Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2124
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: 73828
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:1457 original size:39 final size:40
Alignment explanation
Indices: 1380--1533 Score: 122
Period size: 40 Copynumber: 3.9 Consensus size: 40
1370 TAGCTCCTCG
* * *
1380 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATATTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATATAAACTCA
* *
1420 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
** *
1459 CACGAATGCCTTCGGGACTTAACCCGGAATTAGTAT---CTCG
1 TTC-AATGCCTTCGGGACTTAACCCGG-ATTA-TATAAACTCA
** *
1499 CACAAAGGCCTTCGGGACTTAACCCGGATTA-ATAA
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATATAA
1534 CTCGCACAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
37 2 0.02
39 29 0.30
40 61 0.63
41 3 0.03
42 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
Found at i:1485 original size:79 final size:79
Alignment explanation
Indices: 1386--1552 Score: 187
Period size: 79 Copynumber: 2.1 Consensus size: 79
1376 CTCGTTCAAG
* * * ** *
1386 TGCCTTCGGGACATAGCCCGG-TTATATTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGGAAT-TAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA--
*
1449 TTAA-AACTCGCACGAA
63 TTAATAACTCGCACAAA
* * *
1465 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGATTA
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGATTA
1530 ATAACTCGCACAAA
66 ATAACTCGCACAAA
*
1544 TACCTTCGG
1 TGCCTTCGG
1553 ATCTTAGTCC
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 4 0.05
79 46 0.62
80 24 0.32
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (79 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGATTA
ATAACTCGCACAAA
Found at i:1550 original size:39 final size:39
Alignment explanation
Indices: 1423--1604 Score: 183
Period size: 40 Copynumber: 4.6 Consensus size: 39
1413 TAACTCATTC
*
1423 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA--TTAATAACTCGCACA
* *
1463 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTAATAACTCGCACA
*
1503 AAGGCCTTCGGGACTTAACCCGGATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTAATAACTCGCACA
* ** * * *
1542 AATACCTTC-GGATCTTAGTCC-GATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAT-TAATAAC-TCGCACA
*
1582 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
1605 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
38 6 0.05
39 47 0.39
40 66 0.55
41 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTAATAACTCGCACA
Found at i:1583 original size:79 final size:78
Alignment explanation
Indices: 1426--1604 Score: 206
Period size: 78 Copynumber: 2.3 Consensus size: 78
1416 CTCATTCAAT
* *
1426 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGACTTAACCCGGAATTA
1 GCCTTCGGGACTTAACCCGGA-TTTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGAATTA
*
1491 GTATCTCGCACAAA
65 GTATCTAGCACAAA
**
1505 GGCCTTCGGGACTTAACCCGGA-TTAATAACTCGCACAAATACCTTC-GGATCTTAGTCC-G-AT
1 -GCCTTCGGGACTTAACCCGGATTTAA-AACTCGCACAAATACCTTCGGGA-CTTAACCCGGAAT
1566 ATAGTCA-CTTAGCACAAA
63 -TAGT-ATC-TAGCACAAA
*
1584 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
1605 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
77 2 0.02
78 33 0.38
79 32 0.36
80 21 0.24
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (78 bp):
GCCTTCGGGACTTAACCCGGATTTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGAATTAG
TATCTAGCACAAA
Found at i:8483 original size:80 final size:80
Alignment explanation
Indices: 8384--8564 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
8374 CTCATTCAAT
* * *
8384 GCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-A
1 GCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA
*
8446 TTAGT-A-TCTCGCACAAA
64 -TAGTCACT-TAGCACAAA
**
8463 GGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATAT
1 -GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATAT
8528 AGTCACTTAGCACAAA
65 AGTCACTTAGCACAAA
*
8544 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
8565 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:8524 original size:40 final size:40
Alignment explanation
Indices: 8381--8564 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
8371 TAACTCATTC
* *
8381 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
8421 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
8461 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
8501 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
8542 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
8565 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:13697 original size:44 final size:46
Alignment explanation
Indices: 13649--13751 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 46
13639 TATCTTTGAC
* * * *
13649 ATGGACTTACATGAATTATTCCTGTCTCTAATG-C-TATATATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGTCATATATATAAT
* * *
