Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168136.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_379, 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: 29959
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Found at i:828 original size:26 final size:26
Alignment explanation
Indices: 792--844 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
782 CCAGTTAGAT
*
792 CTTAGACTGGGAATGAACTTCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
*
818 CTTAGACTGGGGATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
844 C
1 C
845 CTAAGTCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTCCGTATG
Found at i:1678 original size:159 final size:156
Alignment explanation
Indices: 1310--1727 Score: 466
Period size: 159 Copynumber: 2.6 Consensus size: 156
1300 ACTCCATATG
* * * * * *
1310 CTTAGACATGGAATAAACTCCGTATGCCTTAGCCAACCCATGAAACAAGCGTACAGGCGCTCAGT
1 CTTAGACATGGAATAAACTCCATATGCCTAAGCCAACCCATGAAACGAGCGTGCGGGCGCTCAGC
* * * *
1375 CGGTTGGAGAGACAGAATGCGTAAG-TCGAGGATCGACCCGATCCCACCTACGTGCTGTCGATCC
66 CGGTCGGAGAGGCAGAATGCGCAAGCT-G-GGATCGACCCGATCCCACCTACGTGCTGCCGATCC
* * * * *
1439 TGCTACCGCAACCTCAGTTTGGTTTGAT
129 CGCTACCACAACCTCAGTCTGGCTGGAT
* * * *
1467 CTTAGAC-TGGGAATAAACTCCATATGCGTAAGTCAACCCATAAAACGAGCGTGCGGGCGCTGAG
1 CTTAGACAT-GGAATAAACTCCATATGCCTAAGCCAACCCATGAAACGAGCGTGCGGGCGCTCAG
* * * *
1531 CCGGTCGAAGAGGCATAATGCACAAGCTGGGAATCGACCCGATCCCCCTCTACGTGCTGCC-AGT
65 CCGGTCGGAGAGGCAGAATGCGCAAGCTGGG-ATCGACCCGATCCCAC-CTACGTGCTGCCGA-T
* * *
1595 CCCGCTCCCACAACCCTCTGTCTGGCTGGGT
127 CCCGCTACCACAA-CCTCAGTCTGGCTGGAT
* * *
1626 CTTAGACATCGAATGAACTGCC-TATGCCTAAGCCAACCCATGAAACGGGCGTGCGGGCGCTCAG
1 CTTAGACATGGAATAAACT-CCATATGCCTAAGCCAACCCATGAAACGAGCGTGCGGGCGCTCAG
1690 CCGGTCGGAGAGGCAGAATGCGCAAGCTGGGGATCGAC
65 CCGGTCGGAGAGGCAGAATGCGCAAGCT-GGGATCGAC
1728 TCGGTTCCTC
Statistics
Matches: 216, Mismatches: 36, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
156 3 0.01
157 89 0.41
158 23 0.11
159 95 0.44
160 6 0.03
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (156 bp):
CTTAGACATGGAATAAACTCCATATGCCTAAGCCAACCCATGAAACGAGCGTGCGGGCGCTCAGC
CGGTCGGAGAGGCAGAATGCGCAAGCTGGGATCGACCCGATCCCACCTACGTGCTGCCGATCCCG
CTACCACAACCTCAGTCTGGCTGGAT
Found at i:2431 original size:11 final size:11
Alignment explanation
Indices: 2415--2440 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2405 CTGTTTGGCT
2415 CTTCGGCGATG
1 CTTCGGCGATG
2426 CTTCGGCGATG
1 CTTCGGCGATG
2437 CTTC
1 CTTC
2441 AACGATGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (11 bp):
CTTCGGCGATG
Found at i:2728 original size:26 final size:26
Alignment explanation
Indices: 2699--2751 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
2689 CCGGTTAGAT
2699 CTTAGACTGGGAATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
*
2725 CTTAGACTGGGGATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
