Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012884.1 Corchorus capsularis cultivar CVL-1 contig12905, 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: 77944
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:5681 original size:30 final size:31
Alignment explanation
Indices: 5647--5715 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
5637 ATGCAATTTG
5647 GGATATAACGTTA-CAAAAAAAAGCAATTAA
1 GGATATAACGTTACCAAAAAAAAGCAATTAA
***
5677 GGATATAACGTTACCAAAAGCCAGCAATTAA
1 GGATATAACGTTACCAAAAAAAAGCAATTAA
5708 GGATATAA
1 GGATATAA
5716 TCCGTTAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 13 0.37
31 22 0.63
ACGTcount: A:0.51, C:0.13, G:0.16, T:0.20
Consensus pattern (31 bp):
GGATATAACGTTACCAAAAAAAAGCAATTAA
Found at i:6964 original size:31 final size:31
Alignment explanation
Indices: 6914--7054 Score: 135
Period size: 31 Copynumber: 4.6 Consensus size: 31
6904 TAGATGATAA
* * **
6914 GCAAGCAATTTA-GATATAACATTTTCTACC
1 GCAAGCAATTAAGGATATAACGTTTTCTATT
* **
6944 GCAAGCAATTAAGGATATAACG-TTAC-AAA
1 GCAAGCAATTAAGGATATAACGTTTTCTATT
* * *
6973 ACAAGCAATTCAGGATATAACGTTTTTTATT
1 GCAAGCAATTAAGGATATAACGTTTTCTATT
* * *
7004 TCGAGCAATTAAGGATATAACGTTTTCGATT
1 GCAAGCAATTAAGGATATAACGTTTTCTATT
*
7035 TCAAGCAATTAAGGATATAA
1 GCAAGCAATTAAGGATATAA
7055 TCAGTTAGAG
Statistics
Matches: 91, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
29 21 0.23
30 16 0.18
31 54 0.59
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (31 bp):
GCAAGCAATTAAGGATATAACGTTTTCTATT
Found at i:7267 original size:29 final size:31
Alignment explanation
Indices: 7201--7267 Score: 102
Period size: 29 Copynumber: 2.2 Consensus size: 31
7191 TCTAACGGAC
7201 TATATCCTTAATTGCTCGATTTTCGTAACGT
1 TATATCCTTAATTGCTCGATTTTCGTAACGT
* *
7232 TATATCCTTAATTG-TTGGTTTT-GTAACGT
1 TATATCCTTAATTGCTCGATTTTCGTAACGT
7261 TATATCC
1 TATATCC
7268 CAAATTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 6 0.18
31 14 0.41
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGATTTTCGTAACGT
Found at i:7890 original size:32 final size:33
Alignment explanation
Indices: 7849--7915 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
7839 CCATGTATTG
*
7849 AACCTTTGTGATTGTTCTGGCCAAAA-AAAAAA
1 AACCTTTGTGATTGTTCTGGCAAAAAGAAAAAA
7881 AACCTTTGTGATTGTTCTGGCAAAAAGAAAAAA
1 AACCTTTGTGATTGTTCTGGCAAAAAGAAAAAA
7914 AA
1 AA
7916 AACCTGTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 25 0.76
33 8 0.24
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (33 bp):
AACCTTTGTGATTGTTCTGGCAAAAAGAAAAAA
Found at i:7924 original size:33 final size:31
Alignment explanation
Indices: 7849--7959 Score: 100
Period size: 32 Copynumber: 3.5 Consensus size: 31
7839 CCATGTATTG
*
7849 AACCTTTGTGATTGTTCTGGCCAAAAAAAAAA
1 AACC-TTGTGATTGTTCTGGCAAAAAAAAAAA
7881 AACCTTTGTGATTGTTCTGGCAAAAAGAAAAAAAA
1 AACC-TTGTGATTGTTCTGGC--AAA-AAAAAAAA
** * * *
7916 AACC-TGTGATTG-AATGTCAGAAAAAAAAG
1 AACCTTGTGATTGTTCTGGCAAAAAAAAAAA
7945 AACCTTTGTGATTGT
1 AACC-TTGTGATTGT
7960 GTGATTGAGA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
