Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1733
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: 59764
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:3146 original size:20 final size:20
Alignment explanation
Indices: 3121--3169 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3111 CAAGGTCTAA
3121 TATCGATACATTCACTTATG
1 TATCGATACATTCACTTATG
* *
3141 TATCGACACATTTACTTATG
1 TATCGATACATTCACTTATG
*
3161 TATCAATAC
1 TATCGATAC
3170 CTTAACTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (20 bp):
TATCGATACATTCACTTATG
Found at i:3177 original size:20 final size:20
Alignment explanation
Indices: 3121--3191 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
3111 CAAGGTCTAA
* *
3121 TATCGATACATTCACTTATG
1 TATCAATACATTAACTTATG
* * *
3141 TATCGACACATTTACTTATG
1 TATCAATACATTAACTTATG
* *
3161 TATCAATACCTTAACTTGTTG
1 TATCAATACATTAACTT-ATG
3182 TATCAATACA
1 TATCAATACA
3192 AATTATAGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 31 0.74
21 11 0.26
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.39
Consensus pattern (20 bp):
TATCAATACATTAACTTATG
Found at i:5848 original size:20 final size:20
Alignment explanation
Indices: 5814--5869 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
5804 GTTGGGCTCA
* *
5814 ATGTATTGATTCAATGCACT
1 ATGTATCGATACAATGCACT
* *
5834 ATGTATCGATACAATTCATT
1 ATGTATCGATACAATGCACT
* *
5854 AGGTATCGATATAATG
1 ATGTATCGATACAATG
5870 TATCGATACA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACAATGCACT
Found at i:5950 original size:32 final size:33
Alignment explanation
Indices: 5907--5971 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
5897 TGCCAATTTT
*
5907 ATGTATTGATACCAAG-AACATGTATCGATACA
1 ATGTATAGATACCAAGCAACATGTATCGATACA
* *
5939 ATGTATAGATACTAAGCAATATGTATCGATACA
1 ATGTATAGATACCAAGCAACATGTATCGATACA
5972 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (33 bp):
ATGTATAGATACCAAGCAACATGTATCGATACA
Found at i:6737 original size:56 final size:56
Alignment explanation
Indices: 6663--6778 Score: 205
Period size: 56 Copynumber: 2.1 Consensus size: 56
6653 CCCTTTATAG
* * *
6663 AACAATTTTTCTCCACCTTAACAAAACATTTATTAACAACTACTCCCTTTTTCTAA
1 AACAACTTTTCTCCACCTTAACAAAACATTTATTAACAACAACTCCCCTTTTCTAA
6719 AACAACTTTTCTCCACCTTAACAAAACATTTATTAACAACAACTCCCCTTTTCTAA
1 AACAACTTTTCTCCACCTTAACAAAACATTTATTAACAACAACTCCCCTTTTCTAA
6775 AACA
1 AACA
6779 TTTATCAACT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (56 bp):
AACAACTTTTCTCCACCTTAACAAAACATTTATTAACAACAACTCCCCTTTTCTAA
Found at i:19086 original size:31 final size:31
Alignment explanation
Indices: 19043--19118 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
19033 TATAATAAAA
* *
19043 AATGTATCGATACATTTGGGTCAAAACCCAT
1 AATGTATCGATACATATGGGTCAAAACCCAG
*
19074 AATGTATTGATACATATGGGTCAAAACCCAG
1 AATGTATCGATACATATGGGTCAAAACCCAG
19105 AATGTATCGATACA
1 AATGTATCGATACA
19119 ATGAAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (31 bp):
AATGTATCGATACATATGGGTCAAAACCCAG
Found at i:23643 original size:19 final size:19
Alignment explanation
Indices: 23619--23673 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
23609 TGTATCGATA
*
23619 CATTGTATCTATACATGTT
1 CATTGTATCGATACATGTT
23638 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGTT
*
23657 AATTGTATCGATACATG
1 CATTGTATCGATACATG
23674 AAACTGGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (19 bp):
CATTGTATCGATACATGTT
Found at i:23737 original size:13 final size:13
Alignment explanation
Indices: 23719--23770 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
23709 GATACATAGC
23719 ACATTGTATCGAT
