Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1847
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: 28654
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Found at i:5429 original size:15 final size:16
Alignment explanation
Indices: 5395--5436 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
5385 GAATAAATCA
5395 AAAATTGTTGAAAATG
1 AAAATTGTTGAAAATG
*
5411 -AAATTCTTGAAAA-G
1 AAAATTGTTGAAAATG
5425 AAAATTGTTGAA
1 AAAATTGTTGAA
5437 CTAGAAAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (16 bp):
AAAATTGTTGAAAATG
Found at i:9045 original size:79 final size:80
Alignment explanation
Indices: 8962--9116 Score: 233
Period size: 79 Copynumber: 1.9 Consensus size: 80
8952 TAAAATCAAA
* * * *
8962 GTTGGAGTATCC-CTGATTGTGAAAAATTGGTGTTTTGGAAATAAAA-CTGGGGGTGGAGTATCC
1 GTTGGAGTATCCTC-GATTGTGAAAAATCGATGTTTTGAAAATAAAACCCGGGGGTGGAGTATCC
9025 CCTCGAAAATAATAGG
65 CCTCGAAAATAATAGG
*
9041 GTTGGAGTATCCTCGATTGTGAAAAATCGATGTTTTGAAAATAAAACCCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCTCGATTGTGAAAAATCGATGTTTTGAAAATAAAACCCGGGGGTGGAGTATCCC
*
9106 CTCGGAAATAA
66 CTCGAAAATAA
9117 AAGCATGAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
79 41 0.60
80 27 0.40
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (80 bp):
GTTGGAGTATCCTCGATTGTGAAAAATCGATGTTTTGAAAATAAAACCCGGGGGTGGAGTATCCC
CTCGAAAATAATAGG
Found at i:9077 original size:130 final size:127
Alignment explanation
Indices: 8835--9086 Score: 324
Period size: 130 Copynumber: 2.0 Consensus size: 127
8825 AAATAACGGG
* *
8835 GTTGGAGTATCCCCAATGGTGAAAAATCGATGTTTTAAAAAAAACTGGGGTTGAGTATCTCCTCG
1 GTTGGAGTATCCCCAATGGTGAAAAATCGATGTTTTAAAAAAAACTGGGGTGGAGTATCCCCTCG
* * * *
8900 AAAATAACGGGGTCGGAGTATCCCCGATTATGGAAGATTGATATTTTGAAAATAAAATCAAA
66 AAAATAACAGGGTCGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAATCAAA
** * * * *
8962 GTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAACTGGGGGTGGAGTATCCCC
1 GTTGGAGTATCCCCAATGGTGAAAAATCGATGTTTT--AAAAAAAACT-GGGGTGGAGTATCCCC
* * * * *
9027 TCGAAAATAATAGGGTTGGAGTATCCTCGATTGTGAAAAATCGATGTTTTGAAAATAAAA
63 TCGAAAATAACAGGGTCGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAA
9087 CCCGGGGTTG
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
127 31 0.30
129 9 0.09
130 65 0.62
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.29
Consensus pattern (127 bp):
GTTGGAGTATCCCCAATGGTGAAAAATCGATGTTTTAAAAAAAACTGGGGTGGAGTATCCCCTCG
AAAATAACAGGGTCGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAATCAAA
Found at i:11490 original size:20 final size:18
Alignment explanation
Indices: 11445--11496 Score: 79
Period size: 17 Copynumber: 2.8 Consensus size: 18
11435 AAAGTGCCTG
11445 AATGTATCGATACATTGA
1 AATGTATCGATACATTGA
11463 AA-GTATCGATACATTGAGA
1 AATGTATCGATACATT--GA
11482 AATGTATCGATACAT
1 AATGTATCGATACAT
11497 CTGGGTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.42
18 2 0.06
19 4 0.13
20 12 0.39
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (18 bp):
AATGTATCGATACATTGA
Found at i:11518 original size:30 final size:29
Alignment explanation
Indices: 11482--11620 Score: 89
Period size: 20 Copynumber: 5.3 Consensus size: 29
11472 TACATTGAGA
11482 AATGTATCGATACATCTGGGTAAAACCCAG
1 AATGTATCGATACAT-TGGGTAAAACCCAG
* *
11512 AATGTATCGATA-A---AGT-GAA---A-
1 AATGTATCGATACATTGGGTAAAACCCAG
11532 AATGTATCGATACATTTGGGTAAAACCCAG
1 AATGTATCGATACA-TTGGGTAAAACCCAG
*
