Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008490.1 Corchorus capsularis cultivar CVL-1 contig08511, 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: 71401
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2336 original size:2 final size:2
Alignment explanation
Indices: 2329--2354 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2319 CAATGCTTTC
2329 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
2355 GAAAGAAAGT
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):
AT
Found at i:3916 original size:35 final size:35
Alignment explanation
Indices: 3877--3965 Score: 151
Period size: 35 Copynumber: 2.5 Consensus size: 35
3867 TGAGGAGAAT
3877 AAAGGCTAGACAAAACCCAAATATTAATGTCAAAA
1 AAAGGCTAGACAAAACCCAAATATTAATGTCAAAA
*
3912 AAAGGCTAGACAAAACCCAAATGTTAATGTCAAAA
1 AAAGGCTAGACAAAACCCAAATATTAATGTCAAAA
* *
3947 AAGGGTTAGACAAAACCCA
1 AAAGGCTAGACAAAACCCA
3966 CTCTGCCAGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.16
Consensus pattern (35 bp):
AAAGGCTAGACAAAACCCAAATATTAATGTCAAAA
Found at i:9952 original size:31 final size:30
Alignment explanation
Indices: 9914--10018 Score: 122
Period size: 31 Copynumber: 3.5 Consensus size: 30
9904 ACTATAGGCT
* * *
9914 AAATGCTCAATTTGGTACCAAACCTTTGACG
1 AAATGCTCAATTTGATACTAAACCTTTCA-G
*
9945 AAATGCTCAATTTGATACTAAACC-TTCAA
1 AAATGCTCAATTTGATACTAAACCTTTCAG
*
9974 AAATGCTCAATTTGATACTAAACCTTTTAGG
1 AAATGCTCAATTTGATACTAAACCTTTCA-G
**
10005 ATCTGCTCAATTTG
1 AAATGCTCAATTTG
10019 GTACGATTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 24 0.38
30 6 0.09
31 34 0.53
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.33
Consensus pattern (30 bp):
AAATGCTCAATTTGATACTAAACCTTTCAG
Found at i:9987 original size:29 final size:30
Alignment explanation
Indices: 9914--9999 Score: 120
Period size: 29 Copynumber: 2.9 Consensus size: 30
9904 ACTATAGGCT
* * * *
9914 AAATGCTCAATTTGGTACCAAACCTTTGACG
1 AAATGCTCAATTTGATACTAAACC-TTCACA
9945 AAATGCTCAATTTGATACTAAACCTTCA-A
1 AAATGCTCAATTTGATACTAAACCTTCACA
9974 AAATGCTCAATTTGATACTAAACCTT
1 AAATGCTCAATTTGATACTAAACCTT
10000 TTAGGATCTG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 26 0.51
30 3 0.06
31 22 0.43
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.31
Consensus pattern (30 bp):
AAATGCTCAATTTGATACTAAACCTTCACA
Found at i:11870 original size:29 final size:30
Alignment explanation
Indices: 11812--11916 Score: 122
Period size: 31 Copynumber: 3.5 Consensus size: 30
11802 GAAATCGTAC
* * *
11812 CAAATTGAGCAAATCCTGAAAGGTTTAGTAT
1 CAAATTGAGC-ATTTCTCAAAGGTTTAGTAT
**
11843 CAAATTGAGCATTT-TTGAAGGTTTAGTAT
1 CAAATTGAGCATTTCTCAAAGGTTTAGTAT
* *
11872 CAAATTGAGCATTTCGTCAAAGGTTTGGTAC
1 CAAATTGAGCATTTC-TCAAAGGTTTAGTAT
11903 CAAATTGAGCATTT
1 CAAATTGAGCATTT
11917 AGCCATAAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 27 0.42
30 2 0.03
31 35 0.55
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.34
Consensus pattern (30 bp):
CAAATTGAGCATTTCTCAAAGGTTTAGTAT
