Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1637
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: 53263
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:3533 original size:2 final size:2
Alignment explanation
Indices: 3526--3554 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3516 TTTCTTTCTT
3526 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3555 GATTTTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3781 original size:29 final size:28
Alignment explanation
Indices: 3748--3804 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
3738 AAAAATATAT
3748 ATATATAATTATTAA-AAATTATATTTTAA
1 ATATATAATTA-TAACAAA-TATATTTTAA
* *
3777 ATATATTATTATAACTAATATATTTTAA
1 ATATATAATTATAACAAATATATTTTAA
3805 TAAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
ATATATAATTATAACAAATATATTTTAA
Found at i:9308 original size:6 final size:6
Alignment explanation
Indices: 9285--9324 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
9275 ATCAATTTTC
* * *
9285 CCACCA CCACCG CCACCT CCACCT CTACCT CCACCT CCAC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCAC
9325 TGTCACCACC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.20, C:0.65, G:0.03, T:0.12
Consensus pattern (6 bp):
CCACCT
Found at i:12016 original size:12 final size:12
Alignment explanation
Indices: 11985--12063 Score: 78
Period size: 11 Copynumber: 7.0 Consensus size: 12
11975 CGGCACTATT
11985 ATATAAAATATA
1 ATATAAAATATA
*
11997 AT-TAAAATATG
1 ATATAAAATATA
*
12008 ATATAAAATATG
1 ATATAAAATATA
12020 ATAT--AATATA
1 ATATAAAATATA
*
12030 ATATAAAAAATA
1 ATATAAAATATA
* *
12042 ACAT-AAATAAA
1 ATATAAAATATA
12053 ATAT-AAATATA
1 ATATAAAATATA
12064 CGAATTTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
10 9 0.16
11 24 0.43
12 23 0.41
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (12 bp):
ATATAAAATATA
Found at i:12028 original size:17 final size:17
Alignment explanation
Indices: 11991--12063 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 17
11981 TATTATATAA
11991 AATATAAT-TAAAATAT
1 AATATAATATAAAATAT
* * **
12007 GATATAAAATATGATAT
1 AATATAATATAAAATAT
*
12024 AATATAATATAAAAAAT
1 AATATAATATAAAATAT
*
12041 AACATAA-ATAAAATAT
1 AATATAATATAAAATAT
12057 AAATATA
1 -AATATA
12064 CGAATTTATT
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
16 14 0.33
17 29 0.67
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (17 bp):
AATATAATATAAAATAT
Found at i:12033 original size:10 final size:10
Alignment explanation
Indices: 11987--12058 Score: 60
Period size: 10 Copynumber: 7.1 Consensus size: 10
11977 GCACTATTAT
11987 ATAAAATATA
1 ATAAAATATA
11997 ATTAAAATATGA
1 A-TAAAATAT-A
*
12009 TATAAAATATG
1 -ATAAAATATA
*
12020 ATATAATATA
1 ATAAAATATA
12030 ATATAAA-A-A
1 ATA-AAATATA
*
12039 ATAACATA-A
1 ATAAAATATA
12048 ATAAAATATA
1 ATAAAATATA
12058 A
1 A
12059 ATATACGAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
8 2 0.04
9 13 0.26
10 15 0.30
11 10 0.20
12 9 0.18
13 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (10 bp):
ATAAAATATA
Found at i:12307 original size:2 final size:2
Alignment explanation
Indices: 12300--12337 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12290 AATAATTTGA
12300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12338 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14219 original size:2 final size:2
Alignment explanation
Indices: 14206--14241 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
14196 TTGTTAAATG
*
14206 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14242 TAGAATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14770 original size:2 final size:2
Alignment explanation
Indices: 14763--14800 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14753 AAACATAGTA
14763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14801 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19566 original size:22 final size:21
Alignment explanation
Indices: 19518--19566 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
19508 TTAAAAAGTT
19518 TTCAAACAAAACAATATTTTA
1 TTCAAACAAAACAATATTTTA
* * *
19539 TACAAACAAATATAATTTTTTA
1 TTCAAACAAA-ACAATATTTTA
19561 TTCAAA
1 TTCAAA
19567 ATTTGATATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (21 bp):
TTCAAACAAAACAATATTTTA
Found at i:24763 original size:19 final size:19
Alignment explanation
Indices: 24739--24788 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 19
24729 AGCTGAACTT
*
24739 TAATATTTTAATATAAAAA
1 TAATATTTTAATAAAAAAA
*
24758 TAATA--TTACTAAAAAAA
1 TAATATTTTAATAAAAAAA
24775 TAATATTTTAATAA
1 TAATATTTTAATAA
24789 TATTATAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 15 0.58
19 11 0.42
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATATTTTAATAAAAAAA
Found at i:25626 original size:14 final size:15
Alignment explanation
Indices: 25607--25638 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
25597 GTTCATACAA
25607 TTATTTTTAA-AAAT
1 TTATTTTTAATAAAT
25621 TTATTTTTAATAAAT
1 TTATTTTTAATAAAT
25636 TTA
1 TTA
25639 AATTTTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTTTTAATAAAT
Found at i:25702 original size:2 final size:2
Alignment explanation
Indices: 25692--25735 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
25682 TTTTTTTTTG
* * *
25692 TA TA CA TA TA TC TA TA TA TC TA TA TA TA TA TA TA TA 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
25734 TA
1 TA
25736 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:25740 original size:2 final size:2
Alignment explanation
Indices: 25735--25799 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
25725 ATATATATAT
25735 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25777 AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
