Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1729
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: 65229
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Found at i:3552 original size:31 final size:30
Alignment explanation
Indices: 3503--3561 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
3493 AATTAAATAA
* *
3503 ATTTTTAATAATTATTATTATTATATTTTT
1 ATTTTAAATAAATATTATTATTATATTTTT
3533 ATTTTAAATAAATATTTATTATTATATTT
1 ATTTTAAATAAATA-TTATTATTATATTT
3562 CATTACACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
ATTTTAAATAAATATTATTATTATATTTTT
Found at i:3747 original size:2 final size:2
Alignment explanation
Indices: 3742--3774 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3732 ACACACACAC
3742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3775 AATGGATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5251 original size:148 final size:146
Alignment explanation
Indices: 4983--5301 Score: 403
Period size: 148 Copynumber: 2.2 Consensus size: 146
4973 CCAATGCTTG
* * * * *
4983 TTGAGCAATGATAAAAGAGAAT-AAGTACAACATAATTTATGTCCTCTAAAATAGAAGGAAAAAA
1 TTGAGCAATGATAAAAGAGAATAAAGCAAAAAATAATTTATATCCTCTAAAATAGAAGAAAAAAA
*
5047 AAAGATTCATAACATTTGAATGGAAATATGTTTTCATTTGATAACATTTTCATGATCCATTGCTT
66 AAAGATTCATAACATTTGAATGAAAATATGTTTTCATTTGATAACATTTTCATGATCCATTGCTT
*
5112 GTTAGTAGGGAATACT
131 GTTAGTAGGAAATACT
* * * *
5128 TTAGAGCAATGGTAAAAGAGAATAAAGCAAAAAAGTTATTTATATCCTTTAAAATAGGAGAAAAA
1 TT-GAGCAATGATAAAAGAGAATAAAGCAAAAAA-TAATTTATATCCTCTAAAATAGAAGAAAAA
* * *
5193 AAAAAGATTGATAACATTTGAATTAAAATAT-TCTTAT-ATTTTAT-ACTATTTTCATGATCCAT
64 AAAAAGATTCATAACATTTGAATGAAAATATGT-TT-TCATTTGATAAC-ATTTTCATGATCCAT
* *
5255 TGCTTGTTGGTAGGAAATTCT
126 TGCTTGTTAGTAGGAAATACT
*
5276 TTGTAACAATGATAAAAGAGAATAAA
1 TTG-AGCAATGATAAAAGAGAATAAA
5302 TTAAAATGCT
Statistics
Matches: 149, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
145 2 0.01
146 19 0.13
147 11 0.07
148 116 0.78
149 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (146 bp):
TTGAGCAATGATAAAAGAGAATAAAGCAAAAAATAATTTATATCCTCTAAAATAGAAGAAAAAAA
AAAGATTCATAACATTTGAATGAAAATATGTTTTCATTTGATAACATTTTCATGATCCATTGCTT
GTTAGTAGGAAATACT
Found at i:6234 original size:22 final size:22
Alignment explanation
Indices: 6208--6250 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6198 AAATTTTATT
*
6208 TAAAT-TTAATTATAAACATATA
1 TAAATATTAA-TATAAAAATATA
6230 TAAATATTAATATAAAAATAT
1 TAAATATTAATATAAAAATAT
6251 TATTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:7192 original size:2 final size:2
Alignment explanation
Indices: 7185--7217 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
7175 TTACTAGGTG
*
7185 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7218 TAATTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7621 original size:2 final size:2
Alignment explanation
Indices: 7614--7656 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
7604 ATGGATATTA
7614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7656 A
1 A
7657 ACGGATTTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9132 original size:147 final size:150
Alignment explanation
Indices: 8922--9323 Score: 485
Period size: 147 Copynumber: 2.7 Consensus size: 150
8912 ATAAAAAGGA
** * * *
8922 AACATTTGAACGGAAATATGCCTCTATTTGAT-ATATTTTCATGATCCATTGCTTGTTACTAGGG
1 AACATTTGAATAGAAATATGCTTCTATTTGATAACATTTTCATGATCCATTGCTTGTTAGTAGGG