Found at i:12517 original size:13 final size:13
Alignment explanation
Indices: 12499--12523 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12489 TCACCCATAA
12499 GTTTTTTTTTTTT
1 GTTTTTTTTTTTT
12512 GTTTTTTTTTTT
1 GTTTTTTTTTTT
12524 GAGAAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
GTTTTTTTTTTTT
Found at i:19394 original size:14 final size:14
Alignment explanation
Indices: 19375--19401 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19365 AAAATTCTAG
19375 TTATTATTATTATA
1 TTATTATTATTATA
19389 TTATTATTATTAT
1 TTATTATTATTAT
19402 CATGACACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:19668 original size:38 final size:38
Alignment explanation
Indices: 19582--19657 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
19572 CCGTTAAACC
* *
19582 TCGCATGTATAGTCTAGTCTGTTAAATTCCACTCACAA
1 TCGCATGTGTAGTCTAGTCTGCTAAATTCCACTCACAA
19620 TCGCATGTGTAGTCTAGGT-TGCTAAATTCCACTCACAA
1 TCGCATGTGTAGTCTA-GTCTGCTAAATTCCACTCACAA
19658 CGTATAGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 33 0.94
39 2 0.06
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (38 bp):
TCGCATGTGTAGTCTAGTCTGCTAAATTCCACTCACAA
Found at i:19789 original size:159 final size:159
Alignment explanation
Indices: 19459--19778 Score: 538
Period size: 159 Copynumber: 2.0 Consensus size: 159
19449 CCGTTAAATC
19459 TCGCATGTGTAGTCTAATCTGCTAAATTCCACTCACAACGTACGTATAGTGTATTGTATAATTTT
1 TCGCATGTGTAGTCTAATCTGCTAAATTCCACTCACAAC--ACGTATAGTGTATTGTATAATTTT
19524 CCTATTATTTTTTTTTGCTACTCATGAACATCATATTGAAATGGACTACCGTTAAACCTCGCATG
64 CCTATTATTTTTTTTTGCTACTCATGAACATCATATTGAAATGGACTACCGTTAAACCTCGCATG
*
19589 TATAGTCTAGTCTGTTAAATTCCACTCACAA
129 TATAGTCTAGTCTGCTAAATTCCACTCACAA
*
19620 TCGCATGTGTAGTCTAGGT-TGCTAAATTCCACTCAC-A-ACGTATAGTGTATTGTATAATTTTC
1 TCGCATGTGTAGTCTA-ATCTGCTAAATTCCACTCACAACACGTATAGTGTATTGTATAATTTTC
*
19682 CTATTATTTTTTTTTTTGCTACTCATGGACATCATATTGAAATGGACTACCGTTAAACCTCGCAT
65 CTATTA--TTTTTTTTTGCTACTCATGAACATCATATTGAAATGGACTACCGTTAAACCTCGCAT
*
19747 GTGTAGTCTAGTCTGCTAAATTCCACTCACAA
128 GTATAGTCTAGTCTGCTAAATTCCACTCACAA
19779 CGTATAGTGT
Statistics
Matches: 152, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
157 31 0.20
159 86 0.57
160 1 0.01
161 33 0.22
162 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (159 bp):
TCGCATGTGTAGTCTAATCTGCTAAATTCCACTCACAACACGTATAGTGTATTGTATAATTTTCC
TATTATTTTTTTTTGCTACTCATGAACATCATATTGAAATGGACTACCGTTAAACCTCGCATGTA
TAGTCTAGTCTGCTAAATTCCACTCACAA
Found at i:19903 original size:124 final size:119
Alignment explanation
Indices: 19620--19969 Score: 578
Period size: 124 Copynumber: 2.9 Consensus size: 119
19610 CCACTCACAA
19620 TCGCATGTGTAGTCTAGGT-TGCTAAATTCCACTCACAACGTATAGTGTATTGTATAATTTTCCT
1 TCGCATGTGTAGTCTA-GTCTGCTAAATTCCACTCACAACGTATAGTGTATTGTATAATTTTCCT
*
19684 ATTATTTTTTTTTTTGCTACTCATGGACATCATATTGAAAT-GGACTACCGTTAAACC
65 ATTA---TTTTTTTTGCTACTCATGAACATCATATTGAAATGGGACTACCGTTAAACC
19741 TCGCATGTGTAGTCTAGTCTGCTAAATTCCACTCACAACGTATAGTGTATTGTATAATTTTCCTA
