Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016324.1 Corchorus capsularis cultivar CVL-1 contig16345, 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: 90306
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2715 original size:17 final size:17
Alignment explanation
Indices: 2690--2723 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2680 CACCCTTCTT
2690 GAAAATTCAAAAATTCA
1 GAAAATTCAAAAATTCA
*
2707 GAAACTTCAAAAATTCA
1 GAAAATTCAAAAATTCA
2724 TAGTTTGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
GAAAATTCAAAAATTCA
Found at i:9125 original size:141 final size:141
Alignment explanation
Indices: 8871--9156 Score: 572
Period size: 141 Copynumber: 2.0 Consensus size: 141
8861 AGATTAAGGT
8871 AGAAAGACACGTGAGAAAGAAGTGAGATATTGAACCTGAAAGCAGACAAAATGGAGAGAAAAAGA
1 AGAAAGACACGTGAGAAAGAAGTGAGATATTGAACCTGAAAGCAGACAAAATGGAGAGAAAAAGA
8936 AATCACCTGGAGGATTTACCAACCCAGTCTCTCTCTCATCCCAAACCCACCAGCTCAGCAACAAG
66 AATCACCTGGAGGATTTACCAACCCAGTCTCTCTCTCATCCCAAACCCACCAGCTCAGCAACAAG
9001 ACAAGATTGGA
131 ACAAGATTGGA
9012 AGAAAGACACGTGAGAAAGAAGTGAGATATTGAACCTGAAAGCAGACAAAATGGAGAGAAAAAGA
1 AGAAAGACACGTGAGAAAGAAGTGAGATATTGAACCTGAAAGCAGACAAAATGGAGAGAAAAAGA
9077 AATCACCTGGAGGATTTACCAACCCAGTCTCTCTCTCATCCCAAACCCACCAGCTCAGCAACAAG
66 AATCACCTGGAGGATTTACCAACCCAGTCTCTCTCTCATCCCAAACCCACCAGCTCAGCAACAAG
9142 ACAAGATTGGA
131 ACAAGATTGGA
9153 AGAA
1 AGAA
9157 TAAGCCAATT
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 145 1.00
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.15
Consensus pattern (141 bp):
AGAAAGACACGTGAGAAAGAAGTGAGATATTGAACCTGAAAGCAGACAAAATGGAGAGAAAAAGA
AATCACCTGGAGGATTTACCAACCCAGTCTCTCTCTCATCCCAAACCCACCAGCTCAGCAACAAG
ACAAGATTGGA
Found at i:10161 original size:12 final size:12
Alignment explanation
Indices: 10141--10174 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
10131 CAAGACCGGC
10141 CAACGCATGGAG
1 CAACGCATGGAG
*
10153 CATCGCATGGAG
1 CAACGCATGGAG
10165 CAACGCATGG
1 CAACGCATGG
10175 GGGAACCGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.32, T:0.12
Consensus pattern (12 bp):
CAACGCATGGAG
Found at i:16421 original size:19 final size:18
Alignment explanation
Indices: 16397--16432 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16387 TGAAGATTTC
16397 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
16416 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
16433 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:23125 original size:43 final size:43
Alignment explanation
Indices: 23077--23177 Score: 166
Period size: 43 Copynumber: 2.3 Consensus size: 43
23067 CAAGCATGAC
*
23077 CCGGACATCACCGAGCCATGCCATGTACCCCAGCCGGACAGCA
1 CCGGACATCACCGAGCCATGCCATGCACCCCAGCCGGACAGCA
* *
23120 CCGGACATCACCGAGCCATGCCATGCACTCCAGCCGGCCAGCA
1 CCGGACATCACCGAGCCATGCCATGCACCCCAGCCGGACAGCA
*
23163 CCAGACATCACCGAG
1 CCGGACATCACCGAG
23178 ATAGCACCAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.26, C:0.43, G:0.23, T:0.09
Consensus pattern (43 bp):
CCGGACATCACCGAGCCATGCCATGCACCCCAGCCGGACAGCA
Found at i:26359 original size:19 final size:18
Alignment explanation
Indices: 26335--26370 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
26325 TGAAGATTTC
26335 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
26354 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
26371 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:28700 original size:17 final size:17
Alignment explanation
Indices: 28675--28708 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28665 CACCCTTCTT
28675 GAAAATTCAAAAATTCA
1 GAAAATTCAAAAATTCA
*
28692 GAAACTTCAAAAATTCA
1 GAAAATTCAAAAATTCA
28709 TAGCCGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
GAAAATTCAAAAATTCA
Found at i:30362 original size:33 final size:33
Alignment explanation
Indices: 30267--30368 Score: 125
Period size: 33 Copynumber: 3.1 Consensus size: 33
30257 TTGGAAAGAG
* *
30267 TGTTTT-AGATGTTGTTTACGATGATACTAAACC
1 TGTTTTAAG-TGTTGTTTGCGATGATACTAAATC
** * *
30300 TAATTTAAGTGTTGTTTGCAATGACACTAAATC
1 TGTTTTAAGTGTTGTTTGCGATGATACTAAATC
*