* * *
8986 GATGCTTTAGAGCAATGGTAAAAGAGAATAAAGTAAAAAAATTATTCATGTCCTCTAAAATT-AA
66 AATGCTTTAGAGCAATGGTAAAAGAGAATAAAATAAAAAAATTATTCATGTCCCCTAAAATTAAA
*
9050 AAAA-ACAA-AAAGATTCAT
131 AAAAGAAAAGAAAGATTCAT
*
9068 AACATTTGAATAGAAATATACTTCTATTTGATAACATTTTCATGATCCATTGCTTGTTAGTAGGG
1 AACATTTGAATAGAAATATGCTTCTATTTGATAACATTTTCATGATCCATTGCTTGTTAGTAGGG
* *
9133 AATGCTTTAGAGCAATGGTAAAAGAGAATAAAAT-AAAAAGTTATTTATGTCCCCTAAAATTAAA
66 AATGCTTTAGAGCAATGGTAAAAGAGAATAAAATAAAAAAATTATTCATGTCCCCTAAAATT---
*
9197 AACAAAAAAGAAAAGAAAGATTGAT
128 -A-AAAAAAGAAAAGAAAGATTCAT
* * * * *
9222 AACATTTGAATGAAAAATATGCTTATATTTGATATCATTTTCGTGA-CCATT-CTTGTTGGTAGG
1 AACATTTGAAT-AGAAATATGCTTCTATTTGATAACATTTTCATGATCCATTGCTTGTTAGTAGG
* * * ** *
9285 GAATTCTTTATAACAATAATAAAAGAGAATAAATTAAAA
65 GAATGCTTTAGAGCAATGGTAAAAGAGAATAAAATAAAA
9324 TGCTTTAGAT
Statistics
Matches: 220, Mismatches: 25, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
146 52 0.24
147 62 0.28
152 6 0.03
153 43 0.20
154 28 0.13
155 29 0.13
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (150 bp):
AACATTTGAATAGAAATATGCTTCTATTTGATAACATTTTCATGATCCATTGCTTGTTAGTAGGG
AATGCTTTAGAGCAATGGTAAAAGAGAATAAAATAAAAAAATTATTCATGTCCCCTAAAATTAAA
AAAAGAAAAGAAAGATTCAT
Found at i:11773 original size:18 final size:19
Alignment explanation
Indices: 11750--11788 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
11740 ATCAGTAATT
11750 ATCTTTAAAAG-ATTAAAA
1 ATCTTTAAAAGTATTAAAA
*
11768 ATCTTTAAAAGTTTTAAAA
1 ATCTTTAAAAGTATTAAAA
11787 AT
1 AT
11789 GAAAAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (19 bp):
ATCTTTAAAAGTATTAAAA
Found at i:12539 original size:157 final size:156
Alignment explanation
Indices: 12377--12677 Score: 383
Period size: 156 Copynumber: 1.9 Consensus size: 156
12367 TAAATGATAG
* *
12377 AAGAGAATAAAATACAAAGTAATTTATATCCTCTAAAATAAAGGGAAAAAATAAAATAAAAAG-A
1 AAGAGAATAAAATAAAAAGTAATTTATATCCTCTAAAATAAA---AAAAAAGAAAA-AAAAAGAA
* * * *
12441 AGATTGACAACATTTGAATG-GAAATATGCATCTATTTGATA-CATTTTCATGATCAATTGCTTA
62 AGATTAACAACATTTGAATGAAAAAAATACATCTATTTGATATCATTTTCATGATCAATTGCTTA
12504 TTAGTAGGGAATGCTTTACGGCAATGGTAA
127 TTAGTAGGGAATGCTTTACGGCAATGGTAA
* * * ** *
12534 AAGAGAATAAAGTAAAAAGTTATTTATGTCCTCTAAAATTTAAAAAAAGAAAAGAAAAGAAAGAT
1 AAGAGAATAAAATAAAAAGTAATTTATATCCTCTAAAATAAAAAAAAAGAAAAAAAAAGAAAGAT
* * * * *
12599 TAATAACATTTGAATGAAAAAAATACTTCTATTTGATATCATTTTCATGATCTATTGCTTGTTGG
66 TAACAACATTTGAATGAAAAAAATACATCTATTTGATATCATTTTCATGATCAATTGCTTATTAG
*
12664 TAGGGAATTCTTTA
131 TAGGGAATGCTTTA
12678 TAACAATGAG
Statistics
Matches: 123, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
153 5 0.04
154 29 0.24
155 17 0.14
156 36 0.29
157 36 0.29
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.32
Consensus pattern (156 bp):
AAGAGAATAAAATAAAAAGTAATTTATATCCTCTAAAATAAAAAAAAAGAAAAAAAAAGAAAGAT
TAACAACATTTGAATGAAAAAAATACATCTATTTGATATCATTTTCATGATCAATTGCTTATTAG
TAGGGAATGCTTTACGGCAATGGTAA
Found at i:13117 original size:3 final size:3
Alignment explanation
Indices: 13109--13147 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
13099 TCTAAAAAAT
*
13109 TAA TAA TAA TAA AAA TAA TAA TAA TAA TAA TATA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA
13148 CTGTCCTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:13241 original size:17 final size:18
Alignment explanation
Indices: 13214--13248 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
