Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1525
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: 28013
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Found at i:429 original size:47 final size:46
Alignment explanation
Indices: 273--493 Score: 235
Period size: 47 Copynumber: 4.8 Consensus size: 46
263 AAAAGGATGT
* * *
273 CAATGTGCTGATT-AAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-AT----AAGGTGC
324 CAATATGCTGATTC-AGGCCAGCT-TATTGGACTT--A-AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAATAAGGTGC
*
365 CAATGTGCTGATTCAAGG-CAGCTATATT-GACTTAAAGTGAACGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-T-AA-GGTGC
412 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATATAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAA-ATAAGGTGC
* *
459 CAATATGCTGATTCAAGGCCGGCTACATTGG-CTTA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
494 GAAGGTTGCC
Statistics
Matches: 151, Mismatches: 7, Indels: 29
0.81 0.04 0.16
Matches are distributed among these distances:
41 30 0.20
42 7 0.05
43 1 0.01
46 7 0.05
47 56 0.37
48 12 0.08
49 8 0.05
50 9 0.06
51 21 0.14
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (46 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAATAAGGTGC
Found at i:472 original size:94 final size:92
Alignment explanation
Indices: 264--488 Score: 289
Period size: 92 Copynumber: 2.4 Consensus size: 92
254 AAAGATGAGA
*
264 AAAGGATGTCAATGTGCTGATT-AAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGG-CAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
328 ATGCTGATTCAGGCCAGCTTATTGGACTT
64 ATGCTGATTCAGGCCAGCTTATTGGACTT
* *
357 AAAGGTGCCAATGTGCTGATTCAAGGCAGCTATATTG-ACTTAAAG-T-G-AACGGTGCCAATAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATAT
418 GCTGATTCAAGGCCAGCTATATTGGACTTAAT
66 GCTGATTC-AGGCCAGCT-TATTGGAC-T--T
* *
450 ATAAGGTGCCAATATGCTGATTCAAGGCCGGCTACATTG
1 A-AAGGTGCCAATGTGCTGATTCAAGG-CAGCTACATTG
489 GCTTAGAAGG
Statistics
Matches: 118, Mismatches: 6, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
88 21 0.18
89 10 0.08
90 9 0.08
91 9 0.08
92 25 0.21
93 11 0.09
94 24 0.20
95 9 0.08
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATAT
GCTGATTCAGGCCAGCTTATTGGACTT
Found at i:535 original size:31 final size:29
Alignment explanation
Indices: 488--600 Score: 117
Period size: 27 Copynumber: 3.9 Consensus size: 29
478 CGGCTACATT
* *
488 GGCTTAGAAGGTTGCCACCGACTTGTGTG
1 GGCTTGGAAGGTTGCCACTGACTTGTGTG
*
517 GGCTTGGAAAAGGGTGCCACTGA-TT-TGTG
1 GGCTTGG--AAGGTTGCCACTGACTTGTGTG
*
546 GGCTTTGAAGGTTGCCACTGAC-T-TGTG
1 GGCTTGGAAGGTTGCCACTGACTTGTGTG
**
573 GGCTTTTAAAGGTTGCCACTGACTTGTG
1 GGC-TTGGAAGGTTGCCACTGACTTGTG
601 GGCTTTTGAA
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
27 21 0.29
28 18 0.25
29 17 0.24
30 4 0.06
31 12 0.17
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.31
Consensus pattern (29 bp):
GGCTTGGAAGGTTGCCACTGACTTGTGTG
Found at i:593 original size:28 final size:28
Alignment explanation
Indices: 495--690 Score: 188
Period size: 29 Copynumber: 7.0 Consensus size: 28
485 ATTGGCTTAG
* **
495 AAGGTTGCCACCGACTTGTGTGGGCTTGGAA
1 AAGGTTGCCACTGAC-T-TGTGGGCTT-TTA
* * *
526 AAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAGGTTGCCACTGACTTGTGGGCTTTTA
553 AAGGTTGCCACTGACTTGTGGGCTTTTA
1 AAGGTTGCCACTGACTTGTGGGCTTTTA
581 AAGGTTGCCACTGACTTGTGGGCTTTTGA
1 AAGGTTGCCACTGACTTGTGGGCTTTT-A
* *
610 AA-ATATGCCACTGACTTGTGGCCTTTTGA
1 AAGGT-TGCCACTGACTTGTGGGCTTTT-A
639 ACAGG-TGCCACT-ACTTGT-GGCTTTT-
1 A-AGGTTGCCACTGACTTGTGGGCTTTTA
* * *
664 AAGGTTGCCACTAAATTATGGGCTTTT
1 AAGGTTGCCACTGACTTGTGGGCTTTT
691 GAAAAATTAT
Statistics
Matches: 142, Mismatches: 15, Indels: 20
0.80 0.08 0.11
Matches are distributed among these distances:
24 3 0.02
25 8 0.06
26 4 0.03
27 34 0.24
28 38 0.27
29 41 0.29
30 2 0.01
31 12 0.08
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (28 bp):
AAGGTTGCCACTGACTTGTGGGCTTTTA
Found at i:628 original size:29 final size:28
Alignment explanation
Indices: 531--694 Score: 185
Period size: 28 Copynumber: 5.9 Consensus size: 28
521 TGGAAAAGGG
* *
531 TGCCACTGATTTGTGGGC-TTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAGT
558 TGCCACTGACTTGTGGGCTTTT-AAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAA-GT
*
586 TGCCACTGACTTGTGGGCTTTTGAAAAT
1 TGCCACTGACTTGTGGGCTTTTGAAAGT
* *
614 ATGCCACTGACTTGTGGCCTTTTGAACAGG
1 -TGCCACTGACTTGTGGGCTTTTGAA-AGT
*
644 TGCCACT-ACTTGT-GGCTTTT-AAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAGT
* * *
669 TGCCACTAAATTATGGGCTTTTGAAA
1 TGCCACTGACTTGTGGGCTTTTGAAA
695 AATTATACCC
Statistics
Matches: 117, Mismatches: 12, Indels: 15
0.81 0.08 0.10
Matches are distributed among these distances:
25 8 0.07
26 6 0.05
27 32 0.27
28 36 0.31
29 34 0.29
30 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.35
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTTGAAAGT
Found at i:648 original size:86 final size:84
Alignment explanation
Indices: 495--749 Score: 243
Period size: 86 Copynumber: 3.0 Consensus size: 84
485 ATTGGCTTAG
* * ** *
495 AAGGTTGCCACCGACTTGTGTGGGC-TTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGG
1 AAGGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAGTATGCCACTGACTTGT-GGCTTTTGAAAGG
*
557 TTGCCACTGACTTGTGGGCTTTT
63 ATGCCACT-ACTTGTGGGCTTTT
580 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAA-TATGCCACTGACTTGTGGCCTTTTGAACAGG
1 -AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGTATGCCACTGACTTGTGG-CTTTTGAA-AGG
644 -TGCCACTACTTGT-GGCTTTT
63 ATGCCACTACTTGTGGGCTTTT
* * * * * * *
664 AAGGTTGCCACTAAATTATGGGCTTTTGAAAAATTATACCCACTGACCTGTGGCTGTTGAAAGGG
1 AAGGTTGCCACTGACTTGTGGGCTTTTG-AAAAGTAT-GCCACTGACTTGTGGCTTTTGAAA--G
729 GATGCCACTAACTTGTGGGCT
62 GATGCCACT-ACTTGTGGGCT
750 GAAAGGAGTG
Statistics
Matches: 145, Mismatches: 11, Indels: 23
0.81 0.06 0.13
Matches are distributed among these distances:
83 27 0.19
84 33 0.23
85 28 0.19
86 37 0.26
87 10 0.07
88 6 0.04
89 4 0.03
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (84 bp):
AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGTATGCCACTGACTTGTGGCTTTTGAAAGGATG
CCACTACTTGTGGGCTTTT
Found at i:655 original size:57 final size:55
Alignment explanation
Indices: 529--663 Score: 177
Period size: 57 Copynumber: 2.4 Consensus size: 55
519 CTTGGAAAAG
* ** *
529 GGTGCCACTGATTTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTTTAAA
1 GGTGCCACTGACTTGTGGGCTTTTGAAAATTGCCACTGACTTGTGGCCTTTTAAA
583 GGTTGCCACTGACTTGTGGGCTTTTGAAAATATGCCACTGACTTGTGGCCTTTTGAACA
1 GG-TGCCACTGACTTGTGGGCTTTTGAAAAT-TGCCACTGACTTGTGGCCTTTT-AA-A
642 GGTGCCACT-ACTTGT-GGCTTTT
1 GGTGCCACTGACTTGTGGGCTTTT
664 AAGGTTGCCA
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
54 2 0.03
55 17 0.24
56 14 0.19
57 27 0.38
58 9 0.12
59 3 0.04
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (55 bp):
GGTGCCACTGACTTGTGGGCTTTTGAAAATTGCCACTGACTTGTGGCCTTTTAAA
Found at i:693 original size:83 final size:84
Alignment explanation
Indices: 531--749 Score: 232
Period size: 84 Copynumber: 2.5 Consensus size: 84
521 TGGAAAAGGG
* * * *
531 TGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGAC
1 TGCCACTGACTTGTGGCCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTAAA
*
596 TTGTGGGCTTTTGAAAATA
66 TTATGGGCTTTTGAAAATA
615 TGCCACTGACTTGTGGCCTTTTGAACAGG-TGCCACT-ACTTGT-GGCTTTT-AAGGTTGCCACT
1 TGCCACTGACTTGTGGCC-TTTG-A-AGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACT
676 AAATTATGGGCTTTTGAAAAATTA
