Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014928.1 Corchorus capsularis cultivar CVL-1 contig14949, 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: 42028
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3125 original size:7 final size:7
Alignment explanation
Indices: 3113--3159 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
3103 GGAGAGAAAT
3113 AGAAAGA
1 AGAAAGA
*
3120 AGAAAGC
1 AGAAAGA
*
3127 ATAAA-A
1 AGAAAGA
*
3133 AAAAAGA
1 AGAAAGA
3140 AGAAAGA
1 AGAAAGA
3147 AG-AAGA
1 AGAAAGA
3153 AGAAAGA
1 AGAAAGA
3160 GTCGAGAGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
6 10 0.30
7 23 0.70
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.02
Consensus pattern (7 bp):
AGAAAGA
Found at i:3158 original size:20 final size:20
Alignment explanation
Indices: 3107--3159 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3097 GGAACTGGAG
* *
3107 AGAAATAGAAAGAAGAAAGC
1 AGAAAAAGAAAGAAGAAAGA
* *
3127 ATAAAAAAAAAGAAGAAAGA
1 AGAAAAAGAAAGAAGAAAGA
*
3147 AGAAGAAGAAAGA
1 AGAAAAAGAAAGA
3160 GTCGAGAGAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAAAGAAGAAAGA
Found at i:10373 original size:24 final size:24
Alignment explanation
Indices: 10346--10393 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
10336 TTTTTGTTTT
* *
10346 GTATACTTTATTTAATCAACAAAA
1 GTATACTATATTTAATCAAAAAAA
* *
10370 GTATTCTATATTTATTCAAAAAAA
1 GTATACTATATTTAATCAAAAAAA
10394 ATTCAATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (24 bp):
GTATACTATATTTAATCAAAAAAA
Found at i:10397 original size:22 final size:24
Alignment explanation
Indices: 10354--10402 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
10344 TTGTATACTT
* *
10354 TATTTAATCAACAAAAGTATTCTA
1 TATTTAATCAACAAAAGAATTCAA
*
10378 TATTTATTCAA-AAAA-AATTCAA
1 TATTTAATCAACAAAAGAATTCAA
10400 TAT
1 TAT
10403 ACTTCTTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 8 0.36
23 4 0.18
24 10 0.45
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (24 bp):
TATTTAATCAACAAAAGAATTCAA
Found at i:13545 original size:22 final size:22
Alignment explanation
Indices: 13520--13576 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
13510 ATCACACTAA
13520 GAAATTTTGATAACCTACCCAC
1 GAAATTTTGATAACCTACCCAC
* * * ** *
13542 GAAATTTTAATAGCCTTCTTAT
1 GAAATTTTGATAACCTACCCAC
13564 GAAATTTTGATAA
1 GAAATTTTGATAA
13577 TGAAACTATG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
GAAATTTTGATAACCTACCCAC
Found at i:13688 original size:22 final size:22
Alignment explanation
Indices: 13648--13703 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
13638 GTTAGTTTGC
* **
13648 CTATAAAATTGTGTTAACCTC-
1 CTATAAAATTTTGAAAACCTCA
13669 CTTATAAAATTTTGAAAACCTCA
1 C-TATAAAATTTTGAAAACCTCA
*
13692 CTATTAAATTTT
1 CTATAAAATTTT
13704 AGTAAGCACA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (22 bp):
CTATAAAATTTTGAAAACCTCA
Found at i:17643 original size:13 final size:13
Alignment explanation
Indices: 17598--17644 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
17588 ATCATTTTTA
17598 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
17611 CT-TTTTACTAATT
