Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2690
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: 72955
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:6752 original size:13 final size:13
Alignment explanation
Indices: 6734--6759 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6724 CAATTTTTGG
6734 TGTATCGATACAT
1 TGTATCGATACAT
6747 TGTATCGATACAT
1 TGTATCGATACAT
6760 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6776 original size:32 final size:33
Alignment explanation
Indices: 6714--6777 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
6704 TACAAGCCAA
**
6714 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
*
6747 TGTATCGATAC-ATACTTGGTGTATTGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
6778 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:9335 original size:13 final size:13
Alignment explanation
Indices: 9313--9353 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
9303 ATAATCACCC
9313 TGTATCGATACAT
1 TGTATCGATACAT
* *
9326 TGTATTGATACAA
1 TGTATCGATACAT
9339 TGTATCGATACAT
1 TGTATCGATACAT
9352 TG
1 TG
9354 AATTTCCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9342 original size:26 final size:25
Alignment explanation
Indices: 9313--9375 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 25
9303 ATAATCACCC
*
9313 TGTATCGATACATTGTATTGATACA-A
1 TGTATCGATACATTGAATT--TACAGA
*
9339 TGTATCGATACATTGAATTTCCAGA
1 TGTATCGATACATTGAATTTACAGA
9364 TGTATCGATACA
1 TGTATCGATACA
9376 CAGAAACATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 3 0.09
25 13 0.38
26 18 0.53
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (25 bp):
TGTATCGATACATTGAATTTACAGA
Found at i:13272 original size:21 final size:21
Alignment explanation
Indices: 13243--13287 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
13233 AAGTTTTTAT
*
13243 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
13263 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
13285 TTT
1 TTT
13288 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:15524 original size:13 final size:13
Alignment explanation
Indices: 15506--15531 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15496 CAATTTTTGG
15506 TGTATCGATACAT
1 TGTATCGATACAT
15519 TGTATCGATACAT
1 TGTATCGATACAT
15532 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:15543 original size:32 final size:33
Alignment explanation
Indices: 15486--15549 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
15476 TACAAGCCAA
**
15486 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
15519 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
15550 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:15556 original size:19 final size:18
Alignment explanation
Indices: 15486--15556 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
15476 TACAAGCCAA
15486 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
15506 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
15519 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
15538 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
15557 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:15958 original size:13 final size:13
Alignment explanation
Indices: 15940--15965 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15930 ATTTGCCTGC
15940 ATGTATCGATACA
1 ATGTATCGATACA
15953 ATGTATCGATACA
1 ATGTATCGATACA
15966 TTTGAGTAAT
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:16067 original size:33 final size:32
Alignment explanation
Indices: 16008--16072 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
15998 TAGCTTAAAT
16008 TGTATCGATACAAATCTTATGCATCGATACAA
1 TGTATCGATACAAATCTTATGCATCGATACAA
* *
16040 TGTATCGATACAATATTTTATGTATCGATACAA
1 TGTATCGATACAA-ATCTTATGCATCGATACAA
16073 ATCGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAATCTTATGCATCGATACAA
Found at i:16911 original size:104 final size:100
Alignment explanation
Indices: 16789--17076 Score: 395
Period size: 104 Copynumber: 2.9 Consensus size: 100
16779 TTTTAAAGAT
* *
16789 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGCTGCCAAAGGCGTCA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG-TGCCAAAGGCGTCA
16854 ATATGCTGATTCAAGGCTAGCTACATTGAACTTAAA
65 ATATGCTGATTCAAGGCTAGCTACATTGAACTTAAA
*
16890 GATGGAAAAGGTGCCAATATGCTTATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAAAGGCG
1 GAT-G--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-GTGCCAAAGGCG
* * * *
16955 TCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
62 TCAATATGCTGATTCAAGGCTAGCTACATTGAACTTAAA
