Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168052.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_302, whole genome shotgun sequence
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: 36914
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:2647 original size:3 final size:3
Alignment explanation
Indices: 2625--2662 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
2615 TCTTCTTTTG
2625 TAT T-T TAT GTAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2663 GTATATCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2679 original size:4 final size:4
Alignment explanation
Indices: 2670--2696 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2660 TATGTATATC
2670 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
2697 TTATTCAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3275 original size:19 final size:19
Alignment explanation
Indices: 3239--3275 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3229 CAGTTTCCGG
* *
3239 TTGAATTTTTCGGTGAAAC
1 TTGAATTTTCCGGCGAAAC
3258 TTGAATTTTCCGGCGAAA
1 TTGAATTTTCCGGCGAAA
3276 TTTCCGGCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (19 bp):
TTGAATTTTCCGGCGAAAC
Found at i:3867 original size:22 final size:23
Alignment explanation
Indices: 3835--3879 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3825 TCTTATTTTA
3835 TTTTTAGTTTTGTTTACTTTTCT
1 TTTTTAGTTTTGTTTACTTTTCT
* *
3858 TTTTTA-TTTTTTTTATTTTTCT
1 TTTTTAGTTTTGTTTACTTTTCT
3880 ATTCTTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.80
Consensus pattern (23 bp):
TTTTTAGTTTTGTTTACTTTTCT
Found at i:4026 original size:57 final size:57
Alignment explanation
Indices: 3916--4026 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
3906 AAAGTTCCGA
* * * *
3916 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAATACTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTACAAAAAAATTTCC
*
3973 AAAAAATACTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTACAAAAAAATT
1 AAAAAATACTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTACAAAAAAATT
4027 ATTCTTTCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (57 bp):
AAAAAATACTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTACAAAAAAATTTCC
Found at i:7868 original size:7 final size:7
Alignment explanation
Indices: 7847--7903 Score: 57
Period size: 7 Copynumber: 8.3 Consensus size: 7
7837 AAAAGATGAT
7847 GAAAAAA
1 GAAAAAA
*
7854 AAAAAAA
1 GAAAAAA
7861 GAAAAAA
1 GAAAAAA
7868 G---AAA
1 GAAAAAA
*
7872 GAAAGAA
1 GAAAAAA
7879 GAAAAAA
1 GAAAAAA
7886 TGAAAAAA
1 -GAAAAAA
7894 TGAAAAAA
1 -GAAAAAA
7902 GA
1 GA
7904 GATCCAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 4 0.10
7 23 0.55
8 15 0.36
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.04
Consensus pattern (7 bp):
GAAAAAA
Found at i:9287 original size:80 final size:80
Alignment explanation
Indices: 9089--10006 Score: 1437
Period size: 80 Copynumber: 11.5 Consensus size: 80
9079 GTCTAGGAGT
9089 ATTTACTTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTA-TTTTCAAAGTTCGTTG
1 ATTTAC-TTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTTG
9151 CCT-TGTTTAGAGGAGCA