1 ACATTGTATCGAT
23732 ACATTGTATCGAT
1 ACATTGTATCGAT
23745 ACA-TG-AT---T
1 ACATTGTATCGAT
23753 A-ATTGTATCGAT
1 ACATTGTATCGAT
23765 ACATTG
1 ACATTG
23771 CTTCTAACGG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
7 1 0.03
8 4 0.12
9 2 0.06
11 2 0.06
12 4 0.12
13 20 0.61
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:23744 original size:33 final size:33
Alignment explanation
Indices: 23702--23770 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
23692 CTACCACTGT
23702 TTGTATCGATACAT-AGCACATTGTATCGATACA
1 TTGTATCGATACATGAGCA-ATTGTATCGATACA
**
23735 TTGTATCGATACATGATTAATTGTATCGATACA
1 TTGTATCGATACATGAGCAATTGTATCGATACA
23768 TTG
1 TTG
23771 CTTCTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGAGCAATTGTATCGATACA
Found at i:25990 original size:20 final size:20
Alignment explanation
Indices: 25967--26039 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
25957 ACAATTCAAA
25967 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
25987 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
26008 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
26028 GTATCGATACAT
1 GTATCGATACAT
26040 AAAAAAAGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:26017 original size:41 final size:42
Alignment explanation
Indices: 25967--26061 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 42
25957 ACAATTCAAA
*
25967 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
*
26008 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
26050 GTATCGATACAT
1 GTATCGATACAT
26062 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 32 0.63
42 19 0.37
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:26118 original size:13 final size:13
Alignment explanation
Indices: 26100--26125 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26090 TACAGCAAGT
26100 ATGTATCGATACA
1 ATGTATCGATACA
26113 ATGTATCGATACA
1 ATGTATCGATACA
26126 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:30207 original size:15 final size:15
Alignment explanation
Indices: 30187--30217 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30177 TAAAAATGTC
*
30187 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
30202 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
30217 C
1 C
30218 CAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:32310 original size:20 final size:21
Alignment explanation
Indices: 32231--32309 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
32221 AATGTCCAAA
*
32231 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
32251 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
32276 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
32296 TTGTATCGATACAT
1 ATGTATCGATACAT
32310 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:32314 original size:13 final size:13
Alignment explanation
Indices: 32296--32334 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
32286 ACATTTTTCT
32296 TTGTATCGATACA
1 TTGTATCGATACA
32309 TTGTATCGATACA
1 TTGTATCGATACA
*
32322 CTGTATCGATACA
1 TTGTATCGATACA
32335 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:34803 original size:20 final size:20
Alignment explanation
Indices: 34780--34852 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
34770 ACAATTCAAA
34780 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
34800 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
34821 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
34841 GTATCGATACAT
1 GTATCGATACAT
34853 AAAAAAAGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:34831 original size:41 final size:42
Alignment explanation