63 AAATTATGGGCTTTTG-AAAA-TA
* * * *
700 TACCCACTGACCTGTGG-CTGTTGAAAGGGGATGCCACTAACTTGTGGGCT
1 T-GCCACTGACTTGTGGCCT-TTG-AA--GGTTGCCACTGACTTGTGGGCT
750 GAAAGGAGTG
Statistics
Matches: 116, Mismatches: 7, Indels: 19
0.82 0.05 0.13
Matches are distributed among these distances:
83 25 0.22
84 29 0.25
85 19 0.16
86 23 0.20
87 10 0.09
88 6 0.05
89 4 0.03
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (84 bp):
TGCCACTGACTTGTGGCCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTAAA
TTATGGGCTTTTGAAAATA
Found at i:928 original size:30 final size:28
Alignment explanation
Indices: 825--961 Score: 105
Period size: 29 Copynumber: 4.7 Consensus size: 28
815 GAAACGATGC
* *
825 CCACCGACTTGTGGGCTTCGAAAAAGGGTG
1 CCACCGACTTGTGGGCTTTGAAAAA--ATG
* * ***
855 CCACGGATTTGTGGGCTTTG-AAGGTTG
1 CCACCGACTTGTGGGCTTTGAAAAAATG
*
882 CCACTTGACGTTGTGGGCTTTTCGAAAAAATG
1 CCAC-CGAC-TTGTGGGC-TTT-GAAAAAATG
*
914 CCACCGACTTGTGGGCTTTGAAAAAAATA
1 CCACCGACTTGTGGGCTTTG-AAAAAATG
* *
943 CCACTGACTTGTGGACTTT
1 CCACCGACTTGTGGGCTTT
962 TGAAGGTGAT
Statistics
Matches: 86, Mismatches: 15, Indels: 13
0.75 0.13 0.11
Matches are distributed among these distances:
27 6 0.07
28 3 0.03
29 37 0.43
30 28 0.33
31 4 0.05
32 8 0.09
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (28 bp):
CCACCGACTTGTGGGCTTTGAAAAAATG
Found at i:2437 original size:7 final size:7
Alignment explanation
Indices: 2399--2480 Score: 73
Period size: 7 Copynumber: 11.6 Consensus size: 7
2389 CCGGACCCCC
2399 TTTTTTG
1 TTTTTTG
2406 -TTTTTG
1 TTTTTTG
2412 TTTGTTTG
1 TTT-TTTG
*
2420 TTTATTG
1 TTTTTTG
2427 -TTTTTG
1 TTTTTTG
*
2433 TTTTTTT
1 TTTTTTG
2440 TTCCTTTTG
1 TT--TTTTG
2449 TTTTTTTTG
1 --TTTTTTG
2458 TTTTTTG
1 TTTTTTG
2465 TTTTTT-
1 TTTTTTG
2471 TTTTTT-
1 TTTTTTG
2477 TTTT
1 TTTT
2481 CATTTTTTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
6 21 0.33
7 25 0.39
8 7 0.11
9 9 0.14
11 2 0.03
ACGTcount: A:0.01, C:0.02, G:0.11, T:0.85
Consensus pattern (7 bp):
TTTTTTG
Found at i:2458 original size:38 final size:37
Alignment explanation
Indices: 2407--2479 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 37
2397 CCTTTTTTGT
2407 TTTTGTTTGTTTGTTTATTGTTTTTGTTTTTTTTTCC
1 TTTTGTTTGTTTGTTTATTGTTTTTGTTTTTTTTTCC
* * *
2444 TTTTGTTTTTTTTGTTTTTTGTTTTTTTTTTTTTTT
1 TTTTG-TTTGTTTGTTTATTGTTTTTGTTTTTTTTT
2480 TCATTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 5 0.16
38 27 0.84
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (37 bp):
TTTTGTTTGTTTGTTTATTGTTTTTGTTTTTTTTTCC
Found at i:2468 original size:32 final size:33
Alignment explanation
Indices: 2412--2473 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
2402 TTTGTTTTTG
2412 TTTGTTTGTTTATTGTTTTTGTTTTTTTTTCCT
1 TTTGTTTGTTTATTGTTTTTGTTTTTTTTTCCT
2445 TTTGTTT-TTT-TTGTTTTTTGTTTTTTTTT
1 TTTGTTTGTTTATTG-TTTTTGTTTTTTTTT
2474 TTTTTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
31 3 0.11
32 18 0.64
33 7 0.25
ACGTcount: A:0.02, C:0.03, G:0.11, T:0.84
Consensus pattern (33 bp):
TTTGTTTGTTTATTGTTTTTGTTTTTTTTTCCT
Found at i:2478 original size:16 final size:16
Alignment explanation
Indices: 2399--2479 Score: 90
Period size: 16 Copynumber: 4.9 Consensus size: 16
2389 CCGGACCCCC
*
2399 TTTTTTGTTTTTGTTTG
1 TTTTTT-TTTTTTTTTG
* *
2416 TTTGTTTATTGTTTTTG
1 TTT-TTTTTTTTTTTTG
**
2433 TTTTTTTTTCCTTTTG
1 TTTTTTTTTTTTTTTG
*
2449 TTTTTTTTGTTTTTTG
1 TTTTTTTTTTTTTTTG
2465 TTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTT
2480 TCATTTTTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
16 37 0.70
17 13 0.25
18 3 0.06
ACGTcount: A:0.01, C:0.02, G:0.11, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTTTTTTTG
Found at i:2486 original size:17 final size:17
Alignment explanation