63 CCTCTGTTTAGAGGAGCA
* *
9168 ATTTATTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTA-TTTTCAAAGTCGTGGTA
1 ATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT--TG
9230 CCTCTGTTTAGAGGAGCA
63 CCTCTGTTTAGAGGAGCA
9248 ATTTACTTTTCAAAGTCGTGGT-CCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGC
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT--TGC
9312 CTCTG-TTAGAGGAGCA
64 CTCTGTTTAGAGGAGCA
* *
9328 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTAC
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT--TGC
9393 CTCTG-TTAGAGGAGCA
64 CTCTGTTTAGAGGAGCA
9409 ATTTACTTTTCAAA---GTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGC
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT--TGC
9471 CTCTGTTTAGAGGAGCA
64 CTCTGTTTAGAGGAGCA
9488 ATATT--TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAGTCGTTGC
1 AT-TTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCGTTGC
9551 CTCTGTTTAGAGGAGCA
64 CTCTGTTTAGAGGAGCA
*
9568 ATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCT
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCT
9633 CTGTTTAGAGGAGCA
66 CTGTTTAGAGGAGCA
*
9648 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCT
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCT
9713 CTG-TTAGAGGAGCA
66 CTGTTTAGAGGAGCA
9727 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCT
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCT
*
9792 CTGTTGAGAGGAGCA
66 CTGTTTAGAGGAGCA
*
9807 ATTTA-TTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTTGCC
1 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCC
9871 TCTGTTTAGAGGAGCA
65 TCTGTTTAGAGGAGCA
*
9887 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTAC-TTTCAAAGTCCGTTGC
1 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT-CGTTGC
9951 CTCTGTTTAGAGGAGCA
64 CTCTGTTTAGAGGAGCA
9968 ATTTAC-TTTCAAAAGTCGTGAGT--CTCTGTTTAGAGGAGC
1 ATTTACTTTTC-AAAGTCGTG-GTGCCTCTGTTTAGAGGAGC
10007 TTCGGCCAAA
Statistics
Matches: 801, Mismatches: 17, Indels: 42
0.93 0.02 0.05
Matches are distributed among these distances:
77 4 0.00
78 107 0.13
79 126 0.16
80 311 0.39
81 245 0.31
82 8 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (80 bp):
ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCT
CTGTTTAGAGGAGCA
Found at i:9499 original size:159 final size:157
Alignment explanation
Indices: 9110--10006 Score: 1363
Period size: 159 Copynumber: 5.6 Consensus size: 157
9100 CAAAGTTCGT
9110 TGCCTCTGTTTAGAGGAGCAATTTA-TTTTCAAAGTTCGTTGCCT-TGTTTAGAGGAGCAATTTA
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAGAGGAGCAATTTA
*
9173 TTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTA-TTTTCAAAGTCGTGGTACCTCT
65 -TTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT--TGCCTCT
9235 GTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGG
126 GTTTAGAGGAGCAATTTACTTTTCAAA--CGTGG
9269 T-CCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG-TTAGAGGAGCAATTT
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCAATTT
* *
9332 ACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTACCTCT
64 A-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT--TGCCTCT
