Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000532.1 Hibiscus syriacus cultivar Beakdansim tig00001027_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: 65517
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:9903 original size:34 final size:34
Alignment explanation
Indices: 9860--9927 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
9850 TGAACACTTA
9860 GGCTTGGATGAGCATCTAAAATCTCCCGAGCCTC
1 GGCTTGGATGAGCATCTAAAATCTCCCGAGCCTC
9894 GGCTTGGATGAGCATCTAAAATCTCCCGAGCCTC
1 GGCTTGGATGAGCATCTAAAATCTCCCGAGCCTC
9928 AGCAAGGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (34 bp):
GGCTTGGATGAGCATCTAAAATCTCCCGAGCCTC
Found at i:9937 original size:34 final size:34
Alignment explanation
Indices: 9865--9938 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
9855 ACTTAGGCTT
* **
9865 GGATGAGCATCTAAAATCTCCCGAGCCTCGGCTT
1 GGATGAGCATCTAAAATCTCCCGAGCCTCAGCAA
9899 GGATGAGCATCTAAAATCTCCCGAGCCTCAGCAA
1 GGATGAGCATCTAAAATCTCCCGAGCCTCAGCAA
9933 GGATGA
1 GGATGA
9939 AGCGTAGCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.20
Consensus pattern (34 bp):
GGATGAGCATCTAAAATCTCCCGAGCCTCAGCAA
Found at i:10952 original size:20 final size:20
Alignment explanation
Indices: 10927--11025 Score: 162
Period size: 20 Copynumber: 5.0 Consensus size: 20
10917 AATTTGTAAA
*
10927 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
10947 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
10967 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
10987 TCGCAACACAGAAATCAAAT
1 TCGCAACACAGAAGTCAAAT
11007 TCGCAACACAGAAGTCAAA
1 TCGCAACACAGAAGTCAAA
11026 GCGCATTTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.47, C:0.25, G:0.11, T:0.16
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:16016 original size:20 final size:20
Alignment explanation
Indices: 15979--16017 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15969 AGATTGAGTG
* * *
15979 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
15999 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
16018 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:16215 original size:21 final size:21
Alignment explanation
Indices: 16176--16215 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16166 CAGAACCCCA
* *
16176 GGGGGGTATCGATTTCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
16197 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
16216 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.10, C:0.23, G:0.40, T:0.28
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:16224 original size:23 final size:22
Alignment explanation
Indices: 16198--16256 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
16188 TTTCCCTGTG
16198 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TCAAA
*
16221 GGGGGAATCAGTT-CCCTCAAA
1 GGGGGAATCGGTTCCCCTCAAA
*
16242 GGGGG-ATCGATTCCC
1 GGGGGAATCGGTTCCC
16257 TCTGCACCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 5 0.16
21 12 0.38
22 3 0.09
23 12 0.38
ACGTcount: A:0.22, C:0.25, G:0.32, T:0.20
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCTCAAA
Found at i:16242 original size:21 final size:23
Alignment explanation
Indices: 16198--16247 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
16188 TTTCCCTGTG
*
16198 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCAGTTCCCCTTCAAA
16221 GGGGGAATCAGTT-CCC-TCAAA
1 GGGGGAATCAGTTCCCCTTCAAA
16242 GGGGGA
1 GGGGGA