2751 C
1 C
2752 CTAAGTCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTCCGTATG
Found at i:3567 original size:26 final size:26
Alignment explanation
Indices: 3538--3590 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3528 TCGGTTAGAT
*
3538 CTTAGACTGGGAATGAACTTCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
3564 CTTAGACTGGGAATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
3590 C
1 C
3591 CTAAGTCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTCCGTATG
Found at i:5715 original size:26 final size:26
Alignment explanation
Indices: 5664--5716 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
5654 CTGGTTTGAT
**
5664 CTTAGACTGGGAATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCAATATG
5690 CTTAGACTGGTG-ATGAACTCAATATG
1 CTTAGACTGG-GAATGAACTCAATATG
5716 C
1 C
5717 CTAAGTCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTCAATATG
Found at i:6017 original size:171 final size:171
Alignment explanation
Indices: 5702--6017 Score: 384
Period size: 171 Copynumber: 1.8 Consensus size: 171
5692 TAGACTGGTG
* **
5702 ATGAACTCAATATGCCTAAGTCAACCCATGAAACGAGCGTAGGGGCACTCAGCCGACCGAAGAAG
1 ATGAACTCAATATGCCTAAGCCAACCCACAAAACGAGCGTAGGGGCACTCAGCCGACCGAAGAAG
* * *
5767 CATAATACGCAAGTCAGGGATCAACCCGGTCCCCCTCTGTGTGCTACCGATCCCGCTGCCGGTCC
66 CAGAATACGCAAGCCAGGGATCAACCCGGTCCCCCTCTGTATGCTACCGATCCCGCTGCCGGTCC
*
5832 TGCTGCCACAACCCTTGGTCCAACTGGGACTTAGACATGGA
131 TACTGCCACAACCCTTGGTCCAACTGGGACTTAGACATGGA
** * * *
5873 ATGAACTCCGTATGCCTAAGCCAACCCACAAAACGAGCGT-GCGGGCGCTCAGCCGA-CGGAGAG
1 ATGAACTCAATATGCCTAAGCCAACCCACAAAACGAGCGTAG-GGGCACTCAGCCGACCGAAGAA
* ** * * *** * *
5936 GCAGAATGCGCAAGCCAGGGATCGGCCTGGTCCCCCCTCTGTATGTTGTTGATCCTGCTGCTGGT
65 GCAGAATACGCAAGCCAGGGATCAACCCGGT-CCCCCTCTGTATGCTACCGATCCCGCTGCCGGT
* *
6001 CCTACTTCCGCAACCCT
129 CCTACTGCCACAACCCT
6018 CAGTTCGGTC
Statistics
Matches: 119, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
170 31 0.26
171 88 0.74
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.19
Consensus pattern (171 bp):
ATGAACTCAATATGCCTAAGCCAACCCACAAAACGAGCGTAGGGGCACTCAGCCGACCGAAGAAG
CAGAATACGCAAGCCAGGGATCAACCCGGTCCCCCTCTGTATGCTACCGATCCCGCTGCCGGTCC
TACTGCCACAACCCTTGGTCCAACTGGGACTTAGACATGGA
Found at i:6563 original size:26 final size:26
Alignment explanation
Indices: 6534--6586 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
6524 CTAGTCCGAT
6534 CTTAGACTGGGAATGAAATCCGTATG
1 CTTAGACTGGGAATGAAATCCGTATG
* *
6560 CTTAGACTGGGGATGAACTCCGTATG
1 CTTAGACTGGGAATGAAATCCGTATG
6586 C
1 C
6587 CTAAGTCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (26 bp):
CTTAGACTGGGAATGAAATCCGTATG
Found at i:7640 original size:26 final size:26
Alignment explanation
Indices: 7611--7663 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
7601 CCGGTTCGAT
* *
7611 CTTAGACTGGGAATGAACTCCGTATG
1 CTTAAACTGGGAATGAACTCCGAATG
