Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015190.1 Corchorus olitorius cultivar O-4 contig15223, 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: 54040
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:535 original size:24 final size:24
Alignment explanation
Indices: 504--598 Score: 154
Period size: 24 Copynumber: 4.0 Consensus size: 24
494 TGCTCCGGCC
504 GATGATGCACCGGCACCACCAGCT
1 GATGATGCACCGGCACCACCAGCT
528 GATGATGCACCGGCACCACCAGCT
1 GATGATGCACCGGCACCACCAGCT
* * *
552 GATGATGCACCTGCACCGCCAGCC
1 GATGATGCACCGGCACCACCAGCT
*
576 GATGATGCACCAGCACCACCAGC
1 GATGATGCACCGGCACCACCAGC
599 CAAAAACTGA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.25, C:0.39, G:0.24, T:0.12
Consensus pattern (24 bp):
GATGATGCACCGGCACCACCAGCT
Found at i:1369 original size:19 final size:19
Alignment explanation
Indices: 1345--1382 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1335 CATCGTCAAT
1345 GGAGTTTAATCTAAACGGG
1 GGAGTTTAATCTAAACGGG
*
1364 GGAGTTTAGTCTAAACGGG
1 GGAGTTTAATCTAAACGGG
1383 TCCTGAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (19 bp):
GGAGTTTAATCTAAACGGG
Found at i:1475 original size:29 final size:29
Alignment explanation
Indices: 1433--1701 Score: 356
Period size: 29 Copynumber: 9.2 Consensus size: 29
1423 GACGGTGACA
1433 TGACATGTATAGGCCCTGAAGCTGAAGGG
1 TGACATGTATAGGCCCTGAAGCTGAAGGG
*
1462 TGACATGTATAGGCCCTGAAGCGCCTAAATGGG
1 TGACATGTATAGGCCCTGAA--G-CTGAA-GGG
* *
1495 T-AC-TG-A-A----CTGAATGGTGACGGTG
1 TGACATGTATAGGCCCTGAA-GCTGAAGG-G
1518 ACATGACATGTATAGGCCCTGAAGCTGAAGGG
1 ---TGACATGTATAGGCCCTGAAGCTGAAGGG
1550 TGACATGTATAGGCCCTGAAGCTGAAGGG
1 TGACATGTATAGGCCCTGAAGCTGAAGGG
*
1579 TGACATGTATAGGCCCTGAAGCTGAAGGT
1 TGACATGTATAGGCCCTGAAGCTGAAGGG
1608 TGACATGTATAGGCCCTGAAGCTGAAGGG
1 TGACATGTATAGGCCCTGAAGCTGAAGGG
1637 TGACATGTATAGGCCCTGAAGCTGAAGGG
1 TGACATGTATAGGCCCTGAAGCTGAAGGG
*
1666 TGACATGTATAGGCCCTGAAGCTGAAGGT
1 TGACATGTATAGGCCCTGAAGCTGAAGGG
1695 TGACATG
1 TGACATG
1702 ACATGTGTAC
Statistics
Matches: 214, Mismatches: 10, Indels: 32
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.01
23 3 0.01
24 1 0.00
25 5 0.02
26 1 0.00
27 2 0.01
28 2 0.01
29 171 0.80
30 2 0.01
31 3 0.01
32 7 0.03
33 10 0.05
34 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (29 bp):
TGACATGTATAGGCCCTGAAGCTGAAGGG
Found at i:1545 original size:88 final size:88
Alignment explanation
Indices: 1396--1658 Score: 364
Period size: 88 Copynumber: 3.0 Consensus size: 88
1386 TGAAGTTGAA
1396 GCCTAAATGGGTACTGAACTGAATGGTGACGGTGACATGACATGTATAGGCCCTGAAGCTGAAGG
1 GCCTAAATGGGTACTGAACTGAATGGTGACGGTGACATGACATGTATAGGCCCTGAAGCTGAAGG
1461 GTGACATGTATAGGCCCTGAAGC
66 GTGACATGTATAGGCCCTGAAGC
1484 GCCTAAATGGGTACTGAACTGAATGGTGACGGTGACATGACATGTATAGGCCCTGAAGCTGAAGG
1 GCCTAAATGGGTACTGAACTGAATGGTGACGGTGACATGACATGTATAGGCCCTGAAGCTGAAGG
1549 GTGACATGTATAGGCCCTGAA--
