Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008251.1 Corchorus capsularis cultivar CVL-1 contig08272, 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: 58828
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2760 original size:30 final size:30
Alignment explanation
Indices: 2726--2877 Score: 114
Period size: 30 Copynumber: 4.9 Consensus size: 30
2716 CTAGTTGTCC
2726 CATTTGATTCTTAAGGTTTGTGAGCTCCTA
1 CATTTGATTCTTAAGGTTTGTGAGCTCCTA
* *
2756 CATTTGATTCTTAATGTTTGTGAGCTCCCCA
1 CATTTGATTCTTAAGGTTTGTGAGCT-CCTA
* ** * ** *
2787 TCATGTCCTTCCTAAGG-AAGCAACT-AGTTGTCC--
1 -CATTTGATTCTTAAGGTTTG----TGAG--CTCCTA
2820 CATTTGATTCTTAAGGTTTGTGAGCTCCTA
1 CATTTGATTCTTAAGGTTTGTGAGCTCCTA
*
2850 CATTTGATTCTTAATGTTTGTGAGCTCC
1 CATTTGATTCTTAAGGTTTGTGAGCTCC
2878 CCATCATGTC
Statistics
Matches: 92, Mismatches: 18, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
28 3 0.03
29 1 0.01
30 54 0.59
31 4 0.04
32 23 0.25
33 1 0.01
34 2 0.02
35 3 0.03
36 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.41
Consensus pattern (30 bp):
CATTTGATTCTTAAGGTTTGTGAGCTCCTA
Found at i:2859 original size:94 final size:94
Alignment explanation
Indices: 2698--2887 Score: 380
Period size: 94 Copynumber: 2.0 Consensus size: 94
2688 TAATCTTCGA
2698 TCCTTCCTAAGGAAGCAACTAGTTGTCCCATTTGATTCTTAAGGTTTGTGAGCTCCTACATTTGA
1 TCCTTCCTAAGGAAGCAACTAGTTGTCCCATTTGATTCTTAAGGTTTGTGAGCTCCTACATTTGA
2763 TTCTTAATGTTTGTGAGCTCCCCATCATG
66 TTCTTAATGTTTGTGAGCTCCCCATCATG
2792 TCCTTCCTAAGGAAGCAACTAGTTGTCCCATTTGATTCTTAAGGTTTGTGAGCTCCTACATTTGA
1 TCCTTCCTAAGGAAGCAACTAGTTGTCCCATTTGATTCTTAAGGTTTGTGAGCTCCTACATTTGA
2857 TTCTTAATGTTTGTGAGCTCCCCATCATG
66 TTCTTAATGTTTGTGAGCTCCCCATCATG
2886 TC
1 TC
2888 TAATAGTTTT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 96 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (94 bp):
TCCTTCCTAAGGAAGCAACTAGTTGTCCCATTTGATTCTTAAGGTTTGTGAGCTCCTACATTTGA
TTCTTAATGTTTGTGAGCTCCCCATCATG
Found at i:7066 original size:64 final size:64
Alignment explanation
Indices: 6961--7081 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 64
6951 GGGAAAAAAA
* * * * *
6961 CTCGCTAAGTTGAAAATCCTGTAAAGAACGGTTTAGGCAAAAGTTAGAGCAAAAAAAAAAAGGC
1 CTCGCTAAGTTGAAAATCCTGAAAAGAACGGCTTAGACAAAACTTAGAACAAAAAAAAAAAGGC
* *
7025 CTCGCTAAGTTGACAATCCTGGAAAAG-ACGGCTTAGACAAAACTTAGAACACAAAAA
1 CTCGCTAAGTTGAAAATCCT-GAAAAGAACGGCTTAGACAAAACTTAGAACAAAAAAA
7082 TAAATGAACT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
64 44 0.90
65 5 0.10
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (64 bp):
CTCGCTAAGTTGAAAATCCTGAAAAGAACGGCTTAGACAAAACTTAGAACAAAAAAAAAAAGGC
Found at i:8705 original size:55 final size:55
Alignment explanation
Indices: 8646--8915 Score: 373
Period size: 54 Copynumber: 4.9 Consensus size: 55
8636 CATGATGAGT
*
8646 ACTAGGGCGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAAC
1 ACTAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAAC
* * *
8701 ACTAGGACGAGC-AAAAATAAATTTTGATCGCTTGAGCCCTGGTTGAAATCAGATGAAC
1 ACTAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCG--A--AGATGAAC
* ** *
8759 ACTAGGACGATCGAATAATAAATTTTGATAACTTGAGCCCTAGTCAAAGATGAAC
1 ACTAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAAC
* * *
8814 ACTAGGACGAGGGAATAAT-AATTTTAATCGCTTGAGCCCTAATCGAAGATGAAC
1 ACTAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAAC
* *
8868 ACTAGGACGAGAGAATAATAAATTTTGATCGCTTGAGCCCTGGTCGAA
1 ACTAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAA
8916 AGCAGATGAG
Statistics
Matches: 187, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
54 78 0.42
55 61 0.33
56 1 0.01
57 1 0.01
58 19 0.10
59 27 0.14
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (55 bp):
ACTAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAAC
Found at i:8802 original size:113 final size:112
Alignment explanation
Indices: 8646--9107 Score: 533
Period size: 113 Copynumber: 4.0 Consensus size: 112
8636 CATGATGAGT
*
8646 ACTAGGGCGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCG-A-AGATGAACACTAGGAC
1 ACTAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAACAGATGAACACTAGGAC
* * *
8709 GAGC-AAAAATAAATTTTGATCGCTTGAGCCCTGGTTGAAATCAGATGAAC
66 GAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCG--A--AGATGAAC
* **
8759 ACTAGGACGATCGAATAATAAATTTTGATAACTTGAGCCCTAGTC-AA-AGATGAACACTAGGAC
1 ACTAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAACAGATGAACACTAGGAC
* * *
8822 GAGGGAATAAT-AATTTTAATCGCTTGAGCCCTAATCGAAGATGAAC
66 GAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAAC
* *
8868 ACTAGGACGAGAGAATAATAAATTTTGATCGCTTGAGCCCTGGTCGAAAGCAGATGAGAGCAAAT
1 ACTAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCG-AA-CAGAT----G---A-
*
8933 GAGCACTAGGACGAGCGGATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAAC
56 -A-CACTAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAAC
* * * * * *
8992 ACCAGGACGAGTGAATAATAAATTTTGATCGTTTGACCCCT-GATCGAAAGCAGATGAGCACTAA
1 ACTAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAG-TCG-AA-CAGATGAACACTAG
9056 GACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAAC
63 GACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAAC
9106 AC
1 AC
9108 CATAACAAAC
Statistics
Matches: 305, Mismatches: 26, Indels: 35
0.83 0.07 0.10
Matches are distributed among these distances:
109 48 0.16
111 3 0.01
113 87 0.29
114 61 0.20
117 2 0.01
120 2 0.01
122 1 0.00
123 19 0.06
124 82 0.27
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (112 bp):
ACTAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAACAGATGAACACTAGGAC
GAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAAC
Found at i:9039 original size:55 final size:55
Alignment explanation
Indices: 8931--9132 Score: 226
Period size: 55 Copynumber: 3.6 Consensus size: 55
8921 ATGAGAGCAA
* * *
8931 ATGAGCACTAGGACGAGCGGATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAG
1 ATGAACACCAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAG
* * *
8986 ATGAACACCAGGACGAGTGAATAATAAATTTTGATCGTTTGACCCCT-GATCGAAAGCAG
1 ATGAACACCAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAG-TCG--A--AG
* * *
9045 ATGAGCACTAAGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAG
1 ATGAACACCAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAG
** * * *
9100 ATGAACACCATAACAAACGAATAATAAAATTTG
1 ATGAACACCAGGACGAGCGAATAATAAATTTTG
9133 GTCACCTGGG
Statistics
Matches: 122, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
54 1 0.01
55 72 0.59
57 2 0.02
59 46 0.38
60 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (55 bp):
ATGAACACCAGGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAG
Found at i:9150 original size:114 final size:114
Alignment explanation
Indices: 8926--9140 Score: 304
Period size: 114 Copynumber: 1.9 Consensus size: 114
8916 AGCAGATGAG
* *
8926 AGCAAATGAGCACTAGGACGAGCGGATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAA
1 AGCAAATGAGCACTAAGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAA
* * ** * *** *
8991 CACCAGGACGAGTGAATAATAAATTTTGATCGTTTGACCCCTGATCGAA
66 CACCAGAACAAACGAATAATAAAATTTGATCACCTGACCCCTGATCAAA
*
9040 AGCAGATGAGCACTAAGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAA
1 AGCAAATGAGCACTAAGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAA
* *
9105 CACCATAACAAACGAATAATAAAATTTGGTCACCTG
66 CACCAGAACAAACGAATAATAAAATTTGATCACCTG
9141 GGTCTTGATC
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
114 88 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.23
Consensus pattern (114 bp):
AGCAAATGAGCACTAAGACGAGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCGAAGATGAA
CACCAGAACAAACGAATAATAAAATTTGATCACCTGACCCCTGATCAAA
Found at i:11275 original size:23 final size:22
Alignment explanation
Indices: 11212--11275 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 22
11202 AATTATTATT
11212 AAACAAGATAGGCAC--AAAAA
1 AAACAAGATAGGCACAAAAAAA
*** *
11232 AAACAAGATAAATAAATAAAAAA
1 AAACAAGATAGGCACA-AAAAAA
*
11255 AAACAAGATAGGCACTAAAAA
1 AAACAAGATAGGCACAAAAAA
11276 TCAACAAATT
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
20 11 0.34
22 5 0.16
23 16 0.50
ACGTcount: A:0.69, C:0.11, G:0.11, T:0.09
Consensus pattern (22 bp):
AAACAAGATAGGCACAAAAAAA