9397 G-TTAGAGGAGCAATTTACTTTTCAAA-GTGG
126 GTTTAGAGGAGCAATTTACTTTTCAAACGTGG
9427 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATAT
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCAAT-T
9492 T-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAGTCGTTGCCTCTG
63 TATTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCGTTGCCTCTG
*
9556 TTTAGAGGAGCAATTTATTTTTCAAAGTCGTGG
127 TTTAGAGGAGCAATTTACTTTTCAAA--CGTGG
9589 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTTAC
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTTA-
*
9654 TTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTG-TT
65 TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTT
9718 AGAGGAGCAATTTACTTTTCAAAGTCGTGG
130 AGAGGAGCAATTTACTTTTCAAA--CGTGG
*
9748 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTGAGAGGAGCAATTTAT
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTTAT
*
9813 TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTTGCCTCTGTTT
66 TTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTT
9878 AGAGGAGCAATTTACTTTTCCAAAGTCGTGG
130 AGAGGAGCAATTTACTTTT-CAAA--CGTGG
*
9909 TGCCTCTGTTGAGAGGAGCAATTTAC-TTTCAAAGTCCGTTGCCTCTGTTTAGAGGAGCAATTTA
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT-CGTTGCCTCTGTTTAGAGGAGCAATTTA
*
9973 CTTTCAAAAGTCGTGAGT--CTCTGTTTAGAGGAGC
65 TTTTC-AAAGTCGTG-GTGCCTCTGTTTAGAGGAGC
10007 TTCGGCCAAA
Statistics
Matches: 703, Mismatches: 12, Indels: 45
0.93 0.02 0.06
Matches are distributed among these distances:
158 43 0.06
159 282 0.40
160 136 0.19
161 174 0.25
162 68 0.10
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (157 bp):
TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTTAT
TTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTTA
GAGGAGCAATTTACTTTTCAAACGTGG
Found at i:10031 original size:9 final size:9
Alignment explanation
Indices: 10017--10097 Score: 83
Period size: 9 Copynumber: 8.9 Consensus size: 9
10007 TTCGGCCAAA
10017 AAAAAAAAC
1 AAAAAAAAC
10026 AAAAAAAAC
1 AAAAAAAAC
*
10035 AAAAACAA-
1 AAAAAAAAC
*
10043 AAAAAAATC
1 AAAAAAAAC
*
10052 AAAAAAATC
1 AAAAAAAAC
*
10061 AAAAAAATC
1 AAAAAAAAC
*
10070 AAAAAAATAA
1 AAAAAAA-AC
*
10080 AAACAAAAAT
1 AAA-AAAAAC
10090 AAAAAAAA
1 AAAAAAAA
10098 ATCAAAATAA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
8 6 0.10
9 46 0.73
10 7 0.11
11 4 0.06
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:10086 original size:49 final size:47
Alignment explanation
Indices: 10013--10104 Score: 141
Period size: 49 Copynumber: 1.9 Consensus size: 47
10003 GAGCTTCGGC
10013 CAAAAAAAAAAACAAAAAAAACAAAAACAAAAAAAAATCAAAAAAAT
1 CAAAAAAAAAAACAAAAAAAACAAAAACAAAAAAAAATCAAAAAAAT
*
10060 CAAAAAAATCAAAA-AAATAAAAACAAAAATAAAAAAAAATCAAAA
1 CAAAAAAA--AAAACAAA-AAAAACAAAAACAAAAAAAAATCAAAA
10105 TAAAAATGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
47 8 0.20
48 3 0.07
49 30 0.73
ACGTcount: A:0.84, C:0.10, G:0.00, T:0.07
Consensus pattern (47 bp):
CAAAAAAAAAAACAAAAAAAACAAAAACAAAAAAAAATCAAAAAAAT
Found at i:10104 original size:9 final size:9
Alignment explanation
Indices: 10017--10082 Score: 84
Period size: 9 Copynumber: 7.6 Consensus size: 9
