Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015324.1 Corchorus olitorius cultivar O-4 contig15357, 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: 64767
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:3221 original size:21 final size:21
Alignment explanation
Indices: 3166--3232 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
3156 CCAAGCCATT
* *
3166 ACCGGCCATTCACCGTGACACC
1 ACCGGCCATGC-CCGTGCCACC
** *
3188 ACCGGTTAAGCCCGTGCCACC
1 ACCGGCCATGCCCGTGCCACC
*
3209 ACCGGCCATGCCCGTGCCATC
1 ACCGGCCATGCCCGTGCCACC
3230 ACC
1 ACC
3233 ATTCCAAACC
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 29 0.81
22 7 0.19
ACGTcount: A:0.19, C:0.46, G:0.21, T:0.13
Consensus pattern (21 bp):
ACCGGCCATGCCCGTGCCACC
Found at i:6501 original size:15 final size:16
Alignment explanation
Indices: 6471--6509 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
6461 TTACTTTGCT
6471 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
6487 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
6502 TTGCTTTT
1 TTG-TTTT
6510 TGTCAATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.67
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:7391 original size:9 final size:9
Alignment explanation
Indices: 7377--7426 Score: 100
Period size: 9 Copynumber: 5.6 Consensus size: 9
7367 TTGTTAATAC
7377 AAACCGCCA
1 AAACCGCCA
7386 AAACCGCCA
1 AAACCGCCA
7395 AAACCGCCA
1 AAACCGCCA
7404 AAACCGCCA
1 AAACCGCCA
7413 AAACCGCCA
1 AAACCGCCA
7422 AAACC
1 AAACC
7427 AACCTAACCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.46, C:0.44, G:0.10, T:0.00
Consensus pattern (9 bp):
AAACCGCCA
Found at i:10270 original size:21 final size:20
Alignment explanation
Indices: 10237--10280 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
10227 CCTTGATTCT
* *
10237 AAACAGCAATATCACTAAAA
1 AAACAACAATATCACAAAAA
*
10257 AAACAACACATATCCCAAAAA
1 AAACAACA-ATATCACAAAAA
10278 AAA
1 AAA
10281 TGATAACAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.64, C:0.23, G:0.02, T:0.11
Consensus pattern (20 bp):
AAACAACAATATCACAAAAA
Found at i:11171 original size:9 final size:9
Alignment explanation
Indices: 11157--11184 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
11147 CGACCGCCGT
11157 CGGTTTTGG
1 CGGTTTTGG
11166 CGGTTTTGG
1 CGGTTTTGG
11175 CGGTTTTGG
1 CGGTTTTGG
11184 C
1 C
11185 ACCGACTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.14, G:0.43, T:0.43
Consensus pattern (9 bp):
CGGTTTTGG
Found at i:11203 original size:71 final size:71
Alignment explanation
Indices: 11113--11255 Score: 268
Period size: 71 Copynumber: 2.0 Consensus size: 71
11103 TAACACCGAA
* *
11113 CACCGACTGCTATATATACTAAACCGCCATGTACCGACCGCCGTCGGTTTTGGCGGTTTTGGCGG
1 CACCGACTGCTATACATACTAAACCGCCATGTACCGACCGCCATCGGTTTTGGCGGTTTTGGCGG
11178 TTTTGG
66 TTTTGG
11184 CACCGACTGCTATACATACTAAACCGCCATGTACCGACCGCCATCGGTTTTGGCGGTTTTGGCGG
1 CACCGACTGCTATACATACTAAACCGCCATGTACCGACCGCCATCGGTTTTGGCGGTTTTGGCGG
11249 TTTTGG
66 TTTTGG
11255 C
1 C
11256 GGTTTGTATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (71 bp):
CACCGACTGCTATACATACTAAACCGCCATGTACCGACCGCCATCGGTTTTGGCGGTTTTGGCGG
TTTTGG
Found at i:11242 original size:9 final size:9
Alignment explanation
Indices: 11228--11260 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
11218 CGACCGCCAT
11228 CGGTTTTGG
1 CGGTTTTGG
11237 CGGTTTTGG
1 CGGTTTTGG
11246 CGGTTTTGG
1 CGGTTTTGG
11255 CGGTTT
1 CGGTTT
11261 GTATTAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.00, C:0.12, G:0.42, T:0.45
Consensus pattern (9 bp):
CGGTTTTGG
Found at i:14177 original size:19 final size:19
Alignment explanation
Indices: 14155--14196 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
14145 TATTTCATTC
*
14155 ATCAATATCAGAT-TCATCA
1 ATCAACATCA-ATATCATCA
*
14174 ATCACCATCAATATCATCA
1 ATCAACATCAATATCATCA
14193 ATCA
1 ATCA
14197 TTTACTTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.29