Found at i:14894 original size:71 final size:71
Alignment explanation
Indices: 14805--15057 Score: 384
Period size: 71 Copynumber: 3.6 Consensus size: 71
14795 AAAGAAAATC
* * * *
14805 AAGAAGAGTAAAGTCTTAATTCAGGATAATTAAGAAAAGAAAGTACAGTTAAAGTCATAA-TCT-
1 AAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGT-TG
*
14868 GGAAGATT
65 GGCA-ATT
* * * *
14876 AAGAAGAGTAAAATCTTAATTCAGGGTAATTAAGAAAATAGAGTATAGTCAAGGTCCTAAGTTGG
1 AAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGG
14941 GCAATT
66 GCAATT
*
14947 AAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAGGGTCCTAAGTTGG
1 AAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGG
15012 GCAATT
66 GCAATT
15018 AAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGA
1 AAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGA
15058 CATGGGCAAT
Statistics
Matches: 166, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
71 162 0.98
72 4 0.02
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.25
Consensus pattern (71 bp):
AAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGG
GCAATT
Found at i:14908 original size:31 final size:31
Alignment explanation
Indices: 14873--14982 Score: 78
Period size: 31 Copynumber: 3.3 Consensus size: 31
14863 AATCTGGAAG
14873 ATTAAGAAGAGTAAAATCTTAATTCAGGGTA
1 ATTAAGAAGAGTAAAATCTTAATTCAGGGTA
* * * *
14904 ATTAAGAAAATAGAGTATAGTCAAGGTCCTAAGT-TGGGCA
1 ATTAAG---A-AGAGTA-A---AA--TCTTAATTCAGGGTA
*
14944 ATTAAGAAGAGTAAAGTCTTAATTCAGGGTA
1 ATTAAGAAGAGTAAAATCTTAATTCAGGGTA
14975 ATTAAGAA
1 ATTAAGAA
14983 AAGAAAGTAC
Statistics
Matches: 59, Mismatches: 9, Indels: 22
0.66 0.10 0.24
Matches are distributed among these distances:
30 6 0.10
31 18 0.31
32 1 0.02
34 1 0.02
35 7 0.12
36 7 0.12
37 1 0.02
39 2 0.03
40 10 0.17
41 6 0.10
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (31 bp):
ATTAAGAAGAGTAAAATCTTAATTCAGGGTA
Found at i:15085 original size:51 final size:51
Alignment explanation
Indices: 15009--15107 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
14999 GGTCCTAAGT
15009 TGGGCAATTAAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGACA
1 TGGGCAATTAAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGACA
*
15060 TGGGCAATTAAGAAGAGTAAAGTCTTTATTCAGGGTAATTAAGAAAAG
1 TGGGCAATTAAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAG
15108 GAAGTACAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.25
Consensus pattern (51 bp):
TGGGCAATTAAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGACA
Found at i:15221 original size:41 final size:41
Alignment explanation
Indices: 15175--15436 Score: 262
Period size: 41 Copynumber: 6.4 Consensus size: 41
15165 TAATTTGGAT
*
15175 AGTCAAACATAGTTAAAGTTTTAATCCATGGCGATTAAGAA
1 AGTCAAACATAGTTAAAGTTTTAATCCAGGGCGATTAAGAA
15216 AGTCAAACATAGTTAAAGTTTTAATCCAGGGCGATTAA-AA
1 AGTCAAACATAGTTAAAGTTTTAATCCAGGGCGATTAAGAA
* * *
15256 GAGTCAGACATAGTTAAATTTTTAATCCAGGGTGATTAAGAAA
1 -AGTCAAACATAGTTAAAGTTTTAATCCAGGGCGATTAAG-AA
* * *
15299 AATCAAACATAATTAAAGTTTTAATCCAGGGTGATTAAGAA
1 AGTCAAACATAGTTAAAGTTTTAATCCAGGGCGATTAAGAA
* * ** * * *
15340 AG-GAAAAATAGTTAAAGTCCTAATTCAGGG-TAGTTAGGAA
1 AGTCAAACATAGTTAAAGTTTTAATCCAGGGCGA-TTAAGAA
* * * * **
15380 AGTCAAGCATAGTTAAGGTCTGAAGT-CAGGGTAATTAAGAA
1 AGTCAAACATAGTTAAAGTTTTAA-TCCAGGGCGATTAAGAA
* *
15421 AGTCCAATATAGTTAA
1 AGTCAAACATAGTTAA
15437 GAACTTAATT
Statistics
Matches: 186, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.01
40 32 0.17
41 114 0.61
42 37 0.20
43 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (41 bp):
AGTCAAACATAGTTAAAGTTTTAATCCAGGGCGATTAAGAA
Found at i:15530 original size:37 final size:38
Alignment explanation
Indices: 15439--15760 Score: 256
Period size: 37 Copynumber: 8.7 Consensus size: 38
15429 ATAGTTAAGA
** * * * *
15439 ACTTAATTCAAGGCAATTAAGTAAAAGC-GGT-TAAGA
1 ACTTAATTCTGGGTAATTAAGTAAAGGCAGGTAAAAGG
* *
15475 ACTTAATTCAGGGCAATTAAGTAAAGGCAGGTAAAAGG
1 ACTTAATTCTGGGTAATTAAGTAAAGGCAGGTAAAAGG
* ** *
15513 -CTTAATTCTGGGAAATTAAGTAAACACA-GTCAAAGG
1 ACTTAATTCTGGGTAATTAAGTAAAGGCAGGTAAAAGG
** *
15549 ACTTAATTCTGGGTAATTAAGTAAACACA-GTAAAGGG
