Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007385.1 Corchorus capsularis cultivar CVL-1 contig07406, 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: 8884
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:6054 original size:17 final size:16
Alignment explanation
Indices: 6032--6078 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 16
6022 AGAGTCATGG
6032 TTTTCAAAAATGCTTTT
1 TTTTCAAAAATG-TTTT
6049 TTTTCAAAAATG---T
1 TTTTCAAAAATGTTTT
6062 TTTTCAAAAATGTTTT
1 TTTTCAAAAATGTTTT
6078 T
1 T
6079 CAAAAAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 13 0.48
16 2 0.07
17 12 0.44
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (16 bp):
TTTTCAAAAATGTTTT
Found at i:6070 original size:12 final size:13
Alignment explanation
Indices: 6048--6144 Score: 79
Period size: 13 Copynumber: 6.8 Consensus size: 13
6038 AAAATGCTTT
6048 TTTTTCAAAAATG
1 TTTTTCAAAAATG
6061 TTTTTCAAAAATG
1 TTTTTCAAAAATG
6074 TTTTTCAAAAAAAGGTCATG
1 TTTTTC---AAAA----ATG
* *
6094 GTTTTCAAAAATA
1 TTTTTCAAAAATG
6107 TTTTTC-AAAATG
1 TTTTTCAAAAATG
6119 TTTTCTTCAAAAAATG
1 -TTT-TTC-AAAAATG
6135 TTTTTCAAAA
1 TTTTTCAAAA
6145 GAGAGTCATG
Statistics
Matches: 69, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
12 5 0.07
13 33 0.48
14 6 0.09
15 3 0.04
16 10 0.14
17 4 0.06
20 8 0.12
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.43
Consensus pattern (13 bp):
TTTTTCAAAAATG
Found at i:6140 original size:61 final size:60
Alignment explanation
Indices: 6022--6166 Score: 179
Period size: 61 Copynumber: 2.3 Consensus size: 60
6012 GGAATATTAG
*
6022 AGAGTCATGGTTTTCAAAAATGCTTTTTTTTCAAAAATGTTTTTCAAAAATGTTTTTCAAAAA
1 AGAGTCATGGTTTTCAAAAA---TTATTTTTCAAAAATGTTTTTCAAAAATGTTTTTCAAAAA
*
6085 A-AGGTCATGGTTTTCAAAAA-TATTTTTC-AAAATGTTTTCTTCAAAAAATGTTTTTCAAAAG
1 AGA-GTCATGGTTTTCAAAAATTATTTTTCAAAAATG-TTT-TTC-AAAAATGTTTTTCAAAAA
6146 AGAGTCATGGTTTTCAGAAAA
1 AGAGTCATGGTTTTCA-AAAA
6167 AACACAAAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
58 6 0.08
59 10 0.14
60 3 0.04
61 31 0.42
62 6 0.08
63 18 0.24
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (60 bp):
AGAGTCATGGTTTTCAAAAATTATTTTTCAAAAATGTTTTTCAAAAATGTTTTTCAAAAA
Found at i:7933 original size:24 final size:24
Alignment explanation
Indices: 7906--7952 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
7896 ATAATCTCTT
7906 TCTTCAACTATTCAATGCTTCAAA
1 TCTTCAACTATTCAATGCTTCAAA
* * *
7930 TCTTCCATTATTCAATTCTTCAA
1 TCTTCAACTATTCAATGCTTCAA
7953 TTCACTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.02, T:0.43
Consensus pattern (24 bp):