* * * * *
16994 GATGAA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA--GAC-AAGGTGCCAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGTGCCAAAGGCGTCAA
17055 TATGCTGATTCAAGGCTAGCTA
66 TATGCTGATTCAAGGCTAGCTA
17077 TATTAGGCTT
Statistics
Matches: 168, Mismatches: 15, Indels: 13
0.86 0.08 0.07
Matches are distributed among these distances:
96 28 0.17
97 2 0.01
100 39 0.23
101 5 0.03
102 1 0.01
103 1 0.01
104 91 0.54
105 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (100 bp):
GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGTGCCAAAGGCGTCAA
TATGCTGATTCAAGGCTAGCTACATTGAACTTAAA
Found at i:17034 original size:48 final size:50
Alignment explanation
Indices: 16781--17089 Score: 349
Period size: 52 Copynumber: 6.1 Consensus size: 50
16771 TCATTGGGTT
* *
16781 TTAAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGAC
1 TTAAAGATGA--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * * * * *
16833 TTAAAGCTGCCAAAGGCGTCAATATGCTGATTCAAGGCTAGCTACATTGAAC
1 TTAAAGATG--AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
*
16885 TTAAAGATGGAAAAGGTGCCAATATGCTTATTCAAGGCCAGCTATATTGGAC
1 TTAAAGAT-G-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * * *
16937 TTAAAGGTGCCAAAGGCGTCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG--AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
16989 TTAAAGATG-AA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
17037 TTAAAGA--CAAGGTGCCAATATGCTGATTCAAGGCTAGCTATATTAGG-C
1 TTAAAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATT-GGAC
17085 TTAAA
1 TTAAA
17090 AGAAGATGCC
Statistics
Matches: 219, Mismatches: 31, Indels: 18
0.82 0.12 0.07
Matches are distributed among these distances:
47 2 0.01
48 75 0.34
49 4 0.02
51 1 0.00
52 135 0.62
53 1 0.00
54 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (50 bp):
TTAAAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
Found at i:17247 original size:30 final size:29
Alignment explanation
Indices: 17109--17260 Score: 161
Period size: 28 Copynumber: 5.3 Consensus size: 29
17099 CACCAACTTG
17109 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACT
1 TGTGGGCTTTTGAAAGG-TTGCCACT-AACT
* *
17138 TGTGTGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTAACT
* * *
17166 TGTGGGCTTTT-AAAGATTGCTACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTAACT
* *
17194 TGTGCGCTTTT-AAAAGTTGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTAACT
*
17222 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTG-AAAGGTTGCCACTAACT
*
17252 TGTTGGCTT
1 TGTGGGCTT
17261 AAACGGAAAA
Statistics
Matches: 104, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
27 3 0.03
28 66 0.63
29 12 0.12
30 23 0.22
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGTTGCCACTAACT
Found at i:17344 original size:29 final size:28
Alignment explanation
Indices: 17303--17445 Score: 135
Period size: 29 Copynumber: 5.0 Consensus size: 28
17293 TTACAAAAGA
* * *
17303 AAAAGAGTGCCACGGAGTTGTGGACTTTAG
1 AAAAGA-TGCCACTGACTTGTGGGCTTT-G
* *
17333 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTT-TG
* *
17362 AAAAGGGTGCCACTGATTTGTGGGCTTTG
1 AAAA-GATGCCACTGACTTGTGGGCTTTG
* * * *
17391 -AAGGTTGCCACTGACTTGTAGACTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
17418 AAAAAGATGCCACTGACTTGTGGGCTTT
1 -AAAAGATGCCACTGACTTGTGGGCTTT
17446 TGAAGGGTGA
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
27 20 0.22
28 2 0.02
29 45 0.49
30 25 0.27
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.27
Consensus pattern (28 bp):
AAAAGATGCCACTGACTTGTGGGCTTTG
Found at i:17423 original size:57 final size:57
Alignment explanation
Indices: 17301--17451 Score: 151
Period size: 57 Copynumber: 2.6 Consensus size: 57
17291 GCTTACAAAA
* * * * * * *
17301 GAAAAAGAGTGCCACGGAGTTGTGGACTTTAGAAAAGATGCCACCGACTTGTGGGCTTC
1 GAAAAAGGGTGCCACTGACTTGTGGGCTTT-G-AAGGATGCCACCGACTTGTAGACTTC
* * * * *
17360 GGAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTAGACTTT
1 GAAAAAGGGTGCCACTGACTTGTGGGCTTTGAAGGATGCCACCGACTTGTAGACTTC
*
17417 GAAAAA-GATGCCACTGACTTGTGGGCTTTTGAAGG
1 GAAAAAGGGTGCCACTGACTTGTGGGC-TTTGAAGG
17452 GTGAGGAATG
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
56 18 0.23
57 33 0.43
58 1 0.01
59 25 0.32
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (57 bp):
GAAAAAGGGTGCCACTGACTTGTGGGCTTTGAAGGATGCCACCGACTTGTAGACTTC
Found at i:18919 original size:20 final size:21
Alignment explanation
Indices: 18896--18953 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
18886 GTTGTTGTTG
18896 TTGTTGT-TTTTTTTTCTTTT
