TCAATGTTTCAAT--TTCAATATTTC-AATGC
19392 TCAATGTTTCAATTTCAATATTTCAATGC
1 TCAATGTTTCAATTTCAATATTTCAATGC
* *
19421 TTCAA--TTTCAATTCTTAA-AATTCAATGC
1 -TCAATGTTTCAATT-TCAATATTTCAATGC
* *
19449 TTCAA--TTTCAACTCTTTAA-A-TTCAATTC
1 -TCAATGTTTCAA-T-TTCAATATTTCAATGC
*
19477 TTCAATGTTTCAATTTCAATATCTCAATGC
1 -TCAATGTTTCAATTTCAATATTTCAATGC
* *
19507 TTCAATGCTTCAAATTCAAT-TCTTCAAT
1 -TCAATGTTTCAATTTCAATAT-TTCAAT
19535 TTCAATCCTT
Statistics
Matches: 121, Mismatches: 11, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
28 53 0.44
29 16 0.13
30 52 0.43
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (29 bp):
TCAATGTTTCAATTTCAATATTTCAATGC
Found at i:19494 original size:22 final size:22
Alignment explanation
Indices: 19392--19547 Score: 98
Period size: 22 Copynumber: 7.2 Consensus size: 22
19382 ATTCCGAATG
19392 TCAATGTTTCAATTTCAATAT-T
1 TCAATGTTTCAATTTCAAT-TCT
*
19414 TCAATGCTTCAATTTCAATTCT
1 TCAATGTTTCAATTTCAATTCT
**
19436 T-AA-AATTCAATGCTTCAA-T-T
1 TCAATGTTTCAAT--TTCAATTCT
* *
19456 TCAACTCTTT-AAATTCAATTCT
1 TCAA-TGTTTCAATTTCAATTCT
19478 TCAATGTTTCAATTTCAATATC-
1 TCAATGTTTCAATTTCAAT-TCT
* *
19500 TCAATGCTTCAATGCTTCAA--AT
1 TCAATGTTTCAAT--TTCAATTCT
*
19522 TCAAT-TCTTCAATTTCAATCCT
1 TCAATGT-TTCAATTTCAATTCT
19544 TCAA
1 TCAA
19548 ATTCAATCCT
Statistics
Matches: 106, Mismatches: 12, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
20 18 0.17
21 11 0.10
22 68 0.64
23 4 0.04
24 5 0.05
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.44
Consensus pattern (22 bp):
TCAATGTTTCAATTTCAATTCT
Found at i:19555 original size:14 final size:14
Alignment explanation
Indices: 19507--19558 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
19497 ATCTCAATGC
*
19507 TTCAATGCTTCAAA
1 TTCAATCCTTCAAA
* *
19521 TTCAATTCTTCAAT
1 TTCAATCCTTCAAA
19535 TTCAATCCTTCAAA
1 TTCAATCCTTCAAA
19549 TTCAATCCTT
1 TTCAATCCTT
19559 AATGTTTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.02, T:0.42
Consensus pattern (14 bp):
TTCAATCCTTCAAA
Found at i:19597 original size:79 final size:80
Alignment explanation
Indices: 19427--19615 Score: 249
Period size: 79 Copynumber: 2.4 Consensus size: 80
19417 ATGCTTCAAT
* * *
19427 TTCAATTCTTAAAATTCAATGCTTCAATTTCAACTCTTTAAATTCAATTCTTCAATGTTTCAATT
1 TTCAATTCTTCAAATTCAATGCTTCAATTTCAACTCTTCAAATTCAATCCTTCAATGTTTCAATT
19492 TCAATATCTCAATGC
66 TCAATATCTCAATGC
* *
19507 TTCAATGCTTCAAATTCAATTCTTCAATTTCAA-TCCTTCAAATTCAATCCTT-AATGTTTCAAT
1 TTCAATTCTTCAAATTCAATGCTTCAATTTCAACT-CTTCAAATTCAATCCTTCAATGTTTCAAT
* *
19570 TTCAATTTGTCAATGC
65 TTCAATATCTCAATGC
** *
19586 TTTGATTCTTCAATTTCGAA-GCTTCAATTT
1 TTCAATTCTTCAAATTC-AATGCTTCAATTT
19616 ACTTCAACGA
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
79 48 0.51
80 47 0.49