*
7637 CTTAAACTGGGGATGAACTCCGAATG
1 CTTAAACTGGGAATGAACTCCGAATG
7663 C
1 C
7664 CTAAGTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (26 bp):
CTTAAACTGGGAATGAACTCCGAATG
Found at i:7847 original size:26 final size:26
Alignment explanation
Indices: 7818--7869 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
7808 TCCGGTCCGA
*
7818 TCTTAGAC-TGGGAATGAACTCCGTAT
1 TCTTAGACAT-GGAACGAACTCCGTAT
7844 TCTTAGACATGGAACGAACTCCGTAT
1 TCTTAGACATGGAACGAACTCCGTAT
7870 GCCTAAGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (26 bp):
TCTTAGACATGGAACGAACTCCGTAT
Found at i:8704 original size:159 final size:158
Alignment explanation
Indices: 8333--8706 Score: 400
Period size: 158 Copynumber: 2.4 Consensus size: 158
8323 AATTCCGTAT
* *
8333 GCTTAGACATGGAATGAACTCCGTATGCCTAAGCCAACCCATGAAACGAGCGTGCGGGGCCTCAG
1 GCTTAGACATGGAATGAACTCCCTATGCCTAAGCCAACCCATGAAACGAGCGTGCGGCGCCTCAG
* * * *
8398 CCGACCGGAGAGGCAAAATGCAAAAGTCGGGGATCGACCCGGTCCCTCCTACGTGCTGTCAATCC
66 CCGACCGAAGAGGCAAAATGCAAAAGCCGGGGATCGAACCGGTCCCTCCTACGTGCTGCCAATCC
* **
8463 TGCTACTGCAACCCTCGGTCCGGTCTGA
131 CGCTACCACAACCCTCGGTCCGGTCTGA
* * ** * *
8491 TCTTAGAC-TGGGAATGAAC-CCCGTATACAAAAGTCAACCCATGAAACGAGCGTGCAGGCG-TT
1 GCTTAGACAT-GGAATGAACTCCC-TATGCCTAAGCCAACCCATGAAACGAGCGTGC-GGCGCCT
* * *** * *
8553 GAGCCGACCGAAGAGGCATAATGTGCAAGCCGGGGATTGAACCGGTCACC-CTCTGCGTGCTGCC
63 CAGCCGACCGAAGAGGCAAAATGCAAAAGCCGGGGATCGAACCGGTC-CCTC-CTACGTGCTGCC
* * *
8617 GATCCCGCTGCCACAACCCTCGGTCCGGT-TGGG
126 AATCCCGCTACCACAACCCTCGGTCCGGTCT-GA
* *
8650 GCTTACACATGGAATGAACTCCCTATGCCTAAGCCAACCCACGAAACG-GTCGTGCGG
1 GCTTAGACATGGAATGAACTCCCTATGCCTAAGCCAACCCATGAAACGAG-CGTGCGG
8707 GCACTTAGTC
Statistics
Matches: 175, Mismatches: 32, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
157 3 0.02
158 88 0.50
159 80 0.46
160 4 0.02
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.18
Consensus pattern (158 bp):
GCTTAGACATGGAATGAACTCCCTATGCCTAAGCCAACCCATGAAACGAGCGTGCGGCGCCTCAG
CCGACCGAAGAGGCAAAATGCAAAAGCCGGGGATCGAACCGGTCCCTCCTACGTGCTGCCAATCC
CGCTACCACAACCCTCGGTCCGGTCTGA
Found at i:8742 original size:159 final size:157
Alignment explanation
Indices: 8333--8750 Score: 423
Period size: 159 Copynumber: 2.6 Consensus size: 157
8323 AATTCCGTAT
* *
8333 GCTTAGACATGGAATGAACTCCGTATGCCTAAGCCAACCCATGAAACGAGCGTGCGGGGCCTCAG
1 GCTTAGACATGGAATGAACTCCCTATGCCTAAGCCAACCCATGAAACGAGCGTGC-GGGCCTTAG
* * * *
8398 CCGACCGGAGAGGCAAAATGCAAAAGTCGGGGATCGACCCGGTCCCTCCTACGTGCTGTCAATCC
65 CCGACCGGAGAGGCAAAATGCGAAAGCCGGGGATCGAACCGGTCCCTCCTACGTGCTGCCAATCC
* **
8463 TGCTACTGCAACCCTCGGTCCGGTCTGA
130 CGCTACCACAACCCTCGGTCCGGTCTGA
* * ** * * *
8491 TCTTAGAC-TGGGAATGAAC-CCCGTATACAAAAGTCAACCCATGAAACGAGCGTGCAGGCGTTG
1 GCTTAGACAT-GGAATGAACTCCC-TATGCCTAAGCCAACCCATGAAACGAGCGTGCGGGCCTT-
* * * * * * *
8554 AGCCGACCGAAGAGGCATAATGTGCAAGCCGGGGATTGAACCGGTCACC-CTCTGCGTGCTGCCG