1 TTGTTGTGTTTTTTTTCTTTT
*
18916 TTGTTTTGTTTTTTTTCTTTTT
1 TTGTTGTGTTTTTTTTC-TTTT
* *
18938 TTCTTCTGTTTTTTTT
1 TTGTTGTGTTTTTTTT
18954 TGTGGAGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 6 0.18
21 9 0.27
22 18 0.55
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (21 bp):
TTGTTGTGTTTTTTTTCTTTT
Found at i:18924 original size:22 final size:22
Alignment explanation
Indices: 18893--18954 Score: 83
Period size: 21 Copynumber: 2.8 Consensus size: 22
18883 TTTGTTGTTG
18893 TTGTTGTTGTTTTTTTTTCTTTT
1 TTGTT-TTGTTTTTTTTTCTTTT
18916 TTGTTTTG-TTTTTTTTCTTTT
1 TTGTTTTGTTTTTTTTTCTTTT
18937 TT-TCTTCTGTTTTTTTTT
1 TTGT-TT-TGTTTTTTTTT
18955 GTGGAGGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.03
21 17 0.47
22 5 0.14
23 13 0.36
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (22 bp):
TTGTTTTGTTTTTTTTTCTTTT
Found at i:20841 original size:52 final size:52
Alignment explanation
Indices: 20763--20912 Score: 223
Period size: 52 Copynumber: 2.9 Consensus size: 52
20753 CGAAATATGA
* *
20763 AAATTTACTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
* *
20815 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
20867 AAATTTGCCTGCATGTATCGATACA--AAGATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTTA-AT-AGTGTATCGATACAT
20913 TGTATCGATA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:20918 original size:13 final size:13
Alignment explanation
Indices: 20900--20926 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20890 CAAAGATCAG
20900 TGTATCGATACAT
1 TGTATCGATACAT
20913 TGTATCGATACAT
1 TGTATCGATACAT
20926 T
1 T
20927 TGAGTAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:21005 original size:33 final size:33
Alignment explanation
Indices: 20966--21032 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
20956 AGTAGCTTAA
20966 ATTGTACCGATACAAAAAAATATGTATCGATAC
1 ATTGTACCGATACAAAAAAATATGTATCGATAC
* ***
20999 ATTGTACCGATACAACACTTTATGTATCGATAC
1 ATTGTACCGATACAAAAAAATATGTATCGATAC
21032 A
1 A
21033 AAGTCTCACC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (33 bp):
ATTGTACCGATACAAAAAAATATGTATCGATAC
Found at i:26250 original size:79 final size:78
Alignment explanation
Indices: 26154--26645 Score: 431
Period size: 79 Copynumber: 6.2 Consensus size: 78
26144 ATGGGGTCAA
* * *
26154 AGTACCCCCTC-AGAAATAACGGGGTT-GAGGTATCTCCAATGGTGAAAAATCGATGTTTTGAAA
1 AGTATCCCCTCGA-AAATAACGGGGTTGGA-GTATCCCCAATTGTGAAAAATCGATGTTTTGAAA
*
26217 ATAAAACTAGGGTTAG
64 ATAAAA-TAGGGTTGG
* * ** *
26233 AGTATCCCCTCAAAAATAACGAGGTTGGAGTATCATCGATTGTGAAAAATCG-TGTTTT-AGAAA
1 AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTTTTGA-AAA
*
26296 TAAAATCGAGGTTGG
65 TAAAATAG-GGTTGG
*** * * * * * *
26311 AGTATCTTTTCGAAAATAACAGGGTTGGGGTATCCTCAATTCTGAAAAATTGATGTTTTGGAAAT
1 AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTTTTGAAAAT
* *
26376 AAAACCAAGGTTGG
66 AAAA-TAGGGTTGG
* * * *
26390 AGTATCCCTTCGAAAATAATGGGGTTGGAGTATCCCCAATTGTGAAAAATCGGTGTTTTGGAAAT
1 AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTTTTGAAAAT
* *
26455 AAAACTGGGGGTGG
66 AAAA-TAGGGTTGG
* * * * * * *
26469 ATTATCCCCTCTG-AAGTAACGGGGTTGAAGTATCCCCAATTATGGAAAAT-TAGTGTTTTGGAA
1 AGTATCCCCTC-GAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGA-TGTTTTGAAA
*
26532 ATAAAATCGGGGTTGG
64 ATAAAAT-AGGGTTGG
* * * * * * * *
26548 AGTGTCCCATCGGACAGAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAAT
1 AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTTTTGAAAAT
26613 AAAA-ACGGAGTTGG
66 AAAATA-GG-GTTGG
*
26627 AGTATCCCCTCGGAAATAA
1 AGTATCCCCTCGAAAATAA
26646 AAATATGAAT
Statistics
Matches: 335, Mismatches: 64, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
77 3 0.01
78 64 0.19
79 264 0.79
80 4 0.01
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (78 bp):
AGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTTTTGAAAAT
AAAATAGGGTTGG
Found at i:26357 original size:157 final size:158
Alignment explanation
Indices: 26167--26458 Score: 408
Period size: 157 Copynumber: 1.9 Consensus size: 158
26157 ACCCCCTCAG
* * * *
26167 AAATAACGGGGTTGAGGTATCTCCAATGGTGAAAAATCGATGTTTTGAAAATAAAACTAGGGTTA
1 AAATAACAGGGTTGAGGTATCTCCAATGCTGAAAAATCGATGTTTTGAAAATAAAACCAAGGTTA
* *
26232 GAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCATCGATTGTGAAAAATC-GTGTTTTAGAAA
66 GAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCACCAATTGTGAAAAATCGGTGTTTTAGAAA
26296 TAAAATCGAGGTTGGAGTATCTTTTCGA
131 TAAAATCGAGGTTGGAGTATCTTTTCGA
* * * *
26324 AAATAACAGGGTTGGGGTATC-CTCAATTCTGAAAAATTGATGTTTTGGAAATAAAACCAAGGTT