1 TCGCATGTGTAGTCTAGTCTGCTAAATTCCACTCACAACGTATAGTGTATTGTATAATTTTCCTA
*
19806 TTATTTTTTTTACTACTCATGAACATCATATTGAAATGGGTTAGGGCTACCGTTAAACC
66 TTATTTTTTTTGCTACTCATGAACATCATATTGAAATGGG--A---CTACCGTTAAACC
19865 TCGCATGTGTAGTCTAGTCTGCTAAATTCCACTCACAACGTATAGTGTATTGTATAATTTTCCTA
1 TCGCATGTGTAGTCTAGTCTGCTAAATTCCACTCACAACGTATAGTGTATTGTATAATTTTCCTA
*
19930 TTATTTTTTTTGCTACTCATGAACATCATATTGAGATGGG
66 TTATTTTTTTTGCTACTCATGAACATCATATTGAAATGGG
19970 CTATATAATA
Statistics
Matches: 218, Mismatches: 4, Indels: 11
0.94 0.02 0.05
Matches are distributed among these distances:
118 32 0.15
119 2 0.01
120 2 0.01
121 66 0.30
124 116 0.53
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (119 bp):
TCGCATGTGTAGTCTAGTCTGCTAAATTCCACTCACAACGTATAGTGTATTGTATAATTTTCCTA
TTATTTTTTTTGCTACTCATGAACATCATATTGAAATGGGACTACCGTTAAACC
Found at i:24881 original size:30 final size:29
Alignment explanation
Indices: 24845--24928 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
24835 TAGGCTTCCT
24845 GGAGGAGGAGGCGGAGGTGGAGGTGCACC
1 GGAGGAGGAGGCGGAGGTGGAGGTGCACC
* * *
24874 AGGAGGAGGAGGAGGTGGTGGAGGGGCACC
1 -GGAGGAGGAGGCGGAGGTGGAGGTGCACC
* *
24904 GG-GTATTGGAGGCGGAGCTGGAGGT
1 GGAGGA--GGAGGCGGAGGTGGAGGT
24929 TTTCCAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 2 0.05
29 2 0.05
30 40 0.91
ACGTcount: A:0.20, C:0.11, G:0.58, T:0.11
Consensus pattern (29 bp):
GGAGGAGGAGGCGGAGGTGGAGGTGCACC
Found at i:26211 original size:6 final size:6
Alignment explanation
Indices: 26200--26230 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
26190 TGTTGGTTTC
*
26200 TTTCTT TTTCTT TTTCTT TTTTTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
26231 CTTTCTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTCTT
Found at i:26217 original size:16 final size:17
Alignment explanation
Indices: 26196--26239 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
26186 AGCTTGTTGG
26196 TTTCTTTCTTTTTCTT-
1 TTTCTTTCTTTTTCTTC
*
26212 TTTCTTT-TTTTTTTTC
1 TTTCTTTCTTTTTCTTC
26228 TTTCTTTCTTTT
1 TTTCTTTCTTTT
26240 ATAAGATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 7 0.28
16 14 0.56
17 4 0.16
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTCTTTCTTTTTCTTC
Found at i:27231 original size:12 final size:12
Alignment explanation
Indices: 27214--27238 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27204 ATCAGTTTAA
27214 CCTCTTCTTCCT
1 CCTCTTCTTCCT
27226 CCTCTTCTTCCT
1 CCTCTTCTTCCT
27238 C
1 C
27239 AATCTGTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (12 bp):
CCTCTTCTTCCT
Found at i:29557 original size:32 final size:32
Alignment explanation
Indices: 29481--29545 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
29471 AAAGAAAAAG
29481 ACATAAACAGAAATAAAGGTACAGTGCTCCAT
1 ACATAAACAGAAATAAAGGTACAGTGCTCCAT
29513 ACATAAACAGAAATAAAGGTACAGTGCTCCAT
1 ACATAAACAGAAATAAAGGTACAGTGCTCCAT
29545 A
1 A
29546 TATATAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (32 bp):
ACATAAACAGAAATAAAGGTACAGTGCTCCAT
Found at i:30061 original size:45 final size:45