10007 TTCGGCCAAA
*
10017 AAAAAAAAC
1 AAAAAAATC
*
10026 AAAAAAAAC
1 AAAAAAATC
10035 AAAAACAA--
1 AAAAA-AATC
10043 AAAAAAATC
1 AAAAAAATC
10052 AAAAAAATC
1 AAAAAAATC
10061 AAAAAAATC
1 AAAAAAATC
10070 AAAAAAAT-
1 AAAAAAATC
10078 AAAAA
1 AAAAA
10083 CAAAAATAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
7 2 0.04
8 10 0.19
9 40 0.74
10 2 0.04
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (9 bp):
AAAAAAATC
Found at i:10109 original size:12 final size:10
Alignment explanation
Indices: 10014--10111 Score: 71
Period size: 9 Copynumber: 9.9 Consensus size: 10
10004 AGCTTCGGCC
10014 AAAAAAAA-A
1 AAAAAAAATA
*
10023 AACAAAAA-A
1 AAAAAAAATA
* *
10032 AACAAAAACA
1 AAAAAAAATA
10042 AAAAAAAAT-
1 AAAAAAAATA
*
10051 CAAAAAAAT-
1 AAAAAAAATA
*
10060 CAAAAAAATCA
1 AAAAAAAAT-A
10071 AAAAAATAA-A
1 AAAAAA-AATA
*
10081 AACAAAAATA
1 AAAAAAAATA
10091 AAAAAAAATCA
1 AAAAAAAAT-A
10102 AAATAAAAAT
1 AAA-AAAAAT
10112 GTTGAGTTGA
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
9 35 0.47
10 23 0.31
11 9 0.12
12 8 0.11
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:10110 original size:1 final size:1
Alignment explanation
Indices: 10014--10098 Score: 62
Period size: 1 Copynumber: 85.0 Consensus size: 1
10004 AGCTTCGGCC
* * * ** ** ** *
10014 AAAAAAAAAAACAAAAAAAACAAAAACAAAAAAAAATCAAAAAAATCAAAAAAATCAAAAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
10079 AAAACAAAAATAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAA
10099 TCAAAATAAA
Statistics
Matches: 63, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.86, C:0.08, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:10238 original size:20 final size:21
Alignment explanation
Indices: 10199--10239 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
10189 TGTAGACACC
*
10199 CAATTGGGTCCGGGCCCAAAT
1 CAATTGGGTCCGGACCCAAAT
*
10220 CAATTGGG-CCTGACCCAAAT
1 CAATTGGGTCCGGACCCAAAT
10240 GGGTAAGGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (21 bp):
CAATTGGGTCCGGACCCAAAT
Found at i:10925 original size:19 final size:19
Alignment explanation
Indices: 10889--10925 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10879 CAGTTTCCGG
**
10889 TTGAATTTTCCGGTGAAAC
1 TTGAATTTTCCGACGAAAC
10908 TTGAATTTTCCGACGAAA
1 TTGAATTTTCCGACGAAA
10926 TTTCCGGCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGAATTTTCCGACGAAAC
Found at i:11503 original size:11 final size:11
Alignment explanation
Indices: 11457--11510 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
11447 TTCTTTTATC
*
11457 TTTATTTTATT
1 TTTATTTTTTT
* *
11468 TTTAGTTTTGT
1 TTTATTTTTTT
11479 TTTACTTTTCTTT
1 TTTA-TTTT-TTT
11492 TTTA-TTTTTT
1 TTTATTTTTTT
11502 TTTATTTTT
1 TTTATTTTT
11511 CTATTTTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 7 0.20
11 19 0.54
12 3 0.09
13 6 0.17
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.81
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:11510 original size:18 final size:18
Alignment explanation
Indices: 11489--11523 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11479 TTTACTTTTC
*
11489 TTTTT-TATTTTTTTTTA
1 TTTTTCTATTTTTCTTTA
11506 TTTTTCTATTTTTCTTTA