13204 GAAATATAGC
13214 TTATCTTTTCTTAATTTT
1 TTATCTTTTCTTAATTTT
*
13232 TTAT-TTTTCTTTATTTT
1 TTATCTTTTCTTAATTTT
13249 CTCTATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (18 bp):
TTATCTTTTCTTAATTTT
Found at i:16702 original size:24 final size:24
Alignment explanation
Indices: 16675--16725 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
16665 TTCTTGTGTC
16675 ATGAATCTTTGGTTGATTCTATAT
1 ATGAATCTTTGGTTGATTCTATAT
16699 ATGAATCTTTGGTTGATTCTATAT
1 ATGAATCTTTGGTTGATTCTATAT
16723 ATG
1 ATG
16726 TTCCTTCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (24 bp):
ATGAATCTTTGGTTGATTCTATAT
Found at i:17901 original size:24 final size:24
Alignment explanation
Indices: 17874--17943 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
17864 AATAAAAATT
*
17874 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAAAA
*
17898 AGCCA-TAATTTTTGACAAACAAAA
1 AGCCACCAA-TTTTGACAAACAAAA
*
17922 AGGAACCACCATTTTTGACAAA
1 A-G--CCACCAATTTTGACAAA
17944 TACAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 20 0.54
25 1 0.03
27 13 0.35
28 1 0.03
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAAAA
Found at i:17943 original size:27 final size:27
Alignment explanation
Indices: 17876--17972 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
17866 TAAAAATTAG
* *
17876 CCACCAATTTTGACAAACAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
**
17900 CCATAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * *
17927 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
17954 CCACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
17973 CATGGTGGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
24 19 0.32
25 1 0.02
27 39 0.66
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:17991 original size:24 final size:25
Alignment explanation
Indices: 17960--18017 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
17950 GTAACCACCA
*
17960 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
*
17984 TTGTTGACAAACACAAAGGGTGGTTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
18010 TTGTTGAC
1 TTGTTGAC
18018 TAGCCACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.47
26 16 0.53
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:19908 original size:21 final size:22
Alignment explanation
Indices: 19882--19927 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
19872 ATCTGTTGAA
* *
19882 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
19903 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
19925 ACT
1 ACT
19928 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:22499 original size:24 final size:24
Alignment explanation
Indices: 22472--22541 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
22462 AATAAAAATT
*
22472 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAAAA
*
22496 AGCCA-TAATTTTTGACAAACAAAA
1 AGCCACCAA-TTTTGACAAACAAAA
*
22520 AGGAACCACCATTTTTGACAAA
1 A-G--CCACCAATTTTGACAAA
22542 TACAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 20 0.54
25 1 0.03
27 13 0.35
28 1 0.03
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAAAA
Found at i:22541 original size:27 final size:27
Alignment explanation
Indices: 22474--22570 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
22464 TAAAAATTAG
* *
22474 CCACCAATTTTGACAAACAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