66 GTGACATGTATAGGCCCTGAAGC
* * *
1570 G-CTGAA-GGGTGACATGTATAGGCCCTGAA-GCTGAAGGT----TGACATGTATAGGCCCTGAA
1 GCCTAAATGGGT-AC-TG-A-A----CTGAATGGTGACGGTGACATGACATGTATAGGCCCTGAA
1628 GCTGAAGGGTGACATGTATAGGCCCTGAAGC
58 GCTGAAGGGTGACATGTATAGGCCCTGAAGC
1659 TGAAGGGTGA
Statistics
Matches: 162, Mismatches: 3, Indels: 19
0.88 0.02 0.10
Matches are distributed among these distances:
84 4 0.02
85 6 0.04
86 3 0.02
87 50 0.31
88 87 0.54
91 7 0.04
92 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.22
Consensus pattern (88 bp):
GCCTAAATGGGTACTGAACTGAATGGTGACGGTGACATGACATGTATAGGCCCTGAAGCTGAAGG
GTGACATGTATAGGCCCTGAAGC
Found at i:1770 original size:19 final size:19
Alignment explanation
Indices: 1746--1782 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1736 CTCCACGACC
1746 CGAAGTCCAAAATTTACAT
1 CGAAGTCCAAAATTTACAT
1765 CGAAGTCCAAAATTTACA
1 CGAAGTCCAAAATTTACA
1783 CCGGTATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.24
Consensus pattern (19 bp):
CGAAGTCCAAAATTTACAT
Found at i:3361 original size:36 final size:36
Alignment explanation
Indices: 3304--3493 Score: 84
Period size: 36 Copynumber: 5.6 Consensus size: 36
3294 AATCCACCCT
* *
3304 CACCACCTAAGGCT-CCGTCGCCAAAAGCACCTCCAC
1 CACCACCAAAGG-TACCATCGCCAAAAGCACCTCCAC
** ** *
3340 CACCACCAAAGGTACCATCGCC---TCCTTCACCAC
1 CACCACCAAAGGTACCATCGCCAAAAGCACCTCCAC
* * * * *
3373 CATCACCTAAGGCACCGTCGCCAAAATCACC-CTCAC
1 CACCACCAAAGGTACCATCGCCAAAAGCACCTC-CAC
* **
3409 CACCACCAAAGGTA-CAT--TC----G--CCTCCTT
1 CACCACCAAAGGTACCATCGCCAAAAGCACCTCCAC
* * *
3436 CACCACCAAAGGCACCTTCGCCAAAAGCACCTACAC
1 CACCACCAAAGGTACCATCGCCAAAAGCACCTCCAC
* *
3472 CACCGCCAAACGTACCATCGCC
1 CACCACCAAAGGTACCATCGCC
3494 TCCTCCTTCA
Statistics
Matches: 106, Mismatches: 33, Indels: 30
0.63 0.20 0.18
Matches are distributed among these distances:
27 16 0.15
28 3 0.03
30 1 0.01
33 25 0.24
34 1 0.01
35 4 0.04
36 56 0.53
ACGTcount: A:0.29, C:0.46, G:0.12, T:0.13
Consensus pattern (36 bp):
CACCACCAAAGGTACCATCGCCAAAAGCACCTCCAC
Found at i:3373 original size:30 final size:30
Alignment explanation
Indices: 3337--3443 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
3327 AAAGCACCTC
3337 CACCACCACCAAAGGTACCATCGCCTCCTT
1 CACCACCACCAAAGGTACCATCGCCTCCTT
* * * *
3367 CACCACCATCACCTAAGGCACCGTCGCCAAAATCACCCT
1 CACCA-C--CACCAAAGGTACCATCGCC----T--CCTT
3406 CACCACCACCAAAGGTA-CATTCGCCTCCTT
1 CACCACCACCAAAGGTACCA-TCGCCTCCTT
3436 CACCACCA
1 CACCACCA
3444 AAGGCACCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
30 16 0.27
31 1 0.02
32 1 0.02
33 16 0.27
35 1 0.02
36 14 0.24
37 1 0.02
38 1 0.02
39 8 0.14
ACGTcount: A:0.29, C:0.47, G:0.09, T:0.15
Consensus pattern (30 bp):
CACCACCACCAAAGGTACCATCGCCTCCTT
Found at i:3373 original size:33 final size:33
Alignment explanation
Indices: 3336--3443 Score: 101
Period size: 33 Copynumber: 3.2 Consensus size: 33