30333 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTTAAGTGTTGTTTGCGATGATACTAAATC
30366 TGT
1 TGT
30369 CTTGGATGCT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 55 0.96
34 2 0.04
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (33 bp):
TGTTTTAAGTGTTGTTTGCGATGATACTAAATC
Found at i:32358 original size:32 final size:32
Alignment explanation
Indices: 32289--32351 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
32279 GGGTATACCT
* *
32289 TTATATAGTGGTGTCTAAAGAACAAAACGCCC
1 TTATATAGCGGCGTCTAAAGAACAAAACGCCC
*
32321 TTATATAGCGGCGTCTAACGAACAAAACGCC
1 TTATATAGCGGCGTCTAAAGAACAAAACGCC
32352 GCTATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (32 bp):
TTATATAGCGGCGTCTAAAGAACAAAACGCCC
Found at i:32431 original size:24 final size:24
Alignment explanation
Indices: 32399--32467 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
32389 AAAATTGCAT
*
32399 ATAGCGGCGTCCAGACGCCGCAAA
1 ATAGGGGCGTCCAGACGCCGCAAA
*
32423 ATAGGGGCGT-CAGGACGCCGCCAA
1 ATAGGGGCGTCCA-GACGCCGCAAA
* *
32447 ATAGGGGTGTCCAGATGCCGC
1 ATAGGGGCGTCCAGACGCCGC
32468 TACATTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.05
24 35 0.90
25 2 0.05
ACGTcount: A:0.25, C:0.29, G:0.35, T:0.12
Consensus pattern (24 bp):
ATAGGGGCGTCCAGACGCCGCAAA
Found at i:32540 original size:24 final size:24
Alignment explanation
Indices: 32508--32556 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
32498 ATTGGAAAAA
32508 TTATATGACGGCGTCTAAACGCCG
1 TTATATGACGGCGTCTAAACGCCG
* *
32532 TTATATGACGGCGTTTAGACGCCG
1 TTATATGACGGCGTCTAAACGCCG
32556 T
1 T
32557 AATGTAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (24 bp):
TTATATGACGGCGTCTAAACGCCG
Found at i:33011 original size:36 final size:36
Alignment explanation
Indices: 32732--33371 Score: 686
Period size: 36 Copynumber: 17.4 Consensus size: 36
32722 AAAGCACATA
* * *
32732 CTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGA
1 CTTAATTTCAAGGAAACTAGGT-AAAGAA-A-AGACTGG
* * * *
32771 CTTAATTTCAAGGGAATTAGGTAAAAGAAGACTGACTGC
1 CTTAATTTCAAGGAAACTAGGT-AAAGAA-A-AGACTGG
* * * *
32810 CTTAATTTCAACGAAATTAGGTAAAAGAAGACTGACTGA
1 CTTAATTTCAAGGAAACTAGGT-AAAGAA-A-AGACTGG
* *
32849 CTTAATTTCAAGGAAATTAGGTAAAAGAAGACCA-ACTGA
1 CTTAATTTCAAGGAAACTAGGT-AAAGAA-A--AGACTGG
* *
32888 CTTAATTTCAAGGAAATTAGGTAAA-AGAAGACTGATTG
1 CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTG---G
* *
32926 CCTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGG
1 -CTTAATTTCAAGGAAACTAGGT-AAAGAA-A-AGACTGG
*
32966 CTTAATTTCAAGGAAACTAAGTAAAGAAAAGACTGG
1 CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGG
*
33002 CTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGG
1 CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGG
*
33038 CTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTAGG
1 CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACT-GG
*
33075 CTTAATTTCAAGGAAACTAGGTAAA-AAAAGACTGC
1 CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGG
*
33110 CTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGG
1 CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGG
*
33146 CTTAATTTCAAGGAAATTAGGTAAAGAAAAGACTGG
1 CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGG
* * * *
33182 CTTAATTTCAATGAAATTAAGTAAAGAAAAGACTAG
1 CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGG
* * *
33218 CTTAGTTTCAAGGAAACTAGGTAGAGAAAATACTGG
1 CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGG
* * * *
33254 CTTAATTTCAACGAAATTAGGTAAAG-ATAGATTGG
1 CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGG
*
33289 C-TAGTTTCAAGGAAACTAGGTAAAG-AAAGACTGG
1 CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGG
* * *
33323 CTTAATTTCAAGGAAATTAAGT--A-AAAAGACAGG
1 CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGG
33356 CTTAATTTCAAGGAAA
1 CTTAATTTCAAGGAAA
33372 GAAATTAAGT
Statistics
Matches: 539, Mismatches: 48, Indels: 34
0.87 0.08 0.05
Matches are distributed among these distances:
33 25 0.05
34 30 0.06
35 53 0.10
36 210 0.39
37 28 0.05
38 9 0.02
39 172 0.32
40 5 0.01
41 1 0.00
42 1 0.00
43 5 0.01
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (36 bp):
CTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTGG
Found at i:36552 original size:30 final size:30
Alignment explanation
Indices: 36516--36578 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
36506 TTTTCAAGGG
*
36516 GGAGGGAATGATGCGTCCAAGG-CTTATCAT
1 GGAGGGAATAATGCG-CCAAGGACTTATCAT
36546 GGAGGGAATAATGCGCCAAGGACTTATCAT
1 GGAGGGAATAATGCGCCAAGGACTTATCAT
36576 GGA
1 GGA
36579 CTTGAAGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.30, C:0.16, G:0.33, T:0.21
Consensus pattern (30 bp):
GGAGGGAATAATGCGCCAAGGACTTATCAT
Found at i:40161 original size:22 final size:22
Alignment explanation
Indices: 40124--40167 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40114 GAATTTCAGG
*
40124 ACAACTTCGGCCCAGAACTTGT
1 ACAACTTCGGCACAGAACTTGT
* *
40146 ACAACTTCGGGACAGAAGTTGT
1 ACAACTTCGGCACAGAACTTGT
40168 TGCAGGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (22 bp):
ACAACTTCGGCACAGAACTTGT
Found at i:40893 original size:11 final size:12
Alignment explanation
Indices: 40865--40892 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
40855 AGTTATATCG
40865 AAAAATATAAAA
1 AAAAATATAAAA
40877 AAAAATATAAAA
1 AAAAATATAAAA
40889 AAAA
1 AAAA
40893 TTTCGACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAATATAAAA
Found at i:42326 original size:33 final size:33
Alignment explanation
Indices: 42273--42359 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
42263 CAAAGAATGT
* * *
42273 TTTAGATGTTGTTTGCGATGATACTAAACCTAA
1 TTTAGGTGTTGTTTGTGATGACACTAAACCTAA
* *
42306 TTT-GAGTGTTGTTTGTGATGACACTAAATCTGA
1 TTTAG-GTGTTGTTTGTGATGACACTAAACCTAA
42339 TTTAGGTGTTGTTTGTGATGA
1 TTTAGGTGTTGTTTGTGATGA
42360 AAATAAATTC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 1 0.02
33 45 0.96
34 1 0.02
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (33 bp):
TTTAGGTGTTGTTTGTGATGACACTAAACCTAA
Found at i:42397 original size:33 final size:33
Alignment explanation
Indices: 42357--42505 Score: 198
Period size: 33 Copynumber: 4.6 Consensus size: 33
42347 TTGTTTGTGA
42357 TGAAAATAAATTC-GTTTTGGTTGATCATAGCAT
1 TGAAAAT-AATTCTGTTTTGGTTGATCATAGCAT
* * *
42390 TGCAAATAATTCTGTTTTGGTTGACCATAACAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
42423 TAAAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
* * *
42456 TGGAAATAATTTTGTTTTGGTTG---ATGGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
42486 TGAAAATAATTCTGTTTTGG
1 TGAAAATAATTCTGTTTTGG
42506 GTGACGAGAA
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
30 24 0.24
32 5 0.05
33 73 0.72
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
Found at i:44658 original size:22 final size:22
Alignment explanation
Indices: 44621--44664 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
44611 GAATTTCAGG
*
44621 ACAACTTCGGCCCAGAACTTGT
1 ACAACTTCGGCACAGAACTTGT
* *
44643 ACAACTTCGGGACAGAAGTTGT
1 ACAACTTCGGCACAGAACTTGT
44665 TGCAGGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (22 bp):
ACAACTTCGGCACAGAACTTGT
Found at i:59556 original size:27 final size:27
Alignment explanation
Indices: 59526--59594 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
59516 TATCACCATC
* *
59526 TACATTCTGACCATTGTCATCATTATT
1 TACATTCTCACCATTGTCACCATTATT
59553 TACATTCTCACCATTGTCACCATTATT
1 TACATTCTCACCATTGTCACCATTATT
59580 TACATTCTCACCATT
1 TACATTCTCACCATT
59595 CTTGATACGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.26, C:0.28, G:0.04, T:0.42
Consensus pattern (27 bp):
TACATTCTCACCATTGTCACCATTATT
Found at i:65113 original size:6 final size:6
Alignment explanation
Indices: 65102--65128 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
65092 AAAGCAAAGC
65102 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
65129 GCAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:65143 original size:13 final size:13
Alignment explanation
Indices: 65125--65172 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
65115 AATCTAAATC
*
65125 TAAAGCAGATTAA
1 TAAAGCAAATTAA
65138 TAAAGCAAATTAA
1 TAAAGCAAATTAA
65151 TAAAGCAAATTAA
1 TAAAGCAAATTAA
65164 TAAAGCAAA
1 TAAAGCAAA
65173 CAATAATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:66110 original size:10 final size:10