TCTTCAACTATTCAATGCTTCAAA
Found at i:8020 original size:58 final size:58
Alignment explanation
Indices: 7930--8061 Score: 167
Period size: 58 Copynumber: 2.3 Consensus size: 58
7920 ATGCTTCAAA
* * * *
7930 TCTTCCATTATTCAATTCTTCAATTCACTTCAATGACCCAGGGTGGTCTTTCTT-CGTT
1 TCTTCAATTATTCAATGCTTCAATTCACTTCAATGACACAGGGTGGTCTGTCTTCCG-T
** * *
7988 TCTTCAATTATTCAATGCTTCAATTTGCTTCAATGATACATGGTGGTCTGTCTTCCGT
1 TCTTCAATTATTCAATGCTTCAATTCACTTCAATGACACAGGGTGGTCTGTCTTCCGT
*
8046 TCCTCAATTATTCAAT
1 TCTTCAATTATTCAAT
8062 ACCTTAATTC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 62 0.97
59 2 0.03
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.43
Consensus pattern (58 bp):
TCTTCAATTATTCAATGCTTCAATTCACTTCAATGACACAGGGTGGTCTGTCTTCCGT
Found at i:8081 original size:22 final size:22
Alignment explanation
Indices: 8056--8177 Score: 72
Period size: 22 Copynumber: 5.6 Consensus size: 22
8046 TCCTCAATTA
8056 TTCAATACCTT-AATTCCAAATC
1 TTCAATA-CTTCAATTCCAAATC
* *
8078 TTCAATACTTCAATTTCAATTC
1 TTCAATACTTCAATTCCAAATC
** * *
8100 TTCAATGTTTC--TTTCAATTC
1 TTCAATACTTCAATTCCAAATC
* * * *
8120 TTTAATGCTTCAGTTTCAATAT-
1 TTCAATACTTCAATTCCAA-ATC
* * *
8142 TTCAATGCTTCAATTTCAATTC
1 TTCAATACTTCAATTCCAAATC
*
8164 TTCAATATTTCAAT
1 TTCAATACTTCAAT
8178 GCTCCGATTT
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
20 18 0.22
21 4 0.05
22 60 0.72
23 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (22 bp):
TTCAATACTTCAATTCCAAATC
Found at i:8145 original size:30 final size:30
Alignment explanation
Indices: 8134--8506 Score: 147
Period size: 30 Copynumber: 12.9 Consensus size: 30
8124 ATGCTTCAGT
*
8134 TTCAATATTTCAATGCTTCAATTTCAATTC
1 TTCAATATTTCAATGCTTCAATTTCAAGTC
* * *
8164 TTCAATATTTCAATGCTCCGATTTCAATTC
1 TTCAATATTTCAATGCTTCAATTTCAAGTC
* * * *
8194 TTC-A-AGTTCAGTCCTTCTATGTTTCAA-T-
1 TTCAATATTTCAATGCTTC-A-ATTTCAAGTC
* * * * *
8222 TCCAATATTTCAATTCTTCAAATCCAATTC
1 TTCAATATTTCAATGCTTCAATTTCAAGTC
* *
8252 TTC-A-ATTTCAATACTTCAATGCTTCGA-T-
1 TTCAATATTTCAATGCTTCAAT--TTCAAGTC
* *
8280 TTCAATATTTCAATGTTTCAATTTCAATTC
1 TTCAATATTTCAATGCTTCAATTTCAAGTC
*
8310 TTCAA-ATTCCAAATG--TCAA--T--A--C
1 TTCAATATTTC-AATGCTTCAATTTCAAGTC
* *
8332 TTCAATATTTTAATTCTTCAAATGCTTCAA-T-
1 TTCAATATTTCAATGCTTC-AAT--TTCAAGTC
* * * *
8363 TTCAATAGTTCAACGCTTCAAGTTCAA-TT
1 TTCAATATTTCAATGCTTCAATTTCAAGTC
*
8392 TTCCAA-A-TTCAATTCTTCAATGTCTCAA-T-
1 TT-CAATATTTCAATGCTTCAAT-T-TCAAGTC
* *
8421 TTCAATATTTCAATGCTTCAATCTCAAATC
1 TTCAATATTTCAATGCTTCAATTTCAAGTC
*
8451 TTCAA-A-TTCAATTCTTCAATGTTTCAA-T-
1 TTCAATATTTCAATGCTTCAA--TTTCAAGTC