3326 AAAAGCACCT
3336 CCACCACCACCAAAGGTACCATCGCCTCCTTCA
1 CCACCACCACCAAAGGTACCATCGCCTCCTTCA
* * * * ****
3369 CCACCATCACCTAAGGCACCGTCGCCAAAATCA
1 CCACCACCACCAAAGGTACCATCGCCTCCTTCA
3402 CCCTCACCACCACCAAAGGTA-CATTCGCCTCCTTCA
1 --C-CACCACCACCAAAGGTACCA-TCGCCTCCTTCA
3438 CCACCA
1 CCACCA
3444 AAGGCACCTT
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
33 30 0.55
34 1 0.02
35 2 0.04
36 22 0.40
ACGTcount: A:0.29, C:0.47, G:0.09, T:0.15
Consensus pattern (33 bp):
CCACCACCACCAAAGGTACCATCGCCTCCTTCA
Found at i:3395 original size:69 final size:66
Alignment explanation
Indices: 3312--3535 Score: 262
Period size: 69 Copynumber: 3.3 Consensus size: 66
3302 CTCACCACCT
*
3312 AAGGCTCCGTCGCCAAAAGCACCTCCACCACCACCAAAGGTACCATCGCCTCCTTCACCACCATC
1 AAGGCACCGTCGCCAAAAGCACCTCCACCACCACCAAAGGTACCATCGCCTCCTTCACCACCATC
3377 A
66 A
*
3378 CCTAAGGCACCGTCGCCAAAATCACC-CTCACCACCACCAAAGGTA-CATTCGCCTCCTTCACCA
1 ---AAGGCACCGTCGCCAAAAGCACCTC-CACCACCACCAAAGGTACCA-TCGCCTCCTTCACCA
3441 -C--CA
61 CCATCA
* * * *
3444 AAGGCACCTTCGCCAAAAGCACCTACACCACCGCCAAACGTACCATCGCCTCCTCCTTCACCACC
1 AAGGCACCGTCGCCAAAAGCACCTCCACCACCACCAAAGGTACCATCG---CCTCCTTCACCACC
3509 ATCA
63 ATCA
*
3513 AAGGCACCAG-CACCAAAAGCACC
1 AAGGCACC-GTCGCCAAAAGCACC
3536 CACGCCAATA
Statistics
Matches: 135, Mismatches: 9, Indels: 22
0.81 0.05 0.13
Matches are distributed among these distances:
63 39 0.29
64 2 0.01
66 14 0.10
67 1 0.01
68 4 0.03
69 75 0.56
ACGTcount: A:0.30, C:0.45, G:0.12, T:0.13
Consensus pattern (66 bp):
AAGGCACCGTCGCCAAAAGCACCTCCACCACCACCAAAGGTACCATCGCCTCCTTCACCACCATC
A
Found at i:3506 original size:63 final size:62
Alignment explanation
Indices: 3307--3506 Score: 213
Period size: 63 Copynumber: 3.1 Consensus size: 62
3297 CCACCCTCAC
* *
3307 CACCTAAGGCTCCGTCGCCAAAAGCACCTCCACCACCACCAAAGGTACCATCGCCTCCTTCACCA
1 CACCAAAGGCACCGTCGCCAAAAGCACCT-CACCACCACCAAAGGTACCATCGCCTCC-T-----
3372 CCAT
59 CCAT
* * * *
3376 CACCTAAGGCACCGTCGCCAAAATCACCCTCACCACCACCAAAGGTA-CATTCGCCTCCTTCAC
1 CACCAAAGGCACCGTCGCCAAAAGCA-CCTCACCACCACCAAAGGTACCA-TCGCCTCCTCCAT
* * * *
3439 CACCAAAGGCACCTTCGCCAAAAGCACCTACACCACCGCCAAACGTACCATCGCCTCCTCCTT
1 CACCAAAGGCACCGTCGCCAAAAGCACCT-CACCACCACCAAAGGTACCATCGCCTCCTCCAT
3502 CACCA
1 CACCA
3507 CCATCAAAGG
Statistics
Matches: 115, Mismatches: 12, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
62 3 0.03
63 55 0.48
64 2 0.02
68 3 0.03
69 49 0.43
70 3 0.03
ACGTcount: A:0.28, C:0.46, G:0.11, T:0.14
Consensus pattern (62 bp):
CACCAAAGGCACCGTCGCCAAAAGCACCTCACCACCACCAAAGGTACCATCGCCTCCTCCAT
Found at i:3569 original size:69 final size:69
Alignment explanation
Indices: 3496--3698 Score: 298
Period size: 69 Copynumber: 2.9 Consensus size: 69
3486 CCATCGCCTC
* * * *
3496 CTCCTTCACCACCATCAAAGGCACCAGCACCAAAAGCACCCACGCCAATACCATCACCAAAGCCA
1 CTCCTTCGCCACCGTCAAAGGCACCACCACCAAAAGCACCCACGCCAATACCATCACCAAAACCA