29 11 0.16
30 2 0.03
31 8 0.12
32 24 0.36
33 8 0.12
34 2 0.03
35 12 0.18
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (31 bp):
AACCTTGTGATTGTTCTGGCAAAAAAAAAAA
Found at i:7999 original size:44 final size:44
Alignment explanation
Indices: 7936--8022 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
7926 TGAATGTCAG
7936 AAAAAAAAGAACCTTTGTGATTGTGTGATTGAGAGTGATTGTTC
1 AAAAAAAAGAACCTTTGTGATTGTGTGATTGAGAGTGATTGTTC
7980 AAAAAAAAGAACCTTTGTGATTGTGTGATTGAGAGTGATTGTT
1 AAAAAAAAGAACCTTTGTGATTGTGTGATTGAGAGTGATTGTT
8023 GGTATTCTCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (44 bp):
AAAAAAAAGAACCTTTGTGATTGTGTGATTGAGAGTGATTGTTC
Found at i:8040 original size:2 final size:2
Alignment explanation
Indices: 8033--8058 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8023 GGTATTCTCG
8033 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
8059 AATGGACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17552 original size:36 final size:35
Alignment explanation
Indices: 17512--17623 Score: 126
Period size: 36 Copynumber: 3.2 Consensus size: 35
17502 TAGATTAAAC
* *
17512 TCTTTATTAACTTCAGTTAATTACCTTGAATTAAGT
1 TCTTTATT-ACTTCACTTAATTACCCTGAATTAAGT
17548 TCTTTATT-C-T-ACTTAATTACCCTGAATTAAG-
1 TCTTTATTACTTCACTTAATTACCCTGAATTAAGT
*
17579 CCTTTTATTGACTTCACTTAATTACCCTGAATTATA-T
1 TC-TTTATT-ACTTCACTTAATTACCCTGAATTA-AGT
17616 TCTTTATT
1 TCTTTATT
17624 TTACTTAATT
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
31 1 0.02
32 25 0.38
33 1 0.02
34 2 0.03
35 1 0.02
36 33 0.51
37 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (35 bp):
TCTTTATTACTTCACTTAATTACCCTGAATTAAGT
Found at i:17574 original size:32 final size:32
Alignment explanation
Indices: 17528--17633 Score: 117
Period size: 32 Copynumber: 3.2 Consensus size: 32
17518 TTAACTTCAG
*
17528 TTAATTACCTTGAATTAAGTTCTTTATTCTAC
1 TTAATTACCCTGAATTAAGTTCTTTATTCTAC
*
17560 TTAATTACCCTGAATTAAG-CCTTTTATTGACTTCAC
1 TTAATTACCCTGAATTAAGTTC-TTTATT--C-T-AC
*
17596 TTAATTACCCTGAATTATA-TTCTTTATTTTAC
1 TTAATTACCCTGAATTA-AGTTCTTTATTCTAC
17628 TTAATT
1 TTAATT
17634 TCCTTTCCTG
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
31 1 0.02
32 32 0.51
33 1 0.02
34 1 0.02
35 1 0.02
36 25 0.40
37 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (32 bp):
TTAATTACCCTGAATTAAGTTCTTTATTCTAC
Found at i:17709 original size:36 final size:36
Alignment explanation
Indices: 17637--18021 Score: 470
Period size: 36 Copynumber: 10.7 Consensus size: 36
17627 CTTAATTTCC
* * * * * *
17637 TTTCC-TGAAATTAAGCCTGTGTCTT-TTTACTTAA
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* * *
17671 TTTCCTTGAAATTAAGCCAGTCTTTCCTTTACCTAA
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* *
17707 TTTCCTTGAAATTAAGCAAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
17743 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* * * * * *
17779 TTTTCTTGAAACTAAGCCAATTTTTTTTTTTACTTAA
1 TTTCCTTGAAACTAAGCC-AGTCTTTTCTTTACCTAG
* * * *
17816 TTTCCTTGAAATTAAACTAGTCTATTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