11562 AATGTATCGATACAAT--G----A---AG
1 AATGTATCGATACATTGGGTAAAACCCAG
* *
11582 AATGTATCGATACATTTGGTAAAACCTAG
1 AATGTATCGATACATTGGGTAAAACCCAG
11611 AATGTATCGA
1 AATGTATCGA
11621 GACAATGAAG
Statistics
Matches: 84, Mismatches: 6, Indels: 39
0.65 0.05 0.30
Matches are distributed among these distances:
20 29 0.35
21 2 0.02
22 1 0.01
23 1 0.01
24 2 0.02
25 4 0.05
26 3 0.04
27 1 0.01
29 15 0.18
30 26 0.31
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (29 bp):
AATGTATCGATACATTGGGTAAAACCCAG
Found at i:11626 original size:49 final size:49
Alignment explanation
Indices: 11465--11693 Score: 300
Period size: 49 Copynumber: 4.6 Consensus size: 49
11455 TACATTGAAA
* *
11465 GTATCGATACATTG-AGAAATGTATCGATACATCTGGGTAAAACCCAGAAT
1 GTATCGATACAATGAAG-AATGTATCGATACAT-TTGGTAAAACCCAGAAT
*
11515 GTATCGATA-AAGTGAAAAATGTATCGATACATTTGGGTAAAACCCAGAAT
1 GTATCGATACAA-TGAAGAATGTATCGATACATTT-GGTAAAACCCAGAAT
*
11565 GTATCGATACAATGAAGAATGTATCGATACATTTGGTAAAACCTAGAAT
1 GTATCGATACAATGAAGAATGTATCGATACATTTGGTAAAACCCAGAAT
* * ***
11614 GTATCGAGACAATGAAGAATGTATCAATACATTTGGTAAAATGTAGAAT
1 GTATCGATACAATGAAGAATGTATCGATACATTTGGTAAAACCCAGAAT
* * *
11663 GTATCGAGATAATGAAGAATGTATTGATACA
1 GTATCGATACAATGAAGAATGTATCGATACA
11694 AATTGTGAAA
Statistics
Matches: 163, Mismatches: 12, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
49 89 0.55
50 71 0.44
51 3 0.02
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (49 bp):
GTATCGATACAATGAAGAATGTATCGATACATTTGGTAAAACCCAGAAT
Found at i:12388 original size:61 final size:62
Alignment explanation
Indices: 12202--12504 Score: 423
Period size: 62 Copynumber: 4.9 Consensus size: 62
12192 TGGAAAGGTT
* * *
12202 TGCCACCAACTCGTGGGGGTTTTGAAAAGAAAAAGGTGTCCTACTCTTTGAGGACTAAAGGG
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAGGG
* *
12264 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTACTCTTTGAAGATTAAAGGG
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAGGG
* * * * *
12326 TGCCATCAACTCGTGTTGGCCTTGAAAA-AAAAAGGCATCCTGCTCTTTGAGGACTAAAGGG
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAGGG
* *
12387 TGCCACCAACTCGTGTGGGCTTTG-AAA-AAAAAGGCGTTCTACTCTTTAAGGACTAAAGGG
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAGGG
* ** * * *
12447 TGCCATCAACTCGACTTGGCTTTGAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAA
1 TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAA
12505 GGAAAAAGGA
Statistics
Matches: 212, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
60 52 0.25
61 53 0.25
62 107 0.50
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (62 bp):
TGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTACTCTTTGAGGACTAAAGGG
Found at i:12535 original size:41 final size:41
Alignment explanation
Indices: 12485--12627 Score: 160
Period size: 43 Copynumber: 3.4 Consensus size: 41
12475 GAAAAAGGCA
* * *
12485 TCCTGCTCTTTGAGGACTAAGGAAAAAGGAGATAAAATGCG
1 TCCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAGTGCG
* * * *
12526 TCCTACTCTTTGAGGACAAAGGAAAAGAAAGAAATTAAGTGTG
1 TCCTGCTCTTTGAGGACAAAGG-AAA-AAGGAAATAAAGTGCG
* *
12569 TCCTGCTCTTTGAGGACAAAAGAGAAAAGGAAATAAAGTGCA
1 TCCTGCTCTTTGAGGACAAAGGA-AAAAGGAAATAAAGTGCG
* *
12611 TCCTGCTTTTTAAGGAC
1 TCCTGCTCTTTGAGGAC
12628 TAAAAGGTGC
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
41 20 0.24
42 31 0.37
43 33 0.39
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (41 bp):
TCCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAGTGCG
Found at i:12759 original size:61 final size:61
Alignment explanation
Indices: 12611--13064 Score: 538
Period size: 61 Copynumber: 7.4 Consensus size: 61
12601 ATAAAGTGCA
* * * * **
12611 TCCTGCTTTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGA-AA-ACG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGTG
* * * * *
12670 TCCTGCTGTTTGAGGACTCAAAGTTGCCACCAACTTGTGTGGGGTTTAAAAAGAGAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGTG
* *
12731 TCCTGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAGAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGTG
* * **
12792 TCCTGCTCTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGTG
* ** *
12853 TTCTGCTCTTTGAGGACTGAAAGGTGCCTTCAACTTGTGTGGGCTTTAAAAGGAAAAGGGAAAGT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG---A--GAAGGT
12918 G
61 G
* * * **
12919 TCCTGCTCTTTGGGGACT-AGAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGGAGAAAGCA
1 TCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGTG
* * * * *
12980 ACCTGCTCTTTGAAGACTGGAAA-TTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGTG
13041 TCCTGCTCTTTGAGGACTGAAAGG
1 TCCTGCTCTTTGAGGACTGAAAGG
13065 ATAAAAGGTT
Statistics
Matches: 337, Mismatches: 47, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
59 47 0.14
60 6 0.02
61 229 0.68
62 2 0.01
63 2 0.01
64 1 0.00
65 1 0.00
66 49 0.15
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGTG
Found at i:12974 original size:188 final size:183
Alignment explanation
Indices: 12608--13064 Score: 600
Period size: 188 Copynumber: 2.5 Consensus size: 183
12598 GAAATAAAGT
* * * *
12608 GCATCCTGCT-TTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA--CG
1 GCATCCTGCTCTTTGAA-GACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * * * *
12670 TCCTGCTGTTTGAGGACTCAAAGTTGCCACCAACTTGTGTGGGGTTTAAAAAGAGAAGGTGTCCT
65 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAAGTGTCCT
* *
12735 GCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAGAAG
130 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAGAAA
**
12789 GTGTCCTGCTCTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCAT
1 GCATCCTGCTCTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCAT
* ** *
12854 TCTGCTCTTTGAGGACTGAAAGGTGCCTTCAACTTGTGTGGGCTTTAAAAGGAAAAGGGAAAGTG
66 CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---A--AAAAGAGAAAGTG
* * *
12919 TCCTGCTCTTTGGGGACT-AGAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGGAGAAA
126 TCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAGAAA
* * *
12977 GCAACCTGCTCTTTGAAGACTGGAAA-TTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTA
1 GCATCCTGCTCTTTGAAGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
13041 TCCTGCTCTTTGAGGACTGAAAGG
65 TCCTGCTCTTTGAGGACTGAAAGG
13065 ATAAAAGGTT
Statistics
Matches: 240, Mismatches: 26, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
181 49 0.20
182 5 0.02
183 41 0.17
186 1 0.00
187 1 0.00
188 139 0.58
189 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.27
Consensus pattern (183 bp):
GCATCCTGCTCTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCAT
CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAAGTGTCCTG
CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAGAAA
Found at i:14027 original size:8 final size:8
Alignment explanation
Indices: 14016--14045 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