63 AGCCGACCGGAGAGGCAAAATGCGAAAGCCGGGGATCGAACCGGTC-CCTC-CTACGTGCTGCCA
* *
8618 ATCCCGCTGCCACAACCCTCGGTCCGGT-TGGG
126 ATCCCGCTACCACAACCCTCGGTCCGGTCT-GA
* *
8650 GCTTACACATGGAATGAACTCCCTATGCCTAAGCCAACCCACGAAACG-GTCGTGCGGGCACTTA
1 GCTTAGACATGGAATGAACTCCCTATGCCTAAGCCAACCCATGAAACGAG-CGTGCGGGC-CTTA
* * * * * *
8714 GTCTACCGGAGAGACAGAATGCGTAAGCCAGGGATCG
64 GCCGACCGGAGAGGCAAAATGCGAAAGCCGGGGATCG
8751 GCCCTCGGTT
Statistics
Matches: 207, Mismatches: 43, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
157 7 0.03
158 85 0.41
159 109 0.53
160 6 0.03
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (157 bp):
GCTTAGACATGGAATGAACTCCCTATGCCTAAGCCAACCCATGAAACGAGCGTGCGGGCCTTAGC
CGACCGGAGAGGCAAAATGCGAAAGCCGGGGATCGAACCGGTCCCTCCTACGTGCTGCCAATCCC
GCTACCACAACCCTCGGTCCGGTCTGA
Found at i:8866 original size:119 final size:119
Alignment explanation
Indices: 8633--8873 Score: 299
Period size: 119 Copynumber: 2.0 Consensus size: 119
8623 GCTGCCACAA
* *
8633 CCCTCGGTCCGGTTGGGGCTTACACATGGAATGAACTCCCTATGCCTAAGCCAACCCACGAAACG
1 CCCTCGGTCCGGTTGGGGCTTAAACAAGGAATGAACTCCCTATGCCTAAGCCAACCCACGAAACG
* ** *
8698 GTCGTGCGGGCACTTAGTCTACCGGAGAGACAGAATGCGTAAGCCAGGGATCGG
66 GTCGTGCGGGCACTCAGTCTACCAAAGAGACAGAATGCGCAAGCCAGGGATCGG
* * * *
8752 CCCTCGGTTCGGTTGGGGCTTAAACAAGGAATGAACTCCGTATGCCTTAGCCAACCCACGAAATG
1 CCCTCGGTCCGGTTGGGGCTTAAACAAGGAATGAACTCCCTATGCCTAAGCCAACCCACGAAACG
* ** * *
8817 AG-CGTAG-GGGCGCTCAGTC-AGCCAAAGAGGTAGAGTGCGCAAGCTAGGGATCGG
66 -GTCGT-GCGGGCACTCAGTCTA-CCAAAGAGACAGAATGCGCAAGCCAGGGATCGG
8871 CCC
1 CCC
8874 GATCCCCCCC
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 1 0.01
119 101 0.97
120 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.30, T:0.17
Consensus pattern (119 bp):
CCCTCGGTCCGGTTGGGGCTTAAACAAGGAATGAACTCCCTATGCCTAAGCCAACCCACGAAACG
GTCGTGCGGGCACTCAGTCTACCAAAGAGACAGAATGCGCAAGCCAGGGATCGG
Found at i:9261 original size:159 final size:156
Alignment explanation
Indices: 8967--9459 Score: 521
Period size: 159 Copynumber: 3.1 Consensus size: 156
8957 ACTCTGTATC
*
8967 CTTAGACATGGAATGAACT-CGTATGCCTAAGCCAACCCATGAAACGAGCGTGCGGGCGCTCAGT
1 CTTAGACATGGAATGAACTCCGTATGCCTAAGACAACCCATGAAACGAGCGTGC-GGCGCTCAGT
* * * * ** * *
9031 CGGTCGGAGAGGTAGAATGCGTAAGCTGAGGCCCGGCCCGGTCCCCGCTTGCATGCTATCGATCC
65 -GGCCGGAGAGGTAGAATGCGCAAGCCGGGGATCGGCCCGATCCCC-CTTGCGTGCTATCGATCC
9096 TGCTGCCGCAACCCTCGGTCCGATCCGAT
128 TGCTGCCGCAACCCTCGGTCCGATCCGAT
* * * *
9125 CTTAGA-ATGGGAATGAACTCCGTATGCCTAAGTCAACGCATGAAACGAGCGTGCGAGCACTGAG
1 CTTAGACAT-GGAATGAACTCCGTATGCCTAAGACAACCCATGAAACGAGCGTGCG-GCGCTCAG
* * * * * * * *
9189 CTGGCCAGAGAGGCATAATGTGCAAGCCGGGGATCGGCCCAATCCCTCTTTGCGTGCTGTCGGTC
64 -TGGCCGGAGAGGTAGAATGCGCAAGCCGGGGATCGGCCCGATCCC-CCTTGCGTGCTATCGATC
* * * * **
9254 CCGCTGCCACAACCCTCGGTTCGA-CTGGGG
127 CTGCTGCCGCAACCCTCGGTCCGATC-CGAT
* *