Indices: 34780--34874 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 42
34770 ACAATTCAAA
*
34780 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
*
34821 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
34863 GTATCGATACAT
1 GTATCGATACAT
34875 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 32 0.63
42 19 0.37
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:34931 original size:13 final size:13
Alignment explanation
Indices: 34913--34938 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34903 TACAGCAAGT
34913 ATGTATCGATACA
1 ATGTATCGATACA
34926 ATGTATCGATACA
1 ATGTATCGATACA
34939 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:39385 original size:16 final size:17
Alignment explanation
Indices: 39359--39391 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
39349 ATTATCAAAG
39359 GGGAGAAATTTTTTTAA
1 GGGAGAAATTTTTTTAA
39376 GGGA-AAATTTTTTTAA
1 GGGAGAAATTTTTTTAA
39392 TGAGAGCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (17 bp):
GGGAGAAATTTTTTTAA
Found at i:41371 original size:21 final size:21
Alignment explanation
Indices: 41347--41403 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
41337 ATTACATAGC
41347 TTTAAATAAAATTTATTTTAA
1 TTTAAATAAAATTTATTTTAA
** *
41368 TTTAAATTTAATTTA-ATTAA
1 TTTAAATAAAATTTATTTTAA
41388 TTT--ATAAAA-TTATTTT
1 TTTAAATAAAATTTATTTT
41404 TAAACATTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 3 0.10
18 6 0.21
20 7 0.24
21 13 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAAATAAAATTTATTTTAA
Found at i:41374 original size:16 final size:16
Alignment explanation
Indices: 41355--41385 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41345 GCTTTAAATA
*
41355 AAATTTATTTTAATTT
1 AAATTTAATTTAATTT
41371 AAATTTAATTTAATT
1 AAATTTAATTTAATT
41386 AATTTATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATTTAATTTAATTT
Found at i:42329 original size:29 final size:30
Alignment explanation
Indices: 42300--42356 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 30
42290 AAAATAATTA
*
42300 TATTATTTT-ATTATAT-TTTTAA-ATTTT
1 TATTATTTTAAATATATCTTTTAATATTTT
42327 TATTATTTTAAATATATCTTTTAATATTTT
1 TATTATTTTAAATATATCTTTTAATATTTT
42357 AAATTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.35
28 6 0.23
29 6 0.23
30 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (30 bp):
TATTATTTTAAATATATCTTTTAATATTTT
Found at i:42370 original size:30 final size:28
Alignment explanation
Indices: 42311--42378 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 28
42301 ATTATTTTAT
* *
42311 TATATTTTTAAATTTTTATTATTTTAAA
1 TATATTTTTAAATTTTAATTATTTAAAA
42339 TATATCTTTTAATATTTTAAATT-TTTAAAA
1 TATAT-TTTTAA-ATTTT-AATTATTTAAAA
*
42369 TATTTTTTTA
1 TATATTTTTA
42379 CAATAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 5 0.15
29 11 0.32
30 15 0.44
31 3 0.09
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (28 bp):
TATATTTTTAAATTTTAATTATTTAAAA
Found at i:44551 original size:18 final size:18
Alignment explanation
Indices: 44524--44566 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
44514 CATTATGTAC
*
44524 ATAATAATAA-AAAAAATA
1 ATAATCATAACAAAAAA-A
*
44542 ATAATCATAACAATAAAA
1 ATAATCATAACAAAAAAA
44560 ATAATCA
1 ATAATCA
44567 CGTTAATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAATCATAACAAAAAAA
Found at i:45117 original size:16 final size:16
Alignment explanation
Indices: 45096--45127 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
45086 TTTATATTAC
*
45096 AAAATAATTTTTTAAT
1 AAAATAATTATTTAAT
45112 AAAATAATTATTTAAT
1 AAAATAATTATTTAAT
45128 TTTAAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATAATTATTTAAT
Found at i:45525 original size:24 final size:22
Alignment explanation
Indices: 45471--45525 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
45461 AAAATAAAAT
*
45471 AAAATT-TATTAATATTTTTTA
1 AAAATTATATAAATATTTTTTA
45492 AAAATTTTATATAAATATTTCTTTCA
1 AAAA--TTATATAAATATTT-TTT-A
45518 AAAATTAT
1 AAAATTAT
45526 TTATTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 4 0.14
23 2 0.07
24 14 0.50
25 3 0.11
26 5 0.18
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATTATATAAATATTTTTTA
Found at i:45592 original size:22 final size:23
Alignment explanation
Indices: 45544--45592 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
45534 AAACTTTATC
***
45544 TAAAATTAATCACTTTTTTTTTT
1 TAAAATTAATCACTTTTTTTAAA
*
45567 TAAAATTACTCA-TTTTTTTAAA
1 TAAAATTAATCACTTTTTTTAAA
45589 TAAA
1 TAAA
45593 TATATATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAAATTAATCACTTTTTTTAAA
Found at i:51392 original size:68 final size:67
Alignment explanation
Indices: 51320--51567 Score: 272
Period size: 68 Copynumber: 3.7 Consensus size: 67
51310 ACATCTCGGT
* * *
51320 ATATAAGCAAGTGACACCAAGTCACTTATGCTAATAAATGACCTCAAAGCTTTGATCGACATCTT
1 ATATAAACAAGTGACACCAAGTCACTTATGCTAATAAACGACCTCAAAGATTTGATCGA-ATCTT
51385 AAC
65 AAC
* * * * * *
51388 ATATAAACAAGTGATACCAAGTCACTTATGCTAACAAACCATCTTAAAGATTTGCTCGATAT-TT
1 ATATAAACAAGTGACACCAAGTCACTTATGCTAATAAACGACCTCAAAGATTTGATCGA-ATCTT
51452 CAAC
65 -AAC
* * ** * * * *
51456 ATATAAACGAGTGACACTAAGTCACTTATAATAATAAATGACCTCAAAGGTTTGATTGAATCTCA
1 ATATAAACAAGTGACACCAAGTCACTTATGCTAATAAACGACCTCAAAGATTTGATCGAATCTTA
51521 AC
66 AC
*
51523 ATATAAACAAGTGACA-C---TAACTTATGCTAATAAACGACCTCAAAG
1 ATATAAACAAGTGACACCAAGTCACTTATGCTAATAAACGACCTCAAAG
51568 GTACTTGACG
Statistics
Matches: 148, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
63 24 0.16
67 22 0.15
68 102 0.69
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (67 bp):
ATATAAACAAGTGACACCAAGTCACTTATGCTAATAAACGACCTCAAAGATTTGATCGAATCTTA
AC
Found at i:51493 original size:136 final size:135
Alignment explanation
Indices: 51276--51536 Score: 362
Period size: 136 Copynumber: 1.9 Consensus size: 135
51266 ATAAGTGACG
* *** *
51276 CTTATGCTAACAAACCACCTTAAAACTTTGCTTGACATCTCGGTATATAAGCAAGTGACACCAAG
1 CTTATGCTAACAAACCACCTTAAAACTTTGCTCGACATCTCAACATATAAACAAGTGACACCAAG
** *
51341 TCACTTATGCTAATAAATGACCTCAAAGCTTTGATCGACATCTTAACATATAAACAAGTGATACC
66 TCACTTATAATAATAAATGACCTCAAAGCTTTGATCGA-ATCTCAACATATAAACAAGTGATACC
51406 AAGTCA
130 AAGTCA
* * * * *
51412 CTTATGCTAACAAACCATCTTAAAGA-TTTGCTCGATATTTCAACATATAAACGAGTGACACTAA
1 CTTATGCTAACAAACCACCTTAAA-ACTTTGCTCGACATCTCAACATATAAACAAGTGACACCAA
* *
51476 GTCACTTATAATAATAAATGACCTCAAAGGTTTGATTGAATCTCAACATATAAACAAGTGA
65 GTCACTTATAATAATAAATGACCTCAAAGCTTTGATCGAATCTCAACATATAAACAAGTGA
51537 CACTAACTTA
Statistics
Matches: 109, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
135 21 0.19
136 87 0.80
137 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (135 bp):
CTTATGCTAACAAACCACCTTAAAACTTTGCTCGACATCTCAACATATAAACAAGTGACACCAAG
TCACTTATAATAATAAATGACCTCAAAGCTTTGATCGAATCTCAACATATAAACAAGTGATACCA
AGTCA
Found at i:59725 original size:20 final size:21
Alignment explanation
Indices: 59700--59755 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
59690 AAAACCCTTA
59700 AAAGTATCGATACACAATT-C
1 AAAGTATCGATACACAATTGC
**
59720 AAAGTATCGATACA-TGTTGC
1 AAAGTATCGATACACAATTGC
59740 AAATGTATCGATACAC
1 AAA-GTATCGATACAC
59756 TGAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 18 0.58
21 11 0.35
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (21 bp):
AAAGTATCGATACACAATTGC
Done.