Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010438.1 Corchorus capsularis cultivar CVL-1 contig10459, 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: 53051
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:12718 original size:14 final size:14
Alignment explanation
Indices: 12691--12719 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12681 TCGGTGTTGG
12691 TCGGTGTCGGTTTT
1 TCGGTGTCGGTTTT
12705 TCGGT-TCGGTTTT
1 TCGGTGTCGGTTTT
12718 TC
1 TC
12720 AGTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.00, C:0.17, G:0.31, T:0.52
Consensus pattern (14 bp):
TCGGTGTCGGTTTT
Found at i:12989 original size:3 final size:3
Alignment explanation
Indices: 12981--13018 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
12971 ATATATATAT
12981 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
13019 TTACTATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17150 original size:13 final size:13
Alignment explanation
Indices: 17132--17164 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17122 TTCGAGACCT
17132 TAAAAAAGAGAAA
1 TAAAAAAGAGAAA
*
17145 TAAAAAAGAGAGA
1 TAAAAAAGAGAAA
17158 -AAAAAAG
1 TAAAAAAG
17165 GGTCTTTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (13 bp):
TAAAAAAGAGAAA
Found at i:27836 original size:25 final size:25
Alignment explanation
Indices: 27808--27878 Score: 133
Period size: 25 Copynumber: 2.8 Consensus size: 25
27798 ACCTATGAAA
27808 TTGACAACATGCCCTTAATTGAGCT
1 TTGACAACATGCCCTTAATTGAGCT
*
27833 TTGACAACATGTCCTTAATTGAGCT
1 TTGACAACATGCCCTTAATTGAGCT
27858 TTGACAACATGCCCTTAATTG
1 TTGACAACATGCCCTTAATTG
27879 GTTAGGTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (25 bp):
TTGACAACATGCCCTTAATTGAGCT
Found at i:31868 original size:27 final size:27
Alignment explanation
Indices: 31826--31877 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
31816 AGCATGGTTA
31826 CCTCTCTATCCATGAGTTAGGAATAGT
1 CCTCTCTATCCATGAGTTAGGAATAGT
*
31853 CCTCTCTATCCTTGAGTTAGGAATA
1 CCTCTCTATCCATGAGTTAGGAATA
31878 ACCTAATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (27 bp):
CCTCTCTATCCATGAGTTAGGAATAGT
Found at i:32691 original size:33 final size:32
Alignment explanation
Indices: 32650--32732 Score: 148
Period size: 33 Copynumber: 2.5 Consensus size: 32
32640 CCGGGAGTTC
32650 AAAATCTCGGTTAAGTTCTTCAAAAAAAAAAA
1 AAAATCTCGGTTAAGTTCTTCAAAAAAAAAAA
32682 AAAATTCTCGGTTAAGTTCTTCAAAAAAAAAAAA
1 AAAA-TCTCGGTTAAGTTCTTC-AAAAAAAAAAA
32716 AAAATCTCGGTTAAGTT
1 AAAATCTCGGTTAAGTT
32733 GAAATCAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
32 4 0.08
33 30 0.61
34 15 0.31
ACGTcount: A:0.49, C:0.12, G:0.11, T:0.28
Consensus pattern (32 bp):
AAAATCTCGGTTAAGTTCTTCAAAAAAAAAAA
Found at i:34871 original size:2 final size:2
Alignment explanation
Indices: 34866--34912 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
34856 ATACACACAC
*
34866 AT AT AT AT AT AT AT AT AT AT AC 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 AT AT AT AT
34908 AT AT A
1 AT AT A
34913 CTAGTTTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:35026 original size:21 final size:22
Alignment explanation
Indices: 34976--35027 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
34966 ATTCATATGA
*
34976 AATTATGATAATCTCTCTATTT
1 AATTATGATAATCTCACTATTT
34998 AATTATGATAAT-TACACTATTT
1 AATTATGATAATCT-CACTATTT
*
35020 -TTTATGAT
1 AATTATGAT
35028 CCCATTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.50
Consensus pattern (22 bp):
AATTATGATAATCTCACTATTT
Found at i:35058 original size:22 final size:22
Alignment explanation
Indices: 35033--35512 Score: 169
Period size: 22 Copynumber: 21.6 Consensus size: 22