9284 CTT-GACATGGAATGAACTCCCTATGCCTAAGACAACCCATGAAAC-AGGTGTGCTGGCGCTCAG
1 CTTAGACATGGAATGAACTCCGTATGCCTAAGACAACCCATGAAACGA-GCGTGC-GGCGCTCAG
* * * *
9347 TGGCCGGAGAGGTAGAATGCGCAAGCCGGGGATTGGCCCGATCCCCCTTACGTGTTACCGATCCT
64 TGGCCGGAGAGGTAGAATGCGCAAGCCGGGGATCGGCCCGATCCCCCTTGCGTGCTATCGATCCT
* *
9412 GCTGCCGCAACCCTCGGTCTGATCTGAT
129 GCTGCCGCAACCCTCGGTCCGATCCGAT
*
9440 CTTAGAC-TGGGAAAGAACTC
1 CTTAGACAT-GGAATGAACTC
9460 TATATGCTTA
Statistics
Matches: 271, Mismatches: 52, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
156 37 0.14
157 56 0.21
158 65 0.24
159 111 0.41
160 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.20
Consensus pattern (156 bp):
CTTAGACATGGAATGAACTCCGTATGCCTAAGACAACCCATGAAACGAGCGTGCGGCGCTCAGTG
GCCGGAGAGGTAGAATGCGCAAGCCGGGGATCGGCCCGATCCCCCTTGCGTGCTATCGATCCTGC
TGCCGCAACCCTCGGTCCGATCCGAT
Found at i:9476 original size:26 final size:26
Alignment explanation
Indices: 9440--9490 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
9430 CTGATCTGAT
*
9440 CTTAGACTGGGAAAGAACTCTATATG
1 CTTAGACTGGGAAAGAACTCCATATG
* *
9466 CTTAGACTGGGGATGAACTCCATAT
1 CTTAGACTGGGAAAGAACTCCATAT
9491 ACCTAAGTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (26 bp):
CTTAGACTGGGAAAGAACTCCATATG
Found at i:11470 original size:159 final size:158
Alignment explanation
Indices: 11056--11557 Score: 476
Period size: 158 Copynumber: 3.2 Consensus size: 158
11046 ACTTCGTATG
* * * * * *
11056 CTTAGACCTGTAATGAACTCTGTATGCCTAAGGCAACCCATGAAACGAGCGTGCAGGCGCTCAGT
1 CTTAGA-CTGGAATGAACTCCGTATGCCTAAGGCAACCCACGAAATGAGCGTGCGGGCGCTCAGC
* * * *
11121 CGATCGGAGAGGTAAAATGCGTAAGTTGGGGATCGGCTCGGTCGCCCCT-TGTGTGTTATCGATC
65 CGATCGGAGAGGTAAAATGCGCAAGCTGGGGATCGGCCCGGTC-CCCCTCTGTGTGTTGTCGATC
* * *
11185 TTGCTACCGCAACCCTTGGTCCGATCCAAT
129 TCGCTACCACAACCCTCGGTCCGATCCAAT
*
11215 CTTAGACTGGGAATGAACT-CGTATGCCTAAGTCAACCCACGAAATGAGCGTGCGGGCGCT-ATG
1 CTTAGACT-GGAATGAACTCCGTATGCCTAAGGCAACCCACGAAATGAGCGTGCGGGCGCTCA-G
* * * * * *
11278 CCGATCGGAGAGGCATAATACGCAAGCCGGGGATCGGCCCGGTCCCCCTCTATGTGTTGTCGGTC
64 CCGATCGGAGAGGTAAAATGCGCAAGCTGGGGATCGGCCCGGTCCCCCTCTGTGTGTTGTCGATC
* ** * *
11343 TCGCTGCCACAACCCTCGGTTTGA-CTGAGT
129 TCGCTACCACAACCCTCGGTCCGATC-CAAT
* * * * *
11373 TTTAGACATGGAATGAACTCCCTATGCCTAAGGCAACCCACGAAATGGGCGTGCGGGCTCTCAAC
1 CTTAGAC-TGGAATGAACTCCGTATGCCTAAGGCAACCCACGAAATGAGCGTGCGGGCGCTCAGC
* * * * * * *
11438 CGATCGAAGAGGTAGAATGCGCAAGCTAGGGATTGGACTGGTCCCCC-CTGTGTGCTGTCGATC-
65 CGATCGGAGAGGTAAAATGCGCAAGCTGGGGATCGGCCCGGTCCCCCTCTGTGTGTTGTCGATCT
* ** * * ** *
11501 CTACTGTCGCAACCCTAGGTCCTTTCCGAT
130 C-GCTACCACAACCCTCGGTCCGATCCAAT
*
11531 CTTAGACTGGGAATGAAATCCGTATGC
1 CTTAGACT-GGAATGAACTCCGTATGC
11558 TTAGACTAGG
Statistics
Matches: 276, Mismatches: 57, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
157 9 0.03
158 173 0.63
159 93 0.34
160 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (158 bp):