*
8479 TTCAAT-TCTTCAAATACTTCAATTTCAA
1 TTCAATAT-TTC-AATGCTTCAATTTCAA
8507 TCCCTCAATC
Statistics
Matches: 265, Mismatches: 40, Indels: 77
0.69 0.10 0.20
Matches are distributed among these distances:
22 9 0.03
23 3 0.01
24 3 0.01
25 2 0.01
26 1 0.00
28 81 0.31
29 30 0.11
30 111 0.42
31 25 0.09
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (30 bp):
TTCAATATTTCAATGCTTCAATTTCAAGTC
Found at i:8157 original size:14 final size:14
Alignment explanation
Indices: 8140--8828 Score: 148
Period size: 14 Copynumber: 48.1 Consensus size: 14
8130 CAGTTTCAAT
8140 ATTTCAATGCTTCA
1 ATTTCAATGCTTCA
*
8154 ATTTCAATTCTTCAA
1 ATTTCAATGCTTC-A
* *
8169 TATTTCAATGCTCCG
1 -ATTTCAATGCTTCA
*
8184 ATTTCAATTCTTCA
1 ATTTCAATGCTTCA
* * *
8198 AGTTCAGTCCTTCTA
1 ATTTCAATGCTTC-A
* *
8213 TGTTTCAAT--TCCAA
1 -ATTTCAATGCTTC-A
*
8227 TATTTCAATTCTTCA
1 -ATTTCAATGCTTCA
* * *
8242 AATCCAATTCTTCA
1 ATTTCAATGCTTCA
*
8256 ATTTCAATACTTCA
1 ATTTCAATGCTTCA
*
8270 ATGCTTCGAT--TTCAA
1 AT--TTCAATGCTTC-A
*
8285 TATTTCAATGTTTCA
1 -ATTTCAATGCTTCA
*
8300 ATTTCAATTCTTCAA
1 ATTTCAATGCTTC-A
*
8315 ATTCCAAATG--TCA
1 ATTTC-AATGCTTCA
** *
8328 ATACTTCAATATTTTA
1 AT--TTCAATGCTTCA
8344 ATTCTTCAAATGCTTCA
1 A-T-TTC-AATGCTTCA
8361 ATTTCAATAG-TTCA
1 ATTTCAAT-GCTTCA
8375 A---C---GCTTCA
1 ATTTCAATGCTTCA
* *
8383 AGTTCAAT-TTTCCA
1 ATTTCAATGCTT-CA
* *
8397 AATTCAATTCTTCA
1 ATTTCAATGCTTCA
8411 ATGTCTCAAT--TTCAA
1 AT-T-TCAATGCTTC-A
8426 TATTTCAATGCTTCA
1 -ATTTCAATGCTTCA
*
8441 ATCTCAAAT-CTTCA
1 ATTTC-AATGCTTCA
* *
8455 AATTCAATTCTTCA
1 ATTTCAATGCTTCA
8469 ATGTTTCAAT--TTCA
1 A--TTTCAATGCTTCA
*
8483 ATTCTTCAAATACTTCA
1 A-T-TTC-AATGCTTCA
* *
8500 ATTTCAATCCCTCA
1 ATTTCAATGCTTCA
*
8514 ATCCTTCAAT--TCCAA
1 AT--TTCAATGCTTC-A
*
8529 TATTTCAATGTTTCA
1 -ATTTCAATGCTTCA
*
8544 ATTTCAATTCTTCAA
1 ATTTCAATGCTTC-A
8559 TATTTCAATGCTTCA
1 -ATTTCAATGCTTCA
*
8574 ATGTCAA-GACTTCA
1 ATTTCAATG-CTTCA
* * *
8588 ATTTCGATTCTTCG
1 ATTTCAATGCTTCA
*
8602 A--T--AT--TTTA
1 ATTTCAATGCTTCA
* *
8610 TTTTCCATGCTTCA
1 ATTTCAATGCTTCA
*
8624 ATTCTTCAATGTTTCAA
1 A-T-TTCAATGCTTC-A
* *
8641 TATTTCAATGCCTCG
1 -ATTTCAATGCTTCA
* *
8656 ATTTCATTTCTTCA
1 ATTTCAATGCTTCA
* * *
8670 ATTGCAATTCTTTGA
1 ATTTCAATGC-TTCA
*
8685 TGTTTCAAT--TTCA
1 -ATTTCAATGCTTCA
* *
8698 CTTTCAATGCGTCA
1 ATTTCAATGCTTCA
*
8712 ATTTCAATTCTTCA
1 ATTTCAATGCTTCA
* * *
8726 AATTCAGTCCTTCA
1 ATTTCAATGCTTCA
*
8740 ATGTTTCAATTCTTCA
1 A--TTTCAATGCTTCA
*
8756 ATTTCAACT-CTGCA
1 ATTTCAA-TGCTTCA
* *
8770 AATTCAATCCTTCA
1 ATTTCAATGCTTCA
*
8784 ATGTTTTAAT-C-TCAA
1 A--TTTCAATGCTTC-A