35023 ATGATCCCAT
35033 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
35055 TATGAAATTTTAATAATGATACAC
1 TATGAAATTTTGATAA-CCTTC-C
* **
35079 TATGAAATTTTGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** * *
35101 TAT-AATTTTTTTTAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* *
35122 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
35144 TAAGGAATTTTGA-AGA-TTTCAA
1 TATGAAATTTTGATA-ACCTTC-C
35166 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * ** *
35188 AATGAAACTTTGATAACCAACAA
1 TATGAAATTTTGATAACCTTC-C
*
35211 TAT-AATATGTTGATAACC-TCC
1 TATGAA-ATTTTGATAACCTTCC
* * * *
35232 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * * *
35255 TATGAAAATTTAAAAATC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
35276 ATATG-AATTATAAGTAATC-ACAC
1 -TATGAAATTTTGA-TAACCTTC-C
*
35299 TCTGAAATTTTGATAA--TTACAC
1 TATGAAATTTTGATAACCTT-C-C
* ***
35321 TATGAAATTGTGATAACCAAGC
1 TATGAAATTTTGATAACCTTCC
*
35343 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
35366 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
35389 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* * * *
35411 TATGAGATCTTGATAACATCCC
1 TATGAAATTTTGATAACCTTCC
** * *
35433 TATGATTTTTTAATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* *
35455 TATGAAATTTTGTTAATC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
35476 ATATGAAATTTTGATAACCCTCT
1 -TATGAAATTTTGATAACCTTCC
35499 TATGAAATTTTGAT
1 TATGAAATTTTGAT
35513 TTCCTCCCTG
Statistics
Matches: 333, Mismatches: 100, Indels: 50
0.69 0.21 0.10
Matches are distributed among these distances:
21 25 0.08
22 227 0.68
23 66 0.20
24 15 0.05
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:35373 original size:23 final size:23
Alignment explanation
Indices: 35342--35404 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
35332 GATAACCAAG
* * *
35342 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAACCTCC
35365 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAACCTCC
35388 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
35405 CTTTCTTATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTCC
Found at i:35425 original size:45 final size:45
Alignment explanation
Indices: 35342--35435 Score: 109
Period size: 46 Copynumber: 2.1 Consensus size: 45
35332 GATAACCAAG
* * *
35342 CTATGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTCCTATAAAATCTTGAT-AACATCC
* * * *
35388 CTATAAAATTTTGATAACT-TTCTTATGAGATCTTGATAACATCC
1 CTATAAAATTTTGATAAATCTTCCTATAAAATCTTGATAACATCC
35432 CTAT
1 CTAT
35436 GATTTTTTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 10 0.24
45 14 0.34
46 17 0.41
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (45 bp):
CTATAAAATTTTGATAAATCTTCCTATAAAATCTTGATAACATCC
Found at i:35669 original size:22 final size:22
Alignment explanation
Indices: 35644--35721 Score: 52
Period size: 22 Copynumber: 3.5 Consensus size: 22
35634 ATTTTGAACA
35644 TTTGATAACCTCTTTATAAAAT
1 TTTGATAACCTCTTTATAAAAT
* *
35666 TTTGTTGATCCT-TTTATGAAAA-
1 TTTGAT-AACCTCTTTAT-AAAAT
* * * * **
35688 TCTGATAATCACATTATATGAT
1 TTTGATAACCTCTTTATAAAAT
35710 TTTGATAACCTC
1 TTTGATAACCTC
35722 GCTTTGAAAT
Statistics
Matches: 39, Mismatches: 13, Indels: 8
0.65 0.22 0.13
Matches are distributed among these distances:
21 4 0.10
22 27 0.69
23 8 0.21
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (22 bp):
TTTGATAACCTCTTTATAAAAT
Found at i:35733 original size:22 final size:22
Alignment explanation
Indices: 35708--35761 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
35698 ACATTATATG
** * *
35708 ATTTTGATAACCTCGCTTTGAA
1 ATTTTGATAACAACACTGTGAA