14006 TCTTTTCTCA
14016 TTTTTCTT
1 TTTTTCTT
14024 TTTTTCTT
1 TTTTTCTT
14032 TTTTTCTCT
1 TTTTTCT-T
14041 TTTTT
1 TTTTT
14046 TTGTCGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTCTT
Found at i:14041 original size:10 final size:9
Alignment explanation
Indices: 14000--14047 Score: 53
Period size: 10 Copynumber: 5.2 Consensus size: 9
13990 CTTAAGTAGG
14000 TTCTTTTCTT
1 TTCTTTT-TT
**
14010 TTCTCATTT
1 TTCTTTTTT
14019 TTC-TTTTT
1 TTCTTTTTT
14027 TTCTTTTTT
1 TTCTTTTTT
14036 TCTCTTTTTT
1 T-TCTTTTTT
14046 TT
1 TT
14048 GTCGTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
8 6 0.19
9 12 0.38
10 14 0.44
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:15315 original size:19 final size:21
Alignment explanation
Indices: 15271--15322 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
15261 TTCAATAATT
*
15271 TGTATCGATACATTCAGTACA
1 TGTATCGATACATTAAGTACA
15292 TGTATCGATACA-TAAGTA-A
1 TGTATCGATACATTAAGTACA
15311 TGTATCGATACA
1 TGTATCGATACA
15323 GTGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 5 0.17
21 12 0.40
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATTAAGTACA
Found at i:15409 original size:82 final size:82
Alignment explanation
Indices: 15292--15468 Score: 309
Period size: 82 Copynumber: 2.2 Consensus size: 82
15282 ATTCAGTACA
* *
15292 TGTATCGATACATAAGTAATGTATCGATACAGTGTATCGCTACAAAGCTATTGCCAAGGAAATGT
1 TGTATCGATACATAAGTAATGTATCGATACAGTGTATCGCTACAAAGCTACTACCAAGGAAATGT
*
15357 ATCGATACATCAATCTT
66 ATCAATACATCAATCTT
*
15374 TGTATCGATACATAAGTAATGTATCGATATAGTGTATCGCTACAAAGCTACTACCAAGGAAATGT
1 TGTATCGATACATAAGTAATGTATCGATACAGTGTATCGCTACAAAGCTACTACCAAGGAAATGT
*
15439 ATCAATACATCGATCTT
66 ATCAATACATCAATCTT
15456 TGTATCGATACAT
1 TGTATCGATACAT
15469 CTAGGAAGTT
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 90 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (82 bp):
TGTATCGATACATAAGTAATGTATCGATACAGTGTATCGCTACAAAGCTACTACCAAGGAAATGT
ATCAATACATCAATCTT
Found at i:17883 original size:51 final size:50
Alignment explanation
Indices: 17808--18034 Score: 238
Period size: 51 Copynumber: 4.6 Consensus size: 50
17798 AAGTTTCTCA
* * * *
17808 AATTTT-CATAATCGGGGGTACTCCAACCT-CGGTTTTATTCCTAAAACACT
1 AATTTTCCACAATCGGGGATACTCCAACCTCCGATTTTATT-C-AAAACACC
17858 AATTTTCCACAATCGGGGATACTCCAA-CTCCGATTTTATTTTCAAAACACC
1 AATTTTCCACAATCGGGGATACTCCAACCTCCGATTTTA--TTCAAAACACC
*
17909 AATTTTCCACAATCGGGGATACTCCAACC-CCG--GTT-TTCAAAACACC
1 AATTTTCCACAATCGGGGATACTCCAACCTCCGATTTTATTCAAAACACC
* * * *
17955 AATTTTCTATAATCGGGGATACTCTAA-CTCCGATTTTATTTCCAAAACACTG
1 AATTTTCCACAATCGGGGATACTCCAACCTCCGATTTTA-TT-CAAAACAC-C
*
18007 ACTTTT-CACAATCGGGGATACTCCAACC
1 AATTTTCCACAATCGGGGATACTCCAACC
18035 CCATTATTTT
Statistics
Matches: 150, Mismatches: 14, Indels: 24
0.80 0.07 0.13
Matches are distributed among these distances:
45 1 0.01
46 38 0.25
48 2 0.01
49 2 0.01
50 10 0.07
51 87 0.58
52 8 0.05
53 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (50 bp):
AATTTTCCACAATCGGGGATACTCCAACCTCCGATTTTATTCAAAACACC
Found at i:17975 original size:97 final size:101
Alignment explanation
Indices: 17808--18036 Score: 315
Period size: 97 Copynumber: 2.3 Consensus size: 101
17798 AAGTTTCTCA
* * * *
17808 AATTTTCATAATCGGGGGTACTCCAACCTCGGTTTTATTCCTAAAACACTAATTTTCCACAATCG
1 AATTTTCACAATCGGGGATACTCCAACCCCGG-TTTATTCCTAAAACACCAATTTTCCACAATCG
*