3561 CCTT
66 CCTT
*
3565 CTCCTTCGCCACCGTCAAAGGCACCATCACCAAAAGCACCCACGCCAATACCATCACCAAAACCA
1 CTCCTTCGCCACCGTCAAAGGCACCACCACCAAAAGCACCCACGCCAATACCATCACCAAAACCA
3630 CCTT
66 CCTT
* * * *
3634 CTCCTTCGCCACCGTCAAAGGTGGCACCACCATCAAAAGCACCTACACCGATACCATCACCAAAA
1 CTCCTTCGCCACCGTCAAA---GGCACCACCACCAAAAGCACCCACGCCAATACCATCACCAAAA
3699 GCGCCCTCAC
Statistics
Matches: 122, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
69 84 0.69
72 38 0.31
ACGTcount: A:0.34, C:0.43, G:0.10, T:0.13
Consensus pattern (69 bp):
CTCCTTCGCCACCGTCAAAGGCACCACCACCAAAAGCACCCACGCCAATACCATCACCAAAACCA
CCTT
Found at i:7249 original size:15 final size:15
Alignment explanation
Indices: 7229--7281 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
7219 ATTCTTGCCT
*
7229 CCACCTCCACCGCCG
1 CCACCTCCACCACCG
7244 CCACCTCCACCACCG
1 CCACCTCCACCACCG
* * *
7259 CCACCACCACCTCCC
1 CCACCTCCACCACCG
7274 CCACCTCC
1 CCACCTCC
7282 TTTGCCATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.17, C:0.70, G:0.06, T:0.08
Consensus pattern (15 bp):
CCACCTCCACCACCG
Found at i:7872 original size:12 final size:12
Alignment explanation
Indices: 7855--7924 Score: 88
Period size: 12 Copynumber: 5.8 Consensus size: 12
7845 ATTCCTCATC
7855 CTCATCATCAAA
1 CTCATCATCAAA
7867 CTCATCATCAAA
1 CTCATCATCAAA
* *
7879 TTCATCATCGAA
1 CTCATCATCAAA
**
7891 CTCATCCCCAAA
1 CTCATCATCAAA
7903 CTCATCATCATAA
1 CTCATCATCA-AA
7916 -TCATCATCA
1 CTCATCATCA
7925 CTATCATCTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
12 47 0.96
13 2 0.04
ACGTcount: A:0.37, C:0.34, G:0.01, T:0.27
Consensus pattern (12 bp):
CTCATCATCAAA
Found at i:8065 original size:24 final size:24
Alignment explanation
Indices: 8038--8088 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
8028 CTGCTACAAA
* *
8038 TTGCTGTTGATT-TTGCCCACCTTT
1 TTGCTGCTGATTGTT-CCCACCCTT
8062 TTGCTGCTGATTGTTCCCACCCTT
1 TTGCTGCTGATTGTTCCCACCCTT
8086 TTG
1 TTG
8089 GTGAGATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.08, C:0.27, G:0.18, T:0.47
Consensus pattern (24 bp):
TTGCTGCTGATTGTTCCCACCCTT
Found at i:9022 original size:15 final size:15
Alignment explanation
Indices: 9000--9040 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
8990 CAGAAAGAGA
9000 AAAG-AAGAAGGAAG
1 AAAGAAAGAAGGAAG
*
9014 AAAGAAAGAAAGAAG
1 AAAGAAAGAAGGAAG
*
9029 AAAGAGAGAAGG
1 AAAGAAAGAAGG
9041 CGGTTGTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAGGAAG
Found at i:13735 original size:25 final size:26
Alignment explanation
Indices: 13684--13735 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
13674 TTAGATGACT
* *
13684 TTAATTGATCCAAAATTGAAAATGTG
1 TTAATTGATCCAAAATCGAAAAGGTG
* *
13710 TTAATTGA-CCTAAATCGGAAAGGTG
1 TTAATTGATCCAAAATCGAAAAGGTG
13735 T
1 T
13736 GACCCTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (26 bp):
TTAATTGATCCAAAATCGAAAAGGTG
