Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004458.1 Hibiscus syriacus cultivar Beakdansim tig00009830_pilon, 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: 57720
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2958 original size:50 final size:50
Alignment explanation
Indices: 2896--3008 Score: 172
Period size: 50 Copynumber: 2.3 Consensus size: 50
2886 TAGCGCGGAT
* * *
2896 CAGGGGGCGCGCTATACCCACGTGGCGCCAGATCACCGTATATCGCGGGG
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCATATAACGCGGGG
* * *
2946 CAGGGGGCGCGCTATACCCACGTGGTGCCAAATCAGCATATAACGCGGTG
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCATATAACGCGGGG
2996 CAGGGGGCGCGCT
1 CAGGGGGCGCGCT
3009 TTTCTGCTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.19, C:0.30, G:0.36, T:0.14
Consensus pattern (50 bp):
CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCATATAACGCGGGG
Found at i:4866 original size:15 final size:15
Alignment explanation
Indices: 4824--4866 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 15
4814 ATTTTTACCC
4824 ATATAA-ATTATAT-
1 ATATAATATTATATA
4837 ATAT-ATATTATATA
1 ATATAATATTATATA
*
4851 ATATAATATAATATA
1 ATATAATATTATATA
4866 A
1 A
4867 AAGAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 11 0.42
14 4 0.15
15 10 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATAATATTATATA
Found at i:5532 original size:15 final size:17
Alignment explanation
Indices: 5500--5534 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5490 CATACTTATT
5500 ATATATTATAAATATAA
1 ATATATTATAAATATAA
5517 ATATATT-TAAAT-TAA
1 ATATATTATAAATATAA
5532 ATA
1 ATA
5535 AAGATATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 5 0.28
17 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATTATAAATATAA
Found at i:14391 original size:19 final size:19
Alignment explanation
Indices: 14363--14467 Score: 111
Period size: 19 Copynumber: 5.2 Consensus size: 19
14353 GCGATTTTGA
14363 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
14382 AAAATATGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
14401 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
14421 GAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
14445 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
14464 AAAA
1 AAAA
14468 ATCCAAAATA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
19 50 0.68
20 3 0.04
22 8 0.11
24 3 0.04
25 10 0.14
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:17305 original size:3 final size:3
Alignment explanation
Indices: 17297--17369 Score: 96
Period size: 3 Copynumber: 24.0 Consensus size: 3
17287 AATTTTAATT
*
17297 TTA TTA TTA TTA TTAA GT- TTA TTA TTA TTA TTA TTA TGT- TTA TTAA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T-TA TTA TT-A
17343 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
17370 ATTACATATT
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
2 2 0.03
3 55 0.87
4 6 0.10
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:22521 original size:20 final size:20
Alignment explanation
Indices: 22496--22536 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
22486 GCATTCCCTC
*
22496 TCTTTGAGACCTTGAAACAT
1 TCTTTGACACCTTGAAACAT
22516 TCTTTGACACCTTGAAACAT
1 TCTTTGACACCTTGAAACAT
22536 T
1 T
22537 GCATTTATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (20 bp):
TCTTTGACACCTTGAAACAT
Found at i:24273 original size:4 final size:4
Alignment explanation
Indices: 24266--24411 Score: 260
Period size: 4 Copynumber: 37.0 Consensus size: 4
24256 ATACATCAAA
*
24266 ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24314 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