Alignment explanation
Indices: 29997--30086 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
29987 TTGACAAAGC
29997 TTGAACCCAAACCTTTCAACCAAACTCTCAAAACACCATAATAGT
1 TTGAACCCAAACCTTTCAACCAAACTCTCAAAACACCATAATAGT
30042 TTGAACCCAAACCTTTCAACCAAACTCTCAAAACACCATAATAGT
1 TTGAACCCAAACCTTTCAACCAAACTCTCAAAACACCATAATAGT
30087 ACCAGTATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.31, G:0.04, T:0.22
Consensus pattern (45 bp):
TTGAACCCAAACCTTTCAACCAAACTCTCAAAACACCATAATAGT
Found at i:30402 original size:40 final size:40
Alignment explanation
Indices: 30342--30421 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
30332 AAACAGTTGC
*
30342 GTCCCATAAGATCTCGAACCTAAAATCTGCTTAAATTGGA
1 GTCCCATAAGATCTCAAACCTAAAATCTGCTTAAATTGGA
30382 GTCCCATAAGATCTCAAACCTAAAATCTGCTTAAATTGGA
1 GTCCCATAAGATCTCAAACCTAAAATCTGCTTAAATTGGA
30422 ACAAACCGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (40 bp):
GTCCCATAAGATCTCAAACCTAAAATCTGCTTAAATTGGA
Found at i:44266 original size:3 final size:3
Alignment explanation
Indices: 44258--44284 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44248 TGCAATGTTC
44258 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
44285 TTGAAGCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:44814 original size:2 final size:2
Alignment explanation
Indices: 44807--44833 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44797 TAGAGTTTCA
44807 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
44834 AAGTTCTCAT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:45156 original size:3 final size:3
Alignment explanation
Indices: 45144--45173 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
45134 AAAAGGGAGG
45144 CAC CACC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CA-C CAC CAC CAC CAC CAC CAC CAC CA
45174 GAAAGAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:45236 original size:7 final size:7
Alignment explanation
Indices: 45226--45251 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
45216 GGTCTGCCCT
45226 CTGCCAA
1 CTGCCAA
45233 CTGCCAA
1 CTGCCAA
45240 CTGCCAA
1 CTGCCAA
45247 CTGCC
1 CTGCC
45252 TACCGAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.46, G:0.15, T:0.15
Consensus pattern (7 bp):
CTGCCAA
Found at i:46269 original size:7 final size:7
Alignment explanation
Indices: 46257--46295 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
46247 AGCAGAGCAC
46257 CTCAGGG
1 CTCAGGG
46264 CTCAGGG
1 CTCAGGG
46271 CTCAGGG
1 CTCAGGG
*
46278 CTCAGGC
1 CTCAGGG
46285 CTCA-GG
1 CTCAGGG
46291 CTCAG
1 CTCAG
46296 TCCTCAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.15, C:0.33, G:0.36, T:0.15
Consensus pattern (7 bp):
CTCAGGG
Found at i:46294 original size:13 final size:14
Alignment explanation
Indices: 46256--46301 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
46246 GAGCAGAGCA
46256 CCTCAGGGCTCAGG
1 CCTCAGGGCTCAGG
*
46270 GCTCAGGGCTCAGG
1 CCTCAGGGCTCAGG
*
46284 CCTCA-GGCTCAGT
1 CCTCAGGGCTCAGG