Found at i:15863 original size:21 final size:21
Alignment explanation
Indices: 15837--15912 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
15827 CTGCTCTAAT
15837 AATCTCATCTGTACAGTGTCC
1 AATCTCATCTGTACAGTGTCC
**
15858 AATCTCATCTGTACAGTACCC
1 AATCTCATCTGTACAGTGTCC
*
15879 AATCTAATCTGTACAGTGT--
1 AATCTCATCTGTACAGTGTCC
15898 AATCTCATCTGTACA
1 AATCTCATCTGTACA
15913 ATTGTTAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
19 14 0.29
21 35 0.71
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (21 bp):
AATCTCATCTGTACAGTGTCC
Found at i:22887 original size:14 final size:14
Alignment explanation
Indices: 22868--22894 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22858 GGCCTTTCTC
22868 TTTTAATGTCGTTA
1 TTTTAATGTCGTTA
22882 TTTTAATGTCGTT
1 TTTTAATGTCGTT
22895 GGCCTTTCTT
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:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (14 bp):
TTTTAATGTCGTTA
Found at i:28193 original size:2 final size:2
Alignment explanation
Indices: 28186--28228 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
28176 GAGAGGTGGC
*
28186 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28228 T
1 T
28229 TGGATATACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:34166 original size:17 final size:17
Alignment explanation
Indices: 34135--34177 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
34125 TCCGGAATAG
* * *
34135 AAAAGGAAAAGAAAATA
1 AAAAGAAAAACAAAAGA
*
34152 ATAAGAAAAACAAAAGA
1 AAAAGAAAAACAAAAGA
34169 AAAAGAAAA
1 AAAAGAAAA
34178 GTTTTCTTCC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAGAAAAACAAAAGA
Found at i:51678 original size:29 final size:28
Alignment explanation
Indices: 51606--51689 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 28
51596 TTAATATCCT
*
51606 TTTTGCCCTCTAAATTTGTACGATTTTGACG
1 TTTTGCCCTCTAAATTT-TA--ATTTTGACA
*
51637 TTTTGCCCCCTAAATTTTAATTTTGGACA
1 TTTTGCCCTCTAAATTTTAATTTT-GACA
*
51666 TTTTGCCCTCTAAACTTGTAATTT
1 TTTTGCCCTCTAAA-TTTTAATTT
51690 GAAGTCATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 5 0.11
29 16 0.34
30 10 0.21
31 16 0.34
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.46
Consensus pattern (28 bp):
TTTTGCCCTCTAAATTTTAATTTTGACA
Found at i:52207 original size:26 final size:26
Alignment explanation
Indices: 52154--52203 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
52144 CGTCCATATT
52154 AATTTTTTAAAATAAAATAATAATTA
1 AATTTTTTAAAATAAAATAATAATTA
52180 AATTTTTTAATAA-AAAATAA-AATT
1 AATTTTTTAA-AATAAAATAATAATT
52204 TAAACATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.17
26 17 0.74
27 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTTTTTAAAATAAAATAATAATTA
Found at i:52366 original size:29 final size:30
Alignment explanation
Indices: 52308--52368 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