1 AAATAACAGGGTTGAGGTATCTC-CAATGCTGAAAAATCGATGTTTTGAAAATAAAACCAAGGTT
* * * * * * *
26388 GGAGTATCCCTTCGAAAATAATGGGGTTGGAGTATCCCCAATTGTGAAAAATCGGTGTTTTGGAA
65 AGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCACCAATTGTGAAAAATCGGTGTTTTAGAA
26453 ATAAAA
130 ATAAAA
26459 CTGGGGGTGG
Statistics
Matches: 116, Mismatches: 17, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
156 1 0.01
157 99 0.85
158 16 0.14
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (158 bp):
AAATAACAGGGTTGAGGTATCTCCAATGCTGAAAAATCGATGTTTTGAAAATAAAACCAAGGTTA
GAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCACCAATTGTGAAAAATCGGTGTTTTAGAAA
TAAAATCGAGGTTGGAGTATCTTTTCGA
Found at i:26533 original size:158 final size:157
Alignment explanation
Indices: 26154--26645 Score: 515
Period size: 158 Copynumber: 3.1 Consensus size: 157
26144 ATGGGGTCAA
* * ** * * *
26154 AGTACCCCCTCAGAAATAACGGGGTTGAGGTATCTCCAATGGTGAAAAATCGATGTTTTGAAAAT
1 AGTATCCCCTC-GAAATAACGGGGTTGAGGTATCCCCAATTATGGAAAATTGATGTTTTGGAAAT
* * * * * **
26219 AAAACTAGGGTTAGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCATCGATTGTGAAAAATC
65 AAAACCAGGGTTGGAGTATCCCATCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATC
* *
26284 -GTGTTTTAGAAATAAAATCGAGGTTGG
130 GGTGTTTTGGAAATAAAATCGAGGGTGG
*** * * * * *
26311 AGTATCTTTTCGAAAATAACAGGGTTGGGGTATCCTCAATTCTGAAAAATTGATGTTTTGGAAAT
1 AGTATCCCCTCG-AAATAACGGGGTTGAGGTATCCCCAATTATGGAAAATTGATGTTTTGGAAAT
* * * *
26376 AAAACCAAGGTTGGAGTATCCCTTCGAAAATAATGGGGTTGGAGTATCCCCAATTGTGAAAAATC
65 AAAACCAGGGTTGGAGTATCCCATCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATC
*
26441 GGTGTTTTGGAAATAAAA-CTGGGGGTGG
130 GGTGTTTTGGAAATAAAATC-GAGGGTGG
* * *
26469 ATTATCCCCTCTGAAGTAACGGGGTTGAAGTATCCCCAATTATGGAAAATT-AGTGTTTTGGAAA
1 AGTATCCCCTC-GAAATAACGGGGTTGAGGTATCCCCAATTATGGAAAATTGA-TGTTTTGGAAA
* * * * * *
26533 TAAAATCGGGGTTGGAGTGTCCCATCGGACAGAACGGGGTTGGAGTATCCCCGATTGTGAAAAAT
64 TAAAACCAGGGTTGGAGTATCCCATCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAAT
* * * *
26598 TGGTGTTTTGAAAATAAAAACG-GAGTTGG
129 CGGTGTTTTGGAAATAAAATCGAG-GGTGG
26627 AGTATCCCCTCGGAAATAA
1 AGTATCCCCTC-GAAATAA
26646 AAATATGAAT
Statistics
Matches: 276, Mismatches: 52, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
156 1 0.00
157 109 0.39
158 164 0.59
159 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (157 bp):
AGTATCCCCTCGAAATAACGGGGTTGAGGTATCCCCAATTATGGAAAATTGATGTTTTGGAAATA
AAACCAGGGTTGGAGTATCCCATCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCG
GTGTTTTGGAAATAAAATCGAGGGTGG
Found at i:29047 original size:63 final size:63
Alignment explanation
Indices: 28952--29073 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 63
28942 TGAATGTATC
* * * *
28952 GATACATTGAAAAATGTATCGAAATATTTGGGTACAACCCAGAATGTATCGATACAATGTGTT
1 GATACAATGAAAAATGTATCGAAACATCTGGGTAAAACCCAGAATGTATCGATACAATGTGTT
* * * *
29015 GATACAATGAACAATGTATCGATACATCTGGGTAAAACTCAGAATGTATTGATACAATG
1 GATACAATGAAAAATGTATCGAAACATCTGGGTAAAACCCAGAATGTATCGATACAATG
29074 AACAATGTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (63 bp):
GATACAATGAAAAATGTATCGAAACATCTGGGTAAAACCCAGAATGTATCGATACAATGTGTT
Found at i:29395 original size:11 final size:12
Alignment explanation
Indices: 29374--29399 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29364 CTACACCTCC
29374 TTTTTGTTTTTT
1 TTTTTGTTTTTT
29386 TTTTTGTTTTTT
1 TTTTTGTTTTTT
29398 TT
1 TT
29400 AAGAAAGACG
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:32854 original size:20 final size:20
Alignment explanation
Indices: 32829--32866 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32819 GTAAAAAGAT
*
32829 AGAATGCATCGGTACATTGA
1 AGAATGCATCGATACATTGA
*
32849 AGAATGTATCGATACATT
1 AGAATGCATCGATACATT
32867 CATACATGTG
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:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (20 bp):
AGAATGCATCGATACATTGA
Found at i:32875 original size:20 final size:20
Alignment explanation
Indices: 32851--32905 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
32841 TACATTGAAG
** *
32851 AATGTATCGATACATTCATA
1 AATGTATCGATACATAAAAA
* * *
32871 CATGTGTTGATACATAAAAA
1 AATGTATCGATACATAAAAA
32891 AATGTATCGATACAT
1 AATGTATCGATACAT
32906 CTAGGTAAAA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATAAAAA
Found at i:37344 original size:52 final size:52
Alignment explanation
Indices: 37195--37323 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
37185 CGAAATATGA
*
37195 AAATTTGCCTGCATGTATCGATACATTTTATATTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
*