1 ACTTAATTCTGGGTAATTAAGTAAAGGCAGGTAAAAGG
* *
15586 ACTTAATTCTGGGTAATTAAGTAAA--CACTGTCAAAGG
1 ACTTAATTCTGGGTAATTAAGTAAAGGCA-GGTAAAAGG
* ** * *
15623 ACTTAATTCTAGGTAATTAAGT-AA-GCACAATCAAAGA
1 ACTTAATTCTGGGTAATTAAGTAAAGGCA-GGTAAAAGG
* *
15660 ACTTAATTCTGGGTAATTAAGTAAAGAGCA-GT-TAAGA
1 ACTTAATTCTGGGTAATTAAGTAAAG-GCAGGTAAAAGG
* *
15697 ACTTAATTCAGGGTAATTAAGTAAAGAGCA-GTCAAAAGA
1 ACTTAATTCTGGGTAATTAAGTAAAG-GCAGGT-AAAAGG
*
15736 ATTTAATT-TAGGGTAATTAAGTAAA
1 ACTTAATTCT-GGGTAATTAAGTAAA
15761 TTAAGATAAG
Statistics
Matches: 249, Mismatches: 25, Indels: 21
0.84 0.08 0.07
Matches are distributed among these distances:
35 2 0.01
36 35 0.14
37 177 0.71
38 6 0.02
39 26 0.10
40 3 0.01
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.27
Consensus pattern (38 bp):
ACTTAATTCTGGGTAATTAAGTAAAGGCAGGTAAAAGG
Found at i:15572 original size:74 final size:74
Alignment explanation
Indices: 15475--15760 Score: 298
Period size: 74 Copynumber: 3.8 Consensus size: 74
15465 GCGGTTAAGA
* *
15475 ACTTAATTCAGGGCAATTAAGTAAAGGCAGGTAAAAGGCTTAATTCTGGGAAATTAAGTAAACAC
1 ACTTAATTCAGGGTAATTAAGTAAAGGCAGGTAAAAGGCTTAATTCTGGGTAATTAAGTAAACAC
15540 AGTCAAAGG
66 AGTCAAAGG
* ** *
15549 ACTTAATTCTGGGTAATTAAGTAAACACA-GTAAAGGGACTTAATTCTGGGTAATTAAGTAAACA
1 ACTTAATTCAGGGTAATTAAGTAAAGGCAGGTAAAAGG-CTTAATTCTGGGTAATTAAGTAAACA
*
15613 CTGTCAAAGG
65 CAGTCAAAGG
** * *
15623 ACTTAATTCTA-GGTAATTAAGT-AA-GCACAATCAAAGAACTTAATTCTGGGTAATTAAGTAAA
1 ACTTAATTC-AGGGTAATTAAGTAAAGGCA-GGTAAAAG-GCTTAATTCTGGGTAATTAAGTAAA
* * *
15685 GAGCAGT-TAAGA
63 CA-CAGTCAAAGG
**
15697 ACTTAATTCAGGGTAATTAAGTAAAGAGCA-GTCAAAAGAATTTAATT-TAGGGTAATTAAGTAA
1 ACTTAATTCAGGGTAATTAAGTAAAG-GCAGGT-AAAAG-GCTTAATTCT-GGGTAATTAAGTAA
15760 A
62 A
15761 TTAAGATAAG
Statistics
Matches: 180, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
72 2 0.01
73 10 0.06
74 131 0.73
75 7 0.04
76 27 0.15
77 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.27
Consensus pattern (74 bp):
ACTTAATTCAGGGTAATTAAGTAAAGGCAGGTAAAAGGCTTAATTCTGGGTAATTAAGTAAACAC
AGTCAAAGG
Found at i:15610 original size:111 final size:112
Alignment explanation
Indices: 15435--15760 Score: 378
Period size: 111 Copynumber: 2.9 Consensus size: 112
15425 CAATATAGTT
** * * * *
15435 AAGAACTTAATTCAAGGCAATTAAGTAAA-AGCGGTTAAGAACTTAATTCAGGGCAATTAAGTAA
1 AAGAACTTAATTCTGGGTAATTAAGTAAACAGCAGTAAAGAACTTAATTCAGGGTAATTAAGTAA
* *
15499 AGGCAGGTAAAAGG-CTTAATTCTGGGAAATTAAGTAAACACAGTCA
66 AGGCAGGTAAAAGGACTTAATTCTAGGAAATTAAGTAAACACAATCA
* * *
15545 AAGGACTTAATTCTGGGTAATTAAGTAAACA-CAGTAAAGGGACTTAATTCTGGGTAATTAAGTA
1 AAGAACTTAATTCTGGGTAATTAAGTAAACAGCAGTAAA-GAACTTAATTCAGGGTAATTAAGTA
* * * *
15609 AA--CACTGTCAAAGGACTTAATTCTAGGTAATTAAGTAAGCACAATCA
65 AAGGCA-GGTAAAAGGACTTAATTCTAGGAAATTAAGTAAACACAATCA
* *
15656 AAGAACTTAATTCTGGGTAATTAAGTAAAGAGCAGTTAAGAACTTAATTCAGGGTAATTAAGTAA
1 AAGAACTTAATTCTGGGTAATTAAGTAAACAGCAGTAAAGAACTTAATTCAGGGTAATTAAGTAA
* * *
15721 AGAGCA-GTCAAAAGAATTTAATT-TAGGGTAATTAAGTAAA
66 AG-GCAGGT-AAAAGGACTTAATTCTA-GGAAATTAAGTAAA
15761 TTAAGATAAG
Statistics
Matches: 182, Mismatches: 24, Indels: 17
0.82 0.11 0.08
Matches are distributed among these distances:
109 2 0.01
110 37 0.20
111 107 0.59
112 10 0.05
113 24 0.13
114 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (112 bp):
AAGAACTTAATTCTGGGTAATTAAGTAAACAGCAGTAAAGAACTTAATTCAGGGTAATTAAGTAA
AGGCAGGTAAAAGGACTTAATTCTAGGAAATTAAGTAAACACAATCA
Found at i:15907 original size:36 final size:35
Alignment explanation
Indices: 15832--15913 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
15822 ATTCAGGGTA
**
15832 ATTAAGTAAATCAGCAAAGACTTAGTCCAAAAGACG
1 ATTAAGTAAATCAGCAAAGACTTAACCCAAAAGA-G
* *
15868 ATTAAGTAAGATCAGTTAAAGACTTAACCCAATAG-G
1 ATTAAGTAA-ATCAG-CAAAGACTTAACCCAAAAGAG
15904 ATTAAGTAAA
1 ATTAAGTAAA
15914 GAAAAGGACT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 1 0.03
36 19 0.47
37 5 0.12
38 15 0.38
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (35 bp):
ATTAAGTAAATCAGCAAAGACTTAACCCAAAAGAG
Found at i:15954 original size:37 final size:37
Alignment explanation
Indices: 15904--16021 Score: 148
Period size: 37 Copynumber: 3.2 Consensus size: 37