*
17852 TTTCCTTGAAACTAAGTCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
* *
17888 TTTCCTTGAAACTAAGCC-GATCTTTTCTTTACTTAA
1 TTTCCTTGAAACTAAGCCAG-TCTTTTCTTTACCTAG
* ** *
17924 TTTCCTTGAAATTAAGTTAGTCTATTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
17960 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
*
17996 TTTCCTTGAAACTAAGCTAGTCTTTT
1 TTTCCTTGAAACTAAGCCAGTCTTTT
18022 TTCAGTCTTC
Statistics
Matches: 301, Mismatches: 45, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
34 5 0.02
35 17 0.06
36 251 0.83
37 28 0.09
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (36 bp):
TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAG
Found at i:17787 original size:108 final size:108
Alignment explanation
Indices: 17637--18021 Score: 560
Period size: 108 Copynumber: 3.6 Consensus size: 108
17627 CTTAATTTCC
* * * * * * * *
17637 TTTCC-TGAAATTAAGCCTGTGTCTT-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTCCTT
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTCTT
* * *
17700 TACCTAATTTCCTTGAAATTAAGCAAGTCTTTTCTTTACCTAG
66 TACTTAATTTCCTTGAAATTAAGCTAGTCTATTCTTTACCTAG
* * * *
17743 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAGTTTTCTTGAAACTAAGCCAATTTTTTTTT
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCC-AGTCTTTTCT
*
17808 TTACTTAATTTCCTTGAAATTAAACTAGTCTATTCTTTACCTAG
65 TTACTTAATTTCCTTGAAATTAAGCTAGTCTATTCTTTACCTAG
*
17852 TTTCCTTGAAACTAAGTCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCC-GATCTTTTCT
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAG-TCTTTTCT
*
17916 TTACTTAATTTCCTTGAAATTAAGTTAGTCTATTCTTTACCTAG
65 TTACTTAATTTCCTTGAAATTAAGCTAGTCTATTCTTTACCTAG
*
17960 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCTAGTCTTTT
1 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTT
18022 TTCAGTCTTC
Statistics
Matches: 249, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
106 5 0.02
107 16 0.06
108 129 0.52
109 99 0.40
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (108 bp):
TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTCTT
TACTTAATTTCCTTGAAATTAAGCTAGTCTATTCTTTACCTAG
Found at i:18030 original size:11 final size:11
Alignment explanation
Indices: 18014--18272 Score: 146
Period size: 11 Copynumber: 23.5 Consensus size: 11
18004 AAACTAAGCT
*
18014 AGTCTTTTTTC
1 AGTCTTATTTC
*
18025 AGTCTTCTTTC
1 AGTCTTATTTC
* *
18036 AGTATTCTTTC
1 AGTCTTATTTC
*
18047 AGT-TTAATATC
1 AGTCTT-ATTTC
*
18058 AGTCTAATTTC
1 AGTCTTATTTC
* *
18069 AGTCTAATATC
1 AGTCTTATTTC
* * *
18080 AGTTTTTTTTT
1 AGTCTTATTTC
* **
18091 AGTCTAAGATC
1 AGTCTTATTTC
*
18102 AGTCTTTTTTC
1 AGTCTTATTTC
*
18113 AGTCTAATTTC
1 AGTCTTATTTC
* *
18124 AGTCTAATATC
1 AGTCTTATTTC
*
18135 AGTCTTATATC
1 AGTCTTATTTC
*
18146 AGTCTAATTTC
1 AGTCTTATTTC
* * *
18157 AATCTAATATC
1 AGTCTTATTTC
*
18168 AGTCTTTTTTCC
1 AGTCTTATTT-C
*
18180 AGTCTAATTTC
1 AGTCTTATTTC
* * *
18191 AATCTTCTATC
1 AGTCTTATTTC
*
18202 AGTCTAATTTC
1 AGTCTTATTTC
*
18213 AGTCTTCTATT-
1 AGTCTTAT-TTC
*
18224 AGTCTAATTTC
1 AGTCTTATTTC
* *
18235 AGTCTAACTTC
