Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1511
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: 47894
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1054 original size:20 final size:20
Alignment explanation
Indices: 1029--1080 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1019 AAAACCCAGA
1029 TGTATCGATACAACATTCCT
1 TGTATCGATACAACATTCCT
1049 TGTATCGATACAACATTCCT
1 TGTATCGATACAACATTCCT
1069 TGTATCGATACA
1 TGTATCGATACA
1081 TTGTATCGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAACATTCCT
Found at i:1086 original size:13 final size:13
Alignment explanation
Indices: 1068--1096 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1058 ACAACATTCC
1068 TTGTATCGATACA
1 TTGTATCGATACA
1081 TTGTATCGATACA
1 TTGTATCGATACA
1094 TTG
1 TTG
1097 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3548 original size:19 final size:19
Alignment explanation
Indices: 3524--3579 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
3514 GCATCGATAC
***
3524 ATTGTATCGATACATGTTT
1 ATTGTATCGATACATGACA
3543 ATTGTATCGATACATGGACA
1 ATTGTATCGATACAT-GACA
3563 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
3580 AACTGGCAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:3568 original size:20 final size:20
Alignment explanation
Indices: 3524--3578 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3514 GCATCGATAC
***
3524 ATTGTATCGATACAT-GTTT
1 ATTGTATCGATACATGGACA
3543 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
3563 ATTGTATCGATACATG
1 ATTGTATCGATACATG
3579 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:3633 original size:20 final size:20
Alignment explanation
Indices: 3608--3660 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
3598 TATCATTATT
3608 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
3628 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
3648 TGTATCGATACAT
1 TGTATCGATACAT
3661 TGTATCGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGGTACAA
Found at i:3664 original size:13 final size:13
Alignment explanation
Indices: 3643--3673 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3633 CGATACATGG
*
3643 TACAATGTATCGA
1 TACATTGTATCGA
3656 TACATTGTATCGA
1 TACATTGTATCGA
3669 TACAT
1 TACAT
3674 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:3670 original size:33 final size:32
Alignment explanation
Indices: 3623--3693 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 32
3613 CGATACATGG
*
3623 TACAATGTATCGATACATG-GTACAATGTATCGA
1 TACATTGTATCGATACATGAG-A-AATGTATCGA
3656 TACATTGTATCGATACATGAAGAAATGTATCGA
1 TACATTGTATCGATACATG-AGAAATGTATCGA
3689 TACAT
1 TACAT
3694 AGCTTGTAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
33 33 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (32 bp):
TACATTGTATCGATACATGAGAAATGTATCGA
Found at i:8745 original size:19 final size:19
Alignment explanation
Indices: 8723--8759 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8713 TGGCAGTAGC
*
8723 CAAATTTGTATCGATACAG
1 CAAATATGTATCGATACAG
8742 CAAATATGTATCGATACA
1 CAAATATGTATCGATACA
8760 ATGTATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (19 bp):
CAAATATGTATCGATACAG
Found at i:8765 original size:13 final size:13
Alignment explanation
Indices: 8747--8785 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
8737 TACAGCAAAT
8747 ATGTATCGATACA
1 ATGTATCGATACA
8760 ATGTATCGATACA
1 ATGTATCGATACA
8773 ATGTATCGATACA
1 ATGTATCGATACA
8786 CAAATTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:11033 original size:21 final size:21
Alignment explanation
Indices: 11000--11044 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
10990 TTGCAAGTTG
*
11000 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
11022 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
11042 AAA
1 AAA
11045 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:14971 original size:20 final size:20
Alignment explanation
Indices: 14892--14971 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
14882 AATGTCCAAA
*
14892 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
14912 GTGTATCGATACATCTAGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
14937 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
14957 TTGTATCGATACATT
1 ATGTATCGATACATT
14972 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:14975 original size:13 final size:13
Alignment explanation
Indices: 14957--14995 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
14947 ACATTTTTCT
14957 TTGTATCGATACA
1 TTGTATCGATACA
14970 TTGTATCGATACA
1 TTGTATCGATACA
*
14983 CTGTATCGATACA
1 TTGTATCGATACA
14996 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:17549 original size:13 final size:13
Alignment explanation
Indices: 17531--17556 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17521 TACAGCAAGT
