Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1998
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: 63062
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:5314 original size:50 final size:50
Alignment explanation
Indices: 5190--5437 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
5180 GATAATAACA
* ** * *
5190 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCAT-CTCGG
* * *
5241 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
5291 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
5341 TGCCCATGCCATGTCCCAGACATGGTCTTACA-GGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-CGG
* *
5395 ATGCCAATTCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5438 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
49 11 0.07
50 82 0.49
51 33 0.20
52 2 0.01
53 1 0.01
54 2 0.01
55 30 0.18
56 8 0.05
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:5368 original size:100 final size:103
Alignment explanation
Indices: 5189--5437 Score: 337
Period size: 100 Copynumber: 2.4 Consensus size: 103
5179 TGATAATAAC
**
5189 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
5254 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACA-GGGACCTCTCAATCTTAAGG
* *
5291 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
5354 TCCCAGACATGGTCTTACAGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGACCTCTCA--ATCTTAAGG
** *
5395 ATGCCAATTCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5438 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
99 11 0.08
100 39 0.30
101 36 0.27
102 3 0.02
103 1 0.01
104 2 0.02
105 39 0.30
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (103 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGACCTCTCAATCTTAAGG
Found at i:5553 original size:13 final size:13
Alignment explanation
Indices: 5532--5563 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5522 GCTTGGATCA
*
5532 TCATCAAATAAAT
1 TCATAAAATAAAT
5545 TCATAAAATAAAT
1 TCATAAAATAAAT
5558 TCATAA
1 TCATAA
5564 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:5810 original size:30 final size:29
Alignment explanation
Indices: 5775--5831 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
5765 CCTCGACTCT
*
5775 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTAC-ATTTTGCCCCTA
*
5805 AACTTTTACATAATTACATTTTGCCCC
1 AACTTTTACAAAATTACATTTTGCCCC
5832 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (29 bp):
AACTTTTACAAAATTACATTTTGCCCCTA
Found at i:8164 original size:9 final size:9
Alignment explanation
Indices: 8147--8181 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
8137 TGAGTTTTCG
8147 AATTCGAAT
1 AATTCGAAT
*
8156 AACTCGAAT
1 AATTCGAAT
*
8165 AATTCAAAT
1 AATTCGAAT
8174 AATTCGAA
1 AATTCGAA
8182 CATCAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.29
Consensus pattern (9 bp):
AATTCGAAT
Found at i:8431 original size:30 final size:31
Alignment explanation
Indices: 8397--8456 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
8387 AAACCTTTTA
*
8397 TTTTCC-CTCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCTCT-AAAACTTTTACTCCCTTCCCAC
*
8427 TTTTCCTCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCTCTAAAACTTTTACTCCCTTCCCA
8457 TCTCACCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCTCTAAAACTTTTACTCCCTTCCCAC
Found at i:9573 original size:20 final size:19
Alignment explanation
Indices: 9519--9581 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
9509 TAATTGATTT
*
9519 AAATATTTAAATGAAATTATA
1 AAATATTTAAAT-ATATTA-A
*
9540 AAATA---AAATATATTTA
1 AAATATTTAAATATATTAA
9556 AAATATTTAAATACTATTAA
1 AAATATTTAAATA-TATTAA
9576 AAATAT
1 AAATAT
9582 ACAAAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
16 6 0.17
17 4 0.11
18 4 0.11
19 5 0.14
20 11 0.31
21 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
AAATATTTAAATATATTAA
Found at i:9878 original size:33 final size:34
Alignment explanation
Indices: 9841--9915 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 34
9831 AAAATATTTT
** *
9841 TTTAATTTCTATTATATATATTTTA-TAATTAAA
1 TTTAATTTCTAAAAAATATATTTTATTAATTAAA
* *
9874 TTTAA-GTCTAAAAAATATATTTTATTATTTAAA
1 TTTAATTTCTAAAAAATATATTTTATTAATTAAA
*
9907 TTGAATTTC
1 TTTAATTTC