1 CTCTTTT-CTTACT
17624 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
17638 CTCTTTT
1 CTCTTTT
17645 ATTTATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:17659 original size:29 final size:28
Alignment explanation
Indices: 17595--17672 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
17585 TTTATCATTT
*
17595 TTACTCTTTTCTTACTCT-TTTTACTAA
1 TTACACTTTTCTTACTCTCTTTTACTAA
* * *
17622 TTACTCTTTTCTTACTCTCTTTTATTTA
1 TTACACTTTTCTTACTCTCTTTTACTAA
17650 TTACCAC-TTT-TTACTCTTCTTTT
1 TTA-CACTTTTCTTACTC-TCTTTT
17673 TTCTTATACT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 24 0.53
28 19 0.42
29 2 0.04
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (28 bp):
TTACACTTTTCTTACTCTCTTTTACTAA
Found at i:17729 original size:21 final size:21
Alignment explanation
Indices: 17705--17971 Score: 175
Period size: 21 Copynumber: 12.9 Consensus size: 21
17695 ATTCTTTGAA
*
17705 TTACTGATCACCTTTTACTCT
1 TTACTGATTACCTTTTACTCT
*
17726 TTACTGATTACTATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
*
17747 TTACTAATTACCACTTTT-CTC-
1 TTACTGATTA-C-CTTTTACTCT
*
17768 TTACTGATTACTGTTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
**
17789 TTACTGATTACCTTTTACTGA
1 TTACTGATTACCTTTTACTCT
17810 TTACT-A-T---TTTT-CTCT
1 TTACTGATTACCTTTTACTCT
* *
17825 TTATTGATTACCTTCTTACTTT
1 TTACTGATTACCTT-TTACTCT
*
17847 TTACTGATTACTATTTTACTCT
1 TTACTGATTAC-CTTTTACTCT
*
17869 TTACTGATTACCATTTTGCTC-
1 TTACTGATTACC-TTTTACTCT
* * *
17890 TCATTGATTACCATTTTGCTC-
1 TTACTGATTACC-TTTTACTCT
*
17911 TTACTGATTACTATTTTAC-CTT
1 TTACTGATTAC-CTTTTACTC-T
* * * *
17933 TTACTAATTATC-ATTACTTT
1 TTACTGATTACCTTTTACTCT
*
17953 TTATTGATTACCTTTTACT
1 TTACTGATTACCTTTTACT
17972 ATTTCATTCT
Statistics
Matches: 194, Mismatches: 34, Indels: 36
0.73 0.13 0.14
Matches are distributed among these distances:
15 6 0.03
16 5 0.03
17 1 0.01
19 1 0.01
20 30 0.15
21 90 0.46
22 59 0.30
23 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (21 bp):
TTACTGATTACCTTTTACTCT
Found at i:17745 original size:22 final size:21
Alignment explanation
Indices: 17717--17929 Score: 183
Period size: 21 Copynumber: 10.3 Consensus size: 21
17707 ACTGATCACC
17717 TTTTACTCTTTACTGATTACTA
1 TTTTACTC-TTACTGATTACTA
* *
17739 TTTTACTCTTACTAATTACCA
1 TTTTACTCTTACTGATTACTA
*
17760 CTTTT-CTCTTACTGATTACTG
1 -TTTTACTCTTACTGATTACTA
17781 TTTTACTCTTACTGATTAC--
1 TTTTACTCTTACTGATTACTA
*
17800 -----CTTTTACTGATTACTA
1 TTTTACTCTTACTGATTACTA
* *
17816 TTTTTCTCTTTATTGATTACCT-
1 TTTTACTC-TTACTGATTA-CTA
* *
17838 TCTTACTTTTTACTGATTACTA
1 TTTTAC-TCTTACTGATTACTA
*
17860 TTTTACTCTTTACTGATTACCA
1 TTTTACTC-TTACTGATTACTA
* * * *
17882 TTTTGCTCTCATTGATTACCA
1 TTTTACTCTTACTGATTACTA
*
17903 TTTTGCTCTTACTGATTACTA
1 TTTTACTCTTACTGATTACTA
17924 TTTTAC
1 TTTTAC
17930 CTTTTACTAA
Statistics
Matches: 155, Mismatches: 22, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
14 13 0.08
20 4 0.03
21 77 0.50
22 58 0.37
23 3 0.02
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53
Consensus pattern (21 bp):
TTTTACTCTTACTGATTACTA
Found at i:17849 original size:44 final size:44
Alignment explanation