17531 ATGTATCGATACA
1 ATGTATCGATACA
17544 ATGTATCGATACA
1 ATGTATCGATACA
17557 CAAATTATTG
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:17554 original size:32 final size:33
Alignment explanation
Indices: 17513--17576 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
17503 TAGCCAAATT
17513 TGTATCGATACAGC-AAGTA-TGTATCGATACAA
1 TGTATCGATACA-CAAAGTATTGTATCGATACAA
*
17545 TGTATCGATACACAAATTATTGTATCGATACA
1 TGTATCGATACACAAAGTATTGTATCGATACA
17577 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 1 0.03
32 16 0.55
33 12 0.41
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (33 bp):
TGTATCGATACACAAAGTATTGTATCGATACAA
Found at i:20804 original size:21 final size:21
Alignment explanation
Indices: 20778--20824 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
20768 TGTGGGAAAT
20778 GATGTGAATGAAGACGCTAAA
1 GATGTGAATGAAGACGCTAAA
20799 GATGTGAATGAAGACGCTAAA
1 GATGTGAATGAAGACGCTAAA
20820 GATGT
1 GATGT
20825 AAAAGCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21
Consensus pattern (21 bp):
GATGTGAATGAAGACGCTAAA
Found at i:21621 original size:49 final size:49
Alignment explanation
Indices: 21567--21719 Score: 252
Period size: 49 Copynumber: 3.1 Consensus size: 49
21557 TAAGATGGAA
21567 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
* * *
21616 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G
21666 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
1 --AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
21717 AAG
1 AAG
21720 ATGAGAAAAG
Statistics
Matches: 95, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
49 48 0.51
50 1 0.01
51 1 0.01
52 45 0.47
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.24
Consensus pattern (49 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
Found at i:21694 original size:52 final size:52
Alignment explanation
Indices: 21558--21716 Score: 270
Period size: 52 Copynumber: 3.1 Consensus size: 52
21548 GGTCTTGGTT
21558 AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
1 AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* * *
21610 AAGAT-G--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
1 AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
21659 AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
1 AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
21711 AAGATG
1 AAGATG
21717 AAGATGAGAA
Statistics
Matches: 98, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
49 45 0.46
50 1 0.01
51 1 0.01
52 51 0.52
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (52 bp):
AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
Found at i:21944 original size:49 final size:49
Alignment explanation
Indices: 21802--22659 Score: 1113
Period size: 49 Copynumber: 17.6 Consensus size: 49
21792 GATGTCAACG
* *
21802 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
* *
21854 TGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
*
21897 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
21946 TGCTGATTCCAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* *
21989 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
22038 TGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* *
22081 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
22130 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* *
22179 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
22228 TGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
22277 TGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
22326 TGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
*
22375 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
* *
22427 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
*
22476 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
* *
22528 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
*
22577 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
* *
22629 TGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTA
22660 GAGGGGTTGC
Statistics
Matches: 701, Mismatches: 78, Indels: 54
0.84 0.09 0.06
Matches are distributed among these distances:
43 112 0.16
45 2 0.00
47 3 0.00
48 1 0.00
49 421 0.60
50 3 0.00
51 2 0.00
52 157 0.22
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
Found at i:22198 original size:98 final size:98
Alignment explanation
Indices: 21735--22659 Score: 1355
Period size: 98 Copynumber: 9.4 Consensus size: 98
21725 AAAAGTGATA
* * * * * *
21735 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCAA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G---AAGG-TGCCAA
* * *
21800 CGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
60 TGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* *