CTTAGACTGGAATGAACTCCGTATGCCTAAGGCAACCCACGAAATGAGCGTGCGGGCGCTCAGCC
GATCGGAGAGGTAAAATGCGCAAGCTGGGGATCGGCCCGGTCCCCCTCTGTGTGTTGTCGATCTC
GCTACCACAACCCTCGGTCCGATCCAAT
Found at i:11560 original size:26 final size:26
Alignment explanation
Indices: 11531--11581 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
11521 CCTTTCCGAT
11531 CTTAGACT-GGGAATGAAATCCGTATG
1 CTTAGACTAGGG-ATGAAATCCGTATG
*
11557 CTTAGACTAGGGATGAACTCCGTAT
1 CTTAGACTAGGGATGAAATCCGTAT
11582 ACCTAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (26 bp):
CTTAGACTAGGGATGAAATCCGTATG
Found at i:18689 original size:26 final size:26
Alignment explanation
Indices: 18653--18705 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
18643 CCGGTCCAAT
18653 CTTAGACTAGGAATGAACT-TCGTATG
1 CTTAGACTAGGAATGAACTCT-GTATG
*
18679 CTTAGACTAGGGATGAACTCTGTATG
1 CTTAGACTAGGAATGAACTCTGTATG
18705 C
1 C
18706 CTAAGTCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (26 bp):
CTTAGACTAGGAATGAACTCTGTATG
Found at i:19709 original size:26 final size:26
Alignment explanation
Indices: 19680--19732 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
19670 CCTATCCGAT
*
19680 CTTAGATTGGGAATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
*
19706 CTTAGACTGGGGATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
19732 C
1 C
19733 CTAAGTCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTCCGTATG
Found at i:20240 original size:26 final size:26
Alignment explanation
Indices: 20204--20256 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
20194 ATGGTCCAAT
*
20204 CTTAGTCTGGGAATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
**
20230 CTTAGACTGGGGGTGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
20256 C
1 C
20257 CTAAGTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTCCGTATG
Found at i:21087 original size:26 final size:26
Alignment explanation
Indices: 21049--21101 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
21039 CCGGTCTGAT
*
21049 CTTAGACTGGGAATGAACTTCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
21075 CTTAGACAT-GGAATGAACTCCGTATG
1 CTTAGAC-TGGGAATGAACTCCGTATG
21101 C
1 C
21102 CTAAGCCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTCCGTATG
Found at i:21576 original size:158 final size:155
Alignment explanation
Indices: 21075--21576 Score: 429
Period size: 158 Copynumber: 3.2 Consensus size: 155
21065 ACTTCGTATG
* * * *
21075 CTTAGACATGGAATGAACTCCGTATGCCTAAGCCAACCCACGAAATGAGCGTGCGAGCACTCAAC
1 CTTAGACATGGAATGAACTCCGTATGCCTAAGCCAACCCATGAAACGAGCGTACGAGCACTC-AG
* * * * * * *
21140 CAGTCGGAGAGGTAGAATGCGTAAGCCGAGGACCGGTCCGGTCCCCCCTGCGTGCTGTTGATCCT
65 CAGTCGGAGAGGTAGAATGAGCAAGCTGGGGATCGCT-CGGTCCCCCCTGCGTGCTG-CGATCCT
*** * * *
21205 GCTATTGCAACGCTCGATCCGATCCGGT
128 GCTACCACAACCCTCGGTCCGATCTGGT
* ** * * * *
21233 CTTAGA-TTGGGAATGAACTCCGTATGCCTAATTCAACCCATGAAACGAGTGTTCGGGCACTAAG