24362 ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT AC-- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
24408 ACAT
1 ACAT
24412 GATACATAAA
Statistics
Matches: 136, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.01
4 134 0.99
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:25027 original size:157 final size:157
Alignment explanation
Indices: 24794--25091 Score: 395
Period size: 157 Copynumber: 1.9 Consensus size: 157
24784 GAGACAATTT
* * * *
24794 ATTTCAAAACAAATTTCGTCTCATTTGAGACATTTTTCCTTTGAGATCCAAATTTCGAATTTGTT
1 ATTTCAAAACAAATTGCGTCTCACTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGAT
* * * *
24859 TCACATTAAACAAAGTTGATCTCA-TTTGAGATCG-TATCTATTTCAAAAACAAATTTCGTCTCG
66 TCACATTAAACAAAATTAATCTCACCTT-AGATCGTTATCTATTTC-AAAACAAATTTCGGCTCG
24922 CTTGAGACATTTTTCCACAAATTTTGAGA
129 CTTGAGACATTTTTCCACAAATTTTGAGA
* * * *
24951 ATTTTAAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAGTTTTGAATTTGAT
1 ATTTCAAAACAAATTGCGTCTCACTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGAT
* * * *
25016 TCAC-TTAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTCAAAACAAATTTCGGCTCGC
66 TCACATT-AAACAAAATTAATCTCACCTTAGATCGTTATCTATTTCAAAACAAATTTCGGCTCGC
*
25080 TTGAGACCTTTT
130 TTGAGACATTTT
25092 CCCTTTGAGA
Statistics
Matches: 121, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
156 2 0.02
157 110 0.91
158 9 0.07
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (157 bp):
ATTTCAAAACAAATTGCGTCTCACTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGAT
TCACATTAAACAAAATTAATCTCACCTTAGATCGTTATCTATTTCAAAACAAATTTCGGCTCGCT
TGAGACATTTTTCCACAAATTTTGAGA
Found at i:25097 original size:105 final size:102
Alignment explanation
Indices: 24956--25194 Score: 277
Period size: 105 Copynumber: 2.3 Consensus size: 102
24946 TGAGAATTTT
* * * *
24956 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAGTTTTGAATTTGATTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
*
25020 TTAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 TT-AAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * * *
25061 AAAACAAATTTCGGCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* **
25126 TTAAACAAAGTTGGTCTCACTTGAGATCGTTTTCTCA
66 TTAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
* *
25163 AAAACAAATTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTC
25195 TCTAAAAACA
Statistics
Matches: 115, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
101 2 0.02
102 28 0.24
103 4 0.03
104 4 0.03
105 75 0.65
106 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TTAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:25179 original size:36 final size:34
Alignment explanation
Indices: 25128--25258 Score: 129
Period size: 36 Copynumber: 3.7 Consensus size: 34
25118 GTTTCACATT
* *
25128 AAACAAAGTTGGTCTCACTTGAGATCGTTTTCTCAA
1 AAACAAATTTTGTCTCACTTGAGA-C-TTTTCTCAA
* *
25164 AAACAAATTTTGTCTCGCTTGAGACAATTTCTCTAA
1 AAACAAATTTTGTCTCACTTGAGAC-TTTTCTC-AA
* * *
25200 AAACAAATTTTGTCTCATTTGAGACTGTATCT-TA
1 AAACAAATTTTGTCTCACTTGAGACT-TTTCTCAA
* *
25234 AAGCAAATTTTGTCTCGCTTGAGAC
1 AAACAAATTTTGTCTCACTTGAGAC
25259 ATCATTTTCT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
34 23 0.29
35 7 0.09
36 50 0.62
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (34 bp):
AAACAAATTTTGTCTCACTTGAGACTTTTCTCAA
Found at i:25246 original size:34 final size:35
Alignment explanation
Indices: 25162--25260 Score: 128
Period size: 34 Copynumber: 2.8 Consensus size: 35
25152 TCGTTTTCTC
* *