21840 AAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTG
1 AAGA--TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
*
21899 CTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
64 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
*
21934 AAGATGCCAATATGCTGATTCCAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
21993 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
22026 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
22085 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
22118 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
22183 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
*
22216 AAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
*
22281 GAGTCAAGGCTAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
*
22314 AAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
22379 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* *
22413 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTG
1 --AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
22478 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
64 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* *
22514 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTG
1 --AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
22579 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
64 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* * *
22615 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 --AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
22660 GAGGGGTTGC
Statistics
Matches: 787, Mismatches: 22, Indels: 26
0.94 0.03 0.03
Matches are distributed among these distances:
92 218 0.28
94 4 0.01
95 41 0.05
96 5 0.01
98 241 0.31
99 1 0.00
101 241 0.31
103 1 0.00
105 3 0.00
107 32 0.04
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (98 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
Found at i:22851 original size:34 final size:34
Alignment explanation
Indices: 22726--23132 Score: 465
Period size: 34 Copynumber: 11.9 Consensus size: 34
22716 GGGCTTTGGG
*
22726 AAGGAAAAAAGATGCCACGGAGTTGTGGAC-TTAA
1 AAGGAAAAAAG-TGCCACGGAGTTGTGGGCTTTAA
22760 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAA-AGTGCCACGGAGTTGTGGGCTTTAA
* *
22796 AA-GAAACAAGTGCCACGGAGTTGTGGGC-TTAG
1 AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAA
* *
22828 AAGGAAAAATAGTGCCACAGAGTTGTGGGC-TTAG
1 AAGGAAAAA-AGTGCCACGGAGTTGTGGGCTTTAA
* * *
22862 AAGGAAAAGAGTGCCATGTAGTTGTGGGCTTT-A
1 AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAA
*
22895 AAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTT-AA
*
22930 AAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAA
1 AA-GGAAAAA-AGTGCCACGGAGTTGTGGGCTTTAA
* *
22966 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAA
1 AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAA
*
23000 ACA-GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 A-AGGAAAAAAGTGCCACGGAGTTGTGGGCTTT-AA
* *
23035 AAGAGAAAAAGAGTGCCACAGAGTTGTGGAC-TTAA
1 AAG-GAAAAA-AGTGCCACGGAGTTGTGGGCTTTAA
* *
23070 AAGGAACAAGGTGCCACGGAGTTGTGGGCTTT-A
1 AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAA
* * *
23103 AA-GAAAAAA-TGCCACTGAGTCGTGGACTTT
1 AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTT
23133 GAGACAAAAT
Statistics
Matches: 328, Mismatches: 29, Indels: 35
0.84 0.07 0.09
Matches are distributed among these distances:
31 18 0.05
32 10 0.03
33 92 0.28
34 101 0.31
35 42 0.13
36 26 0.08
37 39 0.12
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (34 bp):
AAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAA
Found at i:23095 original size:104 final size:101
Alignment explanation
Indices: 22713--23134 Score: 550
Period size: 104 Copynumber: 4.1 Consensus size: 101
22703 CACCGACTTG
** *
22713 TGTGGGCTTTGGGAAGGAAAAA-AGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCC
1 TGTGGGCTTTGAAAAGGAAAAAGAG-TGCCACAGAGTTGTGGACTTAAAA-GGAAAAAGAGTGCC
22777 ACGGAGTTGTGGGCTTTAAAAGAAACAAGTGCCACGGAGT
64 ACGGAGTTGTGGGCTTT-AAAGAAA-AAGTGCCACGGAGT
* * * * *
22817 TGTGGGC-TT-AGAAGGAAAAATAGTGCCACAGAGTTGTGGGCTTAGAAGG-AAAAGAGTGCCAT
1 TGTGGGCTTTGAAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCAC
*
22879 GTAGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGT
66 GGAGTTGTGGGCTTTAAA-GAAAA-AGTGCCACGGAGT
* *
22917 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCC
1 TGTGGGCTTTGAAAA-GGAAAAAGAGTGCCACAGAGTTGTGGAC-TTAAAAGGAAAAAGAGTGCC
22981 ACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGT
64 ACGGAGTTGTGGGCTTT-AA-AGAAAAA-GTGCCACGGAGT
*
23022 TGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAACAAG-GTGCCA
1 TGTGGGCTTTGAAAAG-GAAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCA
* *
23086 CGGAGTTGTGGGCTTTAAAGAAAAAATGCCACTGAGT
65 CGGAGTTGTGGGCTTTAAAGAAAAAGTGCCACGGAGT