9916 GGCCCGATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
32 15 0.45
33 16 0.48
34 2 0.06
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (34 bp):
TTTAATTTCTAAAAAATATATTTTATTAATTAAA
Found at i:10497 original size:16 final size:16
Alignment explanation
Indices: 10471--10510 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
10461 GGTCACAAAG
*
10471 AAAAGAAAAAAATGTAAA
1 AAAAG-AAAAAA-GAAAA
10489 AAAAGAAAAAAGAAAA
1 AAAAGAAAAAAGAAAA
10505 AAAAGA
1 AAAAGA
10511 CCAAATTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 6 0.29
18 5 0.24
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.05
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAA
Found at i:19156 original size:3 final size:3
Alignment explanation
Indices: 19148--19182 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19138 TTATATAAAT
19148 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
19183 TAAAAGCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:24583 original size:9 final size:9
Alignment explanation
Indices: 24569--24595 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
24559 TAAAATATAC
24569 TAATAGTAT
1 TAATAGTAT
24578 TAATAGTAT
1 TAATAGTAT
24587 TAATAGTAT
1 TAATAGTAT
24596 CAACATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (9 bp):
TAATAGTAT
Found at i:24675 original size:3 final size:3
Alignment explanation
Indices: 24667--24711 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
24657 TGACTATAAC
24667 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24712 TCTAATGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25086 original size:25 final size:25
Alignment explanation
Indices: 25037--25088 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
25027 AGATAAATTA
*
25037 AAATTATGGGGTAAAAATTAAAACC
1 AAATTATGAGGTAAAAATTAAAACC
25062 AAATTATGAGGTAAAAATTAAAACC
1 AAATTATGAGGTAAAAATTAAAACC
25087 AA
1 AA
25089 TAAAAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.56, C:0.08, G:0.13, T:0.23
Consensus pattern (25 bp):
AAATTATGAGGTAAAAATTAAAACC
Found at i:26759 original size:44 final size:47
Alignment explanation
Indices: 26711--26812 Score: 111
Period size: 50 Copynumber: 2.2 Consensus size: 47
26701 TGATCTACTA
* *
26711 CAACTTCAATGATATAAGATT-C-T-TAGCTTCATTCCAACCCATTG
1 CAACTTCAAGGAGATAAGATTCCGTATAGCTTCATTCCAACCCATTG
* *
26755 CAACTTCAGGGAGATAAGATTCGCTGTCATAGTTTCATTCCAACCCATTG
1 CAACTTCAAGGAGATAAGATTC-C-GT-ATAGCTTCATTCCAACCCATTG
*
26805 TAACTTCA
1 CAACTTCA
26813 GGGCTATAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
44 18 0.38
46 1 0.02
48 1 0.02
50 27 0.57
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (47 bp):
CAACTTCAAGGAGATAAGATTCCGTATAGCTTCATTCCAACCCATTG
Found at i:26853 original size:138 final size:138
Alignment explanation
Indices: 26615--26880 Score: 349
Period size: 138 Copynumber: 1.9 Consensus size: 138
26605 CTTGCTCCAC
* * * *
26615 TGCAACTCTAGGGAGATAAGATTCACCATCGTAGTTTTATTCCAACCCACTGCAACTTTAGGGGT
1 TGCAACTCTAGGGAGATAAGATTCACCATCATAGTTTCATTCCAACCCACTGCAACTTCAGGGCT
* *
26680 ATAGAAATTGTGGCTTCAATCTGATCTACTACAACTTCAATGATATAAGATTCT-TAGCTTCATT
66 ATAGAAATTGTAGCTTCAATCTGATCTACTACAACTTCAAGGATATAAGATT-TGTAGCTTCATT
26744 CCAACCCAT
130 CCAACCCAT
* ** * *
26753 TGCAACT-TCAGGGAGATAAGATTCGCTGTCATAGTTTCATTCCAACCCATTGTAACTTCAGGGC
1 TGCAACTCT-AGGGAGATAAGATTCACCATCATAGTTTCATTCCAACCCACTGCAACTTCAGGGC
* * * *
26817 TATAGAAATTGTAGCTTCAATCTGAT-TCACTGCAACTTTAGGGATATAGGATTTGTAGCTTCAT
65 TATAGAAATTGTAGCTTCAATCTGATCT-ACTACAACTTCAAGGATATAAGATTTGTAGCTTCAT
26881 CTTGCTCTAC
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
137 3 0.03
138 107 0.97
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (138 bp):
TGCAACTCTAGGGAGATAAGATTCACCATCATAGTTTCATTCCAACCCACTGCAACTTCAGGGCT
ATAGAAATTGTAGCTTCAATCTGATCTACTACAACTTCAAGGATATAAGATTTGTAGCTTCATTC
CAACCCAT
Found at i:27958 original size:28 final size:28
Alignment explanation
Indices: 27926--27997 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
27916 TAATGAGATT
* *
27926 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGATTAATTATAA
* *
27954 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTAATTATAA
*
27982 AGCACTAAGTATGCGA
1 AGCACTAAGTGTGCGA