**
22498 CCATAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * *
22525 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
22552 CCACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
22571 CATGGTGGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
24 19 0.32
25 1 0.02
27 39 0.66
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:22589 original size:24 final size:25
Alignment explanation
Indices: 22558--22615 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
22548 GTAACCACCA
*
22558 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
*
22582 TTGTTGACAAACACAAAGGGTGGTTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
22608 TTGTTGAC
1 TTGTTGAC
22616 TAGCCACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.47
26 16 0.53
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:23047 original size:2 final size:2
Alignment explanation
Indices: 23040--23066 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23030 TGAGATAATT
23040 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
23067 TTAATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23763 original size:16 final size:16
Alignment explanation
Indices: 23674--23769 Score: 59
Period size: 16 Copynumber: 5.6 Consensus size: 16
23664 AAATTTATTG
23674 AAATTATATTTATATTAA
1 AAATTATA--TATATTAA
* *
23692 ATAATAAAATACTAATTAA
1 A-AATTATATA-T-ATTAA
* *
23711 AATAATATTTATATTAA
1 AA-ATTATATATATTAA
* *
23728 ATAATTACAAATTATT-A
1 A-AATTATATA-TATTAA
23745 AAATTATATATATTAA
1 AAATTATATATATTAA
23761 AAATTATAT
1 AAATTATAT
23770 TTATACTTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
15 4 0.07
16 17 0.29
17 14 0.24
18 9 0.15
19 15 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTATATATATTAA
Found at i:23848 original size:24 final size:25
Alignment explanation
Indices: 23802--23856 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
23792 AGTATATATC
*
23802 AAAATTATAGTTACTAAATAATAATA
1 AAAATTATAGTTACTAAACAATAA-A
23828 AAAATTATA-TTA-TAAACAATAAA
1 AAAATTATAGTTACTAAACAATAAA
23851 AAAATT
1 AAAATT
23857 GAGAAGAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 7 0.25
24 9 0.32
25 3 0.11
26 9 0.32
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAATTATAGTTACTAAACAATAAA
Found at i:26477 original size:16 final size:15
Alignment explanation
Indices: 26441--26479 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
26431 TTTCAATTCA
26441 AATATTTTTTATATT
1 AATATTTTTTATATT
**
26456 CGTATTTTTATATATT
1 AATATTTTT-TATATT
26472 AATATTTT
1 AATATTTT
26480 ATTGTCACTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (15 bp):
AATATTTTTTATATT
Found at i:34672 original size:14 final size:14
Alignment explanation
Indices: 34655--34682 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34645 TAACTATTAC
34655 ATTTTATGACAAAT
1 ATTTTATGACAAAT
34669 ATTTTATGACAAAT
1 ATTTTATGACAAAT
34683 GCAAATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
ATTTTATGACAAAT
Found at i:38715 original size:103 final size:104
Alignment explanation
Indices: 38530--38718 Score: 292
Period size: 103 Copynumber: 1.8 Consensus size: 104
38520 TCTCTAGATT
* * * * **
38530 TTTCCTTTATTGTTGTTCTAGTATCAACTTACTAAGTCGTCTAATTTTATAAGCTGCATTCCAAG
1 TTTCCTTTATTGTTGTTCTAGTATCAAATTACTAAGTCATCTAATTCTAAAAGCTGCAGGCCAAG
38595 GTTGCTTCAGTCAGTGGAAAAAAATGCTATCTCTCGAGG
66 GTTGCTTCAGTCAGTGGAAAAAAATGCTATCTCTCGAGG
*