Indices: 2449--2489 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2439 TTTCCTTTTG
**
2449 TTTTTTTTGTTTTTTGT
1 TTTTTTTTGTTTTTTCA
*
2466 TTTTTTTTTTTTTTTCA
1 TTTTTTTTGTTTTTTCA
2483 TTTTTTT
1 TTTTTTT
2490 GGAGGACGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.02, C:0.02, G:0.05, T:0.90
Consensus pattern (17 bp):
TTTTTTTTGTTTTTTCA
Found at i:2489 original size:1 final size:1
Alignment explanation
Indices: 2399--2480 Score: 56
Period size: 1 Copynumber: 82.0 Consensus size: 1
2389 CCGGACCCCC
* * * * * * * ** * *
2399 TTTTTTGTTTTTGTTTGTTTGTTTATTGTTTTTGTTTTTTTTTCCTTTTGTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
2464 GTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTT
2481 CATTTTTTTG
Statistics
Matches: 59, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.01, C:0.02, G:0.11, T:0.85
Consensus pattern (1 bp):
T
Found at i:12193 original size:10 final size:10
Alignment explanation
Indices: 12178--12204 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
12168 ATGTATCAAG
12178 CAAAAACAAA
1 CAAAAACAAA
12188 CAAAAACAAA
1 CAAAAACAAA
12198 CAAAAAC
1 CAAAAAC
12205 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:20135 original size:52 final size:52
Alignment explanation
Indices: 20065--20185 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
20055 GAAAATTTAT
*
20065 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
20117 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
20169 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
20186 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:20198 original size:52 final size:51
Alignment explanation
Indices: 20065--20205 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
20055 GAAAATTTAT
20065 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
20117 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
20169 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
20206 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:20212 original size:13 final size:13
Alignment explanation
Indices: 20194--20218 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20184 CAAAGATCAG
20194 TGTATCGATACAA
1 TGTATCGATACAA
20207 TGTATCGATACA
1 TGTATCGATACA
20219 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:20301 original size:13 final size:13
Alignment explanation
Indices: 20283--20307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20273 CAAAAAAATA
20283 TGTATCGATACAT
1 TGTATCGATACAT
20296 TGTATCGATACA
1 TGTATCGATACA
20308 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:20303 original size:33 final size:33
Alignment explanation
Indices: 20261--20327 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
20251 AGTAGCTTAA
20261 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
20294 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
20327 A
1 A
20328 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:27629 original size:20 final size:19
Alignment explanation
Indices: 27604--27676 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
27594 CTACCAATTT
**
27604 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
*
27624 CATGTATCGATGCAATGAA
1 CATGTATCGATACAATGAA
*
27643 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
27664 -ATGTATCGATACA
1 CATGTATCGATACA
27677 TTTGGGTGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:27648 original size:19 final size:20
Alignment explanation
Indices: 27604--27657 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
27594 CTACCAATTT
**
27604 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
*
27624 CATGTATCGATGCAA-TGAA
1 CATGTATCGATACAATTGAA
27643 CATGTATCGATACAA
1 CATGTATCGATACAA
27658 AGCATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Done.