1 CTTAGACAT-GGAATGAACTCCGTATGCCTAAGCCAACCCATGAAACGAGCGTACGAGCACTCAG
* * * * * * * *
21297 CTGACTGGAAAGGCATAATGTGCAAG-TCGGGGATCAGC-CTGGTCCCCCTCTACGTGCTGCTAG
65 CAGTC-GGAGAGGTAGAATGAGCAAGCT-GGGGATC-GCTC-GGTCCCCC-CTGCGTGCTGCGA-
* * *
21360 TCCCGCTGCCACAACCCTCGGTCCGA-CTGGGG
124 TCCTGCTACCACAACCCTCGGTCCGATCT-GGT
* * * * * *
21392 CTTAGACATGTAATGAACTCCCTATGCATAAGCCAACCCATGAAACGGGCGTACCAGCACTCTGT
1 CTTAGACATGGAATGAACTCCGTATGCCTAAGCCAACCCATGAAACGAGCGTACGAGCACTCAG-
* *
21457 CGGTCAGAGAGGTAGAATGAGCAAGCTGGGGATCGACTCGGTCCCCCCTGCGTGCTGCCGATCCT
65 CAGTCGGAGAGGTAGAATGAGCAAGCTGGGGATCG-CTCGGTCCCCCCTGCGTGCTG-CGATCCT
* *
21522 GCTACCACATCCCTCGGTCCGATCTGAT
128 GCTACCACAACCCTCGGTCCGATCTGGT
21550 CTTAGAC-TGGGAATGAACTCCGTATGC
1 CTTAGACAT-GGAATGAACTCCGTATGC
21577 TTAGACTGGG
Statistics
Matches: 266, Mismatches: 62, Indels: 32
0.74 0.17 0.09
Matches are distributed among these distances:
157 7 0.03
158 138 0.52
159 115 0.43
160 6 0.02
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.21
Consensus pattern (155 bp):
CTTAGACATGGAATGAACTCCGTATGCCTAAGCCAACCCATGAAACGAGCGTACGAGCACTCAGC
AGTCGGAGAGGTAGAATGAGCAAGCTGGGGATCGCTCGGTCCCCCCTGCGTGCTGCGATCCTGCT
ACCACAACCCTCGGTCCGATCTGGT
Found at i:21579 original size:26 final size:26
Alignment explanation
Indices: 21550--21602 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
21540 CCGATCTGAT
21550 CTTAGACTGGGAATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
* *
21576 CTTAGACTGGGGATTAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
21602 C
1 C
21603 CTACATCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTCCGTATG
Found at i:21659 original size:13 final size:13
Alignment explanation
Indices: 21641--21665 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21631 GGCACTCAGC
21641 CGGTCGGAGAGGT
1 CGGTCGGAGAGGT
21654 CGGTCGGAGAGG
1 CGGTCGGAGAGG
21666 CATAATGTGC
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:0.16, C:0.16, G:0.56, T:0.12
Consensus pattern (13 bp):
CGGTCGGAGAGGT
Found at i:21959 original size:26 final size:26
Alignment explanation
Indices: 21930--21985 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
21920 CCGGTCTAAT
*
21930 CTTAGAC-TAGGAATGAACTCCGTATG
1 CTTAGACAT-GGAATGAACTCCATATG
*
21956 CTTAGACATGGAATGAACTTCATATG
1 CTTAGACATGGAATGAACTCCATATG
21982 CTTA
1 CTTA
21986 AGCCAACCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (26 bp):
CTTAGACATGGAATGAACTCCATATG
Found at i:22459 original size:26 final size:26
Alignment explanation
Indices: 22430--22482 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
22420 CCAGTCTAAT
*
22430 CTTAGACTGAGAATGAACTCTGTATG
1 CTTAGACTGAGAACGAACTCTGTATG
* *
22456 CTTAGACTGGGGACGAACTCTGTATG
1 CTTAGACTGAGAACGAACTCTGTATG
22482 C
1 C
22483 CTAAATCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (26 bp):
CTTAGACTGAGAACGAACTCTGTATG