8799 TATTTCAATGCTTCA
1 -ATTTCAATGCTTCA
*
8814 ATTTCAATTCTTCA
1 ATTTCAATGCTTCA
8828 A
1 A
8829 ATCCCCAAAT
Statistics
Matches: 503, Mismatches: 94, Indels: 156
0.67 0.12 0.21
Matches are distributed among these distances:
7 1 0.00
8 7 0.01
10 3 0.01
11 2 0.00
12 10 0.02
13 14 0.03
14 285 0.57
15 44 0.09
16 121 0.24
17 15 0.03
18 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (14 bp):
ATTTCAATGCTTCA
Found at i:8188 original size:44 final size:43
Alignment explanation
Indices: 8140--8567 Score: 153
Period size: 44 Copynumber: 9.9 Consensus size: 43
8130 CAGTTTCAAT
* *
8140 ATTTCAATGCTTCAATTTCAATTCTTCAATATTTCAATGCTCC-G
1 ATTTCAATTCTTCAAATTCAATTCTTCAATATTTCAAT--TCCAG
* * * * * *
8184 ATTTCAATTCTTCAAGTTCAGTCCTTCTATGTTTCAATTCCAAT
1 ATTTCAATTCTTCAAATTCAATTCTTCAATATTTCAATTCC-AG
*
8228 ATTTCAATTCTTCAAATCCAATTCTTC-A-ATTTCAA-T----
1 ATTTCAATTCTTCAAATTCAATTCTTCAATATTTCAATTCCAG
* * * * * *
8264 ACTTCAATGCTTCGATTTCAATAT-TTCAATGTTTCAATTTCA-
1 ATTTCAATTCTTCAAATTCAAT-TCTTCAATATTTCAATTCCAG
* * *
8306 ATTCTTCAAATTC--CAAATGTCAATACTTCAATATTTTAATTCTTCAA
1 A-T-TTC-AATTCTTCAAAT-TCAATTCTTCAATATTTCAATTC--CAG
** *
8353 ATGCTTCAA-T-TTCAATAGTTCAACGCTTC-A-AGTTCAATTTTCCA-
1 AT--TTCAATTCTTCAA-A-TTCAATTCTTCAATATTTCAA--TTCCAG
* * *
8397 AATTCAATTCTTCAATGTCTCAA-T-TTCAATATTTCAATGCTTCA-
1 ATTTCAATTCTTCAA-AT-TCAATTCTTCAATATTTCAAT--TCCAG
* * * *
8441 ATCTCAAATCTTCAAATTCAATTCTTCAATGTTTCAATTTCA-
1 ATTTCAATTCTTCAAATTCAATTCTTCAATATTTCAATTCCAG
* * * * ** *
8483 ATTCTTCAAATACTTCAATTTCAATCCCTCAATCCTTCAATTCCAAT
1 A-T-TTC-AATTCTTCAAATTCAATTCTTCAATATTTCAATTCC-AG
*
8530 ATTTCAATGT-TTCAATTTCAATTCTTCAATATTTCAAT
1 ATTTCAAT-TCTTCAAATTCAATTCTTCAATATTTCAAT
8568 GCTTCAATGT
Statistics
Matches: 291, Mismatches: 54, Indels: 78
0.69 0.13 0.18
Matches are distributed among these distances:
36 20 0.07
37 2 0.01
38 6 0.02
39 1 0.00
41 1 0.00
42 28 0.10
43 10 0.03
44 150 0.52
45 43 0.15
46 11 0.04
47 18 0.06
48 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (43 bp):
ATTTCAATTCTTCAAATTCAATTCTTCAATATTTCAATTCCAG
Found at i:8241 original size:22 final size:22
Alignment explanation
Indices: 8127--8258 Score: 62
Period size: 22 Copynumber: 6.0 Consensus size: 22
8117 TTCTTTAATG
* * *
8127 CTTCAGTTTCAATATTTCAATG
1 CTTCAATTCCAATATTTCAATT
*
8149 CTTCAATTTCAAT-TCTTCAATAT
1 CTTCAATTCCAATAT-TTCAAT-T
*
8172 -TTCAATGCTCC--GATTTCAATT
1 CTTCAAT--TCCAATATTTCAATT
* ** *
8193 CTTCAAGTT-CAGTCCTTCTATGT
1 CTTCAA-TTCCAATATTTCAAT-T
8216 -TTCAATTCCAATATTTCAATT
1 CTTCAATTCCAATATTTCAATT
*
8237 CTTCAAATCCAAT-TCTTCAATT
1 CTTCAATTCCAATAT-TTCAATT