Indices: 17796--17970 Score: 150
Period size: 44 Copynumber: 4.1 Consensus size: 44
17786 CTCTTACTGA
* *
17796 TTACCTTTTACTGATTACTATTTTTCTCTTTATTGATTACCTTC
1 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACCTTC
*
17840 TTACTTTTTACTGATTACTATTTTACTCTTTACTGATTACCATT-
1 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACC-TTC
* * * * * * *
17884 TT-GCTCTCATTGATTACCATTTTGCTC-TTACTGATTA-CTATT
1 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACCT-TC
* * *
17926 TTACCTTTTACTAATTA-TCA--TTACTTTTTATTGATTACCTT-
1 TTACCTTTTACTGATTACT-ATTTTACTCTTTACTGATTACCTTC
17967 TTAC
1 TTAC
17971 TATTTCATTC
Statistics
Matches: 105, Mismatches: 19, Indels: 17
0.74 0.13 0.12
Matches are distributed among these distances:
40 1 0.01
41 10 0.10
42 22 0.21
43 30 0.29
44 40 0.38
45 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.54
Consensus pattern (44 bp):
TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACCTTC
Found at i:17942 original size:22 final size:22
Alignment explanation
Indices: 17796--17942 Score: 115
Period size: 22 Copynumber: 6.8 Consensus size: 22
17786 CTCTTACTGA
17796 TTACCTTTTACTGATTACTATT
1 TTACCTTTTACTGATTACTATT
* * *
17818 TT-TCTCTTTATTGATTACCT-TC
1 TTACCT-TTTACTGATTA-CTATT
*
17840 TTACTTTTTACTGATTACTATT
1 TTACCTTTTACTGATTACTATT
*
17862 TTA-CTCTTTACTGATTACCATT
1 TTACCT-TTTACTGATTACTATT
* * * * *
17884 TT-GCTCTCATTGATTACCATT
1 TTACCTTTTACTGATTACTATT
* *
17905 TT-GCTCTTACTGATTACTATT
1 TTACCTTTTACTGATTACTATT
*
17926 TTACCTTTTACTAATTA
1 TTACCTTTTACTGATTA
17943 TCATTACTTT
Statistics
Matches: 100, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
21 38 0.38
22 59 0.59
23 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (22 bp):
TTACCTTTTACTGATTACTATT
Found at i:17999 original size:15 final size:14
Alignment explanation
Indices: 17945--18001 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
17935 ACTAATTATC
*
17945 ATTACTTTTTATTG
1 ATTACTTTTTACTG
*
17959 ATTACCTTTTACT-
1 ATTACTTTTTACTG
*
17972 ATTTCATTCTTTACTG
1 ATTAC-TT-TTTACTG
17988 ATTATCTTTTTACT
1 ATTA-CTTTTTACT
18002 TTTTACTGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.12
14 12 0.35
15 12 0.35
16 5 0.15
17 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.04, T:0.60
Consensus pattern (14 bp):
ATTACTTTTTACTG
Found at i:18022 original size:21 final size:21
Alignment explanation
Indices: 17981--18083 Score: 96
Period size: 21 Copynumber: 5.2 Consensus size: 21
17971 TATTTCATTC
*
17981 TTTACTGATTATCTTTTTACTT
1 TTTACTGATTA-CTCTTTACTT
* *
18003 TTTACTGATTACCCTTTACTC
1 TTTACTGATTACTCTTTACTT
* *
18024 TTTAC-CA-T--TC-TT-C-C
1 TTTACTGATTACTCTTTACTT
18038 TTTACTGATTACTCTTTACTT
1 TTTACTGATTACTCTTTACTT
18059 TTTACTGATT-CTCTTTACTT
1 TTTACTGATTACTCTTTACTT
18079 TTTAC
1 TTTAC
18084 CATTTTTCTG
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
14 6 0.09
15 2 0.03
16 3 0.04
17 1 0.01
18 2 0.03
19 3 0.04
20 17 0.25
21 22 0.33
22 11 0.16
ACGTcount: A:0.17, C:0.22, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTACTGATTACTCTTTACTT
Found at i:18074 original size:20 final size:21
Alignment explanation