27998 ACTTATTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTAATTATAA
Found at i:28686 original size:23 final size:23
Alignment explanation
Indices: 28651--28910 Score: 243
Period size: 23 Copynumber: 11.1 Consensus size: 23
28641 TTTTGGTTTG
* *
28651 AATTTGGTATATATATGCTGCCC
1 AATTTGTTGTATATATGCTGCCC
*
28674 AATTTGTTGTATATATGCTGTCC
1 AATTTGTTGTATATATGCTGCCC
* * * *
28697 AATTTTTGGTGTAAAAATGCTGCTC
1 AA--TTTGTTGTATATATGCTGCCC
*
28722 AATTTGTTGTATTTATGCTGCCC
1 AATTTGTTGTATATATGCTGCCC
* *
28745 AAATTGTTGTATATATGCTGTCC
1 AATTTGTTGTATATATGCTGCCC
* * * * *
28768 AATTTTGATGTAAAAATGCTACTC
1 AA-TTTGTTGTATATATGCTGCCC
* * *
28792 AATTTGGTATATATATGCTTCCC
1 AATTTGTTGTATATATGCTGCCC
*
28815 AATTTGTTGTATATATGCTGTCC
1 AATTTGTTGTATATATGCTGCCC
* * * *
28838 AATTTTTGGTGTAAAAATGCTGCTC
1 AA--TTTGTTGTATATATGCTGCCC
28863 AATTTGTTGTATATATGCTGCCC
1 AATTTGTTGTATATATGCTGCCC
*
28886 AGA-TTGTTGTATATATGCTGTCC
1 A-ATTTGTTGTATATATGCTGCCC
28909 AA
1 AA
28911 ATTTTAGTGT
Statistics
Matches: 188, Mismatches: 43, Indels: 13
0.77 0.18 0.05
Matches are distributed among these distances:
22 1 0.01
23 134 0.71
24 17 0.09
25 36 0.19
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (23 bp):
AATTTGTTGTATATATGCTGCCC
Found at i:28808 original size:141 final size:142
Alignment explanation
Indices: 28651--28969 Score: 509
Period size: 141 Copynumber: 2.3 Consensus size: 142
28641 TTTTGGTTTG
28651 AATTTGGTATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATG
1 AATTTGGTATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATG
*
28716 CTGCTCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGCTGTCC-AATTTT-GATGT
66 CTGCTCAATTTGTTGTATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTAG-TGT
28779 AAAAATGCTACTC-
130 AAAAATGCT-CTCT
*
28792 AATTTGGTATATATATGCTTCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATG
1 AATTTGGTATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATG
* *
28857 CTGCTCAATTTGTTGTATATATGCTGCCCAGATTGTTGTATATATGCTGTCCAAATTTTAGTGTG
66 CTGCTCAATTTGTTGTATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTAGTGTA
*
28922 AAAATGCTGTCT
131 AAAATGCTCTCT
* * * * *
28934 AGTTTGGTATATAAATGCTGTCCAAATTGATGTATA
1 AATTTGGTATATATATGCTGCCCAATTTGTTGTATA
28970 AGAGCTGTCC
Statistics
Matches: 164, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
141 116 0.71
142 47 0.29
143 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (142 bp):
AATTTGGTATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATG
CTGCTCAATTTGTTGTATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTAGTGTA
AAAATGCTCTCT
Found at i:28977 original size:71 final size:71
Alignment explanation
Indices: 28651--28982 Score: 445
Period size: 71 Copynumber: 4.7 Consensus size: 71
28641 TTTTGGTTTG
* *
28651 AATTTGGTATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATG
1 AATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATG
28716 CTGCTC
66 CTGCTC
* * * *
28722 AATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATG
1 AATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATG
*
28786 CTACTC
66 CTGCTC
* * *
28792 AATTTGGTATATATATGCTTCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATG
1 AATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATG
28857 CTGCTC
66 CTGCTC
* * * * *
28863 AATTTGTTGTATATATGCTGCCCAGATTGTTGTATATATGCTGTCCAAATTTTAGTGTGAAAATG
1 AATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATG
28928 CTG-TC
66 CTGCTC
* * * * *
28933 TAGTTTGGTATATAAATGCTGTCCAAATTGATGTATA-AGAGCTGTCCAAA
1 -AATTTGGTATATATATGCTGCCCAAATTGTTGTATATA-TGCTGTCCAAA
28983 CAGGGTAGAT
Statistics
Matches: 227, Mismatches: 31, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
70 65 0.29
71 162 0.71
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (71 bp):
AATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATG
CTGCTC
Found at i:38472 original size:34 final size:34
Alignment explanation
Indices: 38429--38496 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
38419 TTTAGATAGG
38429 ATCATTTGCAAGTGTTCTTCTATCGGCCGAATAC
1 ATCATTTGCAAGTGTTCTTCTATCGGCCGAATAC
38463 ATCATTTGCAAGTGTTCTTCTATCGGCCGAATAC
1 ATCATTTGCAAGTGTTCTTCTATCGGCCGAATAC
38497 TTTCTTGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (34 bp):