Consensus pattern (19 bp):
ATCAACATCAATATCATCA
Found at i:14225 original size:20 final size:20
Alignment explanation
Indices: 14189--14229 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
14179 CATCAATATC
*
14189 ATCAATCATTTACTTAGCAA
1 ATCAATCATATACTTAGCAA
14209 ATCAATCATCATA-TTAGCAA
1 ATCAATCAT-ATACTTAGCAA
14229 A
1 A
14230 AAAGGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (20 bp):
ATCAATCATATACTTAGCAA
Found at i:17422 original size:52 final size:52
Alignment explanation
Indices: 17366--17555 Score: 287
Period size: 52 Copynumber: 3.7 Consensus size: 52
17356 TTTTTAAATT
17366 GGGAAAGTTCCCATCAA-TTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTC
1 GGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGCTC-TTTTCAAGTC
17418 GGGAAAGTTCCCATC-AGTTTTCAAAGTATTCAATTTAGCTCCTTTTCAAGTC
1 GGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGCT-CTTTTCAAGTC
* * * *
17470 GGGAAAGTTCCCATCAAGTTTTCGAAAG-GTTCAACTTAGCTCTTTTCAAATT
1 GGGAAAGTTCCCATCAAGTTTTC-AAAGTATTCAATTTAGCTCTTTTCAAGTC
*
17522 GGGAAAGTTCCCATCAAGTTTTCAAAGTTTTCAA
1 GGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAA
17556 ATTGGGAAGG
Statistics
Matches: 128, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
51 5 0.04
52 100 0.78
53 19 0.15
54 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (52 bp):
GGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGCTCTTTTCAAGTC
Found at i:17553 original size:37 final size:37
Alignment explanation
Indices: 17512--17620 Score: 161
Period size: 34 Copynumber: 3.0 Consensus size: 37
17502 AACTTAGCTC
17512 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAG
* * *
17549 TTTTCAAATTGGGAAGGTTCCCATC-AGGTTT--AGG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAG
17583 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCGAAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTC-AAAG
17621 GTTCAACTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
34 26 0.42
35 5 0.08
36 5 0.08
37 24 0.39
38 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (37 bp):
TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAG
Found at i:17608 original size:123 final size:123
Alignment explanation
Indices: 17460--17736 Score: 520
Period size: 123 Copynumber: 2.3 Consensus size: 123
17450 ATTTAGCTCC
* *
17460 TTTTCAAGTCGGGAAAGTTCCCATCAAGTTTTCGAAAGGTTCAACTTAGCTCTTTTCAAATTGGG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCGAAAGGTTCAACTTAGCTCTTTTCAAATTGGG
17525 AAAGTTCCCATCAAGTTTTCAAAGTTTTCAAATTGGGAAGGTTCCCATCAGGTTTAGG
66 AAAGTTCCCATCAAGTTTTCAAAGTTTTCAAATTGGGAAGGTTCCCATCAGGTTTAGG
17583 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCGAAAGGTTCAACTTAGCTCTTTTCAAATTGGG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCGAAAGGTTCAACTTAGCTCTTTTCAAATTGGG
17648 AAAGTTCCCATCAAGTTTTCAAAGTTTTCAAATTGGGAAGGTTCCCATCAGGTTTAGG
66 AAAGTTCCCATCAAGTTTTCAAAGTTTTCAAATTGGGAAGGTTCCCATCAGGTTTAGG
*
17706 TTTTCAAATTGGGAAAGTTCCCA-CCAGTTTT
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTT
17737 TAAGTTTTAA
Statistics
Matches: 151, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
122 7 0.05
123 144 0.95
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (123 bp):
TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCGAAAGGTTCAACTTAGCTCTTTTCAAATTGGG
AAAGTTCCCATCAAGTTTTCAAAGTTTTCAAATTGGGAAGGTTCCCATCAGGTTTAGG
Found at i:17810 original size:34 final size:34
Alignment explanation
Indices: 17635--17811 Score: 207
Period size: 34 Copynumber: 5.1 Consensus size: 34
17625 AACTTAGCTC
*
17635 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAG
1 TTTTCAAATTGGGAAAGTTCCCATC-AGTTTT--TAG
* *
17672 TTTTCAAATTGGGAAGGTTCCCATCAG-GTTTAGG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTTA-G
*
17706 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTT-AG
* *