37247 AAATTTACCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
*
37299 AAATTTGCCTCCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
37324 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
Found at i:37385 original size:13 final size:13
Alignment explanation
Indices: 37367--37393 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37357 GCTTAAACTT
37367 ATGTATCGATACA
1 ATGTATCGATACA
37380 ATGTATCGATACA
1 ATGTATCGATACA
37393 A
1 A
37394 CACTTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:37782 original size:28 final size:28
Alignment explanation
Indices: 37710--38186 Score: 584
Period size: 28 Copynumber: 16.9 Consensus size: 28
37700 TCTACAGAGT
* *
37710 TGCCACCGACTTGTATGGGCTTTAAAAGGGTA
1 TGCCACTGACTTG--TGGGCTTTGAAA-GG-A
* * *
37742 TGCCATTGACTTGTGGGTTTTGAAA-TA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
37769 GTGCCACTGACTTGTTGGCTTTGAAAGGA
1 -TGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
37798 TGCCACTGACTTATGGGTTTTGAAATGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
37826 TGCCACTAACTTGTGGGCTTTGAAATGG-
1 TGCCACTGACTTGTGGGCTTTGAAA-GGA
*
37854 TGCCACTGACTTGTGGGCTTTGAAATGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
37882 TGCCACTAACTTGTGGGCTTTAAAATGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
37910 TGCCACTGACTTGT-GGCTTTAAAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
37937 TGCCACTAACTTATGGGCTTTTAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
37965 TGCCATTGACTTGTGGGCTTTAAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
37993 TGCCACTGACTTGTGGGCTTTGAAATGG-
1 TGCCACTGACTTGTGGGCTTTGAAA-GGA
* * *
38021 TGCCACTAACTTGTGGTCTTTGAAATGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
38049 TGCCACTAACTTGTGGACTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
38077 TGCCACTGTCTTGTGGGCTTTAAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
38105 TGCTACTGACTTGTGGGCTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
38133 TGCCACTGACTTGTGGGCTTTGAGAAGGA
1 TGCCACTGACTTGTGGGCTTTGA-AAGGA
38162 TGCCACTGACTTGTGGGCTTTGAAA
1 TGCCACTGACTTGTGGGCTTTGAAA
38187 AGGGTCGTAT
Statistics
Matches: 389, Mismatches: 48, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
27 27 0.07
28 310 0.80
29 31 0.08
30 10 0.03
32 11 0.03
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:38215 original size:14 final size:14
Alignment explanation
Indices: 38196--38268 Score: 64
Period size: 13 Copynumber: 5.5 Consensus size: 14
38186 AAGGGTCGTA
38196 TTGACAAAAATTTC
1 TTGACAAAAATTTC
*
38210 TTGAC-AAAGTTTC
1 TTGACAAAAATTTC
*
38223 -TGACAAACA-TTC
1 TTGACAAAAATTTC
* *
38235 TCGAC-AAAAGTTC
1 TTGACAAAAATTTC
* *
38248 TTGACGATAATTTC
1 TTGACAAAAATTTC
38262 TTGACAA
1 TTGACAA
38269 CCATTTATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
12 10 0.22
13 19 0.41
14 17 0.37
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (14 bp):
TTGACAAAAATTTC
Found at i:38229 original size:26 final size:26
Alignment explanation
Indices: 38196--38268 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
38186 AAGGGTCGTA
38196 TTGACAAAAATTTCTTGACAAAGTT-
1 TTGACAAAAATTTCTTGACAAAGTTC
* *
38221 TCTGACAAACA-TTCTCGACAAAAGTTC
1 T-TGACAAAAATTTCTTGAC-AAAGTTC
* *
38248 TTGACGATAATTTCTTGACAA
1 TTGACAAAAATTTCTTGACAA
38269 CCATTTATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
25 8 0.21
26 22 0.58
27 8 0.21
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (26 bp):
TTGACAAAAATTTCTTGACAAAGTTC
Found at i:44113 original size:15 final size:15
Alignment explanation
Indices: 44071--44113 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
44061 GTAGTGTATT
44071 GATGATTTTGTGGTG
1 GATGATTTTGTGGTG
* * **
44086 GGTAATTAGGTGGTG
1 GATGATTTTGTGGTG
44101 GATGATTTTGTGG
1 GATGATTTTGTGG
44114 CAGATTTGGC
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (15 bp):
GATGATTTTGTGGTG
Found at i:46395 original size:45 final size:45
Alignment explanation
Indices: 46335--46425 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
46325 GACCTTTTCT
*
46335 TCCTTTAGTCGGGCAATTTCTGCAATGTATGATGCTCTTTCTTAC
1 TCCTTTAGTCAGGCAATTTCTGCAATGTATGATGCTCTTTCTTAC
46380 TCCTTTAGTCAGGCAATTTCTGCAATGTATGATGCTCTTTCTTAC
1 TCCTTTAGTCAGGCAATTTCTGCAATGTATGATGCTCTTTCTTAC
46425 T
1 T
46426 TGAATTCTCG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (45 bp):
TCCTTTAGTCAGGCAATTTCTGCAATGTATGATGCTCTTTCTTAC
Found at i:51596 original size:20 final size:20
Alignment explanation
Indices: 51571--51746 Score: 84
Period size: 20 Copynumber: 7.7 Consensus size: 20
51561 TTTTAACTAG