17873 GGGATACTCCAACTCCGATTTTATTTTCAAAACAC-C
65 GGGATACTCCAACTCCGATTTTATTTCCAAAACACTC
* *
17909 AATTTTCCACAATCGGGGATACTCCAACCCCGG-TT-TT-C-AAAACACCAATTTTCTATAATCG
1 AATTTT-CACAATCGGGGATACTCCAACCCCGGTTTATTCCTAAAACACCAATTTTCCACAATCG
* *
17970 GGGATACTCTAACTCCGATTTTATTTCCAAAACACTG
65 GGGATACTCCAACTCCGATTTTATTTCCAAAACACTC
*
18007 ACTTTTCACAATCGGGGATACTCCAACCCC
1 AATTTTCACAATCGGGGATACTCCAACCCC
18037 ATTATTTTCG
Statistics
Matches: 116, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
97 77 0.66
98 6 0.05
99 2 0.02
100 2 0.02
101 6 0.05
102 23 0.20
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.31
Consensus pattern (101 bp):
AATTTTCACAATCGGGGATACTCCAACCCCGGTTTATTCCTAAAACACCAATTTTCCACAATCGG
GGATACTCCAACTCCGATTTTATTTCCAAAACACTC
Found at i:18072 original size:79 final size:78
Alignment explanation
Indices: 17969--18299 Score: 425
Period size: 79 Copynumber: 4.2 Consensus size: 78
17959 TTCTATAATC
* * * * *
17969 GGGGATACTCTAACTCCGATTTTATTTCCAAAACACTGACTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACA-TCAATTTTCACAATCGGGGATACTCCAAC
18034 CCCATTATTTTCGA
65 CCCATTATTTTCGA
* * *
18048 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATCTTTCATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAAT-TTTCACAATCGGGGATACTCCAAC
**
18113 CCTGTTA-TTTCTGA
65 CCCATTATTTTC-GA
* * * *
18127 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCGCAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATT-TTCACAATCGGGGATACTCCAAC
* *
18192 CCCTTTATTTCCGA
65 CCCATTATTTTCGA
* * * *
18206 GGGGACACTCCAACCCCGATTTTATTTCTAAAACATCAATTTT-TC-ATCGGGGGTACTCCAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCACAATCGGGGATACTCCAACC
18269 CCATTATTTTCGA
66 CCATTATTTTCGA
18282 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
18300 TTATTTTCGA
Statistics
Matches: 220, Mismatches: 28, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
76 44 0.20
77 1 0.00
78 9 0.04
79 163 0.74
80 3 0.01
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCACAATCGGGGATACTCCAACC
CCATTATTTTCGA
Found at i:18290 original size:28 final size:28
Alignment explanation
Indices: 18254--18326 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
18244 ATTTTTCATC
* *
18254 GGGGGTACTCCAATCCCATTATTTTCGA
1 GGGGATACTCCAACCCCATTATTTTCGA
*
18282 GGGGATACTCCAACCCCGTTATTTTCGA
1 GGGGATACTCCAACCCCATTATTTTCGA
* *
18310 GGGAATACCCCAACCCC
1 GGGGATACTCCAACCCC
18327 GGTTTTATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.25
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTTCGA
Found at i:18305 original size:104 final size:106
Alignment explanation
Indices: 18178--18406 Score: 300
Period size: 104 Copynumber: 2.2 Consensus size: 106
18168 CTCCGCAATC
* * *
18178 GGGGATACTCCAACCCCTTTATTTCCGAGGGGACACTCCAACCCCGATTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGAACACCCCAACCCCGATTTTATTTCTAAAACATC
* * * * * *
18243 AATTT-T-TCATCGGGGGTACTCCAATCCCATTATTTTCGA
66 AATTTCTATAATCGAGGATACTCCAACCCCATTATCTCCGA
* * * * *
18282 GGGGATACTCCAACCCCGTTATTTTCGAGGGAATACCCCAACCCCGGTTTTATTTCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGAACACCCCAACCCCGATTTTATTTCTAAAACATC
*
18347 AATTTCTCATAATCGAGGATACTCCAACCCCGTTATCTCCGA
66 AATTTCT-ATAATCGAGGATACTCCAACCCCATTATCTCCGA
18389 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
18407 GTTTTGTTTC
Statistics
Matches: 107, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
104 62 0.58