15894 ACCCAATAGG
* *
15904 ATTAAGTAAAGAAAAGGACTCAGTTCCAAGGAAGGGA
1 ATTAAGTAGAGAAAAGGACTTAGTTCCAAGGAAGGGA
* *
15941 ATTAAGTAGAGAAAAGGACTTAGTTCTAATGAAGGGA
1 ATTAAGTAGAGAAAAGGACTTAGTTCCAAGGAAGGGA
** * *
15978 ATTAAGTAGAGTTAAGGACTTAATTTCAAGGAA-GGA
1 ATTAAGTAGAGAAAAGGACTTAGTTCCAAGGAAGGGA
16014 AGTTAAGT
1 A-TTAAGT
16022 GAAGTCAGGG
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
36 4 0.06
37 66 0.94
ACGTcount: A:0.43, C:0.07, G:0.26, T:0.24
Consensus pattern (37 bp):
ATTAAGTAGAGAAAAGGACTTAGTTCCAAGGAAGGGA
Found at i:16152 original size:36 final size:37
Alignment explanation
Indices: 16028--16184 Score: 210
Period size: 37 Copynumber: 4.3 Consensus size: 37
16018 AAGTGAAGTC
* * * *
16028 AGGGGCTTAATTCGGGGTAATTAAGCAGCGTGAATAA
1 AGGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAA
*
16065 AGGGACTTAATTCAGGGTAATTAAGTAACGTCAATAA
1 AGGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAA
*
16102 AGGGACTTAATTCAGGGTAATTAAGTAGCGCCAATAA
1 AGGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAA
* * *
16139 A-AGACTTAATTCAGGGTAATTAAGTGGAGTCAATAA
1 AGGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAA
*
16175 AGAG-CTTAAT
1 AGGGACTTAAT
16185 CTGAGAAGAG
Statistics
Matches: 108, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
36 38 0.35
37 70 0.65
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (37 bp):
AGGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAA
Found at i:16171 original size:73 final size:73
Alignment explanation
Indices: 16030--16184 Score: 215
Period size: 73 Copynumber: 2.1 Consensus size: 73
16020 GTGAAGTCAG
* ** *
16030 GGGCTTAATTCGGGGTAATTAAGCAGCGTGAATAAAGGGACTTAATTCAGGGTAATTAAGTAACG
1 GGGCTTAATTCAGGGTAATTAAGCAGCGCCAATAAAGAGACTTAATTCAGGGTAATTAAGTAACG
16095 TCAATAAA
66 TCAATAAA
* *
16103 GGGACTTAATTCAGGGTAATTAAGTAGCGCCAATAAA-AGACTTAATTCAGGGTAATTAAGTGGA
1 GGG-CTTAATTCAGGGTAATTAAGCAGCGCCAATAAAGAGACTTAATTCAGGGTAATTAAGT-AA
16167 -GTCAATAAA
64 CGTCAATAAA
*
16176 GAGCTTAAT
1 GGGCTTAAT
16185 CTGAGAAGAG
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
72 6 0.08
73 37 0.51
74 30 0.41
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (73 bp):
GGGCTTAATTCAGGGTAATTAAGCAGCGCCAATAAAGAGACTTAATTCAGGGTAATTAAGTAACG
TCAATAAA
Found at i:21922 original size:5 final size:5
Alignment explanation
Indices: 21912--21942 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
21902 AAAATCTTAC
21912 TATCT TATCT T-TCT TATCT TATCT TATCT TA
1 TATCT TATCT TATCT TATCT TATCT TATCT TA
21943 CTACTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (5 bp):
TATCT
Found at i:21931 original size:14 final size:15
Alignment explanation
Indices: 21912--21942 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
21902 AAAATCTTAC
21912 TATCTTATCTT-TCT
1 TATCTTATCTTATCT
21926 TATCTTATCTTATCT
1 TATCTTATCTTATCT
21941 TA
1 TA
21943 CTACTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (15 bp):
TATCTTATCTTATCT
Found at i:22015 original size:34 final size:35
Alignment explanation
Indices: 21966--22070 Score: 187
Period size: 34 Copynumber: 3.1 Consensus size: 35
21956 GTACGAACTC
21966 AAAAATCTTAATTAGTCAATTACTAAAATACCCTT
1 AAAAATCTTAATTAGTCAATTACTAAAATACCCTT
*
22001 AAAAATC-TAATTAGTCAATTACTAAAATACCCCT
1 AAAAATCTTAATTAGTCAATTACTAAAATACCCTT
22035 -AAAATCTTAATTAGTCAATTACTAAAATACCCTT
1 AAAAATCTTAATTAGTCAATTACTAAAATACCCTT
22069 AA
1 AA
22071 TATTATAGTA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
33 6 0.09
34 52 0.79
35 8 0.12
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (35 bp):
AAAAATCTTAATTAGTCAATTACTAAAATACCCTT
Found at i:35148 original size:47 final size:47
Alignment explanation
Indices: 35097--35427 Score: 375
Period size: 47 Copynumber: 7.0 Consensus size: 47
35087 GAAACCCGTT
* * ** * *
35097 GACCAACTTTGGTCACTAAATTGTAAACTCGTGTGGCAGCGAGGAAA
1 GACCATCTTTGGTCACTAAATTGCAAACTCGCATGGAAGCGAGAAAA
* * * *
35144 GACCAACTTTGGTCACTAAATCGCAGACTCGCGTGGAAGCGAGAGAAA
1 GACCATCTTTGGTCACTAAATTGCAAACTCGCATGGAAGCGAGA-AAA
* * *
35192 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGTGAGAGAAA
1 GACCATCTTTGGTCACTAAATTGCAAACTCGCATGGAAGCGAGA-AAA
* *
35240 GACCATCTTTGGTCACCAAA-TGAAAAACTCGCATGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTG-CAAACTCGCATGGAAGCGAGAAAA
* * * *
35287 GACCATCTATGGTCACTAAA-TGCCAATTCGCATGGAAGCTAGAAAA
1 GACCATCTTTGGTCACTAAATTGCAAACTCGCATGGAAGCGAGAAAA
* * *
35333 GACCATCTTTGGTCACCAAA-TGCCAATTCGCATGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGCAAACTCGCATGGAAGCGAGAAAA
*
35379 GACCATCTTTGGTCACTAAA-T-CATAGATTCGCATGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGCA-A-ACTCGCATGGAAGCGAGAAAA
35426 GA
1 GA
35428 TTACTTGAAT
Statistics
Matches: 255, Mismatches: 25, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
45 1 0.00
46 84 0.33
47 86 0.34
48 84 0.33
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (47 bp):
GACCATCTTTGGTCACTAAATTGCAAACTCGCATGGAAGCGAGAAAA
Found at i:35211 original size:48 final size:46
Alignment explanation
Indices: 35097--35427 Score: 385
Period size: 46 Copynumber: 7.0 Consensus size: 46
35087 GAAACCCGTT
* * ** * *
35097 GACCAACTTTGGTCACTAAATTGTAAACTCGTGTGGCAGCGAGGAAA
1 GACCATCTTTGGTCACTAAA-TGCAAACTCGCATGGAAGCGAGAAAA
* * *
35144 GACCAACTTTGGTCACTAAATCGCAGACTCGCGTGGAAGCGAGAGAAA
1 GACCATCTTTGGTCACTAAAT-GCAAACTCGCATGGAAGCGAGA-AAA
* * *
35192 GACCATCTTTGGTCACTAAATTGAAAACTCGCGTGGAAGTGAGAGAAA
1 GACCATCTTTGGTCACTAAA-TGCAAACTCGCATGGAAGCGAGA-AAA
* *
35240 GACCATCTTTGGTCACCAAATGAAAAACTCGCATGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATG-CAAACTCGCATGGAAGCGAGAAAA
* * * *
35287 GACCATCTATGGTCACTAAATGCCAATTCGCATGGAAGCTAGAAAA
1 GACCATCTTTGGTCACTAAATGCAAACTCGCATGGAAGCGAGAAAA
* * *
35333 GACCATCTTTGGTCACCAAATGCCAATTCGCATGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATGCAAACTCGCATGGAAGCGAGAAAA
*
35379 GACCATCTTTGGTCACTAAAT-CATAGATTCGCATGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATGCA-A-ACTCGCATGGAAGCGAGAAAA
35426 GA
1 GA
35428 TTACTTGAAT
Statistics
Matches: 255, Mismatches: 23, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
45 1 0.00
46 85 0.33
47 85 0.33
48 83 0.33
49 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (46 bp):
GACCATCTTTGGTCACTAAATGCAAACTCGCATGGAAGCGAGAAAA
Found at i:35644 original size:70 final size:70
Alignment explanation
Indices: 35539--36039 Score: 735
Period size: 70 Copynumber: 7.2 Consensus size: 70
35529 CTCATTGAAC
* *
35539 TTGGCTTATGGAAAAGCC-CATG-TTGCTTGGATGGAACCAATGCTTGAACTGACTCGTATGGAA
1 TTGGCTTGTGGAAAAGCCTC-TGATTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAA
35602 ACGAGT
65 ACGAGT
* * * *
35608 TTGACTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTGTGGAAA
1 TTGGCTTGTGGAAAAGCCTCTGATTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
35673 CGAGT
66 CGAGT
* * * * *
35678 TTGGCTTGTGGAAAAGCCTCT-ATTGCCTGGATGGAACCAAGGTTTGAGCTGACTCGTGTGGAAA
1 TTGGCTTGTGGAAAAGCCTCTGATTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
35742 CGAGT
66 CGAGT
* *
35747 TTGGCTTGTGGAAAAGCCTCTG-TTGCTTGGATGGAACCAAGGGTT-AACTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTCTGATTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
*
35810 CGAGA
66 CGAGT
* *
35815 TTGGCTTGTGGAAAAGCCCCTG-TTGTTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTCTGATTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
*
35879 CGAGA
66 CGAGT
* * *
35884 TTGGCTTGTAGAAAAGCCTCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTGTGGAAA
1 TTGGCTTGTGGAAAAGCCTCTGATTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
35949 CGAGT
66 CGAGT
* *
35954 TTAGCTTGTGGAAAAGCCTCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTCTGATTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
36019 CGAGT
66 CGAGT
* *
36024 TTGACTTATGGAAAAG
1 TTGGCTTGTGGAAAAG
36040 TCGAAGCGTT
Statistics
Matches: 394, Mismatches: 33, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
68 61 0.15
69 146 0.37
70 187 0.47
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (70 bp):
TTGGCTTGTGGAAAAGCCTCTGATTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
CGAGT
Found at i:36057 original size:276 final size:275
Alignment explanation
Indices: 35539--36060 Score: 823