13693 ATGGACTTACATGACTCAATCCTGTCTCCAAAGTCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGTCATATATATAAT
13739 ATGGACTTACATG
1 ATGGACTTACATG
13752 GCTCATTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 28 0.56
45 1 0.02
46 21 0.42
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (46 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGTCATATATATAAT
Found at i:21313 original size:40 final size:40
Alignment explanation
Indices: 21258--21453 Score: 297
Period size: 40 Copynumber: 4.9 Consensus size: 40
21248 GGATATACCT
*
21258 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
21298 ACTGGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
*
21338 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
21378 ACTCGCACAAATGCCTTCGGGGCTTAGCCCGGAATTA-A-TC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG--TTATAGTA
*
21418 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
21454 CATCCGAATA
Statistics
Matches: 144, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
38 3 0.02
40 138 0.96
41 1 0.01
42 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:21380 original size:80 final size:79
Alignment explanation
Indices: 21232--21449 Score: 305
Period size: 80 Copynumber: 2.7 Consensus size: 79
21222 AAACCAAGTA
* * * * *
21232 CCTTCGGGATTTAG-TCGGATATACCTACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATA-ATACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
21296 TAACTGGCACAAATG
65 TAACTCGCACAAATG
*
21311 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAAT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
21376 TAACTCGCACAAATG
65 TAACTCGCACAAATG
* *
21391 CCTTCGGGGCTTAGCCCGGA-ATTAATCACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGGATA-TAAT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
21450 TTATCATCCG
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
79 15 0.12
80 111 0.88
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAATACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
AACTCGCACAAATG
Found at i:29550 original size:40 final size:39
Alignment explanation
Indices: 29480--29617 Score: 172
Period size: 40 Copynumber: 3.5 Consensus size: 39
29470 AAACCAAGTA
* * *
29480 CCTTTGGGATTTAG-CCGGATATAGCTACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATG
29519 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATG
* * *
29559 CCTTTGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACTCGCACAAATG
29599 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
29618 TTATCATCCG
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 14 0.16
40 73 0.84
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATG
Found at i:34484 original size:25 final size:25
Alignment explanation
Indices: 34455--34551 Score: 113
Period size: 25 Copynumber: 3.9 Consensus size: 25
34445 TCCTGTGCAT
* *
34455 GTATGCTCATATGAGCTGTGAATCG
1 GTATGCTCACACGAGCTGTGAATCG
* *
34480 GTATGCTCAAACGAGCTGTGAATCA
1 GTATGCTCACACGAGCTGTGAATCG
* * * *
34505 TTATGCTCACAGGAGTTGTAAATCG
1 GTATGCTCACACGAGCTGTGAATCG
*
34530 GTATGCTCACACGAGCTATGAA
1 GTATGCTCACACGAGCTGTGAA
34552 AATGGGTCTG
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTGAATCG
Found at i:34511 original size:50 final size:50
Alignment explanation
Indices: 34456--34551 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
34446 CCTGTGCATG
* * * *
34456 TATGCTCATATGAGCTGTGAATCGGTATGCTCAAACGAGCTGTGAATCAT
1 TATGCTCACAGGAGCTGTAAATCGGTATGCTCAAACGAGCTATGAATCAT
* *
34506 TATGCTCACAGGAGTTGTAAATCGGTATGCTCACACGAGCTATGAA
1 TATGCTCACAGGAGCTGTAAATCGGTATGCTCAAACGAGCTATGAA
34552 AATGGGTCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (50 bp):
TATGCTCACAGGAGCTGTAAATCGGTATGCTCAAACGAGCTATGAATCAT
Found at i:34563 original size:27 final size:25
Alignment explanation
Indices: 34475--34565 Score: 74
Period size: 25 Copynumber: 3.6 Consensus size: 25
34465 ATGAGCTGTG
* * **
34475 AATCGGTATGCTCAAACGAGCTGTG
1 AATCGGTATGCTCACACGAGTTGAA
** * *
34500 AATCATTATGCTCACAGGAGTTGTA
1 AATCGGTATGCTCACACGAGTTGAA
34525 AATCGGTATGCTCACACGAGCTATGAA
1 AATCGGTATGCTCACACGAG-T-TGAA
* *
34552 AATGGGTCTGCTCA
1 AATCGGTATGCTCA
34566 TATGAGCTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
25 36 0.69
26 1 0.02
27 15 0.29
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (25 bp):
AATCGGTATGCTCACACGAGTTGAA
Found at i:35935 original size:19 final size:19
Alignment explanation
Indices: 35893--35929 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
35883 ACTCTCCCTC
35893 CAAAAGGATTTTTCGTCCT
1 CAAAAGGATTTTTCGTCCT
35912 CAAAAGAGATTTTT-GTCC
1 CAAAAG-GATTTTTCGTCC
35930 CTAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (19 bp):
CAAAAGGATTTTTCGTCCT
Found at i:35936 original size:20 final size:19
Alignment explanation
Indices: 35894--35936 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
35884 CTCTCCCTCC
*
35894 AAAAGGATTTTTCGTCCTC
1 AAAAGGATTTTTCGTCCTA
35913 AAAAGAGATTTTT-GTCCCTA