*
35730 ATTTTGGTAACAACACTGTGAA
1 ATTTTGATAACAACACTGTGAA
35752 ATTTTGATAA
1 ATTTTGATAA
35762 TCCGATCTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (22 bp):
ATTTTGATAACAACACTGTGAA
Found at i:35864 original size:21 final size:23
Alignment explanation
Indices: 35840--35893 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
35830 TAACCTTCAT
* *
35840 ATGAAATTTTGA-TAATCTCC-C
1 ATGAAATTTTGAGTAACCTCCTA
*
35861 ATGAAATATT-AGTAACCTCCTA
1 ATGAAATTTTGAGTAACCTCCTA
35883 ATGAAATTTTG
1 ATGAAATTTTG
35894 TTAACAACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 16 0.62
22 9 0.35
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (23 bp):
ATGAAATTTTGAGTAACCTCCTA
Found at i:35898 original size:22 final size:20
Alignment explanation
Indices: 35825--35894 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
35815 AAATTGAGAC
* *
35825 TTTTATAACCTTCATATGAAA
1 TTTTGTAACCTCCA-ATGAAA
* *
35846 TTTTGATAATCTCCCATGAAA
1 TTTTG-TAACCTCCAATGAAA
*
35867 TATTAGTAACCTCCTAATGAAA
1 T-TTTGTAACCTCC-AATGAAA
35889 TTTTGT
1 TTTTGT
35895 TAACAACACT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 22 0.58
22 16 0.42
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (20 bp):
TTTTGTAACCTCCAATGAAA
Found at i:36009 original size:22 final size:22
Alignment explanation
Indices: 35977--36182 Score: 141
Period size: 22 Copynumber: 9.3 Consensus size: 22
35967 TTGTGATAAT
* *
35977 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
35999 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* *
36021 TAACCTGATCCTATGAAATTTTGA
1 TAACC--AACCTATGAAATTTTAA
**
36045 TAACC-ACGCTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
*
36067 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
*** * **
36089 TAACTTTCATATGAAATTTTGG
1 TAACCAACCTATGAAATTTTAA
*
36111 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* *
36133 TAACC-TCCTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * * *
36155 TAACCATCTTATGAGATTTTGA
1 TAACCAACCTATGAAATTTTAA
36177 TAACCA
1 TAACCA
36183 CATAGAGACA
Statistics
Matches: 152, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
21 4 0.03
22 125 0.82
23 4 0.03
24 19 0.12
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:36129 original size:66 final size:66
Alignment explanation
Indices: 35977--36184 Score: 231
Period size: 66 Copynumber: 3.1 Consensus size: 66
35967 TTGTGATAAT
* ** * *
35977 TAACCACCCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGATCCTATGAAATT
1 TAACCACACTATGAAATTTTGATAACCACA-CTATGAAATTTTAATAA-CT-ATCATATGAAATT
36041 TTGA
63 TTGA
* * * *
36045 TAACCACGCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTTTCATATGAAATTTTG
1 TAACCACACTATGAAATTTTGATAACCACACTATGAAATTTTAATAACTATCATATGAAATTTTG
*
36110 G
66 A
* * * * *
36111 TAACCACACTATGAAATTTTGATAACCTC-CTCATGAAATTATAATAACCATCTTATGAGATTTT
1 TAACCACACTATGAAATTTTGATAACCACACT-ATGAAATTTTAATAACTATCATATGAAATTTT
36175 GA
65 GA
36177 TAACCACA
1 TAACCACA
36185 TAGAGACAAG
Statistics
Matches: 119, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
65 2 0.02
66 75 0.63
67 2 0.02
68 39 0.33
69 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (66 bp):
TAACCACACTATGAAATTTTGATAACCACACTATGAAATTTTAATAACTATCATATGAAATTTTG
A
Found at i:36147 original size:44 final size:43
Alignment explanation
Indices: 35977--36181 Score: 189
Period size: 44 Copynumber: 4.6 Consensus size: 43
35967 TTGTGATAAT
* ** * * **
35977 TAACCACCCTATGAAATTTCAATAACCAACCTAAGAAATTTTAA
1 TAACCACACTATGAAATTTTGATAACC-TCCTATGAAATTTTGG
*
36021 TAACCTGATC-CTATGAAATTTTGATAACCACGCTATGAAATTTTGG
1 TAACC--A-CACTATGAAATTTTGATAACCTC-CTATGAAATTTTGG
* *