* *
23123 CGTGGACTTTGA
1 TGTGGGCTTTGA
23135 GACAAAATGC
Statistics
Matches: 287, Mismatches: 19, Indels: 27
0.86 0.06 0.08
Matches are distributed among these distances:
99 4 0.01
100 50 0.17
101 24 0.08
102 41 0.14
103 33 0.11
104 69 0.24
105 65 0.23
106 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.21
Consensus pattern (101 bp):
TGTGGGCTTTGAAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCAC
GGAGTTGTGGGCTTTAAAGAAAAAGTGCCACGGAGT
Found at i:31448 original size:52 final size:52
Alignment explanation
Indices: 31378--31498 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
31368 GAAAATTTAT
*
31378 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
31430 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
31482 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
31499 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:31511 original size:52 final size:51
Alignment explanation
Indices: 31378--31518 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
31368 GAAAATTTAT
31378 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
31430 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
31482 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
31519 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:31525 original size:13 final size:13
Alignment explanation
Indices: 31507--31531 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31497 CAAAGATCAG
31507 TGTATCGATACAA
1 TGTATCGATACAA
31520 TGTATCGATACA
1 TGTATCGATACA
31532 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:31615 original size:13 final size:13
Alignment explanation
Indices: 31597--31621 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31587 CAAAAAAATA
31597 TGTATCGATACAT
1 TGTATCGATACAT
31610 TGTATCGATACA
1 TGTATCGATACA
31622 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:31617 original size:33 final size:33
Alignment explanation
Indices: 31575--31641 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
31565 AGTAGCTTAA
31575 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
31608 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
31641 A
1 A
31642 AATCGTTGAA
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:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:36743 original size:152 final size:151
Alignment explanation
Indices: 36571--37079 Score: 495
Period size: 152 Copynumber: 3.3 Consensus size: 151
36561 ATTAATAAAT
* * * * *
36571 ACAAAAAAATTCAAAACTCATAAAATAAATTGAA-TTCTCTAAAACTGATTTACTATGAATTTAA
1 ACAAAAAAATT-AAAACTCATAAAATGAATTGAATTTTTC-AAAACTGATTTAATATGAAATAAA
* * * * * * *
36635 TAAAAATATTTGATGTATTTTAAAAATTTTGAA-TTGAGAAAAATCCAACCAA-AAAAATTTATG
64 CAAAAATATTTGAAGAATTTTAAAAATTATAAACTT-AGAAAAATCCAA-CAAGAAAAACTTACG
*
36698 GAATAGAAAA-TCCCGTAATTTGGAA
127 GAACAGAAAACT-CCGTAATTTGGAA
* *
36723 ACAAAAAAATCTATAACTCATAAAATGAATTGAATTTTTCAAAACTAATTTAATATGAAATAAAC
1 ACAAAAAAAT-TAAAACTCATAAAATGAATTGAATTTTTCAAAACTGATTTAATATGAAATAAAC
* * * * * *
36788 AATAATATTTGAAGAATTTTGAAAATTATAAACTTAGAAAAATCCTATAAGAGAAACTTACGGAG
65 AAAAATATTTGAAGAATTTTAAAAATTATAAACTTAGAAAAATCCAACAAGAAAAACTTACGGAA
* **
36853 CAGAAAACTCTGTAATTTGGTC
130 CAGAAAACTCCGTAATTTGGAA
* * *
36875 ACAAGAAAATATACAACTCATAAAATGAATTGAATTTTTCAAAACTGATTTAATATGAAACAAAC
1 ACAAAAAAAT-TAAAACTCATAAAATGAATTGAATTTTTCAAAACTGATTTAATATGAAATAAAC
* * * * * * * * * *
36940 AATAATATTTGAAGAATTTTGAAATTTATAAACTTACAAAAATCCTATAGGAGAAATTTACGGAG
65 AAAAATATTTGAAGAATTTTAAAAATTATAAACTTAGAAAAATCCAACAAGAAAAACTTACGGAA
* ** * *
37005 TAGAAAACTCTATAACTTGGTA
130 CAGAAAACTCCGTAATTTGGAA
* * *
37027 ACAAAAAAAATTCTAAAACTCATAAAATAAATTAAATTTTTCAAAATTGATTT
1 AC-AAAAAAA-T-TAAAACTCATAAAATGAATTGAATTTTTCAAAACTGATTT
37080 TATGGTAATT
Statistics
Matches: 307, Mismatches: 43, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
151 2 0.01
152 254 0.83
153 14 0.05
154 37 0.12
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.31
Consensus pattern (151 bp):
ACAAAAAAATTAAAACTCATAAAATGAATTGAATTTTTCAAAACTGATTTAATATGAAATAAACA
AAAATATTTGAAGAATTTTAAAAATTATAAACTTAGAAAAATCCAACAAGAAAAACTTACGGAAC
AGAAAACTCCGTAATTTGGAA
Found at i:38103 original size:13 final size:13
Alignment explanation
Indices: 38085--38110 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38075 CAATTTTTTG
38085 TGTATCGATACAT
1 TGTATCGATACAT
38098 TGTATCGATACAT
1 TGTATCGATACAT
38111 ACTTAATGTA
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:38174 original size:20 final size:20
Alignment explanation
Indices: 38149--38222 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
38139 CTGCCAAGAA
38149 ATGTATCGATACAACTTTTT
1 ATGTATCGATACAACTTTTT
***
38169 ATGTATCGATAC-A-TTGCAAC
1 ATGTATCGATACAACTT--TTT
*
38189 ATGTATCGATACATCTTTTT
1 ATGTATCGATACAACTTTTT
38209 CATGTATCGATACA