1 AAAAG-GATTTTTCGT-CCTA
35933 AAAA
1 AAAA
35937 TATTACCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (19 bp):
AAAAGGATTTTTCGTCCTA
Found at i:42089 original size:20 final size:20
Alignment explanation
Indices: 42052--42089 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42042 CTTGAAATTC
*
42052 AAATTACTGATTATATGATT
1 AAATTACTGATTACATGATT
*
42072 AAATTACTGTTTACATGA
1 AAATTACTGATTACATGA
42090 ATGAAAGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (20 bp):
AAATTACTGATTACATGATT
Found at i:42473 original size:22 final size:22
Alignment explanation
Indices: 42448--42504 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
42438 CAGCTGGTAT
42448 GAGCTTACTGTTCAACTCAATA
1 GAGCTTACTGTTCAACTCAATA
* *
42470 GAGCCTACCAT-TTCAGCTCAATA
1 GAGCTTA-C-TGTTCAACTCAATA
42493 GAGCTTACTGTT
1 GAGCTTACTGTT
42505 TATTAGCTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 1 0.03
22 9 0.31
23 18 0.62
24 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (22 bp):
GAGCTTACTGTTCAACTCAATA
Found at i:42748 original size:40 final size:40
Alignment explanation
Indices: 42680--42770 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
42670 TGTCGAAATG
* *
42680 AATGAATTACTGTTGAAATGAATGAATTACTATTGA-TACA
1 AATGAATTACTATTGAAATGAATAAATTACTATT-ATTACA
* * *
42720 AATGAATTACTATTGATAT-AGATAAATTACTGTTATTACT
1 AATGAATTACTATTGAAATGA-ATAAATTACTATTATTACA
42760 AATGAATTACT
1 AATGAATTACT
42771 GGTTATACGG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 2 0.05
40 42 0.95
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (40 bp):
AATGAATTACTATTGAAATGAATAAATTACTATTATTACA
Found at i:42771 original size:20 final size:20
Alignment explanation
Indices: 42680--42770 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 20
42670 TGTCGAAATG
* *
42680 AATGAATTACTGTTGA-AAT
1 AATGAATTACTATTGATACT
*
42699 GAATGAATTACTATTGATACA
1 -AATGAATTACTATTGATACT
42720 AATGAATTACTATTGATA-T
1 AATGAATTACTATTGATACT
* *
42739 AGATAAATTACTGTT-ATTACT
1 A-ATGAATTACTATTGA-TACT
42760 AATGAATTACT
1 AATGAATTACT
42771 GGTTATACGG
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.03
20 55 0.92
21 3 0.05
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (20 bp):
AATGAATTACTATTGATACT
Found at i:42784 original size:20 final size:20
Alignment explanation
Indices: 42679--42822 Score: 82
Period size: 20 Copynumber: 7.2 Consensus size: 20
42669 ATGTCGAAAT
* *
42679 GAATGAATTACT-GTTGAAAT
1 GAATGAATTACTGGTT-ATAC
*
42699 GAATGAATTACT-ATTGATAC
1 GAATGAATTACTGGTT-ATAC
* *
42719 AAATGAATTACT-ATTGATA-
1 GAATGAATTACTGGTT-ATAC
* *
42738 TAGATAAATTACT-GTTATTAC
1 GA-ATGAATTACTGGTTA-TAC
*
42759 TAATGAATTACTGGTTATAC
1 GAATGAATTACTGGTTATAC
* * * *
42779 GGATGAACTACTAGTTATAT
1 GAATGAATTACTGGTTATAC
* *
42799 GAATGAATTACAGTTTATAC
1 GAATGAATTACTGGTTATAC
42819 GAAT
1 GAAT
42823 AAAAATGAAT
Statistics
Matches: 101, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.02
20 93 0.92
21 6 0.06
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (20 bp):
GAATGAATTACTGGTTATAC
Found at i:42808 original size:60 final size:60
Alignment explanation
Indices: 42677--42809 Score: 132
Period size: 60 Copynumber: 2.2 Consensus size: 60
42667 CTATGTCGAA
*
42677 ATGAATGAATTACTGTTGAAATGAATGAATTACTATTGATACAAATGAATTACTATTGAT
1 ATGAATGAATTACTGTTGAAATGAATGAATTACTATTGATACAAATGAACTACTATTGAT
* * * **
42737 AT-AGATAAATTACTGTT-ATTACT-AATGAATTACTGGTT-ATACGGATGAACTACTAGTT-AT
1 ATGA-ATGAATTACTGTTGA--AATGAATGAATTACT-ATTGATACAAATGAACTACTA-TTGAT
42797 ATGAATGAATTAC
1 ATGAATGAATTAC
42810 AGTTTATACG
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
59 2 0.03
60 51 0.85
61 7 0.12
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (60 bp):
ATGAATGAATTACTGTTGAAATGAATGAATTACTATTGATACAAATGAACTACTATTGAT
Found at i:46447 original size:46 final size:45
Alignment explanation
Indices: 46397--46573 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 45
46387 TGGTTGAGCA
46397 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
46443 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
*
46488 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
46536 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGGA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA
46574 CGGGTTACAT
Statistics
Matches: 112, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:46553 original size:93 final size:93
Alignment explanation
Indices: 46394--46565 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
46384 GGATGGTTGA
* *
46394 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
46459 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
46487 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
46552 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
46566 CTTATGGACG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:49210 original size:42 final size:42
Alignment explanation
Indices: 49146--49251 Score: 158