36067 TAACCACACTATGAAATTTTGATAACTTTCATATGAAATTTTGG
1 TAACCACACTATGAAATTTTGATAAC-CTCCTATGAAATTTTGG
* **
36111 TAACCACACTATGAAATTTTGATAACCTCCTCATGAAATTATAA
1 TAACCACACTATGAAATTTTGATAACCTCCT-ATGAAATTTTGG
* *
36155 TAACCATC-TTATGAGATTTTGATAACC
1 TAACCA-CACTATGAAATTTTGATAACC
36182 ACATAGAGAC
Statistics
Matches: 138, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
43 4 0.03
44 95 0.69
45 4 0.03
46 34 0.25
47 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.34
Consensus pattern (43 bp):
TAACCACACTATGAAATTTTGATAACCTCCTATGAAATTTTGG
Found at i:36379 original size:19 final size:20
Alignment explanation
Indices: 36348--36385 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
36338 TATTGACATT
36348 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
36367 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
36386 AATAATATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:37186 original size:6 final size:6
Alignment explanation
Indices: 37177--37222 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
37167 AGTATAGATA
*
37177 TATATC TATATC TATATC --TATC TATATC TAAATC TATACTC TATAT
1 TATATC TATATC TATATC TATATC TATATC TATATC TATA-TC TATAT
37223 AAAAGTACGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 4 0.11
6 25 0.71
7 6 0.17
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (6 bp):
TATATC
Found at i:37198 original size:16 final size:16
Alignment explanation
Indices: 37174--37213 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
37164 TATAGTATAG
*
37174 ATATATATCTATATCT
1 ATATCTATCTATATCT
37190 ATATCTATCTATATCT
1 ATATCTATCTATATCT
*
37206 AAATCTAT
1 ATATCTAT
37214 ACTCTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATCTATCTATATCT
Found at i:38283 original size:20 final size:20
Alignment explanation
Indices: 38246--38284 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
38236 TACTATTATT
38246 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
38266 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
38285 AATGTCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:38501 original size:44 final size:43
Alignment explanation
Indices: 38451--39094 Score: 204
Period size: 44 Copynumber: 15.0 Consensus size: 43
38441 GTCTCTGTGT
* * *
38451 GGTTATCAAAATTTCATAAGATGGTGATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCAT-AGGA
* * * *
38495 GGTTATCAAAATTCCAT-AGTGTGGTTACCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAAG-ATGGTTATCAAAATTTCATA-GGA
* * * *
38539 AGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATAG-GA
* * * * *
38583 GGTTACCAAAATTTCATAGGATCAAGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAAGAT--GGTTATCAAAATTTCATAGG-A
** * * * *
38629 GGTTATTGAAATTTCAT-AGTGTGGTTATCATAATTTTATAGAA
1 GGTTATCAAAATTTCATAAG-ATGGTTATCAAAATTTCATAGGA
* * *
38672 GGGT-T----A--TCA-AAGA-GATTATCAAAATGTCATAGCGA
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATAG-GA
* * *
38707 GGTTAT-AAGAATTTCAT-AGTGTGGTTAACAAAATTTCGTAAGGA
1 GGTTATCAA-AATTTCATAAG-ATGGTTATCAAAATTTCAT-AGGA
* ** *
38751 GGTTA-CTAATATTTCATGGGGA-GGTTATCAAAATTTCATAGTGT
1 GGTTATC-AAAATTTCAT-AAGATGGTTATCAAAATTTCATAG-GA
* * * * *
38795 GGTTATCAAAATTT-TTTAGTCTGGTTATTAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAAG-ATGGTTATCAAAATTTCATA-GGA
* * * *
38839 GGTTATAAAAGTCTCAATTTCATAAG--GAG-TACCAAAATTTGATAGAA
1 GGTTAT-CAA-----AATTTCATAAGATG-GTTATCAAAATTTCATAGGA
* * * *
38886 GTTTAT--AGA--T-AT-CG--GATTATCAAAATTT-ATAGGAA
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATAGG-A
* * *
38921 GATTATCAAAATTTCAT-AG-TGTTGTTATCAAAATTTCAAAGCGT
1 GGTTATCAAAATTTCATAAGATG--GTTATCAAAATTTCATAG-GA