1 -ATGTATCGATACA
38223 TTGCAACATG
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 2 0.05
19 1 0.02
20 24 0.57
21 13 0.31
22 2 0.05
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACAACTTTTT
Found at i:38226 original size:41 final size:40
Alignment explanation
Indices: 38149--38241 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 40
38139 CTGCCAAGAA
38149 ATGTATCGATACAACTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTATGTATCGATACATTGCAAC
*
38189 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTT-ATGTATCGATACATTGCAAC
38230 ATGTATCGATAC
1 ATGTATCGATAC
38242 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 19 0.37
41 32 0.63
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (40 bp):
ATGTATCGATACAACTTTTTATGTATCGATACATTGCAAC
Found at i:38234 original size:20 final size:20
Alignment explanation
Indices: 38169--38241 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
38159 ACAACTTTTT
38169 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
38189 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
38210 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
38230 ATGTATCGATAC
1 ATGTATCGATAC
38242 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:38934 original size:53 final size:53
Alignment explanation
Indices: 38849--38955 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
38839 CTCCTTTATC
*
38849 TCCCTCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
1 TCCCCCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
38902 TCCCCCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
1 TCCCCCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
38955 T
1 T
38956 TATTTGCACT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.36
Consensus pattern (53 bp):
TCCCCCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
Found at i:40757 original size:13 final size:13
Alignment explanation
Indices: 40739--40777 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
40729 ATAATCACCC
*
40739 TGTATCGATACAG
1 TGTATCGATACAA
40752 TGTATCGATACAA
1 TGTATCGATACAA
40765 TGTATCGATACAA
1 TGTATCGATACAA
40778 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:40788 original size:20 final size:20
Alignment explanation
Indices: 40763--40841 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
40753 GTATCGATAC
40763 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
40783 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
40808 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
40828 CATGTATCGATACA
1 AATGTATCGATACA
40842 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:42877 original size:15 final size:15
Alignment explanation
Indices: 42857--42887 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42847 ATTTCGTTTG
*
42857 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
42872 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
42887 G
1 G
42888 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:46967 original size:13 final size:13
Alignment explanation
Indices: 46949--46974 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46939 CAATTTTTTG
46949 TGTATCGATACAT
1 TGTATCGATACAT
46962 TGTATCGATACAT
1 TGTATCGATACAT
46975 ACTTAATGTA
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:47072 original size:40 final size:40
Alignment explanation
Indices: 47014--47105 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
47004 TGCCCAAGAA
* *
47014 ATGTATCGATACAACTTTTTATGTATCGATACCTTGCAAC
1 ATGTATCGATACAACTTTTCATGTATCGATACATTGCAAC
*
47054 ATGTATCGATACATCTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTCATGTATCGATACATTGCAAC
47094 ATGTATCGATAC
1 ATGTATCGATAC
47106 TTTGAATTGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (40 bp):
ATGTATCGATACAACTTTTCATGTATCGATACATTGCAAC
Found at i:47087 original size:20 final size:20
Alignment explanation
Indices: 47014--47087 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
47004 TGCCCAAGAA
* *
47014 ATGTATCGATACAACTTTTT
1 ATGTATCGATACATCTTTTC
**
47034 ATGTATCGATAC--CTTGCAAC
1 ATGTATCGATACATCTT--TTC
47054 ATGTATCGATACATCTTTTC
1 ATGTATCGATACATCTTTTC
47074 ATGTATCGATACAT
1 ATGTATCGATACAT
47088 TGCAACATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
18 3 0.07
20 39 0.87
22 3 0.07
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATCTTTTC
Found at i:47096 original size:20 final size:20
Alignment explanation
Indices: 47034--47105 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
47024 ACAACTTTTT
*
47034 ATGTATCGATACCTTGCAAC
1 ATGTATCGATACATTGCAAC
***
47054 ATGTATCGATACATCT-TTTC
1 ATGTATCGATACAT-TGCAAC
47074 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
47094 ATGTATCGATAC
1 ATGTATCGATAC
47106 TTTGAATTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Done.