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.44
Consensus pattern (80 bp):
TTCAATTCTTCAAATTCAATGCTTCAATTTCAACTCTTCAAATTCAATCCTTCAATGTTTCAATT
TCAATATCTCAATGC
Found at i:19723 original size:58 final size:58
Alignment explanation
Indices: 19590--19851 Score: 332
Period size: 58 Copynumber: 4.5 Consensus size: 58
19580 CAATGCTTTG
* *
19590 ATTCTTCAAT--TTCGAA-GCTTCAATTTACTTCAACGATCCAGGGCGGTCTTCTTTTTTCA
1 ATTCTTCAATCATTC-AATGCTTCAATTTACTTCAATGATCCAGGGCGG---TCTTTCTTCA
* * * *
19649 ATTCTTCAATCATTCAATGGTGCAATTTACTTCAATGACCCAGGGTGGTCTTTCTTCA
1 ATTCTTCAATCATTCAATGCTTCAATTTACTTCAATGATCCAGGGCGGTCTTTCTTCA
*
19707 ATTCCTCAATCATTCAATGCTTCAATTTACTTCAATGATCCAGGGCGGTCTTTACTTCA
1 ATTCTTCAATCATTCAATGCTTCAATTTACTTCAATGATCCAGGGCGGTCTTT-CTTCA
* * ** *
19766 ATTCTTCAATTATTCAATGCTTCAATTTACTTTAATGATCCAGGATGATCTTTCTTCA
1 ATTCTTCAATCATTCAATGCTTCAATTTACTTCAATGATCCAGGGCGGTCTTTCTTCA
* *
19824 ATTCTTCAATTATTCAATGCCTCAATTT
1 ATTCTTCAATCATTCAATGCTTCAATTT
19852 CAAATCTTTG
Statistics
Matches: 181, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
58 89 0.49
59 62 0.34
60 2 0.01
61 28 0.15
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (58 bp):
ATTCTTCAATCATTCAATGCTTCAATTTACTTCAATGATCCAGGGCGGTCTTTCTTCA
Found at i:19783 original size:16 final size:16
Alignment explanation
Indices: 19762--19792 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19752 CGGTCTTTAC
*
19762 TTCAATTCTTCAATTA
1 TTCAATGCTTCAATTA
19778 TTCAATGCTTCAATT
1 TTCAATGCTTCAATT
19793 TACTTTAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.48
Consensus pattern (16 bp):
TTCAATGCTTCAATTA
Found at i:19803 original size:117 final size:119
Alignment explanation
Indices: 19606--19851 Score: 361
Period size: 117 Copynumber: 2.1 Consensus size: 119
19596 CAATTTCGAA
** *
19606 GCTTCAATTTACTTCAACGATCCAGGGCGGTCTTCTTTTTTCAATTCTTCAATCATTCAATGGTG
1 GCTTCAATTTACTTCAACGATCCAGGGCGGTCTTCTTACTTCAATTCTTCAATCATTCAATGCTG
* *
19671 CAATTTACTTCAATGACCCAGGGTGGTCTTTCTTCAATTCCTCAATCATTCAAT
66 CAATTTACTTCAATGACCCAGGATGATCTTTCTTCAATTCCTCAATCATTCAAT
* * *
19725 GCTTCAATTTACTTCAATGATCCAGGGCGGTC-T-TTACTTCAATTCTTCAATTATTCAATGCTT
1 GCTTCAATTTACTTCAACGATCCAGGGCGGTCTTCTTACTTCAATTCTTCAATCATTCAATGCTG
* * * *
19788 CAATTTACTTTAATGATCCAGGATGATCTTTCTTCAATTCTTCAATTATTCAAT
66 CAATTTACTTCAATGACCCAGGATGATCTTTCTTCAATTCCTCAATCATTCAAT
*
19842 GCCTCAATTT
1 GCTTCAATTT
19852 CAAATCTTTG
Statistics
Matches: 114, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
117 82 0.72
118 1 0.01
119 31 0.27
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.41
Consensus pattern (119 bp):
GCTTCAATTTACTTCAACGATCCAGGGCGGTCTTCTTACTTCAATTCTTCAATCATTCAATGCTG
CAATTTACTTCAATGACCCAGGATGATCTTTCTTCAATTCCTCAATCATTCAAT