Indices: 18038--18083 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
18028 CCATTCTTCC
18038 TTTACTGATTACTCTTTACTT
1 TTTACTGATTACTCTTTACTT
18059 TTTACTGATT-CTCTTTACTT
1 TTTACTGATTACTCTTTACTT
18079 TTTAC
1 TTTAC
18084 CATTTTTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.17, C:0.20, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTACTGATTACTCTTTACTT
Found at i:18095 original size:49 final size:51
Alignment explanation
Indices: 17932--18111 Score: 174
Period size: 51 Copynumber: 3.5 Consensus size: 51
17922 TATTTTACCT
* * * *
17932 TTTACTAATTA-TCATTACTTTTTATTGATTACCTTTTACTATTT--CATTC
1 TTTACTGATTACTCTTTACTTTTTACTGATTACC-TTTACTTTTTACCATTC
* *
17981 TTTACTGATTATCTTTTTACTTTTTACTGATTACCCTTTACTCTTTACCATTCTTCC
1 TTTACTGATTA-CTCTTTACTTTTTACTGATTA-CCTTTACTTTTTACCA---TT-C
18038 TTTACTGATTACTCTTTACTTTTTACTGATT-CTCTTTACTTTTTACCATT-
1 TTTACTGATTACTCTTTACTTTTTACTGATTAC-CTTTACTTTTTACCATTC
18088 TTT-CTGATTACTTCTTTTACTTTT
1 TTTACTGATTAC-TC-TTTACTTTT
18112 GCTCTTTGGC
Statistics
Matches: 112, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
49 18 0.16
50 5 0.04
51 35 0.31
52 4 0.04
53 2 0.02
54 1 0.01
55 14 0.12
56 21 0.19
57 12 0.11
ACGTcount: A:0.19, C:0.20, G:0.03, T:0.58
Consensus pattern (51 bp):
TTTACTGATTACTCTTTACTTTTTACTGATTACCTTTACTTTTTACCATTC
Found at i:18135 original size:113 final size:113
Alignment explanation
Indices: 18080--18283 Score: 295
Period size: 113 Copynumber: 1.8 Consensus size: 113
18070 TCTTTACTTT
*
18080 TTACCATTTTTCTGATTAC-TTCTTTTACTTTTGCTCTTTGGCTTTTACTGATTACTTCTTTTAC
1 TTACCATTTTTCTGATTACTTTCTTTTACTTTTGCTCTTTGACTTTTACTGATTACTTCTTTTAC
** *
18144 TTTTACTCATTTTACTGATTATTTCTTCTACTGATTACTTCCTCTTGA
66 CATTACTCACTTTACTGATTATTTCTTCTACTGATTACTTCCTCTTGA
* * *
18192 TTACCATTTTTCTGATTACTTTTTTTTACTTTTGCTCTTTTACTTTTACTGATTAGTTCTTTTAC
1 TTACCATTTTTCTGATTACTTTCTTTTACTTTTGCTCTTTGACTTTTACTGATTACTTCTTTTAC
** *
18257 GTTTACTC-CTTTTACTGATTACTTCTT
66 CATTACTCAC-TTTACTGATTATTTCTT
18284 TTGTTTTAAC
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
112 19 0.23
113 64 0.77
ACGTcount: A:0.16, C:0.20, G:0.07, T:0.58
Consensus pattern (113 bp):
TTACCATTTTTCTGATTACTTTCTTTTACTTTTGCTCTTTGACTTTTACTGATTACTTCTTTTAC
CATTACTCACTTTACTGATTATTTCTTCTACTGATTACTTCCTCTTGA
Found at i:18142 original size:16 final size:16
Alignment explanation
Indices: 18121--18285 Score: 94
Period size: 16 Copynumber: 10.3 Consensus size: 16
18111 TGCTCTTTGG
18121 CTTTTACTGATTACTT
1 CTTTTACTGATTACTT
*
18137 CTTTTACT-TTTAC-T
1 CTTTTACTGATTACTT
*
18151 CATTTTACTGATTATTT
1 C-TTTTACTGATTACTT
*
18168 CTTCTACTGATTACTT
1 CTTTTACTGATTACTT
* *
18184 CCTCT--TGATTAC--
1 CTTTTACTGATTACTT
*
18196 CATTTTTCTGATTACTTT
1 C-TTTTACTGATTAC-TT
* * *
18214 TTTTTACTTTTGCTCT-TTT
1 CTTTTAC---TGAT-TACTT
*
18233 ACTTTTACTGATTAGTT
1 -CTTTTACTGATTACTT
* *
18250 CTTTTAC-GTTTACTC
1 CTTTTACTGATTACTT
18265 CTTTTACTGATTACTT
1 CTTTTACTGATTACTT
18281 CTTTT
1 CTTTT
18286 GTTTTAACTC
Statistics
Matches: 113, Mismatches: 20, Indels: 32
0.68 0.12 0.19
Matches are distributed among these distances:
12 1 0.01
13 2 0.02
14 9 0.08
15 30 0.27
16 47 0.42
17 12 0.11