25162 AAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAACAAATTTTGTCTCGCTTGAGAC-ATGTATCT
**
25198 AAAAACAAATTTTGTCTCATTTGAGAC-TGTATCT
1 AAAAACAAATTTTGTCTCGCTTGAGACATGTATCT
* *
25232 TAAAGCAAATTTTGTCTCGCTTGAGACAT
1 AAAAACAAATTTTGTCTCGCTTGAGACAT
25261 CATTTTCTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
34 28 0.52
35 1 0.02
36 25 0.46
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.36
Consensus pattern (35 bp):
AAAAACAAATTTTGTCTCGCTTGAGACATGTATCT
Found at i:25549 original size:28 final size:29
Alignment explanation
Indices: 25509--25638 Score: 167
Period size: 29 Copynumber: 4.6 Consensus size: 29
25499 TTTCTTTTGA
25509 AAAAAAAATCTTTGAGTTTGTTCCTCTT-
1 AAAAAAAATCTTTGAGTTTGTTCCTCTTG
*
25537 AAAAAAAATCTTTGAGTTTGTTCCTTTTG
1 AAAAAAAATCTTTGAGTTTGTTCCTCTTG
* *
25566 AATAAAAATCTTTGAGTTTGTTCCTTTTG
1 AAAAAAAATCTTTGAGTTTGTTCCTCTTG
* * ***
25595 AATAAAAATCTTGGAGTTTGTT--TCGAA
1 AAAAAAAATCTTTGAGTTTGTTCCTCTTG
25622 AAAAAAAATCTTTGAGT
1 AAAAAAAATCTTTGAGT
25639 CTATTTATTT
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
27 16 0.17
28 27 0.29
29 49 0.53
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.42
Consensus pattern (29 bp):
AAAAAAAATCTTTGAGTTTGTTCCTCTTG
Found at i:25572 original size:29 final size:29
Alignment explanation
Indices: 25502--25616 Score: 178
Period size: 29 Copynumber: 4.0 Consensus size: 29
25492 AAGACAATTT
25502 CTTTTGAAAAAAAAATCTTTGAGTTTGTTC
1 CTTTTG-AAAAAAAATCTTTGAGTTTGTTC
*
25532 CTCTT-AAAAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAAAATCTTTGAGTTTGTTC
*
25560 CTTTTGAATAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAAAATCTTTGAGTTTGTTC
* *
25589 CTTTTGAATAAAAATCTTGGAGTTTGTT
1 CTTTTGAAAAAAAATCTTTGAGTTTGTT
25617 TCGAAAAAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
28 27 0.34
29 49 0.61
30 4 0.05
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
CTTTTGAAAAAAAATCTTTGAGTTTGTTC
Found at i:25581 original size:57 final size:59
Alignment explanation
Indices: 25502--25616 Score: 180
Period size: 57 Copynumber: 2.0 Consensus size: 59
25492 AAGACAATTT
*
25502 CTTTTGAAAAAAAAATCTTTGAGTTTGTTCCTCTT-AAAAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAAATCTTGGAGTTTGTTC
* * *
25560 CTTTTG-AATAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTTGTT
1 CTTTTGAAAAAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAAATCTTGGAGTTTGTT
25617 TCGAAAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 26 0.50
58 26 0.50
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.45
Consensus pattern (59 bp):
CTTTTGAAAAAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAAATCTTGGAGTTTGTTC
Found at i:25777 original size:30 final size:30
Alignment explanation
Indices: 25736--25869 Score: 135
Period size: 30 Copynumber: 4.3 Consensus size: 30
25726 GACAATTTTG
25736 TGAAA-AAAAATCTTTGAGATTGTTTCTTT
1 TGAAACAAAAATCTTTGAGATTGTTTCTTT
*
25765 TGAAACAAAAATCTTTGAGTTTGTTTCTTT
1 TGAAACAAAAATCTTTGAGATTGTTTCTTT
* * * *
25795 GGAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTTT
1 TGAAACAAAA------ATCT-TTGAGATTGTTTCTTT
*
25832 TGAAACAAAAATCTTTGAGTTTGTTTCTTT
1 TGAAACAAAAATCTTTGAGATTGTTTCTTT
*
25862 GGAAACAA
1 TGAAACAA
25870 GATTTTGTCT
Statistics
Matches: 85, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
29 5 0.06
30 52 0.61
31 3 0.04
36 3 0.04
37 22 0.26
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (30 bp):
TGAAACAAAAATCTTTGAGATTGTTTCTTT
Found at i:25832 original size:67 final size:67
Alignment explanation
Indices: 25752--25966 Score: 287
Period size: 67 Copynumber: 3.3 Consensus size: 67
25742 AAAATCTTTG
*