16248 TCGATTCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 11 0.42
22 3 0.12
23 12 0.46
ACGTcount: A:0.24, C:0.22, G:0.36, T:0.18
Consensus pattern (23 bp):
GGGGGAATCAGTTCCCCTTCAAA
Found at i:20116 original size:20 final size:20
Alignment explanation
Indices: 20074--20116 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
20064 TTGCTTTCAT
* *
20074 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
20094 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
20114 TTT
1 TTT
20117 CTCAAAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:22987 original size:21 final size:21
Alignment explanation
Indices: 22963--23004 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22953 CGCTATGTGG
* *
22963 TGAGGTATCTACTTTACGTGA
1 TGAGGTAGCTACTCTACGTGA
*
22984 TGAGGTAGCTGCTCTACGTGA
1 TGAGGTAGCTACTCTACGTGA
23005 GATTGTTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (21 bp):
TGAGGTAGCTACTCTACGTGA
Found at i:23110 original size:4 final size:4
Alignment explanation
Indices: 23101--23142 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
23091 TTTTTCGGCA
* *
23101 TTAT TTAT TTAT TTAT TTAT TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
23143 TCAGCAGCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:23333 original size:21 final size:21
Alignment explanation
Indices: 23309--23389 Score: 108
Period size: 21 Copynumber: 3.9 Consensus size: 21
23299 GGCGTTTTCT
*
23309 ATCGTTCAAAAGGCCCCTGTC
1 ATCGTTCAAGAGGCCCCTGTC
**
23330 ATCGTTCAAGAGGCCCCTCCC
1 ATCGTTCAAGAGGCCCCTGTC
*
23351 ACCGTTCAAGAGGCCCCTGTC
1 ATCGTTCAAGAGGCCCCTGTC
* *
23372 ATCGTTCAATAGGTCCCT
1 ATCGTTCAAGAGGCCCCT
23390 CCCACCATTC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTGTC
Found at i:23400 original size:21 final size:21
Alignment explanation
Indices: 23311--23404 Score: 98
Period size: 21 Copynumber: 4.5 Consensus size: 21
23301 CGTTTTCTAT
* ** *
23311 CGTTCAAAAGGCCCCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
23332 CGTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
** *
23353 CGTTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
* *
23374 CGTTCAATAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
*
23395 CATTCAAGAG
1 CGTTCAAGAG
23405 CTCGATTCAC
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:23402 original size:42 final size:42
Alignment explanation
Indices: 23313--23404 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
23303 TTTTCTATCG
* *
23313 TTCAAAAGGCCCCTGTCATCGTTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTGTCATCGTTCAAGAGGCCCCTCCCACCA
* *
23355 TTCAAGAGGCCCCTGTCATCGTTCAATAGGTCCCTCCCACCA
1 TTCAAGAGGCCCCTGTCATCGTTCAAGAGGCCCCTCCCACCA
23397 TTCAAGAG
1 TTCAAGAG
23405 CTCGATTCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCCCTGTCATCGTTCAAGAGGCCCCTCCCACCA
Found at i:24818 original size:64 final size:64
Alignment explanation
Indices: 24707--24862 Score: 258
Period size: 64 Copynumber: 2.4 Consensus size: 64
24697 TTAATTGAAT
*
24707 TTTACATTGATTTGTAAAAGGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTT
1 TTTA-ATTGATTTGTAAAA-GTTGATTTGTTTAATTGAAGAGGAAATAAGAATTATTTTTTGCTT
24772 G
64 G
* * *
24773 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGAAGTGTAAATAAGAATTATTTTTTTCTTG
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGAAGAGGAAATAAGAATTATTTTTTGCTTG
24837 TTTAATTGATTTGTAAAAGTTGATTT
1 TTTAATTGATTTGTAAAAGTTGATTT
24863 ATTGTTTATT
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
64 68 0.79