25800 AGAAAAGAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:26405 original size:2 final size:2
Alignment explanation
Indices: 26398--26430 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
26388 AAATAAAAGA
26398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26431 GGTTGCTGCT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26930 original size:2 final size:2
Alignment explanation
Indices: 26923--26947 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26913 AAATTTAAAC
26923 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
26948 GTTTTGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28734 original size:2 final size:2
Alignment explanation
Indices: 28727--28766 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
28717 TTATATTCTC
* *
28727 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28767 GTCCAATAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34426 original size:2 final size:2
Alignment explanation
Indices: 34421--34454 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
34411 TCAAAATACA
34421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34455 GTAACTCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36533 original size:12 final size:12
Alignment explanation
Indices: 36511--36561 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
36501 AACTGTGCCG
36511 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
36524 TCAATTTGAAAT
1 TCAATTTGAAAT
*
36536 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
36551 TCAATTTGAAA
1 TCAATTTGAAA
36562 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:36573 original size:27 final size:27
Alignment explanation
Indices: 36517--36573 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
36507 GCCGTCAATT
* *
36517 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
36544 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
36571 TTG
1 TTG
36574 CATAGTACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:41217 original size:12 final size:12
Alignment explanation
Indices: 41200--41225 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41190 GAAAACAAAG
41200 GCTGCCAACTGT
1 GCTGCCAACTGT
41212 GCTGCCAACTGT
1 GCTGCCAACTGT
41224 GC
1 GC
41226 CGTCAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.35, G:0.27, T:0.23
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:41250 original size:12 final size:12
Alignment explanation
Indices: 41228--41278 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
41218 AACTGTGCCG
41228 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
41241 TCAATTTGAAAT
1 TCAATTTGAAAT
*
41253 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
41268 TCAATTTGAAA
1 TCAATTTGAAA
41279 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:41290 original size:27 final size:27
Alignment explanation
Indices: 41234--41290 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
41224 GCCGTCAATT
* *
41234 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
41261 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
41288 TTG
1 TTG
41291 CATAGTGTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:43636 original size:24 final size:22
Alignment explanation
Indices: 43580--43628 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
43570 TGGACATGTT
43580 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
43602 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
43624 AAAAA
1 AAAAA
43629 AATGCATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:44594 original size:20 final size:20
Alignment explanation
Indices: 44571--44621 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
44561 TTGTAGAATA
* *
44571 TATCGATACATTCATACATG
1 TATCGATACATTCAAAAATG
* *
44591 TATCGATATATTGAAAAATG
1 TATCGATACATTCAAAAATG
44611 TATCGATACAT
1 TATCGATACAT
44622 CAGGGTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (20 bp):
TATCGATACATTCAAAAATG
Found at i:45190 original size:32 final size:32
Alignment explanation
Indices: 45149--45999 Score: 1533
Period size: 32 Copynumber: 26.6 Consensus size: 32
45139 GATTTGAAAA
* ** **
45149 GGGTTGCCACTGACTTGCATGGGCTTTTAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45181 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
45213 GGGTTGCCACCGACTTGTGTGGGTTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45245 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45277 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45309 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45341 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45373 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45405 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45437 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
45469 GGGCTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
45501 GGGCTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGG-TTGCCACCGACTTGTGTGGGCTTTGGAAT
45534 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45566 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45598 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45630 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45662 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45694 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45726 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
45758 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
45790 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
45822 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45854 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
45886 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
45918 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