* * *
38965 GGTTTATCAAAATTACATAATG-TGATTATCAAAATTTCATAGAGG
1 GG-TTATCAAAATTTCATAA-GATGGTTATCAAAATTTCATAG-GA
* * * * * *
39010 GGTCAACAAAATTTTATAGAGA-GGTTACCAAAATTGCATTAAGA
1 GGTTATCAAAATTTCATA-AGATGGTTATCAAAATTTCA-TAGGA
* *
39054 GGTTATCAAATTTTCA-AA-ATGTGATTACCAAAATTTCATAG
1 GGTTATCAAAATTTCATAAGATG-G-TTATCAAAATTTCATAG
39095 TCGTATTTCC
Statistics
Matches: 442, Mismatches: 99, Indels: 119
0.67 0.15 0.18
Matches are distributed among these distances:
34 19 0.04
35 22 0.05
36 8 0.02
37 3 0.01
38 1 0.00
39 2 0.00
40 4 0.01
41 2 0.00
42 9 0.02
43 27 0.06
44 231 0.52
45 48 0.11
46 33 0.07
47 11 0.02
48 13 0.03
49 1 0.00
50 5 0.01
51 3 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATAGGA
Found at i:38507 original size:22 final size:21
Alignment explanation
Indices: 38451--38682 Score: 176
Period size: 22 Copynumber: 10.5 Consensus size: 21
38441 GTCTCTGTGT
*
38451 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* * *
38472 TGGTGATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
38495 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* *
38517 GGTTACCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATA-GGA
*
38539 AGTTATCAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAGG-A
*
38561 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
38583 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* * *
38607 AGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGG-A
** *
38629 GGTTATTGAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* * *
38651 GGTTATCATAATTTTATAGAA
1 GGTTATCAAAATTTCATAGGA
38672 GGGTTATCAAA
1 -GGTTATCAAA
38683 GAGATTATCA
Statistics
Matches: 164, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
21 4 0.02
22 138 0.84
23 6 0.04
24 16 0.10
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.37
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:38553 original size:66 final size:65
Alignment explanation
Indices: 38447--38682 Score: 267
Period size: 66 Copynumber: 3.5 Consensus size: 65
38437 TCTTGTCTCT
* ** * * * *
38447 GTGTGGTTATCAAAATTTCATAAGATGGTGATTATAATTTCATGAGG-AGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCAT-AGAAAGTTATCAAAATTTCAT-AGGAAGGTTATCAAAATTTCA
38511 TA
64 TA
38513 GTGTGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT
1 GTGTGGTTACCAAAATTTCATA-GAAAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT
38578 A
65 A
* * **
38579 GTGTGGTTACCAAAATTTCATAGGATCAAGTTATTAAAATTTCTTAGGAAGGTTATTGAAATTTC
1 GTGTGGTTACCAAAATTTCATA-GA--AAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTC
38644 ATA
63 ATA
* * * *
38647 GTGTGGTTATCATAATTTTATAGAAGGGTTATCAAA
1 GTGTGGTTACCAAAATTTCATAGAA-AGTTATCAAA
38683 GAGATTATCA
Statistics
Matches: 148, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
65 5 0.03
66 85 0.57
67 2 0.01
68 56 0.38
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (65 bp):
GTGTGGTTACCAAAATTTCATAGAAAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
Found at i:38712 original size:22 final size:22
Alignment explanation
Indices: 38687--38848 Score: 127
Period size: 22 Copynumber: 7.4 Consensus size: 22
38677 ATCAAAGAGA
* *
38687 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
38709 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
38731 TTAACAAAATTTCGTAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * *
38753 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
38775 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
** **
38797 TTATCAAAATTTTTTAGTCTGG
1 TTATCAAAATTTCATAGTGAGG
*
38819 TTATTAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
38841 TTAT-AAAA
1 TTATCAAAA
38849 GTCTCAATTT