Period size: 276 Copynumber: 1.9 Consensus size: 275
35529 CTCATTGAAC
*
35539 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAATGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
* *
35604 GAGTTTGACTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTGTG
66 GAGATTGACTTGTAGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTGTG
* * * * *
35669 GAAACGAGTTTGGCTTGTGGAAAAGCCTCTATTGCCTGGATGGAACCAAGGTTTGAGCTGACTCG
131 GAAACGAGTTTAGCTTGTGGAAAAGCCTCTAATGCCTGGATGGAACCAAAGCTTGAACTGACTCG
* * * **
35734 TGTGGAAACGAGTTTGGCTTGTGGAAAAGCCTCTGTTGCTTGGATGGAACCAAGGGTTAACTGAC
196 TATGGAAACGAGTTTGACTTATGGAAAAG-CTCTGAAGCTTGGATGGAACCAAGGGTTAACTGAC
35799 TCGTATGGAAACGAGA
260 TCGTATGGAAACGAGA
* * *
35815 TTGGCTTGTGGAAAAGCCCCTGTTGTTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
* *
35880 GAGATTGGCTTGTAGAAAAGCCTCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTGTG
66 GAGATTGACTTGTAGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTGTG
*
35945 GAAACGAGTTTAGCTTGTGGAAAAGCCTCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTC
131 GAAACGAGTTTAGCTTGTGGAAAAGCCTCT-AATGCCTGGATGGAACCAAAGCTTGAACTGACTC
36010 GTATGGAAACGAGTTTGACTTATGGAAAAG-TC-GAAGCGTTCGGATGGAACC
195 GTATGGAAACGAGTTTGACTTATGGAAAAGCTCTGAAGC-TT-GGATGGAACC
36061 GAAGCCAAAT
Statistics
Matches: 224, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
274 3 0.01
275 4 0.02
276 161 0.72
277 56 0.25
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (275 bp):
TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
GAGATTGACTTGTAGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTGTG
GAAACGAGTTTAGCTTGTGGAAAAGCCTCTAATGCCTGGATGGAACCAAAGCTTGAACTGACTCG
TATGGAAACGAGTTTGACTTATGGAAAAGCTCTGAAGCTTGGATGGAACCAAGGGTTAACTGACT
CGTATGGAAACGAGA
Found at i:37077 original size:6 final size:6
Alignment explanation
Indices: 37066--37118 Score: 79
Period size: 6 Copynumber: 8.5 Consensus size: 6
37056 TTCACTCTTT
*
37066 TTTTTC TTTTTC TTTTTC TTTTCC TTTCTTC TTTTTC TTTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTT-TTC TTTTTC -TTTTTC TTTTTC
37116 TTT
1 TTT
37119 CATTTTTTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 32 0.74
7 11 0.26
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:37081 original size:13 final size:13
Alignment explanation
Indices: 37065--37118 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
37055 CTTCACTCTT
37065 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
*
37078 -TTTTTCTTTTCC
1 TTTTTTCTTTTTC
*
37090 TTTCTTCTTTTTC
1 TTTTTTCTTTTTC
37103 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
37116 TTT
1 TTT
37119 CATTTTTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
12 11 0.31
13 25 0.69
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:37097 original size:19 final size:17
Alignment explanation
Indices: 37063--37118 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 17
37053 TTCTTCACTC
37063 TTTT-TTTTCTTTTTCT
1 TTTTCTTTTCTTTTTCT
37079 TTTTCTTTTCCTTTCTTCT
1 TTTTCTTTT-CTTT-TTCT
37098 TTTTCTTTTTTCTTTTTCT
1 TTTTC--TTTTCTTTTTCT
37117 TT
1 TT
37119 CATTTTTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.11
17 4 0.11
18 4 0.11
19 15 0.43
20 4 0.11
21 4 0.11
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTCTTTTTCT
Found at i:37126 original size:19 final size:17
Alignment explanation
Indices: 37063--37118 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 17
37053 TTCTTCACTC
37063 TTTTTTTTCTTTTTCTT
1 TTTTTTTTCTTTTTCTT
*
37080 TTTCTTTTCCTTTCTTCTTT
1 TTT-TTTTTCTTT-TTC-TT
37100 TTCTTTTTTCTTTTTCTT
1 TT-TTTTTTCTTTTTCTT
37118 T
1 T
37119 CATTTTTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 3 0.09
18 11 0.33
19 6 0.18
20 12 0.36
21 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTTCTTTTTCTT
Found at i:37734 original size:22 final size:24
Alignment explanation
Indices: 37704--37747 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
37694 AGGTTTTTCA
37704 TTTCCTTTTTCTT-TTT-CTTTTT
1 TTTCCTTTTTCTTCTTTACTTTTT
*
37726 TTTCTTTTTTCTTCTTTACTTT
1 TTTCCTTTTTCTTCTTTACTTT
37748 GAATGCGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 3 0.16