52298 CTTCTAATTA
* **
52308 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATCATATT
*
52338 ATGTATAAATAT-AATTATTTAATCATATT
1 ATGTATAAATATAAATTATTCAATCATATT
52367 AT
1 AT
52369 ATTATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATCATATT
Found at i:53863 original size:330 final size:318
Alignment explanation
Indices: 52780--54032 Score: 1065
Period size: 321 Copynumber: 3.8 Consensus size: 318
52770 TAGTCGGAGC
* * ** * * *
52780 CCCGGTTCAGTGTTGCATGATTTTT--TGCGCCGAGACTCCTTGAAATATCTATATTAATCTAAC
1 CCCGGGTCAGTTTTGCATGATTTTTAGTG-GCTAAAACTCCTTGAAATATCTATATTCATCTAAT
** * * *** * *
52843 CAAATCCCATCCACAATGGATTTAAGGATTTG-TAAAACAAGCATCTGAAT-TATATTTCGATTT
65 CAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT-TGTTTCGATTT
* * * * * *
52906 AATTAGAAATTAATTCAGAAAATAATAGGAAAAACGATACTAGAAGCATGAAAAGCCCTTCAATC
129 AATTAGAAATTAATTCAG-AAA-AATATGAAAAACGATATTAAAAGCGTGAAGAGTCCTTCAAT-
* * ** *
52971 TTTTTCGAGTTGAATTATATA-ATTTTTATGAGTATTGCGGCTAAAACTTGAGGAAATAACTTTA
191 TTTTT-GATTTAAATTATATATA-TTTTATGAGTATTATGG-TAAAAATTGAGGAAA-AA---TA
* * * * * *
53035 TTTCGAG-CTAATTTTTGTAAAATTCTAGCCGAAATTGTGTAATAATCATCACGGATTTTGGTTA
249 TTTCGGGTC-AATTTTTGCAAAATTTTAGCC--------G--A-AATCGTCACGGTTTTTGGCTA
* *
53099 AAAA-A-GTGTTCCGGG-G
302 AAAACACGT-TT-AGGGAT
* * * *
53115 CCTCAGCT-ACGTTTTGCATGATTTTTTA-T-GCTAAAACTCTTTGAAATATCCATATTCATCTA
1 CC-CGGGTCA-GTTTTGCATGA-TTTTTAGTGGCTAAAACTCCTTGAAATATCTATATTCATCTA
* * * * * *
53177 ATCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCTTGTGAATCTGGTTTCGATT
63 ATCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATT
*
53242 TAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTTCAATCT
128 TAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAGAGTCCTTCAAT-T
** * *
53307 TTTTGATGTTAAATTATATATATTTTATGAGTATGTATGCCAAAAATTGACGGAAAAATTTTTTG
192 TTTTGAT-TTAAATTATATATATTTTATGAGTAT-TATGGTAAAAATTGA-GGAAAAATATTTCG
* *
53372 GGTC-ATTTTTAACAAAATTTTAGCCGAAATCGTCACGGTTTTTGGCTAAAAACACGTTTCGGGA
254 GGTCAATTTTT-GCAAAATTTTAGCCGAAATCGTCACGGTTTTTGGCTAAAAACACGTTTAGGGA
53436 T
318 T
* * * * * *
53437 CCCGGTTTATTTTTGCATGATTTTT-G-GCGCTGAGACTCCTTGAAATAGCTATATTCATCTAAT
1 CCCGGGTCAGTTTTGCATGATTTTTAGTG-GCTAAAACTCCTTGAAATATCTATATTCATCTAAT
*
53500 CAAATCTTAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
65 CAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
*
53565 ATTAGAAATTAATTCAGAAAAATATGAAAAAACGATATTAAAAGCGTGAAGAGTCCTCCAATATT
130 ATTAGAAATTAATTCAGAAAAATATG-AAAAACGATATTAAAAGCGTGAAGAGTCCTTCAAT-TT
* * * * * *
53630 TTTGGATTTTAATAATATATATTCTATAAGTATTTTGGTAAAAAATGGAGGAAAAATATTTCGGG
193 TTT-GATTTAAATTATATATATTTTATGAGTATTATGGT-AAAAATTGAGGAAAAATATTTCGGG
*
53695 TCAATTTTTGCAAAATTTTAG-CGAAATCGTGTACCATCACGGTTTTTTTTGGCTAAAAACGCGT
256 TCAATTTTTGCAAAATTTTAGCCGAAATC--G-----TCACGG---TTTTTGGCTAAAAACACG-
*
53759 TTTAGGGCT
310 TTTAGGGAT