Found at i:19949 original size:14 final size:15
Alignment explanation
Indices: 19930--19993 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 15
19920 AATGTCGATG
19930 CTTCAAT-TTCAATT
1 CTTCAATCTTCAATT
*
19944 CTTCAATGCTTAAATT
1 CTTCAAT-CTTCAATT
**
19960 C--CAATCCTTCAACG
1 CTTCAAT-CTTCAATT
19974 CTTCAAT-TTCAATT
1 CTTCAATCTTCAATT
19988 CTTCAA
1 CTTCAA
19994 ATTCCAAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
14 28 0.72
16 11 0.28
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.41
Consensus pattern (15 bp):
CTTCAATCTTCAATT
Found at i:19949 original size:44 final size:43
Alignment explanation
Indices: 19908--20081 Score: 177
Period size: 44 Copynumber: 4.1 Consensus size: 43
19898 AGATTCAACT
*
19908 CTTCAAATTCCAAATGTCGATGCTTCAATTTCAATTCTTCAATG
1 CTTCAAATTCCAAATGTCAATGCTTCAATTTCAATT-TTCAATG
* *
19952 CTT-AAATTCC-AA--TC----CTTCAACGCTTCAA-TTTCAATT
1 CTTCAAATTCCAAATGTCAATGCTTCAA--TTTCAATTTTCAATG
*
19988 CTTCAAATTCCAAATGCCAATGCTTCAATTTCAATATTTCAATG
1 CTTCAAATTCCAAATGTCAATGCTTCAATTTCAAT-TTTCAATG
* * *
20032 CTTCAAATTCCGAATGTCAATGTTTCAATTTCAATATGTCAATG
1 CTTCAAATTCCAAATGTCAATGCTTCAATTTCAAT-TTTCAATG
20076 CTTCAA
1 CTTCAA
20082 TTTCAATTCT
Statistics
Matches: 109, Mismatches: 9, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
36 15 0.14
37 8 0.07
38 7 0.06
40 3 0.03
42 7 0.06
43 7 0.06
44 62 0.57
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (43 bp):
CTTCAAATTCCAAATGTCAATGCTTCAATTTCAATTTTCAATG
Found at i:19952 original size:22 final size:22
Alignment explanation
Indices: 19927--19993 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
19917 CCAAATGTCG
19927 ATGCTTCAATTTCAATTCTTCA
1 ATGCTTCAATTTCAATTCTTCA
* * *
19949 ATGCTTAAATTCCAATCCTTCA
1 ATGCTTCAATTTCAATTCTTCA
*
19971 ACGCTTCAATTTCAATTCTTCA
1 ATGCTTCAATTTCAATTCTTCA
19993 A
1 A
19994 ATTCCAAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.40
Consensus pattern (22 bp):
ATGCTTCAATTTCAATTCTTCA
Found at i:19985 original size:36 final size:36
Alignment explanation
Indices: 19945--20022 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
19935 ATTTCAATTC
19945 TTCAATGCTT-AAATTCC-AATCCTTCAACGCTTCAAT
1 TTCAATGCTTCAAATTCCAAATCC--CAACGCTTCAAT
* * *
19981 TTCAATTCTTCAAATTCCAAATGCCAATGCTTCAAT
1 TTCAATGCTTCAAATTCCAAATCCCAACGCTTCAAT
20017 TTCAAT
1 TTCAAT
20023 ATTTCAATGC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 26 0.70
37 7 0.19
38 4 0.11
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (36 bp):
TTCAATGCTTCAAATTCCAAATCCCAACGCTTCAAT
Found at i:19985 original size:80 final size:81
Alignment explanation
Indices: 19872--20042 Score: 240
Period size: 80 Copynumber: 2.1 Consensus size: 81
19862 ACGCTTCAAT
* * * * * *
19872 TTCAATTTTCAATTCTTCAATGCTTCAGATTCAACTCTTCAAATTCCAAATGTCGATGCTTCAAT