Alignment explanation
Indices: 66095--66119 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
66085 GAGGACTCTA
66095 GAATTTTCTG
1 GAATTTTCTG
66105 GAATTTTCTG
1 GAATTTTCTG
66115 GAATT
1 GAATT
66120 GTGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:69046 original size:38 final size:41
Alignment explanation
Indices: 68974--69057 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 41
68964 CCCTAATTTT
* *
68974 AAAAACGGAAAATAATTTTTATTTTTTTTTAGAAAAATCGG
1 AAAAACGGAAAATAATCTTTATTTTTTTTTAGAAAAAACGG
69015 AAAAACGGAAAA-AA-CTTT-TTTTTTTTTAGAAAAAACGG
1 AAAAACGGAAAATAATCTTTATTTTTTTTTAGAAAAAACGG
69053 AAAAA
1 AAAAA
69058 TCAAAAACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
38 24 0.59
39 3 0.07
40 2 0.05
41 12 0.29
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (41 bp):
AAAAACGGAAAATAATCTTTATTTTTTTTTAGAAAAAACGG
Found at i:69357 original size:6 final size:6
Alignment explanation
Indices: 69346--69372 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
69336 AAAGCAAAGC
69346 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
69373 GCAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:69387 original size:13 final size:13
Alignment explanation
Indices: 69369--69403 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
69359 AATCTAAATC
*
69369 TAAAGCAGATTAA
1 TAAAGCAAATTAA
69382 TAAAGCAAATTAA
1 TAAAGCAAATTAA
69395 TAAAGCAAA
1 TAAAGCAAA
69404 CAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:72310 original size:33 final size:33
Alignment explanation
Indices: 72268--72343 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
72258 TTCTTTTCAC
72268 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
72301 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
72334 CCAAAACAGA
1 CCAAAACAGA
72344 TTTGTTTTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.24
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:72406 original size:33 final size:33
Alignment explanation
Indices: 72369--72473 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 33
72359 ATTAGCATCC
* *
72369 AAAACATATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * *
72402 AAAACAGATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
**
72435 AAATTAGATTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
72468 AAAACA
1 AAAACA
72474 CTCTTTTCAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 1 0.02
33 58 0.98
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:76760 original size:49 final size:49
Alignment explanation
Indices: 76704--77053 Score: 477
Period size: 49 Copynumber: 7.2 Consensus size: 49
76694 AAAAAGGCAT
* * * * ** * *
76704 TTTGGGAAATGGCAGGTGAGAATAAATACCTTCCGTCCGGGAAGGGCGT
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* * *
76753 TTTGGGAAATAGCAAGCAAAAATAAAGGGCTTCCGTCTGGGAAGGGCGT
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* * *
76802 TTTGGGAAATAGCAAGCAAAAACAAATGGCTTGCGTCTGGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* *
76851 TTTGGGAAATAGCAAGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
*
76900 TTTGGGAAATAACAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* *
76949 TTTGGGAAATTGCAAGTAAAAATGAATGGCTTCCGTCTGGGAAGGGCGC
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
* * * * *
76998 TTTGGGAAATTGCAAGTAAAAGTGAATGGCTTCCATCTGGGAAGGGTG-
1 TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
77046 TTTGGGAA
1 TTTGGGAA
77054 GAAACAGCTA
Statistics
Matches: 274, Mismatches: 27, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
48 8 0.03
49 266 0.97
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (49 bp):
TTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGC
Found at i:89762 original size:15 final size:15
Alignment explanation
Indices: 89742--89780 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
89732 TGAGATATTT
89742 TTTTCAAAAAAAATG
1 TTTTCAAAAAAAATG
*
89757 TTTTC-AAGAAAATG
1 TTTTCAAAAAAAATG
*
89771 CTTTCAAAAA
1 TTTTCAAAAA
89781 TGAGTTTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (15 bp):
TTTTCAAAAAAAATG
Done.