46297 CCTCA
1 CCTCA
46302 AAAGGAAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 12 0.41
14 17 0.59
ACGTcount: A:0.15, C:0.37, G:0.30, T:0.17
Consensus pattern (14 bp):
CCTCAGGGCTCAGG
Found at i:57468 original size:17 final size:17
Alignment explanation
Indices: 57446--57500 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
57436 GATTACCCCC
*
57446 AGATCACTAGTGATCTG
1 AGATCACTAGTGATCTA
* * *
57463 AGATCACCAATGATGTA
1 AGATCACTAGTGATCTA
* *
57480 AGATCACTGGTGATCAA
1 AGATCACTAGTGATCTA
57497 AGAT
1 AGAT
57501 TACATGGGTT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (17 bp):
AGATCACTAGTGATCTA
Found at i:59933 original size:15 final size:13
Alignment explanation
Indices: 59902--59926 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59892 TATACTAGTT
59902 CTTTGTTTTTTTC
1 CTTTGTTTTTTTC
59915 CTTTGTTTTTTT
1 CTTTGTTTTTTT
59927 GGCCTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (13 bp):
CTTTGTTTTTTTC
Found at i:65976 original size:2 final size:2
Alignment explanation
Indices: 65969--66003 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
65959 TTTTATTTAG
* *
65969 AT AT AT AT AT AT AT AT AT AG AT AT AG AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66004 AAAAATATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:67096 original size:6 final size:6
Alignment explanation
Indices: 67085--67110 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
67075 AAAAGATTAA
67085 ACTAAC ACTAAC ACTAAC ACTAAC AC
1 ACTAAC ACTAAC ACTAAC ACTAAC AC
67111 GTACAATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (6 bp):
ACTAAC
Found at i:67270 original size:22 final size:22
Alignment explanation
Indices: 67242--67343 Score: 75
Period size: 22 Copynumber: 4.6 Consensus size: 22
67232 TGTCTCTATG
* *
67242 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTCCATAGGA
* **
67264 TGGTTAT-ATAATTTTATGAGGA
1 TGGTTATCAAAATTCCAT-AGGA
*
67286 -GGTTATCAAAATTCCATATTG-
1 TGGTTATCAAAATTCCATA-GGA
*
67307 TGGTTACCAAAATTCCATAGGA
1 TGGTTATCAAAATTCCATAGGA
*
67329 TCAGGTTATTAAAAT
1 T--GGTTATCAAAAT
67344 CTCTTAGGTT
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
21 16 0.26
22 36 0.58
24 10 0.16
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTCCATAGGA
Found at i:67533 original size:22 final size:22
Alignment explanation
Indices: 67473--67538 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
67463 TTCATTAAAT
*
67473 ATTTCATGAG-GAGGTTATCAAA
1 ATTTCAT-AGTGAAGTTATCAAA
* **
67495 ATTTTATAGTGTGGTTATCAAA
1 ATTTCATAGTGAAGTTATCAAA
67517 ATTTCATA-TGAAAGTTAT-AAA
1 ATTTCATAGTG-AAGTTATCAAA
67538 A
1 A
67539 GTCTCATTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
21 8 0.22
22 29 0.78
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (22 bp):
ATTTCATAGTGAAGTTATCAAA
Found at i:67612 original size:22 final size:22
Alignment explanation
Indices: 67578--67814 Score: 119
Period size: 22 Copynumber: 10.7 Consensus size: 22
67568 GATAGAAGGC
*
67578 TATC-AAATCTCATAGAGTGAT
