Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2941
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: 69820
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5250 original size:40 final size:40
Alignment explanation
Indices: 5191--5402 Score: 241
Period size: 40 Copynumber: 5.3 Consensus size: 40
5181 CATTTGAATG
*
5191 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * * * *
5231 TTATCCGGGCCAAGACCCGAAGGCATTTGTACGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATT
*
5271 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
5311 TTATCCGGGCCAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATT
* * * *
5351 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
5391 ATATCC-GGCTAA
1 ATATCCGGGCTAA
5403 ATTCCGAAGA
Statistics
Matches: 139, Mismatches: 29, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
39 9 0.06
40 125 0.90
41 5 0.04
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:5324 original size:80 final size:80
Alignment explanation
Indices: 5191--5398 Score: 344
Period size: 80 Copynumber: 2.6 Consensus size: 80
5181 CATTTGAATG
5191 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCCAAGACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCCAAGACCCGAAGGCA
*
5256 TTTGTACGAGTTGCT
66 TTTGTACGAGTTGAT
5271 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCCAAGACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCCAAGACCCGAAGGCA
*
5336 TTTGTGCGAGTTGAT
66 TTTGTACGAGTTGAT
* * * * * *
5351 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCCGG
1 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGG
5399 CTAAATTCCG
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 120 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCCAAGACCCGAAGGCA
TTTGTACGAGTTGAT
Found at i:8735 original size:69 final size:70
Alignment explanation
Indices: 8603--8735 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 70
8593 TAGTTTATTA
* * * * *
8603 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
8668 CTTAG
66 CTTAG
8673 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
8736 GTTATGTACT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 35 0.60
70 23 0.40
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:10173 original size:47 final size:47
Alignment explanation
Indices: 10119--10624 Score: 796
Period size: 47 Copynumber: 10.6 Consensus size: 47
10109 TATTTGAATA
*
10119 AATGTGAAAGTGTATATATGTGATAAGACCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
10166 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
10213 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
10262 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
10309 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
10356 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
10403 AATGTGAAAGTGTATATATGTGATAAGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATA--T-AT--GTGATAAGGCCTAATGGCCGATGTGATG
* *
10457 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
10504 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCTGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
10551 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
10598 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
10625 TCCCGAAGGG
Statistics
Matches: 427, Mismatches: 23, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
47 329 0.77
49 51 0.12
50 1 0.00
51 1 0.00
52 6 0.01
54 39 0.09
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:10525 original size:195 final size:195
Alignment explanation
Indices: 10119--10625 Score: 880
Period size: 195 Copynumber: 2.6 Consensus size: 195
10109 TATTTGAATA
*
10119 AATGTGAAAGTGTATATATGTGATAAGACCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
10184 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA--T-AT--GTGATAAGGC
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGTGATAAGGC
*
10244 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
131 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATG
10309 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * *
10374 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGTGATAAGGC
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGTGATAAGGC
10439 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATG
131 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATG
*
10504 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * *
10569 TGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAGT
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGT
10626 CCCGAAGGGC
Statistics
Matches: 298, Mismatches: 14, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
190 108 0.36
192 1 0.00
193 2 0.01
195 187 0.63
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (195 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGTGATAAGGC
CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATG
Found at i:16215 original size:24 final size:25
Alignment explanation
Indices: 16188--16239 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
16178 GCCTAGCCTC
16188 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
**
16212 TTTTGGTAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
16237 TTT
1 TTT
16240 CGCACTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:16613 original size:27 final size:27
Alignment explanation
Indices: 16443--16611 Score: 214
Period size: 27 Copynumber: 6.3 Consensus size: 27
16433 GGGGCAAAAT
* *
16443 GGTAATTTTATCCC-ACAAGGGTATCTC
1 GGTAATTCTA-CCCTACAAGGGTATTTC
*
16470 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
16497 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
16524 GATAATTCTACCCTACAAGTGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
16551 GGTAATTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* ** * *
16578 GGTAATTTTACCCTTTAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
16605 GGTAATT
1 GGTAATT
16612 TTGTAAACCA
Statistics
Matches: 124, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 3 0.02
27 121 0.98
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:16684 original size:27 final size:27
Alignment explanation
Indices: 16443--16719 Score: 209
Period size: 27 Copynumber: 10.3 Consensus size: 27
16433 GGGGCAAAAT
* * *
16443 GGTAATTTTATCCCACAAGGGTATCTC
1 GGTAATTCTATCCTACAAGGGTATTTC
* *
16470 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTATCCTACAAGGGTATTTC
* *
16497 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTATCCTACAAGGGTATTTC
* * *
16524 GATAATTCTACCCTACAAGTGTATTTC
1 GGTAATTCTATCCTACAAGGGTATTTC
16551 GGTAATTCTA-CCTTACAAGGGTATTTC
1 GGTAATTCTATCC-TACAAGGGTATTTC
* * ** * *
16578 GGTAATTTTACCCTTTAGGGGTATTTT
1 GGTAATTCTATCCTACAAGGGTATTTC
* * ** *
16605 GGTAATTTTGT-AAACCAAGGGTATTTT
1 GGTAATTCTATCCTA-CAAGGGTATTTC
* * ** *
16632 GGTAATTTTGT-AAACCAAGGGTATTTT
1 GGTAATTCTATCCTA-CAAGGGTATTTC
* * *
16659 GGTAATTCTATCCTACAGGGGCATTTT
1 GGTAATTCTATCCTACAAGGGTATTTC
* * *
16686 AGTAATTCTATCCTATAAGGGCATTTC
1 GGTAATTCTATCCTACAAGGGTATTTC
*
16713 AGTAATT
1 GGTAATT
16720 TTGTAAACTA
Statistics
Matches: 212, Mismatches: 34, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
26 2 0.01
27 207 0.98
28 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38
Consensus pattern (27 bp):
GGTAATTCTATCCTACAAGGGTATTTC
Found at i:23255 original size:20 final size:21
Alignment explanation
Indices: 23218--23256 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
23208 TAAAAGTTAG
* *
23218 AAAAATAATTATTCTAAACGA
1 AAAAATAATTAATATAAACGA
23239 AAAAATAA-TAATATAAAC
1 AAAAATAATTAATATAAAC
23257 TTAATTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.26
Consensus pattern (21 bp):
AAAAATAATTAATATAAACGA
Found at i:24895 original size:16 final size:16
Alignment explanation
Indices: 24858--24911 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
24848 TAATACATGT
*
24858 AAATATTATATTAAATTA
1 AAATATTA-ATTTAA-TA
* *
24876 AAATTTTTATTTAATA
1 AAATATTAATTTAATA
24892 AAATATTAATTTAA-A
1 AAATATTAATTTAATA
24907 AAATA
1 AAATA
24912 CGAATTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 6 0.19
16 14 0.45
17 5 0.16
18 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATTAATTTAATA
Found at i:25815 original size:54 final size:54
Alignment explanation
Indices: 25730--25854 Score: 214
Period size: 54 Copynumber: 2.3 Consensus size: 54
25720 AAGTCGAAAC
*
25730 TGAAGCACCCGCACCCGTTGAAGTCAAGGAAGAAGAGAAGGCCGACCCACCGGT
1 TGAAGCACCCGCACCCGTTGAAGTCAAGGAAGAAGAGAAGGCCGACCCACCGAT
* * *
25784 TGAAGCACCCGCACCCGTTGAAGTCAGGGAAGAAGAGAAGGCCGATCCACCTAT
1 TGAAGCACCCGCACCCGTTGAAGTCAAGGAAGAAGAGAAGGCCGACCCACCGAT
25838 TGAAGCACCCGCACCCG
1 TGAAGCACCCGCACCCG
25855 AGACCGTGGT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.30, C:0.31, G:0.28, T:0.10
Consensus pattern (54 bp):
TGAAGCACCCGCACCCGTTGAAGTCAAGGAAGAAGAGAAGGCCGACCCACCGAT
Found at i:29689 original size:2 final size:2
Alignment explanation
Indices: 29682--29710 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29672 GCAATGCCAA
29682 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 A
29711 GAAAACAAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34476 original size:49 final size:49
Alignment explanation
Indices: 34404--34502 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
34394 AGGTCAGGAG
* *
34404 TTCGAGTCATGATTTTGGAAGCTTTGCTTGTTTAATTTTAATCAATCTC
1 TTCGAGTCACGATTTTGGAAGCTTTGCTAGTTTAATTTTAATCAATCTC
*
34453 TTCGAGTTACGATTTTGGAAGCTTTGCTAGTTTAATTTTAATCAATCTC
1 TTCGAGTCACGATTTTGGAAGCTTTGCTAGTTTAATTTTAATCAATCTC
34502 T
1 T
34503 ACTCTTGGGC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.46
Consensus pattern (49 bp):
TTCGAGTCACGATTTTGGAAGCTTTGCTAGTTTAATTTTAATCAATCTC
Found at i:40103 original size:28 final size:28