1 TTTTTCTATTTTTCTTTA
11524 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTCTATTTTTCTTTA
Found at i:11511 original size:23 final size:25
Alignment explanation
Indices: 11464--11518 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
11454 ATCTTTATTT
11464 TATTTTTAGTTTTGTTTTACTTTTC
1 TATTTTTAGTTTTGTTTTACTTTTC
* *
11489 T-TTTTTA-TTTTTTTTTATTTTTC
1 TATTTTTAGTTTTGTTTTACTTTTC
11512 TATTTTT
1 TATTTTT
11519 CTTTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 15 0.56
24 11 0.41
25 1 0.04
ACGTcount: A:0.11, C:0.05, G:0.04, T:0.80
Consensus pattern (25 bp):
TATTTTTAGTTTTGTTTTACTTTTC
Found at i:19163 original size:16 final size:17
Alignment explanation
Indices: 19142--19177 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
19132 CTACTAATTA
*
19142 TTTTATTTT-ATTTATT
1 TTTTATTTTCATTCATT
19158 TTTTATTTTCATTCATT
1 TTTTATTTTCATTCATT
19175 TTT
1 TTT
19178 ATACTGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTTCATTCATT
Found at i:19865 original size:18 final size:18
Alignment explanation
Indices: 19830--19872 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
19820 AATAAAATAA
* * *
19830 CTTTTTCTTTTTTTTTTT
1 CTTTTTCTTCTCTATTTT
19848 CTTTTTCTTCTCTATTTT
1 CTTTTTCTTCTCTATTTT
*
19866 CTCTTTC
1 CTTTTTC
19873 CCTTTATCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (18 bp):
CTTTTTCTTCTCTATTTT
Found at i:22275 original size:17 final size:18
Alignment explanation
Indices: 22242--22278 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
22232 ATTATCTTTT
22242 TTAAAAAAATCATCTAAAA
1 TTAAAAAAATCA-CTAAAA
22261 TTAAAAAAATC-CTAAAA
1 TTAAAAAAATCACTAAAA
22278 T
1 T
22279 ATATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (18 bp):
TTAAAAAAATCACTAAAA
Found at i:22359 original size:25 final size:26
Alignment explanation
Indices: 22304--22367 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
22294 TTAAAAAATA
*
22304 AAAAATTCTTATTTTTAGACTTTTTT
1 AAAAATTTTTATTTTTAGACTTTTTT
*
22330 GAAAATTTTTAATTTTTA-A-TTTTTT
1 AAAAATTTTT-ATTTTTAGACTTTTTT
*
22355 AAAAATTTATATT
1 AAAAATTTTTATT
22368 ATAAATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 3 0.09
25 14 0.42
26 9 0.27
27 7 0.21
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (26 bp):
AAAAATTTTTATTTTTAGACTTTTTT
Found at i:22374 original size:24 final size:25
Alignment explanation
Indices: 22324--22376 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
22314 ATTTTTAGAC
* * * *
22324 TTTTTTGAAAATTTTTAATTTTTAA
1 TTTTTTAAAAATTTATAATTATAAA
22349 TTTTTTAAAAATTTAT-ATTATAAA
1 TTTTTTAAAAATTTATAATTATAAA
22373 TTTT
1 TTTT
22377 ATTAGAGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTTTAAAAATTTATAATTATAAA
Found at i:22705 original size:6 final size:7
Alignment explanation
Indices: 22686--22715 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
22676 TATAAATTTT
22686 TTAAAAA
1 TTAAAAA
22693 TTAAAAA
1 TTAAAAA
22700 TTAAAAA
1 TTAAAAA
22707 TTAAAAA
1 TTAAAAA
22714 TT
1 TT
22716 TTCAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
TTAAAAA
Found at i:23298 original size:13 final size:13
Alignment explanation
Indices: 23262--23313 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