Period size: 42 Copynumber: 2.5 Consensus size: 42
49136 GCAGAGACAT
* * * *
49146 GGGCATGTGTCTCAGTCGTGTGTGCTACATAGCCTAGAATAC
1 GGGCGTGTGTCTTAGCCGTGTGTGCTACATAGCCTAGAACAC
49188 GGGCGTGTGTCTTAGCCGTGTGTGCTACATAGCCTAGAACAC
1 GGGCGTGTGTCTTAGCCGTGTGTGCTACATAGCCTAGAACAC
* *
49230 GGGCGTGTGTCTTGGCCATGTG
1 GGGCGTGTGTCTTAGCCGTGTG
49252 AATCTGCACC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (42 bp):
GGGCGTGTGTCTTAGCCGTGTGTGCTACATAGCCTAGAACAC
Found at i:52952 original size:80 final size:78
Alignment explanation
Indices: 52868--53039 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 78
52858 GGACTAAGAT
*
52868 CCGAAGGCATTTGTGCGAG-A-TACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAC
1 CCGAAGGCATTTGTGCGAGCATTA-AA--TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATAC
* *
52931 TAAATCCGGGTTAAGTC
62 TAAAACCGGGCTAAGTC
* * * *
52948 CCGAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAG-CATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
53013 AACCGGGCTATGTC
65 AACCGGGCTAAGTC
53027 CCGAAGGCATTTG
1 CCGAAGGCATTTG
53040 AACGAGGAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
79 38 0.47
80 37 0.46
82 3 0.04
83 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGCATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
ACCGGGCTAAGTC
Found at i:53030 original size:39 final size:39
Alignment explanation
Indices: 52815--53037 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
52805 TTGAATGCTG
* * * * * *
52815 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
52855 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
52895 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
52935 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
52975 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
53014 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
53038 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 24, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
39 37 0.24
40 105 0.69
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:53057 original size:79 final size:80
Alignment explanation
Indices: 52895--53072 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
52885 AGATACAAGT
* * * *
52895 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
52960 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
52975 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
53039 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
53054 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
53073 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:60545 original size:39 final size:39
Alignment explanation
Indices: 60375--60598 Score: 222
Period size: 40 Copynumber: 5.7 Consensus size: 39
60365 TTGAATGCTG
* * *
60375 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTAAA
* *
60415 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTAA-A
* * *
60455 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAAA
* * *
60495 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAAA
* *
60534 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAAA
* *
60573 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
60599 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 20, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
38 7 0.04
39 54 0.35
40 84 0.54
41 11 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAAA
Found at i:60620 original size:78 final size:79
Alignment explanation
Indices: 60455--60631 Score: 205
Period size: 78 Copynumber: 2.3 Consensus size: 79
60445 AGATACAAGT
* * * *
60455 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
60520 GTGCGAGTATTAAA
66 GAACGAGGACTAAA
* * * *
60534 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
60598 GAACGAGGAGCTATA
66 GAACGAGGA-CTAAA
*
60613 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
60632 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
78 58 0.70
79 25 0.30
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGACTAAA
Found at i:65831 original size:28 final size:27
Alignment explanation
Indices: 65800--65853 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
65790 TTCGGAGTTA
65800 TTGATTAAAGATGCTGAACAGAAAGTAT
1 TTGATT-AAGATGCTGAACAGAAAGTAT
65828 TTGATTAAGATGCTGAACAGAAAGTA
1 TTGATTAAGATGCTGAACAGAAAGTA
65854 AATGTAATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (27 bp):
TTGATTAAGATGCTGAACAGAAAGTAT
Found at i:72909 original size:27 final size:25
Alignment explanation
Indices: 72856--72915 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
72846 TTCTAAGTTA
*
72856 TTTTAGTTTCTTCTTTTCACCTCTT
1 TTTTAGTTTCGTCTTTTCACCTCTT
*
72881 TTTTAGTTCTCGTCTTTTTCA-C-CAT
1 TTTTAGTT-TCGTC-TTTTCACCTCTT
72906 TTTTAGTTTC
1 TTTTAGTTTC
72916 CCTTAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 2 0.06
25 18 0.58
26 5 0.16
27 6 0.19
ACGTcount: A:0.10, C:0.22, G:0.07, T:0.62
Consensus pattern (25 bp):
TTTTAGTTTCGTCTTTTCACCTCTT
Done.