38634 TTTCC-TTATTGTTGTTCTGGTATCAAATTACTAAGTCATCTAATTCTAAAAGCTGCAGGCCAAG
1 TTTCCTTTATTGTTGTTCTAGTATCAAATTACTAAGTCATCTAATTCTAAAAGCTGCAGGCCAAG
38698 GTTGCTTCAGAT-AGTGGAAAA
66 GTTGCTTCAG-TCAGTGGAAAA
38719 GATGCTGAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
103 71 0.92
104 6 0.08
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (104 bp):
TTTCCTTTATTGTTGTTCTAGTATCAAATTACTAAGTCATCTAATTCTAAAAGCTGCAGGCCAAG
GTTGCTTCAGTCAGTGGAAAAAAATGCTATCTCTCGAGG
Found at i:41666 original size:2 final size:2
Alignment explanation
Indices: 41659--41687 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41649 TTCCACCCAT
41659 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
41688 TCCAGTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:42837 original size:28 final size:28
Alignment explanation
Indices: 42777--42837 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
42767 TTAATAAAAT
*
42777 ATAAATTTAAACTTAAACTCATTTAAAC
1 ATAAATTTAAACTTAAACTCAATTAAAC
*
42805 TTAAATTTAAA-TTAAAAGCTCAATTAAA-
1 ATAAATTTAAACTT-AAA-CTCAATTAAAC
42833 ATAAA
1 ATAAA
42838 AAAGTAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 2 0.07
28 17 0.61
29 9 0.32
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (28 bp):
ATAAATTTAAACTTAAACTCAATTAAAC
Found at i:43259 original size:23 final size:26
Alignment explanation
Indices: 43214--43261 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
43204 TTAGATTTAC
*
43214 TTAATAAAATATGTATTTAATAATTT
1 TTAATAAAATATGTATATAATAATTT
43240 TTAA-AAAATAT-TATAT-ATAATT
1 TTAATAAAATATGTATATAATAATT
43262 GATGTGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 4 0.19
25 7 0.33
26 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TTAATAAAATATGTATATAATAATTT
Found at i:43301 original size:14 final size:15
Alignment explanation
Indices: 43282--43311 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
43272 TATTATATAA
43282 ATTTATTTAAT-TTT
1 ATTTATTTAATATTT
43296 ATTTATTTAATATTT
1 ATTTATTTAATATTT
43311 A
1 A
43312 AAAATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTATTTAATATTT
Found at i:43756 original size:20 final size:20
Alignment explanation
Indices: 43656--43758 Score: 58
Period size: 20 Copynumber: 5.3 Consensus size: 20
43646 ATTATATAAA
43656 ATATAAAATTAATATATATT
1 ATATAAAATTAATATATATT
* *
43676 ATGTAATAA-TAAAAT-TATTT
1 ATATAA-AATTAATATATA-TT
* * *
43696 AGATCAAATTGAAT-TCAAATT
1 ATATAAAATT-AATAT-ATATT
**
43717 -T-TAAAA--AATATATAAA
1 ATATAAAATTAATATATATT
43733 ATATAAAATTAATATATATT
1 ATATAAAATTAATATATATT
43753 ATATAA
1 ATATAA
43759 CAATAAAATG
Statistics
Matches: 58, Mismatches: 14, Indels: 22
0.62 0.15 0.23
Matches are distributed among these distances:
16 5 0.09
17 2 0.03
18 5 0.09
19 8 0.14
20 31 0.53
21 6 0.10
22 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (20 bp):
ATATAAAATTAATATATATT
Found at i:57091 original size:46 final size:41
Alignment explanation
Indices: 57000--57092 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
56990 CTTAACCATG
* *
57000 TCCCCTCCCCCTTTCACTTTCCCTGCTTTCTTACATGACAT
1 TCCCCTCCCCCTTCCACTTTCCCTGCTTTCTTACATCACAT
*
57041 TCCCCTCCCCCTTCCACTTTCCCTTCTTTCTTACATCACAT
1 TCCCCTCCCCCTTCCACTTTCCCTGCTTTCTTACATCACAT
*
57082 TGCCCTCCCCC
1 TCCCCTCCCCC
57093 AGGTTTTAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.11, C:0.49, G:0.03, T:0.37
Consensus pattern (41 bp):
TCCCCTCCCCCTTCCACTTTCCCTGCTTTCTTACATCACAT
Done.