51571 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
51591 ATGTATCGATACATCTGGGTAAAAAGACAAA
1 ATGTATCGATACAT-T--G-----A-A-A-A
*
51622 ATGTATC-AGTACATTGAAGA
1 ATGTATCGA-TACATTGAAAA
* *
51642 ATGTATCGATACATTCATAA
1 ATGTATCGATACATTGAAAA
*
51662 ATGTATCGATACATTAAAAAA
1 ATGTATCGATACATT-GAAAA
*
51683 ATGTAACGATACATCTGGGTAAAAGACAAA
1 ATGTATCGATACA--T---T----GA-AAA
51713 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
51733 ATGTATCGACACAT
1 ATGTATCGATACAT
51747 CTGGGTAAAA
Statistics
Matches: 123, Mismatches: 10, Indels: 46
0.69 0.06 0.26
Matches are distributed among these distances:
20 61 0.50
21 19 0.15
22 1 0.01
23 3 0.02
25 1 0.01
26 1 0.01
28 3 0.02
29 3 0.02
30 18 0.15
31 13 0.11
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.27
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:51672 original size:91 final size:91
Alignment explanation
Indices: 51571--51746 Score: 284
Period size: 91 Copynumber: 1.9 Consensus size: 91
51561 TTTTAACTAG
* *
51571 ATGTATCGATACATT-GAAAAATGTATCGATACATCTGGGTAAAAAGACAAAATGTATC-AGTAC
1 ATGTATCGATACATTAAAAAAATGTAACGATACATCTGGGT-AAAAGACAAAATGTATCGA-TAC
* *
51634 ATTGAAGAATGTATCGATACATTCATAA
64 ATTGAAAAATGTATCGACACATTCATAA
51662 ATGTATCGATACATTAAAAAAATGTAACGATACATCTGGGTAAAAGACAAAATGTATCGATACAT
1 ATGTATCGATACATTAAAAAAATGTAACGATACATCTGGGTAAAAGACAAAATGTATCGATACAT
51727 TGAAAAATGTATCGACACAT
66 TGAAAAATGTATCGACACAT
51747 CTGGGTAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
91 55 0.70
92 24 0.30
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.27
Consensus pattern (91 bp):
ATGTATCGATACATTAAAAAAATGTAACGATACATCTGGGTAAAAGACAAAATGTATCGATACAT
TGAAAAATGTATCGACACATTCATAA
Found at i:51675 original size:40 final size:41
Alignment explanation
Indices: 51620--51696 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
51610 TAAAAAGACA
* * *
51620 AAATGTATCAGTACATT-GAAGAATGTATCGATACATTCAT
1 AAATGTATCAGTACATTAAAAAAATGTAACGATACATTCAT
51660 AAATGTATC-GATACATTAAAAAAATGTAACGATACAT
1 AAATGTATCAG-TACATTAAAAAAATGTAACGATACAT
51697 CTGGGTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 1 0.03
40 15 0.47
41 16 0.50
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (41 bp):
AAATGTATCAGTACATTAAAAAAATGTAACGATACATTCAT
Found at i:51754 original size:50 final size:51
Alignment explanation
Indices: 51660--51756 Score: 160
Period size: 50 Copynumber: 1.9 Consensus size: 51
51650 ATACATTCAT
*
51660 AAATGTATCGATACATTAAAAAAATGTAACGATACATCTGGGTAAAAGACA
1 AAATGTATCGATACATTAAAAAAATGTAACGACACATCTGGGTAAAAGACA
* *
51711 AAATGTATCGATACATT-GAAAAATGTATCGACACATCTGGGTAAAA
1 AAATGTATCGATACATTAAAAAAATGTAACGACACATCTGGGTAAAA
51757 ATATGACTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
50 26 0.60
51 17 0.40
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.25
Consensus pattern (51 bp):
AAATGTATCGATACATTAAAAAAATGTAACGACACATCTGGGTAAAAGACA
Found at i:58317 original size:15 final size:15
Alignment explanation
Indices: 58297--58346 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
58287 TATTGCAGAT
*
58297 GAAGCCAC-CTAGAAA
1 GAAGCCACTCAAG-AA
58312 GAAGCCACTCAAGAA
1 GAAGCCACTCAAGAA
*
58327 GAAGCCATTCAAGAA
1 GAAGCCACTCAAGAA
58342 GAAGC
1 GAAGC
58347 ACCAGAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 29 0.91
16 3 0.09
ACGTcount: A:0.46, C:0.24, G:0.22, T:0.08
Consensus pattern (15 bp):
GAAGCCACTCAAGAA
Found at i:58869 original size:89 final size:89
Alignment explanation
Indices: 58656--58924 Score: 378
Period size: 89 Copynumber: 3.0 Consensus size: 89
58646 GTTCTAATAA
* * * * * *
58656 AATAAAATTCTTGAAACTCCAAAGATGTGATAGATGTATATGGGTATCAGATTTTTTCTGACACG
1 AATAAAATTCTTGGAACTCAAAAGATGTGACAGATGCATGTGGGTATCAGATTATTTCTGACACG
*
58721 ATGAAAAATATTTGACT-ATGCCT
66 ATGAAAAATATTTAACTAATGCCT
* * * ** **
58744 AATAAAGTTCTTGGAATTCGAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTGACATA
1 AATAAAATTCTTGGAACTCAAAAGATGTGACAGATGCATGTGGGTATCAGATTATTTCTGACACG
58809 ATGAAAAATATTTAACTAATGCCT
66 ATGAAAAATATTTAACTAATGCCT
*
58833 AATAAAATTCTTGGAACTCAAAAAATGTGACAGATGCATGTGGGTATCAGATTATTTCTGACACG
1 AATAAAATTCTTGGAACTCAAAAGATGTGACAGATGCATGTGGGTATCAGATTATTTCTGACACG
* *
58898 ACGGAAAATATTTAACTAATGCCT
66 ATGAAAAATATTTAACTAATGCCT
58922 AAT
1 AAT
58925 GTTAGCTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
88 70 0.44
89 88 0.56
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (89 bp):
AATAAAATTCTTGGAACTCAAAAGATGTGACAGATGCATGTGGGTATCAGATTATTTCTGACACG
ATGAAAAATATTTAACTAATGCCT
Found at i:59802 original size:21 final size:21
Alignment explanation