8259 TCAATACTTC
Statistics
Matches: 84, Mismatches: 13, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
20 1 0.01
21 7 0.08
22 71 0.85
23 3 0.04
24 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45
Consensus pattern (22 bp):
CTTCAATTCCAATATTTCAATT
Found at i:8250 original size:58 final size:58
Alignment explanation
Indices: 8142--8314 Score: 181
Period size: 58 Copynumber: 3.0 Consensus size: 58
8132 GTTTCAATAT
* * * *
8142 TTCAATGCTTCAA--TTTCAATTCTTCAATATTTCAATGCTCCGATTTCAATTCTTCAAG
1 TTCAATACTTCAATGTTTCAATTC--CAATATTTCAATTCTTCAATTTCAATTCTTCAAG
* * * * * *
8200 TTCAGTCCTTCTATGTTTCAATTCCAATATTTCAATTCTTCAAATCCAATTCTTCAAT
1 TTCAATACTTCAATGTTTCAATTCCAATATTTCAATTCTTCAATTTCAATTCTTCAAG
* * *
8258 TTCAATACTTCAATGCTTCGATTTCAATATTTCAATGT-TTCAATTTCAATTCTTCAA
1 TTCAATACTTCAATGTTTCAATTCCAATATTTCAAT-TCTTCAATTTCAATTCTTCAA
8315 ATTCCAAATG
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
58 85 0.89
59 1 0.01
60 9 0.09
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.45
Consensus pattern (58 bp):
TTCAATACTTCAATGTTTCAATTCCAATATTTCAATTCTTCAATTTCAATTCTTCAAG
Found at i:8271 original size:22 final size:22
Alignment explanation
Indices: 8246--8672 Score: 151
Period size: 22 Copynumber: 19.2 Consensus size: 22
8236 TCTTCAAATC
8246 CAATTCTTCAATTTCAATACTT
1 CAATTCTTCAATTTCAATACTT
* * *
8268 CAATGCTTCGATTTCAATATTT
1 CAATTCTTCAATTTCAATACTT
*
8290 CAATGT-TTCAATTTCAATTCTT
1 CAAT-TCTTCAATTTCAATACTT
*
8312 CAAATTC--CAAATGTCAATACTT
1 C-AATTCTTC-AATTTCAATACTT
* *
8334 CAATAT-TTTAATTCTTCAAATGCTT
1 CAAT-TCTTCAA-T-TTC-AATACTT
**
8359 CAA-T-TTCAATAGTTCAACGCTT
1 CAATTCTTCAAT--TTCAATACTT
*
8381 CAA--GTTCAATTTTCCAA-A-TT
1 CAATTCTTCAA-TTT-CAATACTT
8401 CAATTCTTCAATGTCTCAAT--TT
1 CAATTCTTCAAT-T-TCAATACTT
8423 CAATAT-TTCAATGCTTCAAT-C-T
1 CAAT-TCTTCAAT--TTCAATACTT
* * *
8445 CAAATCTTCAAATTCAATTCTT
1 CAATTCTTCAATTTCAATACTT
*
8467 CAATGT-TTCAATTTCAATTCTT
1 CAAT-TCTTCAATTTCAATACTT
* * *
8489 CAAATACTTCAATTTCAATCCCT
1 C-AATTCTTCAATTTCAATACTT
* * *
8512 CAATCCTTCAATTCCAATATTT
1 CAATTCTTCAATTTCAATACTT
*
8534 CAATGT-TTCAATTTCAATTCTT
1 CAAT-TCTTCAATTTCAATACTT
*
8556 CAATAT-TTCAATGCTTCAAT--GT
1 CAAT-TCTTCAAT--TTCAATACTT
** * *
8578 CAAGACTTCAATTTCGATTCTT
1 CAATTCTTCAATTTCAATACTT
* * *
8600 CGATATT-TT-ATTTTCCATGCTT
1 C-A-ATTCTTCAATTTCAATACTT
*
8622 CAATTCTTCAATGTTTCAATATTT
1 CAATTCTTCAA--TTTCAATACTT
* * * * *
8646 CAATGCCTCGATTTCATTTCTT
1 CAATTCTTCAATTTCAATACTT
8668 CAATT
1 CAATT
8673 GCAATTCTTT
Statistics
Matches: 309, Mismatches: 56, Indels: 80
0.69 0.13 0.18