1 TTCAAATTCCAATCCTTCAACGCTTCAGATTCAACTCTTCAAATTCCAAATGCCAATGCTTCAAT
19937 TTCAAT-TCTTCAATGC
66 TTCAATAT-TTCAATGC
*
19953 TT-AAATTCCAATCCTTCAACGCTTCA-ATTTCAATTCTTCAAATTCCAAATGCCAATGCTTCAA
1 TTCAAATTCCAATCCTTCAACGCTTCAGA-TTCAACTCTTCAAATTCCAAATGCCAATGCTTCAA
20016 TTTCAATATTTCAATGC
65 TTTCAATATTTCAATGC
20033 TTCAAATTCC
1 TTCAAATTCC
20043 GAATGTCAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
79 1 0.01
80 69 0.86
81 10 0.12
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.39
Consensus pattern (81 bp):
TTCAAATTCCAATCCTTCAACGCTTCAGATTCAACTCTTCAAATTCCAAATGCCAATGCTTCAAT
TTCAATATTTCAATGC
Found at i:20008 original size:22 final size:22
Alignment explanation
Indices: 19982--20081 Score: 105
Period size: 22 Copynumber: 4.5 Consensus size: 22
19972 CGCTTCAATT
*
19982 TCAATTCTTCAAATTCCAAATG
1 TCAATGCTTCAAATTCCAAATG
* * *
20004 CCAATGCTTC-AATTTCAATATT
1 TCAATGCTTCAAATTCCAA-ATG
*
20026 TCAATGCTTCAAATTCCGAATG
1 TCAATGCTTCAAATTCCAAATG
* *
20048 TCAATGTTTC-AATTTCAATATG
1 TCAATGCTTCAAATTCCAA-ATG
20070 TCAATGCTTCAA
1 TCAATGCTTCAA
20082 TTTCAATTCT
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
21 13 0.21
22 42 0.68
23 7 0.11
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (22 bp):
TCAATGCTTCAAATTCCAAATG
Found at i:20028 original size:14 final size:14
Alignment explanation
Indices: 20011--20122 Score: 63
Period size: 14 Copynumber: 7.9 Consensus size: 14
20001 ATGCCAATGC
20011 TTCAATTTCAATAT
1 TTCAATTTCAATAT
20025 TTCAATGCTTCAA-AT
1 TTCAAT--TTCAATAT
* * *
20040 TCCGAATGTCAATGT
1 TTC-AATTTCAATAT
20055 TTCAATTTCAATAT
1 TTCAATTTCAATAT
*
20069 GTCAATGCTTC-A-AT
1 TTCAAT--TTCAATAT
*
20083 TTCAATTCTTCGA-A-
1 TTCAA-T-TTCAATAT
*
20097 TTCAATTTCAATGT
1 TTCAATTTCAATAT
*
20111 TTCAAATTCAAT
1 TTCAATTTCAAT
20123 TCTTCAAAGC
Statistics
Matches: 77, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
12 4 0.05
13 1 0.01
14 50 0.65
15 11 0.14
16 11 0.14
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (14 bp):
TTCAATTTCAATAT
Found at i:20059 original size:80 final size:79
Alignment explanation
Indices: 19888--20066 Score: 238
Period size: 80 Copynumber: 2.2 Consensus size: 79
19878 TTTCAATTCT
* * *
19888 TCAATGCTTCAGA-TTCAACTCTTCAAATTCCAAATGTCGATGCTTCAATTTCAATTCTTCAATG
1 TCAATGCTTCA-ATTTCAATTCTTCAAATTCCAAATGCCAATGCTTCAATTTCAATTCTTCAATG
*
19952 CTTAAATTCCAATCCT
65 CTTAAATTCCAAT-CG
*
19968 TCAACGCTTCAATTTCAATTCTTCAAATTCCAAATGCCAATGCTTCAATTTCAATAT-TTCAATG
1 TCAATGCTTCAATTTCAATTCTTCAAATTCCAAATGCCAATGCTTCAATTTCAAT-TCTTCAATG
20032 CTTCAAATTCCGAAT-G
65 CTT-AAATTCC-AATCG
*
20048 TCAATGTTTCAATTTCAAT
1 TCAATGCTTCAATTTCAAT
20067 ATGTCAATGC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
79 1 0.01
80 76 0.86