1 AGTCTTATTTC
*
18246 AGTCTTCA-ATC
1 AGTCTT-ATTTC
*
18257 AGTCTAATTTC
1 AGTCTTATTTC
18268 AGTCT
1 AGTCT
18273 AACTTTGCCT
Statistics
Matches: 188, Mismatches: 53, Indels: 14
0.74 0.21 0.05
Matches are distributed among these distances:
10 5 0.03
11 170 0.90
12 13 0.07
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (11 bp):
AGTCTTATTTC
Found at i:18059 original size:22 final size:22
Alignment explanation
Indices: 18014--18274 Score: 193
Period size: 22 Copynumber: 11.8 Consensus size: 22
18004 AAACTAAGCT
** *
18014 AGTCTTTTTTCAGTCTTCTTTC
1 AGTCTTTTTTCAGTCTAATATC
* * *
18036 AGTATTCTTTCAGTTTAATATC
1 AGTCTTTTTTCAGTCTAATATC
**
18058 AGTCTAATTTCAGTCTAATATC
1 AGTCTTTTTTCAGTCTAATATC
* * *
18080 AGTTTTTTTTTAGTCTAAGATC
1 AGTCTTTTTTCAGTCTAATATC
*
18102 AGTCTTTTTTCAGTCTAATTTC
1 AGTCTTTTTTCAGTCTAATATC
** * *
18124 AGTCTAATATCAGTCTTATATC
1 AGTCTTTTTTCAGTCTAATATC
** *
18146 AGTCTAATTTCAATCTAATATC
1 AGTCTTTTTTCAGTCTAATATC
*
18168 AGTCTTTTTTCCAGTCTAATTTC
1 AGTCTTTTTT-CAGTCTAATATC
* * * *
18191 AATCTTCTATCAGTCTAATTTC
1 AGTCTTTTTTCAGTCTAATATC
* *
18213 AGTCTTCTATT-AGTCTAATTTC
1 AGTCTT-TTTTCAGTCTAATATC
*** *
18235 AGTCTAACTTCAGTCTTCA-ATC
1 AGTCTTTTTTCAGTC-TAATATC
**
18257 AGTCTAATTTCAGTCTAA
1 AGTCTTTTTTCAGTCTAA
18275 CTTTGCCTAA
Statistics
Matches: 190, Mismatches: 45, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
21 4 0.02
22 166 0.87
23 20 0.11
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (22 bp):
AGTCTTTTTTCAGTCTAATATC
Found at i:18273 original size:11 final size:11
Alignment explanation
Indices: 18043--18274 Score: 182
Period size: 11 Copynumber: 21.0 Consensus size: 11
18033 TTCAGTATTC
*
18043 TTTCAGTTTAA
1 TTTCAGTCTAA
*
18054 TATCAGTCTAA
1 TTTCAGTCTAA
18065 TTTCAGTCTAA
1 TTTCAGTCTAA
* * **
18076 TATCAGTTTTT
1 TTTCAGTCTAA
*
18087 TTTTAGTCTAA
1 TTTCAGTCTAA
** **
18098 GATCAGTCTTT
1 TTTCAGTCTAA
18109 TTTCAGTCTAA
1 TTTCAGTCTAA
18120 TTTCAGTCTAA
1 TTTCAGTCTAA
* *
18131 TATCAGTCTTA
1 TTTCAGTCTAA
*
18142 TATCAGTCTAA
1 TTTCAGTCTAA
*
18153 TTTCAATCTAA
1 TTTCAGTCTAA
* **
18164 TATCAGTCTTT
1 TTTCAGTCTAA
18175 TTTCCAGTCTAA
1 TTT-CAGTCTAA
* **
18187 TTTCAATCTTC
1 TTTCAGTCTAA
*
18198 TATCAGTCTAA
1 TTTCAGTCTAA
**
18209 TTTCAGTCTTC
1 TTTCAGTCTAA
18220 TATT-AGTCTAA
1 T-TTCAGTCTAA
18231 TTTCAGTCTAA
1 TTTCAGTCTAA
*
18242 CTTCAGTCTTCAA
1 TTTCAGTC-T-AA
18255 --TCAGTCTAA
1 TTTCAGTCTAA
18264 TTTCAGTCTAA
1 TTTCAGTCTAA
18275 CTTTGCCTAA
Statistics
Matches: 168, Mismatches: 46, Indels: 14
0.74 0.20 0.06
Matches are distributed among these distances:
9 2 0.01
10 3 0.02
11 149 0.89
12 12 0.07
13 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.46
Consensus pattern (11 bp):
TTTCAGTCTAA
Found at i:18527 original size:41 final size:42
Alignment explanation
Indices: 18416--18550 Score: 206
Period size: 42 Copynumber: 3.3 Consensus size: 42
18406 CTGAATTAGG
* *
18416 ACTATGTTTG-CTTTTCTTAATCACCATGGATTACAACTTCA
1 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA
*
18457 ACTATGTTTAACTTTTCTTAATCACCCTGGATTACAACTTTA