17741 TTTT-AAATTGGAAAAGTTCCCATCAGGTTTTAG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTTAG
* *
17774 TTTTCAATTTAGGGAAAGTTCCCGTCA-TTTTTAG
1 TTTTCAAATT-GGGAAAGTTCCCATCAGTTTTTAG
17808 TTTT
1 TTTT
17812 AGTCTTCAAA
Statistics
Matches: 122, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
33 7 0.06
34 64 0.52
35 24 0.20
36 3 0.02
37 24 0.20
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (34 bp):
TTTTCAAATTGGGAAAGTTCCCATCAGTTTTTAG
Found at i:26530 original size:20 final size:20
Alignment explanation
Indices: 26505--26542 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
26495 AAATACAAAA
26505 GAATAAGACGAAAGGAGCAT
1 GAATAAGACGAAAGGAGCAT
**
26525 GAATAAGGGGAAAGGAGC
1 GAATAAGACGAAAGGAGC
26543 TGGAGCTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.37, T:0.08
Consensus pattern (20 bp):
GAATAAGACGAAAGGAGCAT
Found at i:30218 original size:25 final size:24
Alignment explanation
Indices: 30182--30228 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
30172 TCCTTCTATT
30182 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
30205 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
30229 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:34996 original size:12 final size:12
Alignment explanation
Indices: 34979--35011 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
34969 CTTGTCATCC
34979 TCAAACTGATGG
1 TCAAACTGATGG
34991 TCAAACTGATGG
1 TCAAACTGATGG
35003 TCAAACTGA
1 TCAAACTGA
35012 AGTAGTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (12 bp):
TCAAACTGATGG
Found at i:36654 original size:3 final size:3
Alignment explanation
Indices: 36646--36685 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
36636 TGTGTAATTA
36646 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
36686 ATTTGATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:42462 original size:81 final size:80
Alignment explanation
Indices: 42327--42481 Score: 283
Period size: 81 Copynumber: 1.9 Consensus size: 80
42317 TTTAAGCGTT
42327 ATCACTTACAGACCAGAGGTCCAGGGCTGCGGTGACATGAAATATAGATAGCTTAAACATTGAAT
1 ATCACTTACAGACCAGAGGTCCAGGGCTGCGGTGACATGAAATATAGATAGCTTAAACATT-AAT
42392 TTTTTTTTTTTAAATC
65 TTTTTTTTTTTAAATC
* *
42408 ATCACTTACAGACCAGTGGTCCAGGTCTGCGGTGACATGAAATATAGATAGCTTAAACATTAATT
1 ATCACTTACAGACCAGAGGTCCAGGGCTGCGGTGACATGAAATATAGATAGCTTAAACATTAATT
42473 TTTTTTTTT
66 TTTTTTTTT
42482 AAAAAAAACA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
80 13 0.18
81 59 0.82
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (80 bp):
ATCACTTACAGACCAGAGGTCCAGGGCTGCGGTGACATGAAATATAGATAGCTTAAACATTAATT
TTTTTTTTTTAAATC
Found at i:43962 original size:17 final size:19
Alignment explanation
Indices: 43940--43977 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
43930 TAAATCTCCA
43940 TTGAAA-TCTTTT-TTGGG
1 TTGAAATTCTTTTCTTGGG
43957 TTGAAATTTCTTTTCTTGGG
1 TTGAAA-TTCTTTTCTTGGG
43977 T
1 T
43978 GGCTTCATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.16, C:0.08, G:0.21, T:0.55
Consensus pattern (19 bp):
TTGAAATTCTTTTCTTGGG
Found at i:45182 original size:18 final size:18
Alignment explanation
Indices: 45155--45193 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
45145 TCTCCATTGC
* *
45155 CAACATTTGCAGGTACAA
1 CAACACTTGCAGCTACAA
45173 CAACACTTGCAGCTACAA
1 CAACACTTGCAGCTACAA
45191 CAA
1 CAA
45194 TTCCCAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.18
Consensus pattern (18 bp):
CAACACTTGCAGCTACAA
Found at i:46838 original size:3 final size:3
Alignment explanation
Indices: 46830--46864 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
46820 AAATGATAAG
*
46830 TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
46865 ATTAGTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:48957 original size:21 final size:21
Alignment explanation
Indices: 48933--48972 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
48923 ACCTGGGTGA
*
48933 TCAGGCAAACCATATGGGTCT