65 14 0.16
66 4 0.05
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (64 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGAAGAGGAAATAAGAATTATTTTTTGCTTG
Found at i:24992 original size:20 final size:20
Alignment explanation
Indices: 24967--25018 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
24957 TCGTTACGAT
24967 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACACAAA
* *
24987 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACACAAA
25007 AGTCAAATTCGC
1 AGTCAAATTCGC
25019 GTTGCGGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (20 bp):
AGTCAAATTCGCAACACAAA
Found at i:25112 original size:20 final size:20
Alignment explanation
Indices: 25087--25125 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25077 CGCGATTATC
*
25087 GCGTTGCGAATTTGACTTTT
1 GCGTTGCGAATTTAACTTTT
25107 GCGTTGCGAATTTAACTTT
1 GCGTTGCGAATTTAACTTT
25126 CACATCAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (20 bp):
GCGTTGCGAATTTAACTTTT
Found at i:25924 original size:20 final size:19
Alignment explanation
Indices: 25840--25928 Score: 74
Period size: 20 Copynumber: 4.6 Consensus size: 19
25830 AACTAAAACC
*
25840 TGTTGCGAAATTAAATTCG
1 TGTTGCGAATTTAAATTCG
* *
25859 TG-TGCGAATTCGAAAATCG
1 TGTTGCGAATT-TAAATTCG
* *
25878 AGTTGTGAATTTGAAATTC-
1 TGTTGCGAATTT-AAATTCG
**
25897 AATTGCGAATTTAAATTCAG
1 TGTTGCGAATTTAAATTC-G
25917 TGTTGCGAATTT
1 TGTTGCGAATTT
25929 GGAAAAAGCG
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
18 13 0.24
19 19 0.35
20 22 0.41
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.37
Consensus pattern (19 bp):
TGTTGCGAATTTAAATTCG
Found at i:25988 original size:20 final size:20
Alignment explanation
Indices: 25963--26000 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
25953 TCTTTGTTCT
25963 GATTTACAAATTCGCGTTAC
1 GATTTACAAATTCGCGTTAC
*
25983 GATTTACATATTCGCGTT
1 GATTTACAAATTCGCGTT
26001 GCGAATTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (20 bp):
GATTTACAAATTCGCGTTAC
Found at i:26082 original size:20 final size:20
Alignment explanation
Indices: 26059--26105 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
26049 TGGAAACTGG
*
26059 GTTGCGAAATTGGAGTTCGC
1 GTTGCGAAATTGGAGATCGC
*
26079 GTTGCG-AATTTGAGATCGC
1 GTTGCGAAATTGGAGATCGC
*
26098 GTTACGAA
1 GTTGCGAA
26106 CGTGATGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (20 bp):
GTTGCGAAATTGGAGATCGC
Found at i:39435 original size:174 final size:174
Alignment explanation
Indices: 39134--39481 Score: 660
Period size: 174 Copynumber: 2.0 Consensus size: 174
39124 TGGCAGATTT
39134 GGGTCGAACTCCTCCGTATGTGGAAAGTTAATTCAGTTCTCCCTAATAATCCGAAAGGCTTCTTG
1 GGGTCGAACTCCTCCGTATGTGGAAAGTTAATTCAGTTCTCCCTAATAATCCGAAAGGCTTCTTG
* *
39199 CTTTCTTGGCCGCAATTAAGACCAAACTCGTGTATTTGGAGATTTATTCCAGGAGTTGTTTTGTG
66 CTTTCTTGGCCGCAATTAAGACCAAACTCATGTATTTGGAGATTTATTCCAGGAGCTGTTTTGTG
39264 GTCTGTCTGGCTGTGTAGGAACCAGATTGTATTTAAGAAAGGCA
131 GTCTGTCTGGCTGTGTAGGAACCAGATTGTATTTAAGAAAGGCA
* *
39308 GGGTTGAACTCCTCCGTATGTGGAAAGTTAATTCAGTTCTCCCTAATAATTCGAAAGGCTTCTTG
1 GGGTCGAACTCCTCCGTATGTGGAAAGTTAATTCAGTTCTCCCTAATAATCCGAAAGGCTTCTTG
39373 CTTTCTTGGCCGCAATTAAGACCAAACTCATGTATTTGGAGATTTATTCCAGGAGCTGTTTTGTG
66 CTTTCTTGGCCGCAATTAAGACCAAACTCATGTATTTGGAGATTTATTCCAGGAGCTGTTTTGTG
39438 GTCTGTCTGGCTGTGTAGGAACCAGATTGTATTTAAGAAAGGCA
131 GTCTGTCTGGCTGTGTAGGAACCAGATTGTATTTAAGAAAGGCA
39482 AGTTGGATAG
Statistics