Found at i:23869 original size:26 final size:26
Alignment explanation
Indices: 23833--23885 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
23823 CCGATCTGAT
23833 CTTAGACTGGGAATGAACTCCATATG
1 CTTAGACTGGGAATGAACTCCATATG
* *
23859 CTTAGACTGGGGATGAACTTCATATG
1 CTTAGACTGGGAATGAACTCCATATG
23885 C
1 C
23886 CTAAGTCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTCCATATG
Found at i:24083 original size:26 final size:25
Alignment explanation
Indices: 24042--24093 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
24032 CTGGTCCGAT
24042 CTTAGACTAGAATGAACTCAGTATG
1 CTTAGACTAGAATGAACTCAGTATG
* *
24067 CTTAGACATGGAATGAACTCTGTATG
1 CTTAGAC-TAGAATGAACTCAGTATG
24093 C
1 C
24094 CTAAGCCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (25 bp):
CTTAGACTAGAATGAACTCAGTATG
Found at i:24595 original size:26 final size:26
Alignment explanation
Indices: 24544--24596 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
24534 CCTATCCGAT
*
24544 CTTAGACTGGGAATGAACTTCATATG
1 CTTAGACTGGGAATGAACTCCATATG
* *
24570 CTTAGACTGGGGATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCATATG
24596 C
1 C
24597 CTAAGTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTCCATATG
Found at i:25638 original size:26 final size:26
Alignment explanation
Indices: 25609--25661 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
25599 CCGGTCTGAT
25609 CTTAGACTGGGAATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
*
25635 CTTAGACTGGGGATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTCCGTATG
25661 C
1 C
25662 CTAAGTCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTCCGTATG
Found at i:26880 original size:26 final size:26
Alignment explanation
Indices: 26830--26882 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
26820 CCGGTCCGAT
*
26830 CTTAGACTGGGAATGAACTATGTATG
1 CTTAGACTGGGAATGAACTACGTATG
* *
26856 CTTAGACTGGGGATGAACTCCGTATG
1 CTTAGACTGGGAATGAACTACGTATG
26882 C
1 C
26883 CTAAGTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (26 bp):
CTTAGACTGGGAATGAACTACGTATG
Found at i:28471 original size:26 final size:26
Alignment explanation
Indices: 28442--28494 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
28432 CCAGTCCAAT
28442 CTTAGAC-TGGGAATGAACTCCATATG
1 CTTAGACAT-GGAATGAACTCCATATG
*
28468 CTTAGACATGGAATGAACTCCGTATG
1 CTTAGACATGGAATGAACTCCATATG
28494 C
1 C
28495 CTAAGCCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (26 bp):
CTTAGACATGGAATGAACTCCATATG
Found at i:29014 original size:28 final size:28
Alignment explanation
Indices: 28968--29021 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
28958 TGGTCCTGAT
28968 CTTAGACTGGGAATCAACTCTGTATGGC
1 CTTAGACTGGGAATCAACTCTGTATGGC
* *
28996 CTTAGACTGGGGATGAACTCTGTATG
1 CTTAGACTGGGAATCAACTCTGTATG
29022 CCTAAGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (28 bp):
CTTAGACTGGGAATCAACTCTGTATGGC
Done.