25752 AGATTGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
25817 TA
66 TA
*
25819 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAGATTTTGTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
25884 TA
66 TA
* * * * *
25886 AGATAATTTCTTTTG-AA-AAAAATCTTTGAATCTGTTTCTCTT--AAA-ATGAATTTTGTATCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT-TTGGAAACA-AAATTTTGTCTCT
*
25946 CTTG
64 CTTA
* *
25950 AGACAGTTTCTCTTGAA
1 AGATAGTTTCTTTTGAA
25967 GTAAATCTTT
Statistics
Matches: 133, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
63 1 0.01
64 28 0.21
65 21 0.16
66 4 0.03
67 79 0.59
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.45
Consensus pattern (67 bp):
AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
TA
Found at i:25837 original size:37 final size:37
Alignment explanation
Indices: 25787--25913 Score: 117
Period size: 37 Copynumber: 3.6 Consensus size: 37
25777 CTTTGAGTTT
25787 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* * * * *
25824 GTTTCTTTTGAAACAAAA------ATCT-TTGAGTTT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
*
25854 GTTTCTTTGGAAACAAGATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
25891 ATTTCTTTTGAAA-AAAATCTTTG
1 GTTTCTTTGGAAACAAAAT-TTTG
25914 AATCTGTTTC
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
30 21 0.31
31 3 0.04
36 7 0.10
37 37 0.54
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (37 bp):
GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:26163 original size:120 final size:121
Alignment explanation
Indices: 26025--26250 Score: 280
Period size: 120 Copynumber: 1.9 Consensus size: 121
26015 TTAACAAAAT
* * *
26025 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAAA
**
26088 ACTAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGTGATC
64 AAAAATC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
* ** **
26145 CATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
* * *
26210 AAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
66 AAATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
26251 TCGAGACAAC
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
119 7 0.08
120 66 0.74
121 16 0.18
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (121 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
AAATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
Found at i:26286 original size:66 final size:66
Alignment explanation
Indices: 26146--26272 Score: 193
Period size: 66 Copynumber: 1.9 Consensus size: 66
26136 GATGTGATCC
* *
26146 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAAAA
26211 A
66 A
* * **
26212 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC-TCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAA
26273 TACCCACATT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
65 19 0.35
66 36 0.65
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (66 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAAAA
A
Found at i:26317 original size:40 final size:40
Alignment explanation
Indices: 26254--26333 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
26244 TTGTCTCTCG
26254 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
* * *
26294 AGACAATTTCTTTT-AAAACTACCCACCTTTGAGATTGTTT
1 AGACAACTTCTTTTGAAAA-TACCCACATTTGAGATCGTTT
26334 TTATTAAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
Found at i:26452 original size:15 final size:15
Alignment explanation
Indices: 26429--26472 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
26419 TTTTGAGTCG
*
26429 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