24 4 0.21
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTCCTTTTTCTTCTTTACTTTTT
Found at i:38351 original size:44 final size:44
Alignment explanation
Indices: 38242--38417 Score: 280
Period size: 44 Copynumber: 3.9 Consensus size: 44
38232 CTTCATTGAC
* *
38242 ATCAAAACCTTTTGAACATCATGACTCTTTTTTTGAAAAACCATTTT
1 ATCAAAACCTTTTGAAAACCATGACTC--TTTTTG-AAAACCATTTT
* * *
38289 ATCAAAACCTTTTAAAAACCATGACTCTTTTTGAAAATCGTTTT
1 ATCAAAACCTTTTGAAAACCATGACTCTTTTTGAAAACCATTTT
38333 ATCAAAACCTTTTGAAAACCATGACTCTTTTTGAAAACCATTTT
1 ATCAAAACCTTTTGAAAACCATGACTCTTTTTGAAAACCATTTT
38377 ATCAAAACCTTTTGAAAACCATGACTCTTTTTGAAAACCAT
1 ATCAAAACCTTTTGAAAACCATGACTCTTTTTGAAAACCAT
38418 CGTTGTTTTT
Statistics
Matches: 121, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
44 91 0.75
45 6 0.05
47 24 0.20
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (44 bp):
ATCAAAACCTTTTGAAAACCATGACTCTTTTTGAAAACCATTTT
Found at i:38427 original size:19 final size:19
Alignment explanation
Indices: 38342--38417 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 19
38332 TATCAAAACC
38342 TTTTGAAAACCATGACTCT
1 TTTTGAAAACCATGACTCT
* * *
38361 TTTTGAAAACCATTTTATCAAAACC
1 TTTTGAAAACCA--TGA-C---TCT
38386 TTTTGAAAACCATGACTCT
1 TTTTGAAAACCATGACTCT
38405 TTTTGAAAACCAT
1 TTTTGAAAACCAT
38418 CGTTGTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
19 26 0.58
21 2 0.04
22 2 0.04
23 2 0.04
25 13 0.29
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.37
Consensus pattern (19 bp):
TTTTGAAAACCATGACTCT
Found at i:38445 original size:12 final size:11
Alignment explanation
Indices: 38423--38464 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
38413 ACCATCGTTG
*
38423 TTTTTTTTTTC
1 TTTTTTCTTTC
38434 TCTTTTTCTTTC
1 T-TTTTTCTTTC
38446 TTTTTTC-TTC
1 TTTTTTCTTTC
38456 -TTTTTCTTT
1 TTTTTTCTTT
38465 TTTCATCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 6 0.21
10 5 0.18
11 7 0.25
12 10 0.36
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:38451 original size:20 final size:20
Alignment explanation
Indices: 38427--38464 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
38417 TCGTTGTTTT
38427 TTTTTTC-TCTTTTTCTTTC
1 TTTTTTCTTCTTTTTCTTTC
38446 TTTTTTCTTCTTTTTCTTT
1 TTTTTTCTTCTTTTTCTTT
38465 TTTCATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTCTTTTTCTTTC
Found at i:38476 original size:16 final size:16
Alignment explanation
Indices: 38442--38476 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38432 TCTCTTTTTC
* *
38442 TTTCTTTTTTCTTCTT
1 TTTCTTTTTTCATCAT
38458 TTTCTTTTTTCATCAT
1 TTTCTTTTTTCATCAT
38474 TTT
1 TTT
38477 TATCTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTTTTCATCAT
Found at i:47990 original size:3 final size:3
Alignment explanation
Indices: 47975--48012 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
47965 TAGAGTACAG
47975 ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
48013 ATGATAAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:49960 original size:14 final size:14
Alignment explanation
Indices: 49940--49978 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
49930 GATTCAAACT
49940 AACTGACTCAAAAA
1 AACTGACTCAAAAA
*
49954 AATTGAC-CAAAAA
1 AACTGACTCAAAAA
49967 AACTGACT-AAAA
1 AACTGACTCAAAA
49979 CTCGATAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.59, C:0.18, G:0.08, T:0.15
Consensus pattern (14 bp):
AACTGACTCAAAAA
Found at i:50440 original size:2 final size:2
Alignment explanation
Indices: 50435--50473 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
50425 CTATAGTGTG
*
50435 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50474 ATAATACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53837 original size:12 final size:12
Alignment explanation
Indices: 53803--53839 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
53793 TGAATGATGA
**
53803 TGAGAACAATAA
1 TGAGAACAATGG
53815 TGAGAACAATGG
1 TGAGAACAATGG
53827 TGAGAACAATGG
1 TGAGAACAATGG
53839 T
1 T
53840 AACAATAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.27, T:0.19
Consensus pattern (12 bp):
TGAGAACAATGG
Done.