Matches are distributed among these distances:
20 19 0.06
21 12 0.04
22 206 0.67
23 38 0.12
24 25 0.08
25 9 0.03
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (22 bp):
CAATTCTTCAATTTCAATACTT
Found at i:8369 original size:39 final size:38
Alignment explanation
Indices: 8224--8354 Score: 112
Period size: 36 Copynumber: 3.6 Consensus size: 38
8214 GTTTCAATTC
* *
8224 CAATATTTCAATTCTTCAAA-TCCAATTCTTCAAT--TT
1 CAATATTTCAATTCTTCAAATTCCAAAT-GTCAATACTT
* * * * * **
8260 CAATACTTCAATGCTTC-GATTTCAATATTTCAATGTTT
1 CAATATTTCAATTCTTCAAATTCCAA-ATGTCAATACTT
8298 C-A-ATTTCAATTCTTCAAATTCCAAATGTCAATACTT
1 CAATATTTCAATTCTTCAAATTCCAAATGTCAATACTT
*
8334 CAATATTTTAATTCTTCAAAT
1 CAATATTTCAATTCTTCAAAT
8355 GCTTCAATTT
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
35 1 0.01
36 46 0.61
37 9 0.12
38 19 0.25
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.44
Consensus pattern (38 bp):
CAATATTTCAATTCTTCAAATTCCAAATGTCAATACTT
Found at i:8420 original size:83 final size:82
Alignment explanation
Indices: 8256--8447 Score: 205
Period size: 83 Copynumber: 2.4 Consensus size: 82
8246 CAATTCTTCA
* * * * *
8256 ATTTCAATACTTCAATGCTTCGATTTCAATATTTCAATGTTTCAATTTCAATTCTTCAAATTCCA
1 ATTTCAATACTTCAATGCTTCAATTTCAATAGTTCAACGCTTCAAGTTCAATTCTTCAAATTCCA
8321 AATGTCAATACTTCAAT
66 AATGTCAATACTTCAAT
* *
8338 ATTTTAATTCTTCAAATGCTTCAATTTCAATAGTTCAACGCTTCAAGTTCAATT-TTCCAAATT-
1 ATTTCAATACTTC-AATGCTTCAATTTCAATAGTTCAACGCTTCAAGTTCAATTCTT-CAAATTC
* * *
8401 CAATTCTTCAAT-GTCTC-A-
64 CAAAT-GTCAATACT-TCAAT
* *
8419 ATTTCAATATTTCAATGCTTCAATCTCAA
1 ATTTCAATACTTCAATGCTTCAATTTCAA
8448 ATCTTCAAAT
Statistics
Matches: 92, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
80 15 0.16
81 10 0.11
82 19 0.21
83 48 0.52
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.42
Consensus pattern (82 bp):
ATTTCAATACTTCAATGCTTCAATTTCAATAGTTCAACGCTTCAAGTTCAATTCTTCAAATTCCA
AATGTCAATACTTCAAT
Found at i:8461 original size:36 final size:36
Alignment explanation
Indices: 8416--8493 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
8406 CTTCAATGTC
*
8416 TCAATTTCAATAT-TTCAATGCTTCAATCTCAAATCT
1 TCAAATTCAAT-TCTTCAATGCTTCAATCTCAAATCT
* * *
8452 TCAAATTCAATTCTTCAATGTTTCAATTTCAATTCT
1 TCAAATTCAATTCTTCAATGCTTCAATCTCAAATCT
8488 TCAAAT
1 TCAAAT
8494 ACTTCAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 1 0.03
36 36 0.97
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.44
Consensus pattern (36 bp):
TCAAATTCAATTCTTCAATGCTTCAATCTCAAATCT
Found at i:8536 original size:30 final size:29
Alignment explanation