105 1 0.01
107 44 0.41
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (106 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGAACACCCCAACCCCGATTTTATTTCTAAAACATC
AATTTCTATAATCGAGGATACTCCAACCCCATTATCTCCGA
Found at i:18359 original size:262 final size:263
Alignment explanation
Indices: 18020--18568 Score: 746
Period size: 262 Copynumber: 2.1 Consensus size: 263
18010 TTTCACAATC
* * *
18020 GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTTCGAGGGAATACCCCAACCCCGGTTTTATTTCTAAAACATC
* * *
18085 AATCTTTCATAATC-AGGGATACTCCAACCCTGTTATTTCTGAGGGGATACTCCAACCCCGGTTT
66 AATCTTTCATAATCGA-GGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGTTT
* * *
18149 TATTTCTAAAACACCAATTCTCCGCAATCGGGGATACTCCAACCCCTTTATTTCCGAGGGGACAC
130 TATTTCCAAAACA-CAATTCTCCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACAC
* * * ** *
18214 TCCAACCCCGATTTTATTTCTAAAACATCAATTTTT-CATC-GGGGGTACTCCAATCCCATTATT
194 ACCAACCCCGATTTTATTTCCAAAACATCAATTTTTACAACTGGGGACACTCCAACCCCATTATT
*
18277 TTCGA
259 TTCAA
* *
18282 GGGGATACTCCAACCCCGTTATTTTCGAGGGAATACCCCAACCCCGGTTTTATTTCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTTCGAGGGAATACCCCAACCCCGGTTTTATTTCTAAAACATC
18347 AAT-TTCTCATAATCGAGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGTTT
66 AATCTT-TCATAATCGAGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGTTT
* ** * ** * * **
18411 TGTTTCCAAAACATTATTTTTTATAGTCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATGCA
130 TATTTCCAAAACACAATTCTCCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACA
* * *
18476 CCAATCCCGATTTTATTTCCAAATCATCGATTTTTCACAACTGGGGACACTCCAACCCCATTATT
195 CCAACCCCGATTTTATTTCCAAAACATCAATTTTT-ACAACTGGGGACACTCCAACCCCATTATT
18541 TTCAA
259 TTCAA
*
18546 GGGGATACGCCAACCCCGTTATT
1 GGGGATACTCCAACCCCGTTATT
18569 ATCTCCAAAA
Statistics
Matches: 250, Mismatches: 32, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
261 73 0.29
262 127 0.51
263 4 0.02
264 46 0.18
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.31
Consensus pattern (263 bp):
GGGGATACTCCAACCCCGTTATTTTCGAGGGAATACCCCAACCCCGGTTTTATTTCTAAAACATC
AATCTTTCATAATCGAGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGTTTT
ATTTCCAAAACACAATTCTCCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACAC
CAACCCCGATTTTATTTCCAAAACATCAATTTTTACAACTGGGGACACTCCAACCCCATTATTTT
CAA
Found at i:18374 original size:79 final size:79
Alignment explanation
Indices: 18282--18593 Score: 335
Period size: 79 Copynumber: 3.9 Consensus size: 79
18272 TTATTTTCGA
* * * *
18282 GGGGATACTCCAACCCCGTTATTTTCGAGGGAATACCCCAACCCCGGTTTTATTTCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACACCAACCCCGGTTTTATTTCCAAAATATT
18347 AATTTCTCATAATC
66 AATTTCTCATAATC
* * * * *
18361 GAGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGTTTTGTTTCCAAAACATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACACCAACCCCGGTTTTATTTCCAAAATATT
* * *
18426 -ATTTTTTATAGTC
66 AATTTCTCATAATC
* * *
18439 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATGCACCAATCCCGATTTTATTTCC-AAATCAT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACACCAACCCCGGTTTTATTTCCAAAAT-AT
** * *
18503 CGATTTTTCACAA-C
65 TAATTTCTCATAATC
* * * * * *
18517 TGGGGACACTCCAACCCCATTATTTTCAAGGGGATACGCCAACCCC-GTTATTATCTCCAAAATA
1 -GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACACCAACCCCGGTT-TTATTTCCAAAATA
18581 TTAAATTTCTCAT
64 TT-AATTTCTCAT
18594 CGGGAAATGT