Alignment explanation
Indices: 40062--40149 Score: 115
Period size: 28 Copynumber: 3.2 Consensus size: 28
40052 ATAAAGAATA
* **
40062 ATTTG-ATTTACTCACATGAGTTGTGAT
1 ATTTGAATTTGCTCACACAAGTTGTGAT
*
40089 ATTTGAATTTGCTCACACAAGATGTGAT
1 ATTTGAATTTGCTCACACAAGTTGTGAT
* *
40117 ATTTGAATTTGCTTACACAACTTGTGAT
1 ATTTGAATTTGCTCACACAAGTTGTGAT
40145 ATTTG
1 ATTTG
40150 GGCTGCTCAC
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 5 0.09
28 48 0.91
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (28 bp):
ATTTGAATTTGCTCACACAAGTTGTGAT
Found at i:55791 original size:79 final size:79
Alignment explanation
Indices: 55654--55801 Score: 206
Period size: 79 Copynumber: 1.9 Consensus size: 79
55644 ATCATAAATC
* ** ** *
55654 AGAATCAGTAACAAGCAGTCTAACATGTTCAGATATCGTATATTCCTCATCAACAAAGTAATGTA
1 AGAATCAGTAACAAGCAATCTAACATAATCAGATATCACATATTCCTCATCAACAAAGTAACGTA
55719 GAGGGTTATAAACT
66 GAGGGTTATAAACT
* * * *
55733 AGAATCAGTAACAATCAATCTAACATAATCAGATATCACATATTCTTCATTAATAAAGTAACGTA
1 AGAATCAGTAACAAGCAATCTAACATAATCAGATATCACATATTCCTCATCAACAAAGTAACGTA
55798 GAGG
66 GAGG
55802 CGTACCAACA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 59 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (79 bp):
AGAATCAGTAACAAGCAATCTAACATAATCAGATATCACATATTCCTCATCAACAAAGTAACGTA
GAGGGTTATAAACT
Found at i:58890 original size:30 final size:30
Alignment explanation
Indices: 58850--58910 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
58840 GGGGGTGGGA
*
58850 TGGGAGAGGAGTAAAAGTTTTGGGAGGAAAG
1 TGGGAGAGGAGTAAAAATTTTGGG-GGAAAG
*
58881 TGGGA-AGGAGTAAAAATTTTTGGGGAAAG
1 TGGGAGAGGAGTAAAAATTTTGGGGGAAAG
58910 T
1 T
58911 AAAGAGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.25
30 16 0.57
31 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.41, T:0.23
Consensus pattern (30 bp):
TGGGAGAGGAGTAAAAATTTTGGGGGAAAG
Found at i:58979 original size:9 final size:9
Alignment explanation
Indices: 58959--58995 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
58949 TATAGTTTCG
*
58959 TATTCGATT
1 TATTCGAAT
*
58968 TATTCAAAT
1 TATTCGAAT
58977 TATTCGAAT
1 TATTCGAAT
58986 TATTCGAAT
1 TATTCGAAT
58995 T
1 T
58996 TGAAAACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:59014 original size:18 final size:19
Alignment explanation
Indices: 58987--59048 Score: 74
Period size: 18 Copynumber: 3.3 Consensus size: 19
58977 TATTCGAATT
*
58987 ATTCGAATTTGAAAACCAA
1 ATTCGAATTTGAAAACGAA
**
59006 ATTCG-ATTTGAACTCGAA
1 ATTCGAATTTGAAAACGAA
59024 ATTCGAAATTTGAAAA-GAA
1 ATTCG-AATTTGAAAACGAA
59043 ATTCGA
1 ATTCGA
59049 GTTGACTCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 16 0.44
19 13 0.36
20 7 0.19
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.29
Consensus pattern (19 bp):
ATTCGAATTTGAAAACGAA
Found at i:59045 original size:37 final size:36
Alignment explanation
Indices: 58987--59059 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
58977 TATTCGAATT
*
58987 ATTCGAATTTGAAAACCAAATTCGATTTGAACTCGAA
1 ATTCGAATTTGAAAACCAAATTCGAGTTG-ACTCGAA
*
59024 ATTCGAAATTTGAAAA-GAAATTCGAGTTGACTCGAA
1 ATTCG-AATTTGAAAACCAAATTCGAGTTGACTCGAA
59060 TAATTCGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 7 0.21
37 16 0.48
38 10 0.30
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (36 bp):
ATTCGAATTTGAAAACCAAATTCGAGTTGACTCGAA
Found at i:59065 original size:38 final size:40
Alignment explanation
Indices: 58980--59067 Score: 114
Period size: 38 Copynumber: 2.3 Consensus size: 40
58970 TTCAAATTAT
* *
58980 TCGAATTATTCG-AATTTGAAAACCAAATTCGATTTGAAC
1 TCGAATAATTCGAAATTTGAAAACCAAATTCGAGTTGAAC
*
59019 TCG-A-AATTCGAAATTTGAAAA-GAAATTCGAGTTG-AC
1 TCGAATAATTCGAAATTTGAAAACCAAATTCGAGTTGAAC
59055 TCGAATAATTCGA
1 TCGAATAATTCGA
59068 TTAATTCGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 5 0.12
37 17 0.40
38 18 0.42
39 3 0.07
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (40 bp):
TCGAATAATTCGAAATTTGAAAACCAAATTCGAGTTGAAC
Found at i:59994 original size:10 final size:10
Alignment explanation
Indices: 59979--60003 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
59969 ATGAGAAAAA
59979 AATTTTAAAT
1 AATTTTAAAT
59989 AATTTTAAAT
1 AATTTTAAAT
59999 AATTT
1 AATTT
60004 ATATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AATTTTAAAT
Found at i:62108 original size:43 final size:43
Alignment explanation
Indices: 62047--62158 Score: 206
Period size: 43 Copynumber: 2.6 Consensus size: 43
62037 CCGGCATTAC
* *
62047 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACAGCACCGGCACGAA
62090 GCCTGCTAGGCACGAAGGCCCGAATACACAGCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACAGCACCGGCACGAA
62133 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
62159 TAATACCAGC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.29, C:0.33, G:0.28, T:0.10
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACAGCACCGGCACGAA
Done.