1 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA
*
18499 ACTATGTTTGAC-TTTCTTAATCGCCCTGGATT--AACTTTA
1 ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA
18538 ACTATGTTTGACT
1 ACTATGTTTGACT
18551 ATCCAAATTA
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
39 19 0.22
41 28 0.32
42 40 0.46
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (42 bp):
ACTATGTTTGACTTTTCTTAATCACCCTGGATTACAACTTTA
Found at i:18699 original size:15 final size:14
Alignment explanation
Indices: 18679--18708 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
18669 CCAACTTGGG
18679 ACCTTGACTTTGCTT
1 ACCTTGACTTT-CTT
18694 ACCTTGACTTTCTT
1 ACCTTGACTTTCTT
18708 A
1 A
18709 ATTATCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.17, C:0.27, G:0.10, T:0.47
Consensus pattern (14 bp):
ACCTTGACTTTCTT
Found at i:22163 original size:24 final size:23
Alignment explanation
Indices: 22119--22165 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
22109 GTTTACACTA
22119 TCTTATTCATTCTTTCTGTATTT
1 TCTTATTCATTCTTTCTGTATTT
*
22142 TCTTACTTCCATT-TTTGTGTATTT
1 TCTTA-TT-CATTCTTTCTGTATTT
22166 GTAGTTATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.13, C:0.17, G:0.06, T:0.64
Consensus pattern (23 bp):
TCTTATTCATTCTTTCTGTATTT
Found at i:30788 original size:49 final size:48
Alignment explanation
Indices: 30725--30851 Score: 150
Period size: 49 Copynumber: 2.6 Consensus size: 48
30715 ACATTTCCTG
*
30725 CACTTTTTCTCAATTTTTGAAACAAAATTGAACCTTTAATTTTCCTCA
1 CACTTTTTCTCAATTTTTGAAACAAAATTGAACATTTAATTTTCCTCA
* * * * **
30773 CACCTTTTTCTCAATTTTT-ATGACAAAATTGAATATTTACTTTTCTTTG
1 CA-CTTTTTCTCAATTTTTGA-AACAAAATTGAACATTTAATTTTCCTCA
*
30822 CACTTTTTATCAATTTTTG-AACAAAATTGA
1 CACTTTTTCTCAATTTTTGAAACAAAATTGA
30852 TTGGCACGCT
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
47 10 0.15
48 18 0.27
49 39 0.58
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (48 bp):
CACTTTTTCTCAATTTTTGAAACAAAATTGAACATTTAATTTTCCTCA
Found at i:31692 original size:15 final size:15
Alignment explanation
Indices: 31656--31705 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
31646 TGCTAGGGTG
31656 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
* * *
31671 AACGGTGCAAATAAT
1 AATGGTGCAAACAAC
**
31686 AATGGTGTGAACAAC
1 AATGGTGCAAACAAC
31701 AATGG
1 AATGG
31706 AAACGATGCA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.18
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Found at i:33089 original size:33 final size:32
Alignment explanation
Indices: 33004--33143 Score: 111
Period size: 33 Copynumber: 4.2 Consensus size: 32
32994 AAAGGATCAT
* **
33004 GTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCAA
1 GTGGCCGG-TGTGGCCGGGCATCGCC-ATGTCGC
* * * *
33037 GTGTCCGGGTGTAGTCGGGCATGGCCATGTCGC
1 GTGGCC-GGTGTGGCCGGGCATCGCCATGTCGC
* *
33070 GTGGCCGGTGATGGCCGGGCATCTCCATGTTGC
1 GTGGCCGGTG-TGGCCGGGCATCGCCATGTCGC
* * * *
33103 ATGGCCGGTGTTGCACGGGCATCTCCAAGTCGC
1 GTGGCCGGTGTGGC-CGGGCATCGCCATGTCGC
33136 GTGGCCGG
1 GTGGCCGG
33144 ATCTCCAAGT
Statistics
Matches: 87, Mismatches: 16, Indels: 8
0.78 0.14 0.07