Indices: 59761--59815 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
59751 GTCAGTGACT
*
59761 TGTATCGATATATTCACATAA
1 TGTATCGATACATTCACATAA
*
59782 TGTATCGGTACATT-ACAATAA
1 TGTATCGATACATTCAC-ATAA
*
59803 -GTATCAATACATT
1 TGTATCGATACATT
59816 TTCATGTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCACATAA
Found at i:59903 original size:21 final size:21
Alignment explanation
Indices: 59879--59918 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
59869 CATATGTATT
59879 GATACAAATAGTATTTATATC
1 GATACAAATAGTATTTATATC
***
59900 GATACTTTTAGTATTTATA
1 GATACAAATAGTATTTATA
59919 CTTGAAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (21 bp):
GATACAAATAGTATTTATATC
Found at i:60267 original size:89 final size:89
Alignment explanation
Indices: 60118--60471 Score: 431
Period size: 89 Copynumber: 4.1 Consensus size: 89
60108 AATATGTGTT
* *
60118 TAATACCTAATAAAATTCTTGAAACTCGAAAGATGTGACAGATGCATGT-GAGTATTAGATTCCT
1 TAATGCCTAATAAAATTCTTGAAACTCGAAAGATGTGACAGATGCATGTGGA-TATCAGATTCCT
60182 TCTAACACGATGAAAAATATTTGAC
65 TCTAACACGATGAAAAATATTTGAC
* * * *
60207 TAATGCCTAATAAAATTCTTAAAACTCGAAAGATATGATAGATGCATGTGGATATCAGATTCTTT
1 TAATGCCTAATAAAATTCTTGAAACTCGAAAGATGTGACAGATGCATGTGGATATCAGATTCCTT
* * * * *
60272 TTGACATGA-CAGAAAATATTCGAC
66 CTAACACGATGA-AAAATATTTGAC
* * **
60296 -AATGCCTAATAAATTTCTTGAAACTCGAAAGATGTGACAGATGTATGTAAATATCAGATTCCTT
1 TAATGCCTAATAAAATTCTTGAAACTCGAAAGATGTGACAGATGCATGTGGATATCAGATTCCTT
60360 CTGAA-ACGATGAAAAATATTTGAC
66 CT-AACACGATGAAAAATATTTGAC
* * * * *
60384 TAATGCCTAATAAATTTCTTGAAACTCGAAAGATGTAATAGATGCATATGG--GT---A-TCCTT
1 TAATGCCTAATAAAATTCTTGAAACTCGAAAGATGTGACAGATGCATGTGGATATCAGATTCCTT
60443 CTAACACGATGAAAAATATTTGAC
66 CTAACACGATGAAAAATATTTGAC
60467 TAATG
1 TAATG
60472 ACATGACAAA
Statistics
Matches: 228, Mismatches: 31, Indels: 18
0.82 0.11 0.06
Matches are distributed among these distances:
82 2 0.01
83 31 0.14
84 1 0.00
87 1 0.00
88 72 0.32
89 119 0.52
90 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (89 bp):
TAATGCCTAATAAAATTCTTGAAACTCGAAAGATGTGACAGATGCATGTGGATATCAGATTCCTT
CTAACACGATGAAAAATATTTGAC
Found at i:63876 original size:20 final size:19
Alignment explanation
Indices: 63835--63878 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
63825 GAGACTTAAT
* *
63835 AAAAAATAATGCAAAACTA
1 AAAAAATAAAGCAAAACGA
*
63854 AAAAAATAAAGTAAAATCGA
1 AAAAAATAAAGCAAAA-CGA
63874 AAAAA
1 AAAAA
63879 TTACAAGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.14
Consensus pattern (19 bp):
AAAAAATAAAGCAAAACGA
Found at i:64010 original size:9 final size:9
Alignment explanation
Indices: 63998--64068 Score: 54
Period size: 9 Copynumber: 7.4 Consensus size: 9
63988 AAAAACATAC
63998 TTAAAAAAA
1 TTAAAAAAA
64007 TTAAAAAAA
1 TTAAAAAAA
*
64016 -AAACTAAAAA
1 TTAA--AAAAA
*
64026 CTATAAAATAA
1 -T-TAAAAAAA
64037 TTATAAAAAA
1 TTA-AAAAAA
64047 TTAAAAAAA
1 TTAAAAAAA
**
64056 GGAAAAAAA
1 TTAAAAAAA
64065 TTAA
1 TTAA
64069 TATATTGAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
8 2 0.04
9 26 0.54
10 14 0.29
11 4 0.08
13 2 0.04
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:64054 original size:21 final size:21
Alignment explanation
Indices: 63955--64054 Score: 57
Period size: 21 Copynumber: 4.7 Consensus size: 21
63945 AAAATTCAAA
*
63955 AAAAAATTAATAATATAACTT-T
1 AAAAAATTAA-AAAATAA-TTAT
*
63977 AAAAAACTATAAAAAACATACTTA-
1 AAAAAA-T-T-AAAAA-ATAATTAT
*
64001 AAAAAATTAAAAAA-AA-AACT
1 AAAAAATTAAAAAATAATTA-T
* *
64021 -AAAAACTATAAAATAATTAT
1 AAAAAATTAAAAAATAATTAT
64041 AAAAAATTAAAAAA
1 AAAAAATTAAAAAA
64055 AGGAAAAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 21
0.66 0.10 0.24
Matches are distributed among these distances:
18 1 0.02
19 12 0.20
20 4 0.07
21 17 0.29
22 7 0.12
23 2 0.03
24 11 0.19
25 5 0.08
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAAAAATAATTAT
Found at i:64912 original size:16 final size:16
Alignment explanation
Indices: 64891--64933 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
64881 TTACGTGATT
*
64891 ATATAACATGAATTAA
1 ATATAAAATGAATTAA
64907 ATATAAAAAT-AATTAA
1 ATAT-AAAATGAATTAA
*
64923 ATATAATATGA
1 ATATAAAATGA
64934 TAAAAAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.17
16 15 0.65
17 4 0.17
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (16 bp):
ATATAAAATGAATTAA
Found at i:65018 original size:19 final size:20
Alignment explanation
Indices: 64986--65032 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
64976 TTAAATTATT
64986 AATATAAAAATTT-ATATAA
1 AATATAAAAATTTAATATAA
* *
65005 AATATAATATTTTAGATATAA
1 AATATAAAAATTTA-ATATAA