19 2 0.02
20 9 0.08
21 1 0.01
ACGTcount: A:0.16, C:0.19, G:0.06, T:0.58
Consensus pattern (16 bp):
CTTTTACTGATTACTT
Found at i:18245 original size:37 final size:37
Alignment explanation
Indices: 18215--18324 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 37
18205 GATTACTTTT
* *
18215 TTTTACTTTTGCT-CTTTTACTTTTACTGATTAGTTC
1 TTTTACGTTTACTCCTTTTACTTTTACTGATTAGTTC
*
18251 TTTTACGTTTACT-C-----CTTTTACTGATTACTTC
1 TTTTACGTTTACTCCTTTTACTTTTACTGATTAGTTC
* *
18282 TTTT--GTTTTAACTCCTTTTACTTCTACTGATTACTTC
1 TTTTACG-TTT-ACTCCTTTTACTTTTACTGATTAGTTC
18319 TTTTAC
1 TTTTAC
18325 TTCTTACTAG
Statistics
Matches: 60, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
29 1 0.02
30 3 0.05
31 23 0.38
32 1 0.02
36 12 0.20
37 20 0.33
ACGTcount: A:0.15, C:0.20, G:0.06, T:0.58
Consensus pattern (37 bp):
TTTTACGTTTACTCCTTTTACTTTTACTGATTAGTTC
Found at i:18271 original size:31 final size:31
Alignment explanation
Indices: 18234--18303 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
18224 TGCTCTTTTA
*
18234 CTTTTACTGATTAGTTCTTTTACG-TTT-ACTC
1 CTTTTACTGATTACTTCTTTT--GTTTTAACTC
18265 CTTTTACTGATTACTTCTTTTGTTTTAACTC
1 CTTTTACTGATTACTTCTTTTGTTTTAACTC
18296 CTTTTACT
1 CTTTTACT
18304 TCTACTGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 1 0.03
30 3 0.08
31 32 0.89
ACGTcount: A:0.16, C:0.20, G:0.07, T:0.57
Consensus pattern (31 bp):
CTTTTACTGATTACTTCTTTTGTTTTAACTC
Found at i:18397 original size:24 final size:25
Alignment explanation
Indices: 18370--18426 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
18360 TCTCTTACTT
*
18370 TGAATCTCAATTTCCACTTTAA-TA
1 TGAATCTCAATTACCACTTTAATTA
*
18394 TGAATCTTAATTACCACTTTAATTA
1 TGAATCTCAATTACCACTTTAATTA
*
18419 TCAATCTC
1 TGAATCTC
18427 TTCTTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (25 bp):
TGAATCTCAATTACCACTTTAATTA
Found at i:18802 original size:37 final size:37
Alignment explanation
Indices: 18761--18841 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
18751 TCGCTTTTTA
* *
18761 CTTAATTACTGATTTACTGATTACTATTACTTTGACT
1 CTTAATTACTGAATTACTGATTACCATTACTTTGACT
* *
18798 CTTAATCACTTAATTACTGATTACCATTACTTTGACT
1 CTTAATTACTGAATTACTGATTACCATTACTTTGACT
18835 CTTAATT
1 CTTAATT
18842 TATTGGAGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (37 bp):
CTTAATTACTGAATTACTGATTACCATTACTTTGACT
Found at i:18821 original size:52 final size:52
Alignment explanation
Indices: 18650--18804 Score: 292
Period size: 52 Copynumber: 3.0 Consensus size: 52
18640 TGATTACTAT
*
18650 CTTTTTACTTGATTACTGATTTACTGATTACTATTACTTTGAATCTTAATCG
1 CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGAATCTTAATCG
18702 CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGAATCTTAATCG
1 CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGAATCTTAATCG
*
18754 CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTTAATC
1 CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGAATCTTAATC
18805 ACTTAATTAC
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 101 1.00
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.50
Consensus pattern (52 bp):
CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGAATCTTAATCG
Found at i:20364 original size:18 final size:19
Alignment explanation
Indices: 20317--20364 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
20307 TTTTCTCCAA
*
20317 CTCCCCTTTTTCTTCCTTT
1 CTCCCTTTTTTCTTCCTTT
*
20336 CCCCCTTTTTTCTTCCTTT
1 CTCCCTTTTTTCTTCCTTT
20355 -TCCCTTTTTT
1 CTCCCTTTTTT
20365 TTGCCCCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (19 bp):
CTCCCTTTTTTCTTCCTTT
Found at i:20366 original size:20 final size:19
Alignment explanation
Indices: 20319--20364 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
20309 TTCTCCAACT
20319 CCCC-TTTTTCTTCCTTTC
1 CCCCTTTTTTCTTCCTTTC
20337 CCCCTTTTTTCTTCCTTT-
1 CCCCTTTTTTCTTCCTTTC
*
20355 TCCCTTTTTT
1 CCCCTTTTTT
20365 TTGCCCCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (19 bp):
CCCCTTTTTTCTTCCTTTC
Found at i:22083 original size:22 final size:22
Alignment explanation
Indices: 22058--22101 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
22048 AGGAGACCAT
*
22058 AAGTAGAGAAGACACAATGCAA
1 AAGTAAAGAAGACACAATGCAA
22080 AAGTAAAGAAGACACAATGCAA
1 AAGTAAAGAAGACACAATGCAA
22102 TTTAGTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.20, T:0.09
Consensus pattern (22 bp):
AAGTAAAGAAGACACAATGCAA
Found at i:25274 original size:13 final size:13
Alignment explanation
Indices: 25256--25281 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25246 ATGTTGGAGG
25256 GTTTTCTTTAATT
1 GTTTTCTTTAATT
25269 GTTTTCTTTAATT
1 GTTTTCTTTAATT
25282 TTCTTGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
GTTTTCTTTAATT
Found at i:30426 original size:11 final size:11
Alignment explanation
Indices: 30410--30441 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
30400 AAAGTTCGTG
30410 TTTGAAGATTA
1 TTTGAAGATTA
*
30421 TTTGAAGATAA
1 TTTGAAGATTA
30432 TTTGAAGATT
1 TTTGAAGATT
30442 TGAAGACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:32358 original size:6 final size:6
Alignment explanation
Indices: 32321--32356 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
32311 GAGGCAACCC
* *
32321 AATTTT AATTTT AATTTT AATTTT AGTTTT TATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
32357 TAGGTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (6 bp):
AATTTT
Found at i:36845 original size:13 final size:13
Alignment explanation
Indices: 36827--36852 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36817 ATGTTGGAGG
36827 GTTTTCTTTAATT
1 GTTTTCTTTAATT
36840 GTTTTCTTTAATT
1 GTTTTCTTTAATT
36853 TTCTTGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
GTTTTCTTTAATT
Found at i:40045 original size:12 final size:12
Alignment explanation
Indices: 40028--40094 Score: 89
Period size: 12 Copynumber: 5.5 Consensus size: 12
40018 TTAATACAGG
40028 TATCGACGGATA
1 TATCGACGGATA
40040 TATCGAACGGATA
1 TATCG-ACGGATA
*
40053 TATCGATGGATA
1 TATCGACGGATA
* *
40065 TATCGATGTATA
1 TATCGACGGATA
*
40077 TATCGACGAATA
1 TATCGACGGATA
40089 TATCGA
1 TATCGA
40095 GGTATCGATG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
12 38 0.76
13 12 0.24
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (12 bp):
TATCGACGGATA
Done.