Matches are distributed among these distances:
32 8 0.09
33 77 0.89
34 2 0.02
ACGTcount: A:0.11, C:0.26, G:0.41, T:0.21
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATCGCCATGTCGC
Found at i:52579 original size:49 final size:48
Alignment explanation
Indices: 52509--52640 Score: 169
Period size: 49 Copynumber: 2.8 Consensus size: 48
52499 ATCTTTTACA
*
52509 TTTCC-TGCACTTTTTCTCAATTTTTATAACAAAATTGAACCTTTAAT
1 TTTCCTTGCACTTTTTCTCAATTTTTATAACAAAATTGAACATTTAAT
* * * *
52556 TTTCCTTGCACCTTTTTCTCAATTTTCATGACAAAATTGAATATTTACT
1 TTTCCTTGCA-CTTTTTCTCAATTTTTATAACAAAATTGAACATTTAAT
* * *
52605 TTTCTTTGCACTTTTTATCAATTTTT-GAACAAAATT
1 TTTCCTTGCACTTTTTCTCAATTTTTATAACAAAATT
52641 TATTGGCACG
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
47 13 0.18
48 18 0.25
49 42 0.58
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.48
Consensus pattern (48 bp):
TTTCCTTGCACTTTTTCTCAATTTTTATAACAAAATTGAACATTTAAT
Found at i:56050 original size:22 final size:22
Alignment explanation
Indices: 56010--56069 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
56000 AACTAACTTC
*
56010 TATTATTTGTAATATATACTACA
1 TATTATTTG-AATAAATACTACA
* *
56033 TCTTATTTGAATAAATACTACT
1 TATTATTTGAATAAATACTACA
56055 TATTATTTGAATAAA
1 TATTATTTGAATAAA
56070 CATATGGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 25 0.76
23 8 0.24
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (22 bp):
TATTATTTGAATAAATACTACA
Found at i:57137 original size:33 final size:33
Alignment explanation
Indices: 57070--57178 Score: 125
Period size: 33 Copynumber: 3.4 Consensus size: 33
57060 TTCTCGTCAC
* * *
57070 CCAAAACAGATTTATTTTCAATGC---CATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
57100 CCAAAACAGGATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
* ** *
57133 CCAAAACAAAATTATTTTTAATGCTATGTTCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
57166 CCAAAACAGAATT
1 CCAAAACAGAATT
57179 GTTTTCATCA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
30 21 0.32
33 45 0.68
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.29
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:57238 original size:33 final size:33
Alignment explanation
Indices: 57201--57371 Score: 193
Period size: 33 Copynumber: 5.2 Consensus size: 33
57191 ATTAGCATCC
**
57201 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATTGCAAACAACACTT
*
57234 AAAACAGATTTAGTGTCATTGCAAACAACACTT
1 AAAACAGATTTAGTATCATTGCAAACAACACTT
** * * *
57267 AAATTAGGTTTAGTATCATCGTAAACAACA-TCT
1 AAAACAGATTTAGTATCATTGCAAACAACACT-T
* *
57300 AAAACAGATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTATCATTGCAAACAACACTT
** *
57333 AAATTAGGTTTAGTATCATTGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATTGCAAACAACACT-T
57366 AAAACA
1 AAAACA
57372 TTCTCTTCAA
Statistics
Matches: 112, Mismatches: 23, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
32 2 0.02
33 109 0.97
34 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATTGCAAACAACACTT
Found at i:57293 original size:66 final size:66
Alignment explanation