Matches: 170, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 170 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (174 bp):
GGGTCGAACTCCTCCGTATGTGGAAAGTTAATTCAGTTCTCCCTAATAATCCGAAAGGCTTCTTG
CTTTCTTGGCCGCAATTAAGACCAAACTCATGTATTTGGAGATTTATTCCAGGAGCTGTTTTGTG
GTCTGTCTGGCTGTGTAGGAACCAGATTGTATTTAAGAAAGGCA
Found at i:45510 original size:3 final size:3
Alignment explanation
Indices: 45493--45528 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
45483 CAGTGGCAGC
*
45493 AAG AGG AAG -AG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
45529 GGCGGTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:47682 original size:85 final size:85
Alignment explanation
Indices: 47533--47721 Score: 263
Period size: 85 Copynumber: 2.2 Consensus size: 85
47523 ATCTCCCAGC
*
47533 TTTACAGCATAGCTCAAGGAGAGAAGGGCTATATGTCAACCAAGACCTTCGAGTTCAATTACATT
1 TTTACAGCATAGCTCAAGGAGAGAAGGGCTATATGTCAACAAAGACCTTCGAGTTCAATTACATT
**
47598 CAGCTCAAAGGCATATCAAA
66 CAAATCAAAGGCATATCAAA
* * * * * **
47618 TTTGCGGCATAGCTCAAGGTGAGAAGGGTTATCA-GTCAGCAAAGACCTTCGAGTTTGATTACAT
1 TTTACAGCATAGCTCAAGGAGAGAAGGGCTAT-ATGTCAACAAAGACCTTCGAGTTCAATTACAT
47682 TCAAATCAAAGGCATATCAAA
65 TCAAATCAAAGGCATATCAAA
*
47703 TTTACAGCATAACTCAAGG
1 TTTACAGCATAGCTCAAGG
47722 CGACCAAAAA
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 89 0.99
86 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (85 bp):
TTTACAGCATAGCTCAAGGAGAGAAGGGCTATATGTCAACAAAGACCTTCGAGTTCAATTACATT
CAAATCAAAGGCATATCAAA
Found at i:49626 original size:85 final size:84
Alignment explanation
Indices: 49483--49725 Score: 378
Period size: 85 Copynumber: 2.9 Consensus size: 84
49473 GAAGTTATCA
*
49483 AAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGCTCAAATGCATATCAAATTT
1 AAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAA-GCATATCAAATTT
49548 ACATCATAACTCAAGGCGAG
65 ACATCATAACTCAAGGCGAG
*
49568 AAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTTAAAGACATATCAAATTT
1 AAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAG-CATATCAAATTT
*
49633 ACATCATAATTCAAGGCGAG
65 ACATCATAACTCAAGGCGAG
* * * * *
49653 AAGGGTTATCTATCAACAAATACCTTCGAGTTCGATTCCATTCAGCTCAAGGGCATGTCAAATTT
1 AAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAA-AGCATATCAAATTT
*
49718 ACAGCATA
65 ACATCATA
49726 GCTTAAGTCG
Statistics
Matches: 146, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
84 1 0.01
85 144 0.99
86 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (84 bp):
AAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGCATATCAAATTTA
CATCATAACTCAAGGCGAG
Found at i:49748 original size:85 final size:84
Alignment explanation
Indices: 49483--49786 Score: 367
Period size: 85 Copynumber: 3.6 Consensus size: 84
49473 GAAGTTATCA
* *
49483 AAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGCTCAAATGCATATCAAATTT
1 AAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTT
*
49548 ACATCATAACTCAAGGCGAG
66 ACATCAT-ACTTAAGGCGAG
* *
49568 AAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTTAAAGACATATCAAATTT
1 AAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTT
*
49633 ACATCATAATTCAAGGCGAG
66 ACATCATACTT-AAGGCGAG
* * * * *
49653 AAGGGTTATCTATCAACAAATACCTTCGAGTTCGATTCCATTCAGCTCAAGGGCATGTCAAATTT
1 AAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTT
* * *
49718 ACAGCATAGCTTAAGTCGAT
66 ACATCATA-CTTAAGGCGAG
** * * * * *
49738 AAAAGCTATCTGTCAATAAAAAACTATCGAGTTTGATT-CTATTCAGCTC
1 AAGGGTTATCTGTCAACAAAGACCT-TCGAGTTCGATTAC-ATTCAGCTC
49787 GATGACACAT