45950 GGGTTGCCACTGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
45982 GGG-TGCCACGGAGTTGTG
1 GGGTTGCCACCGACTTGTG
46000 GATTTAAAAG
Statistics
Matches: 799, Mismatches: 19, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
31 13 0.02
32 756 0.95
33 30 0.04
ACGTcount: A:0.14, C:0.19, G:0.37, T:0.31
Consensus pattern (32 bp):
GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
Found at i:46016 original size:27 final size:27
Alignment explanation
Indices: 45982--46664 Score: 1080
Period size: 27 Copynumber: 25.0 Consensus size: 27
45972 GCTTTGAAAT
*
45982 GGGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
46009 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
46036 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
46063 GGGTGCCACAGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
46090 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
46118 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
46145 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
46172 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
46199 GAGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
46226 AGGTGCGACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
46253 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
46280 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
46307 GAGATGCCACGGAGTTGTGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
46335 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
46363 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
46390 GGGTGCCACGGAGTTGTGGACTTTGAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
46418 -GGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
46444 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* * **
46472 GAGTGCCACAGAGTTGTGGACTTTGAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
46499 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
46526 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
46554 GAGTGCCTCGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* * *
46582 GAGTGCCACGGAGTTATGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
46609 GGGTGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
46637 GGATGCCACGGAGTTGTGGACTTCAAAA
1 GGGTGCCACGGAGTTGTGGACTT-AAAA
46665 AGAAATGCCA
Statistics
Matches: 607, Mismatches: 40, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
26 5 0.01
27 415 0.68
28 187 0.31
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:46116 original size:82 final size:81
Alignment explanation
Indices: 45982--46664 Score: 1080
Period size: 82 Copynumber: 8.3 Consensus size: 81
45972 GCTTTGAAAT
* *
45982 GGGTGCCACGGAGTTGTGGATTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
46047 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* *
46063 GGGTGCCACAGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
46128 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
*
46145 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
46210 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* * *
46226 AGGTGCGACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
46291 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
*
46307 GAGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
46372 GGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
* *
46390 GGGTGCCACGGAGTTGTGGACTTTGAAA-GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
46454 GAGTTGTGGACTTTAAAA
65 GAGTTGTGGAC-TTAAAA
* * **
46472 GAGTGCCACAGAGTTGTGGACTTTGAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
46537 AGTTGTGGACTTTAAAA
66 AGTTGTGGAC-TTAAAA
* * * * * *
46554 GAGTGCCTCGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTATGGATTTAAAAGGGTGCCACA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
46619 GAGTTGTGGACTTTAAAA
65 GAGTTGTGGAC-TTAAAA
*
46637 GGATGCCACGGAGTTGTGGACTTCAAAA
1 GGGTGCCACGGAGTTGTGGACTT-AAAA
46665 AGAAATGCCA
Statistics
Matches: 560, Mismatches: 34, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
81 201 0.36
82 226 0.40
83 133 0.24
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.23
Consensus pattern (81 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAA
Found at i:47954 original size:198 final size:198
Alignment explanation
Indices: 47616--48014 Score: 764
Period size: 198 Copynumber: 2.0 Consensus size: 198
47606 GATTGGGATG
47616 AGTCGACCTTTGAAGACCCTTAAGATTTTTCCAAGTTGTTTTGAGTTGCCCCTTGTTTAGGTGTT
1 AGTCGACCTTTGAAGACCCTTAAGATTTTTCCAAGTTGTTTTGAGTTGCCCCTTGTTTAGGTGTT
47681 TAAGAGGTTTTTGACTAGCTTTAGGGTGAAAAAGGTTTTTTTATTTTTTTTTGTAGGATTGGGTG
66 TAAGAGGTTTTTGACTAGCTTTAGGGTGAAAAAGGTTTTTTTATTTTTTTTTGTAGGATTGGGTG
*
47746 AGTTTCAAAGCTTGTGTCTCACCAAGTTTTTTGCTAAAAAGAACATTTCCCTAAAAAATAGGTTC
131 AGTTTCAAAGCTTGTGTCTCACCAAGTTTTTTGCTAAAAAGAACATTTCCCTAAAAAACAGGTTC
47811 ATC
196 ATC
47814 AGTCGACCTTTGAAGACCCTTAAGATTTTTCCAAGTTGTTTTGAGTTGCCCCTTGTTTAGGTGTT
1 AGTCGACCTTTGAAGACCCTTAAGATTTTTCCAAGTTGTTTTGAGTTGCCCCTTGTTTAGGTGTT
*
47879 TAAGAGGTTTTTGACTAGCTTTAGGGTGAAAAAGG-TTTTTTATTTTTTTTTTGTAGGATTGTGT
66 TAAGAGGTTTTTGACTAGCTTTAGGGTGAAAAAGGTTTTTTTA-TTTTTTTTTGTAGGATTGGGT
47943 GAGTTTCAAAGCTTGTGTCTCACCAAGTTTTTTGCTAAAAAGAACATTTCCCTAAAAAACAGGTT
130 GAGTTTCAAAGCTTGTGTCTCACCAAGTTTTTTGCTAAAAAGAACATTTCCCTAAAAAACAGGTT
48008 CATC
195 CATC
48012 AGT
1 AGT
48015 TCACATGACA
Statistics
Matches: 198, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
197 7 0.04
198 191 0.96
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.41
Consensus pattern (198 bp):
AGTCGACCTTTGAAGACCCTTAAGATTTTTCCAAGTTGTTTTGAGTTGCCCCTTGTTTAGGTGTT
TAAGAGGTTTTTGACTAGCTTTAGGGTGAAAAAGGTTTTTTTATTTTTTTTTGTAGGATTGGGTG
AGTTTCAAAGCTTGTGTCTCACCAAGTTTTTTGCTAAAAAGAACATTTCCCTAAAAAACAGGTTC
ATC
Done.