23252 TTATATATAT
**
23262 TATATTAATAAAA
1 TATATTAATTTAA
23275 T-TATT-ATTTAA
1 TATATTAATTTAA
*
23286 TATTTTAATTTAA
1 TATATTAATTTAA
*
23299 GATATTAATTTAA
1 TATATTAATTTAA
23312 TA
1 TA
23314 AAAATATTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 5 0.16
12 7 0.23
13 19 0.61
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
TATATTAATTTAA
Found at i:23496 original size:13 final size:13
Alignment explanation
Indices: 23480--23504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23470 ATCAAAAGAA
23480 AAAAATAATAAAT
1 AAAAATAATAAAT
23493 AAAAATAATAAA
1 AAAAATAATAAA
23505 AAATAGTTTA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAATAATAAAT
Found at i:24073 original size:17 final size:17
Alignment explanation
Indices: 24051--24085 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
24041 GTTTTATAAA
*
24051 TTATAAAATAGATTAAT
1 TTATAAAATAGATCAAT
24068 TTATAAAATAGATCAAT
1 TTATAAAATAGATCAAT
24085 T
1 T
24086 AAGATGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (17 bp):
TTATAAAATAGATCAAT
Found at i:28901 original size:87 final size:88
Alignment explanation
Indices: 28779--28951 Score: 194
Period size: 87 Copynumber: 2.0 Consensus size: 88
28769 TTGAAGATTC
** *
28779 AGATTTTAAGGGTTTAGATTTAAGTTTTAAGGGTTTTAGGG-TTTGGTTT-AAGGTCTGGAATGT
1 AGATTTTAAGGGTTTAGATTTAAAATTTAAGGG-TTTAGGGTTTTGATTTAAAGGTCTGG-AT-T
* *
28842 TTAGG-GTTTTGATTTTAGAGTTTGA
63 TTAGGAGTTTGGATTTAAGAGTTTGA
* * * *
28867 AGATTTT-AGGGTTTCGATTTTAAAATTTGA-GGTTTGGGGTTTTGATTTAAAGGTTTGGATTTT
1 AGATTTTAAGGGTTTAGA-TTTAAAATTTAAGGGTTTAGGGTTTTGATTTAAAGGTCTGGATTTT
28930 AGGAGTTTGGATTTAAGAGTTT
65 AGGAGTTTGGATTTAAGAGTTT
28952 AAAGGTTTGG
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
86 12 0.17
87 36 0.50
88 24 0.33
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.47
Consensus pattern (88 bp):
AGATTTTAAGGGTTTAGATTTAAAATTTAAGGGTTTAGGGTTTTGATTTAAAGGTCTGGATTTTA
GGAGTTTGGATTTAAGAGTTTGA
Found at i:28907 original size:58 final size:59
Alignment explanation
Indices: 28840--28993 Score: 156
Period size: 58 Copynumber: 2.6 Consensus size: 59
28830 GGTCTGGAAT
* *
28840 GTTTAGGGTTTTGATTTTAGA-GTTTGAAGATTTTAGG-GTTTCGATTTTAA-AATTT-GAG
1 GTTTGGGGTTTTGATTTTAGAGGTTTG--GATTTTAGGAGTTTCGA-TTTAAGAATTTAAAG
* * *
28898 GTTTGGGGTTTTGA-TTTAAAGGTTTGGATTTTAGGAGTTTGGATTTAAGAGTTTAAAG
1 GTTTGGGGTTTTGATTTTAGAGGTTTGGATTTTAGGAGTTTCGATTTAAGAATTTAAAG
* *
28956 GTTTGGGATTTTCGATTTTAGGTGGTTTTGGATTTTAG
1 GTTTGGGGTTTT-GATTTTA-GAGG-TTTGGATTTTAG
28994 AGGTTTTGAA
Statistics
Matches: 80, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
56 14 0.17
57 15 0.19
58 31 0.39
59 2 0.03
60 4 0.05
61 2 0.03
62 12 0.15
ACGTcount: A:0.21, C:0.01, G:0.29, T:0.48
Consensus pattern (59 bp):
GTTTGGGGTTTTGATTTTAGAGGTTTGGATTTTAGGAGTTTCGATTTAAGAATTTAAAG
Found at i:28930 original size:15 final size:15
Alignment explanation
Indices: 28905--29092 Score: 60
Period size: 15 Copynumber: 12.3 Consensus size: 15
28895 GAGGTTTGGG
* *
28905 GTTTTGATTTAAAG-
1 GTTTGGATTTTAAGA
*
28919 GTTTGGATTTTAGGA
1 GTTTGGATTTTAAGA
28934 GTTTGGA-TTTAAGA
1 GTTTGGATTTTAAGA
** * **
28948 GTTTAAAGGTTTGGGA