26444 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
26459 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
26473 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:26761 original size:36 final size:34
Alignment explanation
Indices: 26710--26805 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 34
26700 TTTGAGAAAA
* * * *
26710 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTACC
1 ATCTTTGAATCTGTTTCTTT-GAAACAAAA-TAAAC
*
26746 ATCTTTGAATCTGTTTCCCTTGAAACAAAATAAAC
1 ATCTTTGAATCTGTTT-CTTTGAAACAAAATAAAC
26781 ATCTTTGAGATC-GTTTCTCTTGAAA
1 ATCTTTGA-ATCTGTTTCT-TTGAAA
26806 TGAATTTTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
34 1 0.02
35 21 0.41
36 26 0.51
37 3 0.06
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (34 bp):
ATCTTTGAATCTGTTTCTTTGAAACAAAATAAAC
Found at i:26797 original size:35 final size:36
Alignment explanation
Indices: 26731--26805 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
26721 TGTTTCTTTG
* *
26731 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
*
26767 GAAACAAAA-TAAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTGA-ATCTGTTTCCCTT
26802 GAAA
1 GAAA
26806 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
Found at i:27211 original size:40 final size:41
Alignment explanation
Indices: 27156--27519 Score: 218
Period size: 40 Copynumber: 8.4 Consensus size: 41
27146 TGGCCAGTAG
* *
27156 TCCTCATCACATAGGAACCGTGTCATCC-CCTGACCAGACC
1 TCCTCATCACGTAGGAGCCGTGTCATCCACCTGACCAGACC
** *
27196 TCCTCATCACGTAGGAGCCGTGTCATCCTAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCC-ACCTGACCAGACC
* * *
27237 GTCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT---CC-ACCT---GA---CCAGACC
* * * *
27289 TCTTCATCACGTATGAGCAGTGCCATCC-CCTGACCAGACC
1 TCCTCATCACGTAGGAGCCGTGTCATCCACCTGACCAGACC
** * *
27329 TCCTCATCACGTAGGAGCCGTGTCATCCTAGATAACCA-TCC
1 TCCTCATCACGTAGGAGCCGTGTCATCC-ACCTGACCAGACC
* * *
27370 GTCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT---CC-ACCT---GA---CCAGACC
* * * *
27422 TCTTCATCACGTATGAGCAGTGCCATCC-CCTGACCAGACC
1 TCCTCATCACGTAGGAGCCGTGTCATCCACCTGACCAGACC
** *
27462 TCCTCATCACGTAGGAGCCGTGTCATCCTAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCC-ACCTGACCAGACC
27503 GTCCTCATCACGTAGGA
1 -TCCTCATCACGTAGGA
27520 ATCGGGTTAT
Statistics
Matches: 248, Mismatches: 47, Indels: 56
0.71 0.13 0.16
Matches are distributed among these distances:
40 86 0.35
41 6 0.02
42 81 0.33
43 4 0.02
45 10 0.04
46 6 0.02
48 6 0.02
51 47 0.19
52 2 0.01
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.22
Consensus pattern (41 bp):
TCCTCATCACGTAGGAGCCGTGTCATCCACCTGACCAGACC
Found at i:27381 original size:133 final size:133
Alignment explanation
Indices: 27138--27619 Score: 741
Period size: 133 Copynumber: 3.6 Consensus size: 133
27128 AACCATTATC
* * * * * * * * *
27138 CCTAGAGATGGCCAGTAGTCCTCATCACATAGGAACCGTGTCATCCCCTGACCAGACCTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGCCATCCCCTGACCAGACCTCCTCAT
27203 CACGTAGGAGCCGTGTCATCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGCC
66 CACGTAGGAGCCGTGTCATCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGCC
27268 CTA
131 CTA
27271 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGCCATCCCCTGACCAGACCTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGCCATCCCCTGACCAGACCTCCTCAT
*
27336 CACGTAGGAGCCGTGTCATCCTAGATAACCATCCGTCCTCATCACGTAGGAACCGTGTTATCGCC
66 CACGTAGGAGCCGTGTCATCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGCC
27401 CTA
131 CTA
27404 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGCCATCCCCTGACCAGACCTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGCCATCCCCTGACCAGACCTCCTCAT