Statistics
Matches: 190, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
84 2 0.01
85 166 0.87
86 22 0.12
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (84 bp):
AAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTT
ACATCATACTTAAGGCGAG
Found at i:51275 original size:85 final size:85
Alignment explanation
Indices: 50884--51268 Score: 432
Period size: 85 Copynumber: 4.5 Consensus size: 85
50874 ACATGTCATC
* * * * * * * *
50884 GAGCTGAATGGAATCGAACTCAATAGGTTTTTATTGACATATAA-CTTTCCTTGACTTAAGTTAT
1 GAGCTGAATGAAATCGAACTCGA-AGGTCTTTGTTGACATATAACCCTT-CTCGCCTTGAGTTAT
* * *
50948 ACTGTAAATTTGACATGCCCTT
64 GCTATAAATTTGATATGCCCTT
* *
50970 GAGCTGAATGAAATCGAACTCGAATGTATTTGTTGACATATAACCCTTCTCGCCTTGAGTTAT-C
1 GAGCTGAATGAAATCGAACTCGAAGGTCTTTGTTGACATATAACCCTTCTCGCCTTGAGTTATGC
*
51034 ATATAAATTTGATATGCCTTT
66 -TATAAATTTGATATGCCCTT
* * * * ** * *
51055 GAGTTGAATGTAATCGAACTCGAAGGTCTTTGCTGACAGATTGCCCTTCTTGCCTTGAGCTATGC
1 GAGCTGAATGAAATCGAACTCGAAGGTCTTTGTTGACATATAACCCTTCTCGCCTTGAGTTATGC
*
51120 CATAAATTTGATATGCCCTT
66 TATAAATTTGATATGCCCTT
* * * *
51140 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTATCGCCTTGAGTTATGT
1 GAGCTGAATGAAATCGAACTCGAAGGTCTTTGTTGACATATAACCCTTCTCGCCTTGAGTTATGC
* *
51205 TGTAAATTTGATATGCCTTT
66 TATAAATTTGATATGCCCTT
* * * *
51225 GAGCTGAACGAAATCGAACTCAAAAGTCTTCGTTGACATATAAC
1 GAGCTGAATGAAATCGAACTCGAAGGTCTTTGTTGACATATAAC
51269 TTTTATCAAC
Statistics
Matches: 255, Mismatches: 41, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
84 1 0.00
85 229 0.90
86 25 0.10
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGAAATCGAACTCGAAGGTCTTTGTTGACATATAACCCTTCTCGCCTTGAGTTATGC
TATAAATTTGATATGCCCTT
Found at i:52543 original size:38 final size:42
Alignment explanation
Indices: 52467--52545 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 42
52457 GCTTTTTTCC
*
52467 TTTGTTTTTTGTTTCTCTTTTTTATTTTCTCTTTTCTTTTTA
1 TTTGTTTTTTGTTTCTCTTTTTTATCTTCTCTTTTCTTTTTA
52509 TTTG-TTTTTG-TT-TCTTTTTTA-CTTCT-TTTCTCTTTTT
1 TTTGTTTTTTGTTTCTCTTTTTTATCTTCTCTTT-TCTTTTT
52546 GTTCTGATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
37 3 0.09
38 11 0.31
39 9 0.26
40 2 0.06
41 6 0.17
42 4 0.11
ACGTcount: A:0.04, C:0.13, G:0.05, T:0.78
Consensus pattern (42 bp):
TTTGTTTTTTGTTTCTCTTTTTTATCTTCTCTTTTCTTTTTA
Found at i:52730 original size:2 final size:2
Alignment explanation
Indices: 52723--52778 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
52713 ATAACAAGGG
52723 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52765 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
52779 GGATAAATAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54706 original size:3 final size:3
Alignment explanation
Indices: 54698--54727 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
54688 TCCAGATTTC
54698 TCT TCT TCT TCT TCT TCT TCTT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TC-T TCT TCT TC
54728 CCCGTGAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:59740 original size:31 final size:30
Alignment explanation
Indices: 59703--59760 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
59693 ATAAGATATG
59703 TGTGATAAA-GTGATGGAACATGATATGTTTA
1 TGTGATAAAGGT-ATGGAA-ATGATATGTTTA
*
59734 TGTGATAAAGGTATGGAAATTATATGT
1 TGTGATAAAGGTATGGAAATGATATGT
59761 CTATACAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 15 0.60
32 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (30 bp):
TGTGATAAAGGTATGGAAATGATATGTTTA