Statistics
Matches: 112, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
21 9 0.08
22 98 0.88
23 5 0.04
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:38842 original size:66 final size:65
Alignment explanation
Indices: 38692--38848 Score: 165
Period size: 66 Copynumber: 2.4 Consensus size: 65
38682 AGAGATTATC
* *
38692 AAAATGTCATAGCG-AGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCGTAAGGAGGTTA
1 AAAATTTCATAG-GAAGGTTATAA-AATTTCATAGTGTGGTTAACAAAATTTCGTAAGCAGGTTA
38756 CT
64 CT
* * * * * * *
38758 AATATTTCATGGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTT-TTTAGTCTGGTTA
1 AAAATTTCATAGGAAGGTTAT-AAAATTTCATAGTGTGGTTAACAAAATTTCGTAAG-CAGGTTA
*
38822 TT
64 CT
*
38824 AAAATTTCATATGAAGGTTATAAAA
1 AAAATTTCATAGGAAGGTTATAAAA
38849 GTCTCAATTT
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
65 8 0.11
66 65 0.87
67 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.37
Consensus pattern (65 bp):
AAAATTTCATAGGAAGGTTATAAAATTTCATAGTGTGGTTAACAAAATTTCGTAAGCAGGTTACT
Found at i:38948 original size:22 final size:23
Alignment explanation
Indices: 38900--39006 Score: 114
Period size: 22 Copynumber: 4.8 Consensus size: 23
38890 ATAGATATCG
**
38900 GATTATCAAAATTT-ATAG-GAA
1 GATTATCAAAATTTCATAGTGTT
38921 GATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAGTGTT
* * *
38944 G-TTATCAAAATTTCAAAGCGTG
1 GATTATCAAAATTTCATAGTGTT
* * *
38966 GTTTATCAAAATTACATAATG-T
1 GATTATCAAAATTTCATAGTGTT
38988 GATTATCAAAATTTCATAG
1 GATTATCAAAATTTCATAG
39007 AGGGGTCAAC
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
21 14 0.20
22 39 0.56
23 17 0.24
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (23 bp):
GATTATCAAAATTTCATAGTGTT
Found at i:39019 original size:22 final size:22
Alignment explanation
Indices: 38994--39044 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
38984 ATGTGATTAT
*
38994 CAAAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAGAGAGGTCAA
* * *
39016 CAAAATTTTATAGAGAGGTTAC
1 CAAAATTTCATAGAGAGGTCAA
39038 CAAAATT
1 CAAAATT
39045 GCATTAAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTCAA
Found at i:39422 original size:22 final size:22
Alignment explanation
Indices: 39390--39844 Score: 232
Period size: 22 Copynumber: 20.8 Consensus size: 22
39380 AAAGTTTCAG
*
39390 GGAGGATATCAAAATTTCATAT
1 GGAGGTTATCAAAATTTCATAT
*
39412 GAAGGTTATCAAAATTTCATAGT
1 GGAGGTTATCAAAATTTCATA-T
** *
39435 TTA-GTTTTCAAAATTTCATA-
1 GGAGGTTATCAAAATTTCATAT
* **
39455 AGAGAGTTATTGAAATTTCATA-
1 GGAG-GTTATCAAAATTTCATAT
* * * *
39477 GTATGTAGATCAAAATTTCATAG
1 GGAGGT-TATCAAAATTTCATAT
* * *
39500 GGAGATTAACAAAATTTCGTAAT
1 GGAGGTTATCAAAATTTCAT-AT
* *
39523 -GAGGTTATCAAAA-ATCATAG
1 GGAGGTTATCAAAATTTCATAT
39543 GGAGGTTATC-AAA----ATAT
1 GGAGGTTATCAAAATTTCATAT
* * *
39560 GTA-GTTATCAAGATTTCATAA
1 GGAGGTTATCAAAATTTCATAT
* *
39581 GGAGGTTATCAAAATTTTATAG
1 GGAGGTTATCAAAATTTCATAT
*
39603 GGAGGTTTATCAAAATTTTATA-
1 GGAGG-TTATCAAAATTTCATAT
39625 GGAAGGTTTATCAAAATTTCATA-
1 GG-AGG-TTATCAAAATTTCATAT
* *
39648 GCGAGGTTATTACAATTTCATAAT
1 G-GAGGTTATCAAAATTTCAT-AT
*
39672 GTGA--TTATCAAAATTTCAGAGT
1 G-GAGGTTATCAAAATTTCATA-T
*
39694 GTGA--TTA-CTAACAA-TTCATAC
1 G-GAGGTTATC-AA-AATTTCATAT
* * * * *
39715 GGAGATTTTTAAATTTTCATAA
1 GGAGGTTATCAAAATTTCATAT
* * *
39737 CGTGGTTATCAATATATATCATAT
1 GGAGGTTATCAA-A-ATTTCATAT
* *
39761 GGAGGTTATCAACATCTCATAGT
1 GGAGGTTATCAAAATTTCATA-T
**
39784 GTTGGTTATCAAAATTTCAT-T
1 GGAGGTTATCAAAATTTCATAT
*
39805 GGGAAGTTATCAAAATTTCATA-
1 -GGAGGTTATCAAAATTTCATAT
39827 GGAAGGTTATCAAAATTT
1 GG-AGGTTATCAAAATTT
39845 TATAAAAAGA
Statistics
Matches: 333, Mismatches: 69, Indels: 62