Indices: 57209--57371 Score: 274
Period size: 66 Copynumber: 2.5 Consensus size: 66
57199 CCAAAACAGA
* *
57209 TTTAGTATCATCACAAACAACA-CTTAAAACAGATTTAGTGTCATTGCAAACAACACTTAAATTA
1 TTTAGTATCATCGCAAACAACATC-TAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTA
57273 GG
65 GG
*
57275 TTTAGTATCATCGTAAACAACATCTAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAG
1 TTTAGTATCATCGCAAACAACATCTAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAG
57340 G
66 G
*
57341 TTTAGTATCATTGCAAACAACATCTAAAACA
1 TTTAGTATCATCGCAAACAACATCTAAAACA
57372 TTCTCTTCAA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
66 90 0.99
67 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.29
Consensus pattern (66 bp):
TTTAGTATCATCGCAAACAACATCTAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAG
G
Found at i:58764 original size:5 final size:5
Alignment explanation
Indices: 58754--58787 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
58744 TGGTCGAAAA
58754 TTTAT TTTAT TTTAT TTTAT TTTAT TTATAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT-TAT TTT
58788 TCGATATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:58889 original size:8 final size:8
Alignment explanation
Indices: 58861--58894 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
58851 GAATCGGCTA
58861 TGAATTTT
1 TGAATTTT
*
58869 TGAAGTTTC
1 TGAA-TTTT
58878 TGAATTTT
1 TGAATTTT
58886 TGAATTTT
1 TGAATTTT
58894 T
1 T
58895 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:65570 original size:33 final size:32
Alignment explanation
Indices: 65533--65640 Score: 126
Period size: 33 Copynumber: 3.3 Consensus size: 32
65523 AAAGTATCAT
* * ** *
65533 GTGGCCGGTTGTGGCCGGGCATGTCCTTGTTGC
1 GTGGCCGG-TGTAGCCGGGCATCTCCAAGTCGC
65566 GTGGCCGGTGATAGCCGGGCATCTCCAAGTCGC
1 GTGGCCGGTG-TAGCCGGGCATCTCCAAGTCGC
* *
65599 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGTAGC-CGGGCATCTCCAAGTCGC
65632 GTGGCCGGT
1 GTGGCCGGT
65641 CACAAGTGCT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
32 5 0.08
33 60 0.92
ACGTcount: A:0.09, C:0.28, G:0.40, T:0.23
Consensus pattern (32 bp):
GTGGCCGGTGTAGCCGGGCATCTCCAAGTCGC
Found at i:66075 original size:161 final size:165
Alignment explanation
Indices: 65726--66087 Score: 484
Period size: 161 Copynumber: 2.2 Consensus size: 165
65716 TTGGCGCATC
* * * *
65726 ATTAAATAACTAGACTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAA
1 ATTAAATAACTAAACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAA
* * ** * * *
65791 GATCCCTACAAAGGCTTGCTTTTAGAGTTAGAGAACTTATTTTTTTCGTCTTTTCTTATTTGACA
66 GATCCCTACAAAGGATTGATGATAGAGTTAGAGAACTAATCTTTTTCGTCTTTACTTA--TGACA
* * * *
65856 TATTACTTAAATGTCCTAACTTTTGATTGTTGAGGGG
129 GATTACTTAAATGTCCTAACTTTTGATTCTTAAGGAG
* * *
65893 ATTAAATAAGTAATCTTTTTGGTCATTTCTTAATGGACTTGAATAGAGTAGTGGAATTAATAAAA
1 ATTAAATAACTAAACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAA
65958 GATCCC-ATC-AAGGATTGATGAT-GAGTTAGAGAACTAATCTTTTTCGTCTTTAAC-TA-G-CA
66 GATCCCTA-CAAAGGATTGATGATAGAGTTAGAGAACTAATCTTTTTCGTCTTT-ACTTATGACA