Found at i:60051 original size:23 final size:23
Alignment explanation
Indices: 59983--60043 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
59973 CAATCTTATA
* *
59983 TGGCACTACGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
60006 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
60029 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
60044 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:62019 original size:2 final size:2
Alignment explanation
Indices: 62012--62041 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
62002 AAAAGAAAGA
62012 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62042 ATAAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:62436 original size:214 final size:214
Alignment explanation
Indices: 62067--62496 Score: 724
Period size: 214 Copynumber: 2.0 Consensus size: 214
62057 AAAATGTAAT
* * * *
62067 GATCAAAATAGTAAAAACAAAAGGTTAAAGGACTAAAATATCAAAAAGAAATTTAAGGGTTTAAA
1 GATCAAAATAGCAAAAACAAAAGGTTAAAGGACTAAAATATAAAAAAGAAATTTAAGGCTCTAAA
*
62132 CTGGTATTAACAGAAACTAAAATGACTAAACAATAAATACAAATAAATTAGAGCCCAATAATCAA
66 CTGGTATTAACAGAAACTAAAATGACTAAACAATAAATACAAATAAATCAGAGCCCAATAATCAA
*
62197 TTAAAATAAATACAGGGACCAGAAACTAAAATAACCCAAAAATAACATTTACAGATTAAAATAAA
131 TTAAAATAAATACAGGAACCAGAAACTAAAATAACCCAAAAATAACATTTACAGATTAAAATAAA
62262 ATAAACAAGAAACATGGAG
196 ATAAACAAGAAACATGGAG
62281 GATCAAAATAGCAAAAACAAAAGGTTAAAGGACTAAAA-ATTAAAAATAGAAATTTAAGGCTCTA
1 GATCAAAATAGCAAAAACAAAAGGTTAAAGGACTAAAATA-TAAAAA-AGAAATTTAAGGCTCTA
*
62345 AACTGGTA-TAACA-AAACTAAAATGACTAAACAATAATTGTA-AAATAAATCAGAGCCCAATAA
64 AACTGGTATTAACAGAAACTAAAATGACTAAACAATAA--ATACAAATAAATCAGAGCCCAATAA
*
62407 TCAATTAAAATAAATATAGGAACCAGAAACTAAAATAACCCAAAAATAACATTTACAGATTAAAA
127 TCAATTAAAATAAATACAGGAACCAGAAACTAAAATAACCCAAAAATAACATTTACAGATTAAAA
62472 TAAAATAAACAAGAAACATGGAG
192 TAAAATAAACAAGAAACATGGAG
62495 GA
1 GA
62497 CTAAACAATA
Statistics
Matches: 204, Mismatches: 8, Indels: 8
0.93 0.04 0.04
Matches are distributed among these distances:
213 24 0.12
214 155 0.76
215 25 0.12
ACGTcount: A:0.57, C:0.12, G:0.11, T:0.20
Consensus pattern (214 bp):
GATCAAAATAGCAAAAACAAAAGGTTAAAGGACTAAAATATAAAAAAGAAATTTAAGGCTCTAAA
CTGGTATTAACAGAAACTAAAATGACTAAACAATAAATACAAATAAATCAGAGCCCAATAATCAA
TTAAAATAAATACAGGAACCAGAAACTAAAATAACCCAAAAATAACATTTACAGATTAAAATAAA
ATAAACAAGAAACATGGAG
Found at i:65219 original size:29 final size:28
Alignment explanation
Indices: 65142--65219 Score: 70
Period size: 30 Copynumber: 2.7 Consensus size: 28
65132 GTTAATACCA
* *
65142 ATTTTGA-CCCTTAAATTTCTGTTTTGAT
1 ATTTTGATCCTTTACATTT-TGTTTTGAT
* *
65170 ATTTT-AGTCCTTTAACCTTTTGTTTTTGCT
1 ATTTTGA-TCCTTT-ACATTTTG-TTTTGAT
65200 ATTTTGATCCTTTACATTTT
1 ATTTTGATCCTTTACATTTT
65220 TATTTATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
27 1 0.03
28 5 0.12
29 12 0.30
30 21 0.52
31 1 0.03
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.58
Consensus pattern (28 bp):
ATTTTGATCCTTTACATTTTGTTTTGAT
Found at i:65378 original size:26 final size:24
Alignment explanation
Indices: 65342--65392 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
65332 AGACTGAACA
*
65342 TTTTCTTCATTTTTATTTTTATTT
1 TTTTCTTCATTTTTATTGTTATTT
65366 TTTTCTTAACATTTTTATTGTTATTT
1 TTTTCTT--CATTTTTATTGTTATTT
65392 T
1 T
65393 CTCAATTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.29
26 17 0.71
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTCTTCATTTTTATTGTTATTT
Done.