* * * *
53768 -CTGGGTCAGTTTTGCATGATTTTTAGTGGC-AACATTCCTTGAAATATCTATATTCATC-AAAC
1 CCCGGGTCAGTTTTGCATGATTTTTAGTGGCTAAAACTCCTTGAAATATCTATATTCATCTAATC
* * **
53830 TAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTTAATTTA
66 -AAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
* * * * * *
53895 ATTAGAAATTAATTTGAAAACAAATAGGACAAACGATATTAGAAGCGTG-AGAAGCCCTTCAATT
130 ATTAGAAATTAA-TTCAGAA-AAATATGAAAAACGATATTAAAAGCGTGAAG-AGTCCTTCAATT
*** * *
53959 TTTTCCCGTTAAATTATATAT-TTTTATGAGTATTGTGCCTAAAAATTGA-GAAAAATATTTCGG
192 TTTT-GATTTAAATTATATATATTTTATGAGTATTATG-GTAAAAATTGAGGAAAAATATTTCGG
54022 GTCAATTTTTG
255 GTCAATTTTTG
54033 TAGAATTT
Statistics
Matches: 768, Mismatches: 109, Indels: 89
0.80 0.11 0.09
Matches are distributed among these distances:
320 12 0.02
321 183 0.24
322 82 0.11
323 5 0.01
324 1 0.00
327 6 0.01
328 25 0.03
329 24 0.03
330 151 0.20
331 49 0.06
332 24 0.03
333 1 0.00
334 2 0.00
335 78 0.10
336 79 0.10
337 44 0.06
338 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (318 bp):
CCCGGGTCAGTTTTGCATGATTTTTAGTGGCTAAAACTCCTTGAAATATCTATATTCATCTAATC
AAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
TTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAGAGTCCTTCAATTTTTT
GATTTAAATTATATATATTTTATGAGTATTATGGTAAAAATTGAGGAAAAATATTTCGGGTCAAT
TTTTGCAAAATTTTAGCCGAAATCGTCACGGTTTTTGGCTAAAAACACGTTTAGGGAT
Found at i:53898 original size:651 final size:652
Alignment explanation
Indices: 52792--54031 Score: 1471
Period size: 657 Copynumber: 1.9 Consensus size: 652
52782 CGGTTCAGTG
* * *
52792 TTGCATGATTTTTTGCGCCGAGACTCCTTGAAATATCTATATTAATCTAACCAAATCCCATCCAC
1 TTGCATGATTTTTGGCGCCGAGACTCCTTGAAATAGCTATATTAATCTAACCAAATCCCAGCCAC
*
52857 AATGGATTTAAGGATTTGTAAAACAAGCATCTGAATTATATTTCGATTTAATTAGAAATTAATTC
66 AATGAATTTAAGGATTTGTAAAACAAGCATCTGAATTATATTTCGATTTAATTAGAAATTAATTC
* * * * *
52922 AGAAAATAATAGGAAAAACGATACTAGAAGCATGAAAAGCCCTTCAATCTTTTTCGAGTTGAATT
131 AGAAAATAATAGAAAAAACGATACTAAAAGCATGAAAAGCCCTCCAATATTTTTCGAGTTGAATA
* * * *
52987 ATATAATTTTTATGAGTATTGCGGCTAAAACTTGAGGAAATAACTTTATTTCGAGCTAATTTTTG
196 ATATAATTTCTATAAGTATTGCGGCTAAAAATGGAGGAAATAA--TTATTTCGAGCTAATTTTTG
* * * * * *
53052 TAAAATTCTAGCCGAAATTGTGTAATAATCATCACGGATTTTGGTTAAAAAAGTGTTCCGGGGCC
259 CAAAATTCTAGCCGAAATCGTG--ATAACCATCACGGATTTTGGCTAAAAAAGCGTTCCAGGGCC
* *
53117 TCAGCTACGTTTTGCATGATTTTTTATGCTAAAACTCTTTGAAATATCCATATTCATCTAATCAA
322 TCAGCTACGTTTTGCATGATTTTTTATGCTAAAACTCCTTGAAATATCCATATTCATCAAATCAA
* *
53182 ATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCTTGTGAATCTGGTTTCGATTTAATT
387 ATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCTTGTGAATCTGGTTTCAATTTAATT
* * *
53247 AGAAATTAA-TTCAGAA-AAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTTCAATCTTTT
452 AGAAATTAATTTCAAAACAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAAT-TTTT
* * * *