*
65026 ATTATAA
1 AATATAA
65033 CATGAGTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 11 0.48
21 12 0.52
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AATATAAAAATTTAATATAA
Found at i:65468 original size:14 final size:14
Alignment explanation
Indices: 65446--65479 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
65436 TTAAAAATAA
*
65446 AAATAATATATTTT
1 AAATTATATATTTT
*
65460 AAATTATATTTTTT
1 AAATTATATATTTT
65474 AAATTA
1 AAATTA
65480 AAAAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AAATTATATATTTT
Found at i:65529 original size:19 final size:19
Alignment explanation
Indices: 65507--65553 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 19
65497 CTTTTTTAAG
65507 TTTTAATTTTATT-TTATAT
1 TTTTAATTTTATTATTAT-T
65526 TTTTAATTTTATTAATTATT
1 TTTTAATTTTATT-ATTATT
65546 TTTTAATT
1 TTTTAATT
65554 AAATTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.50
20 9 0.35
21 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTAATTTTATTATTATT
Found at i:65559 original size:20 final size:21
Alignment explanation
Indices: 65520--65561 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
65510 TAATTTTATT
**
65520 TTATATTTTTAATTTTATTAA
1 TTATATTTTTAATTAAATTAA
65541 TTAT-TTTTTAATTAAATTAA
1 TTATATTTTTAATTAAATTAA
65561 T
1 T
65562 ATCATTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATATTTTTAATTAAATTAA
Found at i:66847 original size:14 final size:14
Alignment explanation
Indices: 66828--66878 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
66818 GTTACAATTT
66828 TTAAAATATAAATA
1 TTAAAATATAAATA
66842 TTAAAATATTAAAT-
1 TTAAAATA-TAAATA
* *
66856 CTAATAATATAAAAA
1 TTAA-AATATAAATA
66871 TTAAAATA
1 TTAAAATA
66879 CTCTTCTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAATATAAATA
Found at i:68648 original size:54 final size:56
Alignment explanation
Indices: 68585--68693 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 56
68575 CAACGTACTG
*
68585 TAAATTTAAA-GATGATAAGT-AAATGA-TTAAAATAAT-ATTTTTTTCAAAAATAAC
1 TAAATTTAAAGGA-GATAAGTCAAATAATTTAAAA-AATAATTTTTTTCAAAAATAAC
* *
68639 TAAATTTAAAGGAGTTAAGTCAGATAATTTAAAAAATAATTTTTTTCAAAAATAA
1 TAAATTTAAAGGAGATAAGTCAAATAATTTAAAAAATAATTTTTTTCAAAAATAA
68694 TTTTTAGTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
54 16 0.33
55 9 0.19
56 23 0.48
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (56 bp):
TAAATTTAAAGGAGATAAGTCAAATAATTTAAAAAATAATTTTTTTCAAAAATAAC
Found at i:68848 original size:96 final size:97
Alignment explanation
Indices: 68670--68862 Score: 298
Period size: 96 Copynumber: 2.0 Consensus size: 97
68660 AGATAATTTA
*
68670 AAAAATAATTTTTTTCAAAAATAATTTTTAGTTATATGTGCTTTATATATATATATATAACATAT
1 AAAAATAATTTTTTTCAAAAATAATTTTTAGTTATATGTGC-TTACATATATATATATAACATAT
*
68735 TTTAAAATTAAAATTTATATTTACATAAAAAAT
65 TTTAAAAATAAAATTTATATTTACATAAAAAAT
* * * * *
68768 AAAAATGATTTTTTTCAAAAATGATTTTTAGTTATATGTGC-TCCATATATATATGTAGCATATT
1 AAAAATAATTTTTTTCAAAAATAATTTTTAGTTATATGTGCTTACATATATATATATAACATATT
*
68832 TTAAAAATAAAATTTATATTTACGTAAAAAA
66 TTAAAAATAAAATTTATATTTACATAAAAAA
68863 ATAAGATCTT
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
96 48 0.55
98 39 0.45
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (97 bp):
AAAAATAATTTTTTTCAAAAATAATTTTTAGTTATATGTGCTTACATATATATATATAACATATT
TTAAAAATAAAATTTATATTTACATAAAAAAT
Found at i:69242 original size:22 final size:22
Alignment explanation
Indices: 69217--69259 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
69207 TGATATTAAA
69217 ATATAATTTTTAAAAATTATAC
1 ATATAATTTTTAAAAATTATAC
69239 ATATAATTTTTAAAAATTATA
1 ATATAATTTTTAAAAATTATA
69260 AAGTTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATAATTTTTAAAAATTATAC
Found at i:70249 original size:21 final size:21
Alignment explanation
Indices: 70186--70253 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
70176 CAATAATCCA
70186 AGAAATGAGATAAAATAATAT
1 AGAAATGAGATAAAATAATAT
*** *
70207 AGAAAATTTCAT-ATATAATAT
1 AG-AAATGAGATAAAATAATAT
*
70228 AGAAATGAGATAAAATATTAT
1 AGAAATGAGATAAAATAATAT
70249 A-AAAT
1 AGAAAT
70254 AATGTTTTGA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
20 10 0.28
21 20 0.56
22 6 0.17
ACGTcount: A:0.59, C:0.01, G:0.10, T:0.29
Consensus pattern (21 bp):
AGAAATGAGATAAAATAATAT
Found at i:72424 original size:1 final size:1
Alignment explanation
Indices: 72420--72446 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
72410 TTACTTTTTC
72420 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
72447 GCTATGCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.