* * * *
27469 CACGTAGGAGCCGTGTCATCCTAGATAACCAGCCGTCCTCATCACGTAGGAATCGGGTTATCACT
66 CACGTAGGAGCCGTGTCATCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGCC
27534 C-A
131 CTA
* * * * **
27536 TCCTAAAGATGACCAGAACTCTTCATCATGTATGAGCAGTGTCATCCCTTGACCAGATTTCCTCA
1 -CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGCCATCCCCTGACCAGACCTCCTCA
* * *
27601 TCATGTAGGAACCTTGTCA
65 TCACGTAGGAGCCGTGTCA
27620 CCTTTAGACG
Statistics
Matches: 324, Mismatches: 24, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
132 1 0.00
133 323 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.23
Consensus pattern (133 bp):
CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGCCATCCCCTGACCAGACCTCCTCAT
CACGTAGGAGCCGTGTCATCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGCC
CTA
Found at i:27592 original size:40 final size:40
Alignment explanation
Indices: 27545--27666 Score: 120
Period size: 40 Copynumber: 3.0 Consensus size: 40
27535 ATCCTAAAGA
27545 TGACCAGAACTCTTCATCATGTATGAGCAGTGTCATCCCT
1 TGACCAGAACTCTTCATCATGTATGAGCAGTGTCATCCCT
** * * * ** *
27585 TGACCAGATTTCCTCATCATGTAGGAACCTTGTCA-CCTT
1 TGACCAGAACTCTTCATCATGTATGAGCAGTGTCATCCCT
*
27624 TAGACGACCAGAACTCTTCATCATGTATGAGCAGTGTCGTCCC
1 T----GACCAGAACTCTTCATCATGTATGAGCAGTGTCATCCC
27667 CAACAACCAA
Statistics
Matches: 60, Mismatches: 17, Indels: 6
0.72 0.20 0.07
Matches are distributed among these distances:
39 4 0.07
40 28 0.47
43 26 0.43
44 2 0.03
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (40 bp):
TGACCAGAACTCTTCATCATGTATGAGCAGTGTCATCCCT
Found at i:27838 original size:3 final size:3
Alignment explanation
Indices: 27830--27896 Score: 75
Period size: 3 Copynumber: 22.0 Consensus size: 3
27820 AATTTTAATT
* *
27830 TTA TTA TTA TTA TTAA GT- TTA TTA TTA TTA TTA TT- TTGT TTA TTAA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TT-A TTA TT-A
27876 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
27897 ATTACATATT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
2 3 0.05
3 46 0.82
4 7 0.12
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:29091 original size:19 final size:19
Alignment explanation
Indices: 29045--29091 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
29035 CATTAATTTG
*
29045 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
29065 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
29085 TATATTT
1 TATATTT
29092 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:32180 original size:29 final size:28
Alignment explanation
Indices: 32129--32214 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 28
32119 CTTCACAGCA
* *
32129 TAGGTCGCCATGCCCTCCGGGCGACCTT
1 TAGGTCGCCATGCACGCCGGGCGACCTT
* *
32157 CTAGGTCGCCATGCACGCCAGGCGACATGT
1 -TAGGTCGCCATGCACGCCGGGCGACCT-T
* *
32187 TAGGTCGCCATGCATGCTGGGCGACCTT
1 TAGGTCGCCATGCACGCCGGGCGACCTT
32215 GTCCTGCGCC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
28 1 0.02
29 46 0.96
30 1 0.02
ACGTcount: A:0.15, C:0.34, G:0.30, T:0.21
Consensus pattern (28 bp):
TAGGTCGCCATGCACGCCGGGCGACCTT
Found at i:32330 original size:31 final size:31
Alignment explanation
Indices: 32295--32356 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
32285 CATGGCGCAT
*
32295 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGATCGTA
* *
32326 GCAAAGCTTCATCTTCTCGCCACAGATCGTA
1 GCAAAGCTTCATCCTCTCACCACAGATCGTA
32357 TAGAACACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.35, G:0.15, T:0.24
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAGATCGTA
Found at i:35307 original size:42 final size:42
Alignment explanation
Indices: 35257--35339 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
35247 AAAATAATTC
* * *
35257 TGAAAAATA-TTTTCTGATGTTTGATAAATGTAATTGATTTTA
1 TGAAAAATATTTTTCAG-TGTTAGATAAATATAATTGATTTTA
*
35299 TGAAAAATATTTTTCAGTGTTAGATAGATATAATTGATTTT
1 TGAAAAATATTTTTCAGTGTTAGATAAATATAATTGATTTT
35340 TTCAATATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 30 0.83
43 6 0.17
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.47
Consensus pattern (42 bp):
TGAAAAATATTTTTCAGTGTTAGATAAATATAATTGATTTTA
Found at i:35359 original size:17 final size:18
Alignment explanation
Indices: 35326--35359 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35316 TGTTAGATAG
*
35326 ATATAATTGATTTTTTCA
1 ATATAATTGAATTTTTCA
35344 ATATAATT-AATTTTTC
1 ATATAATTGAATTTTTC
35360 TAGTTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (18 bp):
ATATAATTGAATTTTTCA
Found at i:46123 original size:23 final size:23
Alignment explanation
Indices: 46105--46158 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 23
46095 AATAAAATAT
*
46105 ATTTATTTCTTTTATTAAAAGAG
1 ATTTATTGCTTTTATTAAAAGAG
*
46128 ATTTATTGCTTTTTTATTTAAAAGAA
1 ATTTATTGC--TTTTA-TTAAAAGAG
46154 ATTTA
1 ATTTA
46159 ATAGCTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 8 0.31
25 5 0.19
26 13 0.50
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
ATTTATTGCTTTTATTAAAAGAG
Found at i:46157 original size:26 final size:27
Alignment explanation
Indices: 46112--46172 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
46102 TATATTTATT
* *
46112 TCTTTTA-TTAAAAGAGATTT-ATTGC
1 TCTTTTATTTAAAAGAAATTTAATAGC
*
46137 TTTTTTATTTAAAAGAAATTTAATAGC
1 TCTTTTATTTAAAAGAAATTTAATAGC
46164 TCTTTTATT
1 TCTTTTATT
46173 GGAATTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 6 0.20
26 12 0.40
27 12 0.40
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (27 bp):
TCTTTTATTTAAAAGAAATTTAATAGC
Found at i:51584 original size:27 final size:27
Alignment explanation
Indices: 51538--51599 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
51528 GAGATTTATT
*
51538 TCTTTTA-TTAAAAGAGATTTATTACC
1 TCTTTTATTTAAAAGAGATTTAATACC
* *
51564 TCTTTTATTTAAAA-ACTATTTAATAGC
1 TCTTTTATTTAAAAGA-GATTTAATACC
51591 TCTTTTATT
1 TCTTTTATT
51600 AGAATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.26
27 23 0.74
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.52
Consensus pattern (27 bp):
TCTTTTATTTAAAAGAGATTTAATACC
Found at i:54031 original size:34 final size:37
Alignment explanation
Indices: 53966--54035 Score: 92
Period size: 39 Copynumber: 1.9 Consensus size: 37
53956 AAAAGTCCAT
*
53966 AATTAAATAAAAACTTTATAATTGATGGTAAACAACCAA
1 AATTAAATAAAAAC--TATAATTGATAGTAAACAACCAA
54005 AATTAAATAAAAAC-ATAA-TGA-AGTAAACAAC
1 AATTAAATAAAAACTATAATTGATAGTAAACAAC
54036 TCTATCGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 9 0.30
35 3 0.10
36 4 0.13
39 14 0.47
ACGTcount: A:0.59, C:0.10, G:0.07, T:0.24
Consensus pattern (37 bp):
AATTAAATAAAAACTATAATTGATAGTAAACAACCAA
Found at i:56219 original size:29 final size:29
Alignment explanation
Indices: 56182--56252 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
56172 TTTATAATTG
56182 TAAAA-AATAATATAAAAATTTAGTATAA
1 TAAAATAATAATATAAAAATTTAGTATAA
** *
56210 TAAAATAATAA-ATTAATGATTTATTATAA
1 TAAAATAATAATA-TAAAAATTTAGTATAA
* *
56239 TACAATAAAAATAT
1 TAAAATAATAATAT
56253 TTTACCTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 6 0.17
29 28 0.80
30 1 0.03
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (29 bp):
TAAAATAATAATATAAAAATTTAGTATAA
Done.