81 8 0.09
82 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.38
Consensus pattern (79 bp):
TCAATGCTTCAATTTCAATTCTTCAAATTCCAAATGCCAATGCTTCAATTTCAATTCTTCAATGC
TTAAATTCCAATCG
Found at i:20102 original size:20 final size:20
Alignment explanation
Indices: 19975--20123 Score: 80
Period size: 22 Copynumber: 7.3 Consensus size: 20
19965 CCTTCAACGC
19975 TTCAATTTCAAT-TCTTCAAA
1 TTCAATTTCAATGT-TTCAAA
** * *
19995 TTCCAAATGCCAATGCTTCAAT
1 TT-C-AATTTCAATGTTTCAAA
*
20017 TTCAATATTTCAATGCTTCAAA
1 TTC-A-ATTTCAATGTTTCAAA
* *
20039 TTCCGAATGTCAATGTTTCAAT
1 TT-C-AATTTCAATGTTTCAAA
20061 TTCAATATGTCAATG---C---
1 TTCAAT-T-TCAATGTTTCAAA
*
20077 TTCAATTTCAAT-TCTTCGAA
1 TTCAATTTCAATGT-TTCAAA
20097 TTCAATTTCAATGTTTCAAA
1 TTCAATTTCAATGTTTCAAA
20117 TTCAATT
1 TTCAATT
20124 CTTCAAAGCC
Statistics
Matches: 101, Mismatches: 13, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
14 5 0.05
15 1 0.01
16 6 0.06
17 1 0.01
19 1 0.01
20 29 0.29
21 6 0.06
22 50 0.50
23 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (20 bp):
TTCAATTTCAATGTTTCAAA
Found at i:20115 original size:34 final size:36
Alignment explanation
Indices: 20061--20127 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 36
20051 ATGTTTCAAT
*
20061 TTCAATATGTCAATGCTTCAATTTCAATTCTTCGAA
1 TTCAATATGTCAATGCTTCAAATTCAATTCTTCGAA
*
20097 TTCAAT-T-TCAATGTTTCAAATTCAATTCTTC
1 TTCAATATGTCAATGCTTCAAATTCAATTCTTC
20128 AAAGCCTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 22 0.76
35 1 0.03
36 6 0.21
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (36 bp):
TTCAATATGTCAATGCTTCAAATTCAATTCTTCGAA
Found at i:22415 original size:7 final size:7
Alignment explanation
Indices: 22405--22434 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
22395 AATCCAAAAG
22405 AATTCAA
1 AATTCAA
22412 AATTCAA
1 AATTCAA
22419 AATTCAA
1 AATTCAA
*
22426 AAATCAA
1 AATTCAA
22433 AA
1 AA
22435 AAAGAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.23
Consensus pattern (7 bp):
AATTCAA
Found at i:25610 original size:13 final size:13
Alignment explanation
Indices: 25592--25616 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25582 TTAGCTATCC
25592 CCTTTATCAACCT
1 CCTTTATCAACCT
25605 CCTTTATCAACC
1 CCTTTATCAACC
25617 ATGGCAGCAG
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:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (13 bp):
CCTTTATCAACCT
Found at i:29551 original size:19 final size:18
Alignment explanation
Indices: 29518--29554 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
29508 TTGAAATAAT
29518 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
29536 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
29555 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Done.