66017 GATTACTTAAATGTCCTAACTTTTGATTCTTAAGGAG
129 GATTACTTAAATGTCCTAACTTTTGATTCTTAAGGAG
66054 ATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
1 ATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
66088 TGACAAATGA
Statistics
Matches: 172, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
161 66 0.38
162 1 0.01
165 29 0.17
166 11 0.06
167 65 0.38
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (165 bp):
ATTAAATAACTAAACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAA
GATCCCTACAAAGGATTGATGATAGAGTTAGAGAACTAATCTTTTTCGTCTTTACTTATGACAGA
TTACTTAAATGTCCTAACTTTTGATTCTTAAGGAG
Found at i:67603 original size:2 final size:2
Alignment explanation
Indices: 67596--67626 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
67586 CAATTTCCAT
67596 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
67627 GTAGCAGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:70291 original size:2 final size:2
Alignment explanation
Indices: 70284--70322 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
70274 ACATTACCTC
70284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
70323 TATTTTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:71954 original size:2 final size:2
Alignment explanation
Indices: 71947--71980 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
71937 TGAGATTGCC
71947 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71981 TATTTTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73168 original size:2 final size:2
Alignment explanation
Indices: 73161--73193 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
73151 AGATTACCTC
*
73161 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73194 CACACACACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73198 original size:2 final size:2
Alignment explanation
Indices: 73193--73224 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
73183 ATGTATATAT
73193 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
73225 TATATATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:75254 original size:33 final size:32
Alignment explanation
Indices: 75213--75320 Score: 139
Period size: 33 Copynumber: 3.3 Consensus size: 32
75203 GCCGCGCAAC
*
75213 ACCGGCCACGTGACTTGGA-GATGCCCGGCCATC-
1 ACCGGCCACGTGAC-T-GACCATGCCCGGCCA-CA
75246 ACCGGCCACGTGACATGACCATGCCCGGCCACA
1 ACCGGCCACGTGAC-TGACCATGCCCGGCCACA
*
75279 ACCGGCCACATGACTCGACCATGCCCGGCCACA
1 ACCGGCCACGTGACT-GACCATGCCCGGCCACA
75312 ACCGGCCAC
1 ACCGGCCAC
75321 ACGATCCTTT
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
32 4 0.06
33 65 0.94
ACGTcount: A:0.22, C:0.43, G:0.25, T:0.10
Consensus pattern (32 bp):
ACCGGCCACGTGACTGACCATGCCCGGCCACA
Found at i:76586 original size:19 final size:19
Alignment explanation
Indices: 76564--76603 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
76554 GGTTTTCTTG
76564 TGCAATTAA-TCTAATTAAT
1 TGCAA-TAACTCTAATTAAT
*
76583 TGCAATAACTCTAATTTAT
1 TGCAATAACTCTAATTAAT
76602 TG
1 TG
76604 TGTAATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (19 bp):
TGCAATAACTCTAATTAAT
Done.