Indices: 8500--8567 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
8490 AAATACTTCA
8500 ATTTCAATCCCTCAATCCTTCAATTC-CAAT
1 ATTTCAATCCCTCAAT--TTCAATTCTCAAT
***
8530 ATTTCAATGTTTCAATTTCAATTCTTCAAT
1 ATTTCAATCCCTCAATTTCAATTC-TCAAT
8560 ATTTCAAT
1 ATTTCAAT
8568 GCTTCAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 8 0.24
30 25 0.76
ACGTcount: A:0.31, C:0.24, G:0.01, T:0.44
Consensus pattern (29 bp):
ATTTCAATCCCTCAATTTCAATTCTCAAT
Found at i:8576 original size:8 final size:7
Alignment explanation
Indices: 8074--8575 Score: 75
Period size: 8 Copynumber: 68.4 Consensus size: 7
8064 CTTAATTCCA
8074 AATCTTC
1 AATCTTC
8081 AATACTTC
1 AAT-CTTC
8089 AAT-TTC
1 AATCTTC
8095 AATTCTTC
1 AA-TCTTC
*
8103 AATGTT-
1 AATCTTC
8109 --TCTTTC
1 AATC-TTC
*
8115 AATTCTTT
1 AA-TCTTC
8123 AATGCTTC
1 AAT-CTTC
*
8131 AGT-TTC
1 AATCTTC
*
8137 AATATTTC
1 AAT-CTTC
8145 AATGCTTC
1 AAT-CTTC
8153 AAT-TTC
1 AATCTTC
8159 AATTCTTC
1 AA-TCTTC
*
8167 AATATTTC
1 AAT-CTTC
*
8175 AATGCTCC
1 AAT-CTTC
*
8183 GAT-TTC
1 AATCTTC
8189 AATTCTTC
1 AA-TCTTC
*
8197 AA-GTTC
1 AATCTTC
*
8203 AGTCCTTC
1 AAT-CTTC
* *
8211 TATGTTTC
1 AAT-CTTC
*
8219 AAT-TCC
1 AATCTTC
*
8225 AATATTTC
1 AAT-CTTC
8233 AATTCTTC
1 AA-TCTTC
8241 AAATC--C
1 -AATCTTC
8247 AATTCTTC
1 AA-TCTTC
8255 AAT-TTC
1 AATCTTC
8261 AATACTTC
1 AAT-CTTC
8269 AATGCTTC
1 AAT-CTTC
*
8277 GAT-TTC
1 AATCTTC
*
8283 AATATTTC
1 AAT-CTTC
*
8291 AATGTTTC
1 AAT-CTTC
8299 AAT-TTC
1 AATCTTC
8305 AATTCTTC
1 AA-TCTTC
*
8313 AAAT-TCC
1 -AATCTTC
*
8320 AAAT-GTC
1 -AATCTTC
8327 AATACTTC
1 AAT-CTTC
* *
8335 AATATTTT
1 AAT-CTTC
8343 AATTCTTC
1 AA-TCTTC
8351 AAATGCTTC
1 -AAT-CTTC
8360 AAT-TTC
1 AATCTTC
*
8366 AATAGTTC
1 AAT-CTTC
*
8374 AACGCTTC
1 AA-TCTTC
*
8382 AA-GTTC
1 AATCTTC
*
8388 AATTTTCC
1 AATCTT-C
*
8396 AA-ATTC
1 AATCTTC
8402 AATTCTTC
1 AA-TCTTC
*
8410 AATGTCTC
1 AATCT-TC
8418 AAT-TTC
1 AATCTTC
*
8424 AATATTTC
1 AAT-CTTC
8432 AATGCTTC
1 AAT-CTTC
8440 AATC-TC
1 AATCTTC
8446 AAATCTTC
1 -AATCTTC
*
8454 AA-ATTC
1 AATCTTC
8460 AATTCTTC
1 AA-TCTTC
*
8468 AATGTTTC
1 AAT-CTTC
8476 AAT-TTC
1 AATCTTC
8482 AATTCTTC
1 AA-TCTTC
8490 AAATACTTC
1 -AAT-CTTC
8499 AAT-TTC
1 AATCTTC
*
8505 AATCCCTC
1 AAT-CTTC
8513 AATCCTTC
1 AAT-CTTC
*
8521 AAT-TCC
1 AATCTTC
*
8527 AATATTTC
1 AAT-CTTC
*
8535 AATGTTTC
1 AAT-CTTC
8543 AAT-TTC
1 AATCTTC
8549 AATTCTTC
1 AA-TCTTC
*
8557 AATATTTC
1 AAT-CTTC
8565 AATGCTTC
1 AAT-CTTC
8573 AAT
1 AAT
8576 GTCAAGACTT
Statistics
Matches: 374, Mismatches: 58, Indels: 125
0.67 0.10 0.22
Matches are distributed among these distances:
4 1 0.00
5 4 0.01
6 96 0.26