0.72 0.15 0.13
Matches are distributed among these distances:
16 6 0.02
17 7 0.02
20 7 0.02
21 26 0.08
22 201 0.60
23 66 0.20
24 20 0.06
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
GGAGGTTATCAAAATTTCATAT
Found at i:39608 original size:81 final size:82
Alignment explanation
Indices: 39478--39641 Score: 190
Period size: 81 Copynumber: 2.0 Consensus size: 82
39468 AATTTCATAG
* * *
39478 TATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCGTAATGAGG-TTATCAAAA-ATCAT
1 TATGTAGATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAATATCAT
*
39541 AGGGAGG-TTATCAAAA
66 AGGAAGGTTTATCAAAA
* * * * * * *
39557 TATGTAGTTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTT
1 TATGTAG--ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAATATC
39622 ATAGGAAGGTTTATCAAAA
64 ATAGGAAGGTTTATCAAAA
39641 T
1 T
39642 TTCATAGCGA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
79 7 0.10
81 34 0.49
82 9 0.13
83 9 0.13
84 10 0.14
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (82 bp):
TATGTAGATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTTATCAAAATATCAT
AGGAAGGTTTATCAAAA
Found at i:42875 original size:21 final size:21
Alignment explanation
Indices: 42810--42929 Score: 100
Period size: 22 Copynumber: 5.5 Consensus size: 21
42800 AAGGTTTGTT
* *
42810 AAAATTTCATAGTTAGGTTATC
1 AAAATTTCATAGGTA-ATTATC
* *
42832 AAAGTTTCATATGG-AGTTTATC
1 AAAATTTCATA-GGTA-ATTATC
*
42854 ACAATTTCATAGGTAATTATC
1 AAAATTTCATAGGTAATTATC
* *
42875 AAAATTTCAAAAAGTAATTATC
1 AAAATTTC-ATAGGTAATTATC
*
42897 AAAATTTAATAAGGTAATTA-C
1 AAAATTTCAT-AGGTAATTATC
42918 TAAAATTTCATA
1 -AAAATTTCATA
42930 AAAATATTAA
Statistics
Matches: 80, Mismatches: 13, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
21 17 0.21
22 62 0.77
23 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (21 bp):
AAAATTTCATAGGTAATTATC
Found at i:42925 original size:44 final size:44
Alignment explanation
Indices: 42849--42932 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
42839 CATATGGAGT
* *
42849 TTATCACAATTTCATAGGTAATTATCAAAATTTCA-AAAAGTAA
1 TTATCAAAATTTAATAGGTAATTATCAAAATTTCATAAAAGTAA
42892 TTATCAAAATTTAATAAGGTAATTA-CTAAAATTTCATAAAA
1 TTATCAAAATTTAAT-AGGTAATTATC-AAAATTTCATAAAA
42933 ATATTAAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
43 14 0.39
44 18 0.50
45 4 0.11
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTAATAGGTAATTATCAAAATTTCATAAAAGTAA
Found at i:47105 original size:51 final size:51
Alignment explanation
Indices: 47003--47105 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
46993 CATTCTTCAA
* * **
47003 TATTTCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCTTTTAGTGT
1 TATTTCCTTGTTTCAATCTTGTCTCCGAACAAAAGAACACTCGTACAGTGT
* **
47054 TATTTTCTTGTTTCAATCTTGTCTCCGAACGTAAGAACACT-GTACACGTGT
1 TATTTCCTTGTTTCAATCTTGTCTCCGAACAAAAGAACACTCGTACA-GTGT
47105 T
1 T
47106 TCTCTCTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 2 0.05
51 42 0.95
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (51 bp):
TATTTCCTTGTTTCAATCTTGTCTCCGAACAAAAGAACACTCGTACAGTGT
Found at i:52030 original size:2 final size:2
Alignment explanation
Indices: 52023--52050 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52013 TAATTTGACC
52023 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
52051 TACTTGTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52443 original size:2 final size:2
Alignment explanation
Indices: 52436--52462 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52426 TTCCGGCACC
52436 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 T
52463 TTTACGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.