1 TATCAAAATTTCATAGAGTGAT
* * *
67599 TATCGAAATTTCATGGAGATCGGGT
1 TATCAAAATTTCATAGAG-T--GAT
**
67624 TATCAAAATTT-ATAGAAAGAT
1 TATCAAAATTTCATAGAGTGAT
*
67645 TATCAAAATTTCATAGTGTTG-T
1 TATCAAAATTTCATAGAG-TGAT
* * * *
67667 TATCAAAATTTCAAAGCGAGGT
1 TATCAAAATTTCATAGAGTGAT
*
67689 TATCAAAATTACATA-ATGTGAT
1 TATCAAAATTTCATAGA-GTGAT
* *
67711 TATCAGAATTTCATAGAG-CAGT
1 TATCAAAATTTCATAGAGTGA-T
* * * * *
67733 CAACAAAATTTCATAAAGAGGT
1 TATCAAAATTTCATAGAGTGAT
* * * *
67755 TATCAAAATTCCATAAAGAGCT
1 TATCAAAATTTCATAGAGTGAT
* * *
67777 TATCTAATTTTCA-AAATGTGAT
1 TATCAAAATTTCATAGA-GTGAT
67799 TA-CAAAAATTTCATAG
1 TATC-AAAATTTCATAG
67815 TGGTATTTCT
Statistics
Matches: 162, Mismatches: 40, Indels: 26
0.71 0.18 0.11
Matches are distributed among these distances:
21 23 0.14
22 119 0.73
23 4 0.02
24 4 0.02
25 12 0.07
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (22 bp):
TATCAAAATTTCATAGAGTGAT
Found at i:67780 original size:66 final size:65
Alignment explanation
Indices: 67621--67789 Score: 171
Period size: 66 Copynumber: 2.6 Consensus size: 65
67611 ATGGAGATCG
* * ** * * *
67621 GGTTATCAAAATTTATAGAA-AGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCG
1 GGTTATCAAAATTCATA-AAGAGATTATCAAAATTTCATAGAGCAGTCAACAAAATTTCAAAGAG
67685 A
65 A
* * *
67686 GGTTATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGCAGTCAACAAAATTTCATAA-A
1 GGTTATCAAAATT-CATAAAGAGATTATCAAAATTTCATAGAGCAGTCAACAAAATTTCA-AAGA
67750 GA
64 GA
* * *
67752 GGTTATCAAAATTCCATAAAGAGCTTATCTAATTTTCA
1 GGTTATCAAAATT-CATAAAGAGATTATCAAAATTTCA
67790 AAATGTGATT
Statistics
Matches: 84, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
65 14 0.17
66 68 0.81
67 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (65 bp):
GGTTATCAAAATTCATAAAGAGATTATCAAAATTTCATAGAGCAGTCAACAAAATTTCAAAGAGA
Found at i:67910 original size:20 final size:20
Alignment explanation
Indices: 67885--67935 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
67875 TTATGGAGTA
*
67885 ATCAAAATTTCAATGAGGAT
1 ATCAAAATTTCAAGGAGGAT
* *
67905 ATC-AAAGTTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
67924 ATCAAAATTTCA
1 ATCAAAATTTCA
67936 TACAAAGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:67975 original size:44 final size:44
Alignment explanation
Indices: 67924--68091 Score: 191
Period size: 44 Copynumber: 3.8 Consensus size: 44
67914 CAGGGAGGAT
* *
67924 ATCAAAATTTCATACAAAGATTATCAAAATTTCATAGT-T-TAG
1 ATCAAAATTTCATAGAAAGATTAACAAAATTTCATAGTATCTAG
* * *
67966 TTTTCAAAATTTCA-A-AAGAGTGTTATCAAAATTTCATAGTATCTAG
1 --ATCAAAATTTCATAGAA-AG-ATTAACAAAATTTCATAGTATCTAG
**
68012 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAGTATCTAG
1 ATCAAAATTTCATAGAAAGATTAACAAAATTTCATAGTATCTAG
**
68056 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATA
1 ATCAAAATTTCATAGAAAGATTAACAAAATTTCATA
68092 ATGAGGTTAT
Statistics
Matches: 111, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 99 0.89
45 4 0.04
46 3 0.03
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (44 bp):