ATCATTTGCAAGTGTTCTTCTATCGGCCGAATAC
Found at i:41047 original size:48 final size:48
Alignment explanation
Indices: 40991--41087 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
40981 GAGTCCATAC
*
40991 TCCGTAAGTTAGGAGCATGACTCCTCGAATCCTGAAAATAACGAATAT
1 TCCGTAAGTTAGGAGCATGACTCCTCGAATCCTGAAAATAACAAATAT
*
41039 TCCGTAAGTTAGGAGCATGATTCCTCGAATCCTGAAAATAACAAATAT
1 TCCGTAAGTTAGGAGCATGACTCCTCGAATCCTGAAAATAACAAATAT
41087 T
1 T
41088 GCCTCGGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (48 bp):
TCCGTAAGTTAGGAGCATGACTCCTCGAATCCTGAAAATAACAAATAT
Found at i:41372 original size:9 final size:9
Alignment explanation
Indices: 41358--41384 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
41348 TAAAATATAC
41358 TAATAGTAT
1 TAATAGTAT
41367 TAATAGTAT
1 TAATAGTAT
41376 TAATAGTAT
1 TAATAGTAT
41385 CAACATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (9 bp):
TAATAGTAT
Found at i:52166 original size:35 final size:33
Alignment explanation
Indices: 52120--52187 Score: 118
Period size: 35 Copynumber: 2.0 Consensus size: 33
52110 ATTAGATAGG
52120 ATCATTTGCAAGTGTTCTTCTATCGGGCCGAATAC
1 ATCATTTGCAAGTGTTCTTCTATC-GG-CGAATAC
52155 ATCATTTGCAAGTGTTCTTCTATCGGCGAATAC
1 ATCATTTGCAAGTGTTCTTCTATCGGCGAATAC
52188 TTTTTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 7 0.21
34 2 0.06
35 24 0.73
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (33 bp):
ATCATTTGCAAGTGTTCTTCTATCGGCGAATAC
Found at i:54717 original size:48 final size:48
Alignment explanation
Indices: 54661--54757 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
54651 GAGTCCATAC
*
54661 TCCGTAAGTTAGGAGCATGACTCCTCGAATCCTGAAAATAACGAATAT
1 TCCGTAAGTTAGGAGCATGACTCCTCGAATCCTGAAAATAACAAATAT
*
54709 TCCGTAAGTTAGGAGCATGATTCCTCGAATCCTGAAAATAACAAATAT
1 TCCGTAAGTTAGGAGCATGACTCCTCGAATCCTGAAAATAACAAATAT
54757 T
1 T
54758 GCCTCGGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (48 bp):
TCCGTAAGTTAGGAGCATGACTCCTCGAATCCTGAAAATAACAAATAT
Found at i:55038 original size:9 final size:9
Alignment explanation
Indices: 55024--55050 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
55014 TAAAATATAC
55024 TAATAGTAT
1 TAATAGTAT
55033 TAATAGTAT
1 TAATAGTAT
55042 TAATAGTAT
1 TAATAGTAT
55051 CAACATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (9 bp):
TAATAGTAT
Found at i:57588 original size:25 final size:24
Alignment explanation
Indices: 57547--57593 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
57537 TTCACGCATA
57547 TTATATACAACATATAAATATAAC
1 TTATATACAACATATAAATATAAC
*
57571 TTATTTACATACATATAAATATA
1 TTATATACA-ACATATAAATATA
57594 TTTATATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (24 bp):
TTATATACAACATATAAATATAAC
Found at i:59533 original size:17 final size:17
Alignment explanation
Indices: 59494--59527 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
59484 ACATTTTTTA
*
59494 GGTATTATTTGGAAAGG
1 GGTATTATTTGAAAAGG
59511 GGTATTATTTGAAAAGG
1 GGTATTATTTGAAAAGG
59528 TTTATTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (17 bp):
GGTATTATTTGAAAAGG
Found at i:59868 original size:21 final size:22
Alignment explanation
Indices: 59831--59874 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
59821 ATACACTTAT
*
59831 AGACCTTAAATTGAGTTT-AAA
1 AGACCTTAAAATGAGTTTGAAA
59852 AGACCTTAAAAAT-AGTTTGAAA
1 AGACCTT-AAAATGAGTTTGAAA
59874 A
1 A
59875 CAATTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.30
Consensus pattern (22 bp):
AGACCTTAAAATGAGTTTGAAA
Found at i:60336 original size:14 final size:15
Alignment explanation
Indices: 60312--60341 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
60302 TGCCTAACCA
60312 ATATACTTCATTAGC
1 ATATACTTCATTAGC
60327 ATAT-CTTCATTAGC
1 ATATACTTCATTAGC
60341 A
1 A
60342 CAACATTTCA
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:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
ATATACTTCATTAGC
Found at i:61834 original size:15 final size:15
Alignment explanation
Indices: 61814--61842 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
61804 GAAATGTTGT
61814 GCTAATGAAGATATC
1 GCTAATGAAGATATC
61829 GCTAATGAAGATAT
1 GCTAATGAAGATAT
61843 ATTGGTAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (15 bp):
GCTAATGAAGATATC
Done.