1 GTTTGGA-TTTTAAGA
* * * *
28964 TTTTCGATTTTAGGTG
1 GTTTGGATTTTAAG-A
28980 GTTTTGGATTTT-AGA
1 G-TTTGGATTTTAAGA
* * *
28995 GGTTTTGAATTTTAGGG
1 -G-TTTGGATTTTAAGA
* *
29012 GTTTGAATTTAAAGGA
1 GTTTGGATTTTAA-GA
* * * *
29028 TTTTAGATTTTAGGG
1 GTTTGGATTTTAAGA
29043 GTTTCGGATTTT-AGA
1 GTTT-GGATTTTAAGA
*
29058 GTTTTGAATTTTAAGA
1 G-TTTGGATTTTAAGA
* *
29074 TTTTGGATTTTAGGA
1 GTTTGGATTTTAAGA
29089 GTTT
1 GTTT
29093 TAGAAACCTA
Statistics
Matches: 124, Mismatches: 39, Indels: 21
0.67 0.21 0.11
Matches are distributed among these distances:
14 22 0.18
15 49 0.40
16 43 0.35
17 10 0.08
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.48
Consensus pattern (15 bp):
GTTTGGATTTTAAGA
Found at i:28951 original size:29 final size:28
Alignment explanation
Indices: 28780--28951 Score: 104
Period size: 28 Copynumber: 6.0 Consensus size: 28
28770 TGAAGATTCA
* *
28780 GATTTTAAGGGTTTAGATTTAAG-TTTTAAG
1 GATTTT-AGGGTTTGGATTTAAGAGTTT--G
* *
28810 GGTTTTAGGGTTTGG-TTTAAG-GTCTG
1 GATTTTAGGGTTTGGATTTAAGAGTTTG
* *
28836 GAATGTTTAGGGTTTTGATTTTAGAGTTTG
1 G-AT-TTTAGGGTTTGGATTTAAGAGTTTG
* *
28866 AAGATTTTAGGGTTTCGATTTTAA-AATTT-
1 --GATTTTAGGGTTTGGA-TTTAAGAGTTTG
* * *
28895 GAGGTTTGGGGTTTTGATTTAA-AGGTTTG
1 GA-TTTTAGGGTTTGGATTTAAGA-GTTTG
28924 GATTTTAGGAGTTTGGATTTAAGAGTTT
1 GATTTTAGG-GTTTGGATTTAAGAGTTT
28952 AAAGGTTTGG
Statistics
Matches: 112, Mismatches: 18, Indels: 25
0.72 0.12 0.16
Matches are distributed among these distances:
26 2 0.02
27 9 0.08
28 38 0.34
29 30 0.27
30 26 0.23
31 6 0.05
32 1 0.01
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.47
Consensus pattern (28 bp):
GATTTTAGGGTTTGGATTTAAGAGTTTG
Found at i:29000 original size:16 final size:16
Alignment explanation
Indices: 28964--29086 Score: 101
Period size: 15 Copynumber: 7.8 Consensus size: 16
28954 AGGTTTGGGA
* *
28964 TTTTCGATTTTAGGTGG
1 TTTTGGATTTTA-GAGG
28981 TTTTGGATTTTAGAGG
1 TTTTGGATTTTAGAGG
*
28997 TTTTGAATTTTAG-GG
1 TTTTGGATTTTAGAGG
* * *
29012 GTTT-GAATTTAAAGG
1 TTTTGGATTTTAGAGG
* *
29027 ATTTTAGATTTTAGGGG
1 -TTTTGGATTTTAGAGG
*
29044 TTTCGGATTTTAGA-G
1 TTTTGGATTTTAGAGG
* *
29059 TTTTGAATTTTA-AGA
1 TTTTGGATTTTAGAGG
29074 TTTTGGATTTTAG
1 TTTTGGATTTTAG
29087 GAGTTTTAGA
Statistics
Matches: 83, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
14 6 0.07
15 29 0.35
16 29 0.35
17 19 0.23
ACGTcount: A:0.22, C:0.02, G:0.26, T:0.50
Consensus pattern (16 bp):
TTTTGGATTTTAGAGG
Found at i:29069 original size:31 final size:32
Alignment explanation
Indices: 28970--29086 Score: 127
Period size: 31 Copynumber: 3.7 Consensus size: 32
28960 GGGATTTTCG
28970 ATTTTAGGTGGTTTTGGATTTTAGAGGTTTTGA
1 ATTTTAGG-GGTTTTGGATTTTAGAGGTTTTGA
* *
29003 ATTTTAGGGG-TTT-GAATTTAAAGGATTTT-A
1 ATTTTAGGGGTTTTGGATTTTAGAGG-TTTTGA
*
29033 GATTTTAGGGGTTTCGGATTTTAGA-GTTTTGA
1 -ATTTTAGGGGTTTTGGATTTTAGAGGTTTTGA
* *
29065 ATTTTA-AGATTTTGGATTTTAG
1 ATTTTAGGGGTTTTGGATTTTAG
29087 GAGTTTTAGA
Statistics
Matches: 71, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
30 23 0.32
31 27 0.38
32 6 0.08
33 15 0.21
ACGTcount: A:0.23, C:0.01, G:0.26, T:0.50
Consensus pattern (32 bp):
ATTTTAGGGGTTTTGGATTTTAGAGGTTTTGA
Done.