ATCAAAATTTCATAGAAAGATTAACAAAATTTCATAGTATCTAG
Found at i:68104 original size:44 final size:45
Alignment explanation
Indices: 68012--68186 Score: 203
Period size: 44 Copynumber: 4.0 Consensus size: 45
68002 TAGTATCTAG
* ** *
68012 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAGT-ATCTAG
1 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATAAGGTAT
*
68056 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGT-T
1 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATAAGGTAT
** * * * *
68100 ATCAAAAAATCATAGGGAGGTTATCAAAATTTCATATTAAGGTCT
1 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATAAGGTAT
* * *
68145 -TCAAAATTCCTTAAGGAGATTAACAAAATTTCATAATAAGGT
1 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATAAGGT
68187 TAAAAAAAAT
Statistics
Matches: 111, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
44 108 0.97
45 3 0.03
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (45 bp):
ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATAAGGTAT
Found at i:68142 original size:22 final size:22
Alignment explanation
Indices: 67923--68263 Score: 146
Period size: 22 Copynumber: 15.7 Consensus size: 22
67913 TCAGGGAGGA
** *
67923 TATCAAAATTTCATACAAAGAT
1 TATCAAAATTTCATAGTAAGGT
*
67945 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATAG-TAAGGT
* *
67967 TTTCAAAATTTCA-A-AAGAGTGT
1 TATCAAAATTTCATAGTA-AG-GT
**
67989 TATCAAAATTTCATAGT-ATCT
1 TATCAAAATTTCATAGTAAGGT
* ** *
68010 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGTAAGGT
* **
68033 TAACAAAATTTCATAGT-ATCT
1 TATCAAAATTTCATAGTAAGGT
* ** *
68054 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGTAAGGT
* * *
68077 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGTAAGGT
** **
68099 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGTAAGGT
*
68121 TATCAAAATTTCATATTAAGGT
1 TATCAAAATTTCATAGTAAGGT
* * * *
68143 CT-TCAAAATTCCTTAAG-GAGAT
1 -TATCAAAATTTCAT-AGTAAGGT
* *
68165 TAACAAAATTTCATAATAAGGT
1 TATCAAAATTTCATAGTAAGGT
** * *
68187 TAAAAAAAATT-A-A-AAAGGT
1 TATCAAAATTTCATAGTAAGGT
* * * **
68206 TCTCGAAATTCCATAGTATCGT
1 TATCAAAATTTCATAGTAAGGT
* *
68228 TATTAAAATTTCATAGGAA-GT
1 TATCAAAATTTCATAGTAAGGT
68249 TATCAAAATTTCATA
1 TATCAAAATTTCATA
68264 ATGGAATCAT
Statistics
Matches: 232, Mismatches: 70, Indels: 35
0.69 0.21 0.10
Matches are distributed among these distances:
19 10 0.04
20 3 0.01
21 24 0.10
22 187 0.81
23 8 0.03
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (22 bp):
TATCAAAATTTCATAGTAAGGT
Found at i:68277 original size:21 final size:20
Alignment explanation
Indices: 68231--68277 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
68221 GTATCGTTAT
*
68231 TAAAATTTCATAGGAAGTTA
1 TAAAATTTCATAGGAAGTCA
68251 TCAAAATTTCATAATGGAA-TCA
1 T-AAAATTTCAT-A-GGAAGTCA
68273 TAAAA
1 TAAAA
68278 AATAGTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 4 0.17
23 4 0.17
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (20 bp):
TAAAATTTCATAGGAAGTCA
Done.