7 38 0.10
8 215 0.57
9 20 0.05
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (7 bp):
AATCTTC
Found at i:8588 original size:44 final size:42
Alignment explanation
Indices: 8421--8726 Score: 146
Period size: 44 Copynumber: 7.1 Consensus size: 42
8411 ATGTCTCAAT
* *
8421 TTCAATATTTCAATGCTTCAATCTCAA-ATCTTCAAATTCAATTC
1 TTCAATATTTCAAT--TTCAATTTCAAGA-CTTCAATTTCAATTC
* * *
8465 TTCAATGTTTCAATTTCAATTCTTCAAATACTTCAATTTCAATCC
1 TTCAATATTTCAATTTCAA-T-TTC-AAGACTTCAATTTCAATTC
* ** * *
8510 CTCAATCCTTCAATTCCAATATTTCAATG-TTTCAATTTCAATTC
1 TTCAATATTTCAATTTC-A-ATTTCAA-GACTTCAATTTCAATTC
* *
8554 TTCAATATTTCAATGCTTCAATGTCAAGACTTCAATTTCGATTC
1 TTCAATATTTCAAT--TTCAATTTCAAGACTTCAATTTCAATTC
* * * *
8598 TTCGATATTT-TA-TT---TTCCATG-CTTCAATTCTTCAATGT-
1 TTCAATATTTCAATTTCAATTTCAAGACTTCAA-T-TTCAAT-TC
* * *** *
8636 TTCAATATTTCAATGCCTCGATTTCATTTCTTCAATTGCAATTC
1 TTCAATATTTCAAT--TTCAATTTCAAGACTTCAATTTCAATTC
** * * *
8680 TTTGATGTTTCAATTTCACTTTCAATG-CGTCAATTTCAATTC
1 TTCAATATTTCAATTTCAATTTCAA-GACTTCAATTTCAATTC
8722 TTCAA
1 TTCAA
8727 ATTCAGTCCT
Statistics
Matches: 197, Mismatches: 42, Indels: 48
0.69 0.15 0.17
Matches are distributed among these distances:
36 6 0.03
37 5 0.03
38 14 0.07
39 2 0.01
40 2 0.01
42 29 0.15
43 4 0.02
44 85 0.43
45 38 0.19
46 11 0.06
47 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.45
Consensus pattern (42 bp):
TTCAATATTTCAATTTCAATTTCAAGACTTCAATTTCAATTC
Found at i:8758 original size:44 final size:43
Alignment explanation
Indices: 8699--8828 Score: 145
Period size: 44 Copynumber: 3.0 Consensus size: 43
8689 TCAATTTCAC
* *
8699 TTTCAATGCGTCAATTTCAATTCTTCAAATTCAGTCCTTCAATG
1 TTTCAATTC-TCAATTTCAATTCTTCAAATTCAATCCTTCAATG
* *
8743 TTTCAATTCTTCAATTTCAACTCTGCAAATTCAATCCTTCAATG
1 TTTCAATTC-TCAATTTCAATTCTTCAAATTCAATCCTTCAATG
* * * *
8787 TTTTAA-TCTCAATATTTCAATGCTTCAATTTCAATTCTTCAA
1 TTTCAATTCTC-A-ATTTCAATTCTTCAAATTCAATCCTTCAA
8829 ATCCCCAAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.03
43 3 0.04
44 68 0.93
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.43
Consensus pattern (43 bp):
TTTCAATTCTCAATTTCAATTCTTCAAATTCAATCCTTCAATG
Found at i:8798 original size:22 final size:22
Alignment explanation
Indices: 8773--8828 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
8763 CTCTGCAAAT
* * *
8773 TCAATCCTTCAATGTTTTAATC
1 TCAATACTTCAATGCTTCAATC
* *
8795 TCAATATTTCAATGCTTCAATT
1 TCAATACTTCAATGCTTCAATC
*
8817 TCAATTCTTCAA
1 TCAATACTTCAA
8829 ATCCCCAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (22 bp):
TCAATACTTCAATGCTTCAATC
Done.