Statistics
Matches: 191, Mismatches: 36, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
77 3 0.02
78 65 0.34
79 112 0.59
80 11 0.06
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACACCAACCCCGGTTTTATTTCCAAAATATT
AATTTCTCATAATC
Found at i:18424 original size:183 final size:185
Alignment explanation
Indices: 18100--18472 Score: 502
Period size: 183 Copynumber: 2.0 Consensus size: 185
18090 TTCATAATCA
* * *
18100 GGGATACTCCAACCCTGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCA
1 GGGATACTCCAACCCCGTTATTTCTGAGGGAATACCCCAACCCCGGTTTTATTTCTAAAACACCA
* * * *
18165 ATTCTCCGCAATCGGGGATACTCCAACCCCTTTATTTCCGAGGGGACACTCCAACCCCGATTTTA
66 ATTCTCCACAATCGAGGATACTCCAACCCCGTTATCTCCGAGGGGACACTCCAACCCCGATTTTA
* * * *
18230 TTTCTAAAACATCAATTTTT-CA-TCGGGGGTACTCCAATCCCATTATTTTCGAG
131 TTTCCAAAACATCAATTTTTACAGTCGGGGATACTCCAACCCCATTATTTCCGAG
* **
18283 GGGATACTCCAACCCCGTTATTT-TCGAGGGAATACCCCAACCCCGGTTTTATTTCTAAAATATT
1 GGGATACTCCAACCCCGTTATTTCT-GAGGGAATACCCCAACCCCGGTTTTATTTCTAAAACACC
* * *
18347 AATT-TCTCATAATCGAGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGTTT
65 AATTCTC-CACAATCGAGGATACTCCAACCCCGTTATCTCCGAGGGGACACTCCAACCCCGATTT
* * * * *
18411 TGTTTCCAAAACATTATTTTTTATAGTCGGGGATACTCCAACCCCGTTATTTCCGAG
129 TATTTCCAAAACATCAATTTTTACAGTCGGGGATACTCCAACCCCATTATTTCCGAG
18468 GGGAT
1 GGGAT
18473 GCACCAATCC
Statistics
Matches: 164, Mismatches: 22, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
182 3 0.02
183 128 0.78
184 1 0.01
185 32 0.20
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (185 bp):
GGGATACTCCAACCCCGTTATTTCTGAGGGAATACCCCAACCCCGGTTTTATTTCTAAAACACCA
ATTCTCCACAATCGAGGATACTCCAACCCCGTTATCTCCGAGGGGACACTCCAACCCCGATTTTA
TTTCCAAAACATCAATTTTTACAGTCGGGGATACTCCAACCCCATTATTTCCGAG
Found at i:18576 original size:157 final size:157
Alignment explanation
Indices: 18282--18583 Score: 367
Period size: 157 Copynumber: 1.9 Consensus size: 157
18272 TTATTTTCGA
* * * *
18282 GGGGATACTCCAACCCCGTTATTTTCGAGGGAATACCCCAACCCCGGTTTTATTTCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGAATACACCAACCCCGATTTTATTTCTAAAATATC
* * * * *
18347 AATTTCTCATAATCGAGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGTTTT
66 AATTTCTCACAATCGAGGACACTCCAACCCCATTATCTCCAAGGGGATACGCCAACCCCGGTTTT
* *
18412 GTTTCCAAAACATTATTTTTTATAGTC
131 ATCTCCAAAACATTATTTTTTATAGTC
* * * *
18439 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATGCACCAATCCCGATTTTATTTC-CAAATCAT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGAATACACCAACCCCGATTTTATTTCTAAAAT-AT
* * * * *
18503 CGATTTTTCACAA-CTGGGGACACTCCAACCCCATTATTTTCAAGGGGATACGCCAACCCC-GTT
65 CAATTTCTCACAATC-GAGGACACTCCAACCCCATTATCTCCAAGGGGATACGCCAACCCCGGTT
*
18566 ATTATCTCCAAAATATTA
129 -TTATCTCCAAAACATTA
18584 AATTTCTCAT
Statistics
Matches: 121, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
156 8 0.07
157 113 0.93
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (157 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGAATACACCAACCCCGATTTTATTTCTAAAATATC
AATTTCTCACAATCGAGGACACTCCAACCCCATTATCTCCAAGGGGATACGCCAACCCCGGTTTT
ATCTCCAAAACATTATTTTTTATAGTC
Found at i:20604 original size:4 final size:4
Alignment explanation
Indices: 20595--20621 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20585 TTTTGAGGTG
20595 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
20622 GTTTGTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Done.