53310 TGATGTTAAATTATATATATTTTATGAGTATGTATGCC-AAAAATTGACGGAAAAATTTTTTGGG
516 TCACGTTAAATTATATAT-TTTTATGAGTAT-TATGCCTAAAAATTGA--GAAAAATATTTCGGG
53374 TC-ATTTTTAACAAAATTTTAGCCGAAATCGTCACGGTTTTTGGCTAAAAACACGTTTCGGGATC
577 TCAATTTTTAACAAAATTTTAGCCGAAATCGTCACGGTTTTTGGCTAAAAACACGTTTCGGGATC
53438 CCGGTTTATTT
642 CCGGTTTATTT
* * * **
53449 TTGCATGATTTTTGGCGCTGAGACTCCTTGAAATAGCTATATTCATCTAATCAAATCTTAGCCAC
1 TTGCATGATTTTTGGCGCCGAGACTCCTTGAAATAGCTATATTAATCTAACCAAATCCCAGCCAC
* *** * *
53514 ATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCT-TGTTTCGATTTAATTAGAAATTAAT
66 AATGAATTTAAGGATTTG-TAAAACAAGCATCTGAAT-TATATTTCGATTTAATTAGAAATTAAT
* * * * * * *
53578 TCAG-AAA-AATATGAAAAAACGATATTAAAAGCGTGAAGAGTCCTCCAATATTTTTGGATTTTA
129 TCAGAAAATAATA-GAAAAAACGATACTAAAAGCATGAAAAGCCCTCCAATATTTTTCGAGTTGA
** *
53641 ATAATAT-ATATTCTATAAGTATTTTGG-TAAAAAATGGAGGAAA-AA-TATTTCG-GGTCAATT
193 ATAATATAAT-TTCTATAAGTATTGCGGCT-AAAAATGGAGGAAATAATTATTTCGAGCT-AATT
* * * **
53701 TTTGCAAAATTTTAG-CGAAATCGTG-T-ACCATCACGGTTTTTTTTGGCTAAAAACGCGTTTTA
255 TTTGCAAAATTCTAGCCGAAATCGTGATAACCATCACGG---ATTTTGGCTAAAAAAGCGTTCCA
* * * * *
53763 GGG-CTCTGGGT-CAGTTTTGCATGA-TTTTTAGTGGC-AACATTCCTTGAAATATCTATATTCA
317 GGGCCTC-AGCTAC-GTTTTGCATGATTTTTTA-T-GCTAAAACTCCTTGAAATATCCATATTCA
* *
53824 TCAAA-CTAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATT-TGAATCAT-GT
378 TCAAATC-AAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGC-TTGTGAATC-TGGT
* * * * *
53886 TTTAATTTAATTAGAAATTAATTTGAAAACAAATAGGACAAACGATATTAGAAGCGTGAGAAGCC
440 TTCAATTTAATTAGAAATTAATTTCAAAACAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCC
* *
53951 CTTCAATTTTTTCCCGTTAAATTATATATTTTTATGAGTATTGTGCCTAAAAATTGAGAAAAATA
505 CTTCAATTTTTTCACGTTAAATTATATATTTTTATGAGTATTATGCCTAAAAATTGAGAAAAATA
54016 TTTCGGGTCAATTTTT
570 TTTCGGGTCAATTTTT
54032 GTAGAATTT
Statistics
Matches: 493, Mismatches: 70, Indels: 47
0.81 0.11 0.08
Matches are distributed among these distances:
648 9 0.02
649 16 0.03
650 22 0.04
651 146 0.30
652 40 0.08
653 61 0.12
656 9 0.02
657 147 0.30
658 42 0.09
659 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (652 bp):
TTGCATGATTTTTGGCGCCGAGACTCCTTGAAATAGCTATATTAATCTAACCAAATCCCAGCCAC
AATGAATTTAAGGATTTGTAAAACAAGCATCTGAATTATATTTCGATTTAATTAGAAATTAATTC
AGAAAATAATAGAAAAAACGATACTAAAAGCATGAAAAGCCCTCCAATATTTTTCGAGTTGAATA
ATATAATTTCTATAAGTATTGCGGCTAAAAATGGAGGAAATAATTATTTCGAGCTAATTTTTGCA
AAATTCTAGCCGAAATCGTGATAACCATCACGGATTTTGGCTAAAAAAGCGTTCCAGGGCCTCAG
CTACGTTTTGCATGATTTTTTATGCTAAAACTCCTTGAAATATCCATATTCATCAAATCAAATCT
CAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCTTGTGAATCTGGTTTCAATTTAATTAGAA
ATTAATTTCAAAACAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATTTTTTCACG
TTAAATTATATATTTTTATGAGTATTATGCCTAAAAATTGAGAAAAATATTTCGGGTCAATTTTT
AACAAAATTTTAGCCGAAATCGTCACGGTTTTTGGCTAAAAACACGTTTCGGGATCCCGGTTTAT
TT
Done.