1 TCAGACAAACCATATGGGTCT
* *
48954 TCAGACAAACGATGTGGGT
1 TCAGACAAACCATATGGGT
48973 GCCCAGGTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (21 bp):
TCAGACAAACCATATGGGTCT
Found at i:50506 original size:15 final size:15
Alignment explanation
Indices: 50486--50518 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
50476 GAGTTTTATT
50486 TGTTATGAATACACA
1 TGTTATGAATACACA
*
50501 TGTTATGAATATACA
1 TGTTATGAATACACA
50516 TGT
1 TGT
50519 ATATAATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (15 bp):
TGTTATGAATACACA
Found at i:50637 original size:21 final size:21
Alignment explanation
Indices: 50613--50653 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
50603 TGTTCATCCT
50613 CTTGTATTTA-TGATGATGTAC
1 CTTGTATTTATTG-TGATGTAC
50634 CTTGTATTTATTGTGATGTA
1 CTTGTATTTATTGTGATGTA
50654 TCTATGTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.51
Consensus pattern (21 bp):
CTTGTATTTATTGTGATGTAC
Found at i:50994 original size:33 final size:33
Alignment explanation
Indices: 50948--51025 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
50938 TTTTACAAAA
*
50948 TTTCTTTAACATGCATAATCTCCTCCTTCTACC
1 TTTCTTTATCATGCATAATCTCCTCCTTCTACC
50981 TTTCTTTATCATGCATAATCTCCTCCTTCTACC
1 TTTCTTTATCATGCATAATCTCCTCCTTCTACC
51014 TTTCTTTATCAT
1 TTTCTTTATCAT
51026 TAAAAAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.19, C:0.31, G:0.03, T:0.47
Consensus pattern (33 bp):
TTTCTTTATCATGCATAATCTCCTCCTTCTACC
Found at i:52533 original size:38 final size:38
Alignment explanation
Indices: 52482--52560 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
52472 CTATATCGGG
52482 TGTGCAAATTTGATTG-ATGGCTCCGGAAGAGCTAGTAT
1 TGTGCAAATTTGATTGAAT-GCTCCGGAAGAGCTAGTAT
52520 TGTGCAAATTTGATTGAATGCTCCGGAAGAGCTAGTAT
1 TGTGCAAATTTGATTGAATGCTCCGGAAGAGCTAGTAT
52558 TGT
1 TGT
52561 TTTATCTGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 38 0.95
39 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.33
Consensus pattern (38 bp):
TGTGCAAATTTGATTGAATGCTCCGGAAGAGCTAGTAT
Found at i:56083 original size:15 final size:15
Alignment explanation
Indices: 56063--56095 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
56053 CAAGGGGGAG
56063 TGTTATGAATATACA
1 TGTTATGAATATACA
56078 TGTTATGAATATACA
1 TGTTATGAATATACA
56093 TGT
1 TGT
56096 ATATAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (15 bp):
TGTTATGAATATACA
Found at i:56213 original size:21 final size:21
Alignment explanation
Indices: 56189--56230 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
56179 TTGTTCATCC
*
56189 CCTTGTATTTA-TGATGATGTA
1 CCTTATATTTATTG-TGATGTA
56210 CCTTATATTTATTGTGATGTA
1 CCTTATATTTATTGTGATGTA
56231 TCTGTGTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.50
Consensus pattern (21 bp):
CCTTATATTTATTGTGATGTA
Found at i:57496 original size:2 final size:2
Alignment explanation
Indices: 57489--57521 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
57479 TAAAACCGTT
57489 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
57522 AATTATACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:58022 original size:22 final size:21
Alignment explanation
Indices: 57997--58050 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
57987 GAAGTTCGTG
57997 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
58019 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
58038 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
58051 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:61952 original size:11 final size:11
Alignment explanation
Indices: 61936--61969 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
61926 AGCAGTAGGG
61936 TCCTTCCTAGC
1 TCCTTCCTAGC
61947 TCCTTCCTAGC
1 TCCTTCCTAGC
61958 TCCTTCCTAGC
1 TCCTTCCTAGC
61969 T
1 T
61970 TTTACCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.09, C:0.44, G:0.09, T:0.38
Consensus pattern (11 bp):
TCCTTCCTAGC
Done.