Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006853.1 Hibiscus syriacus cultivar Beakdansim tig00017435_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: 95886
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:18280 original size:2 final size:2
Alignment explanation
Indices: 18275--18305 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18265 GTATGTTAAC
*
18275 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18306 TATGGGGGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:18548 original size:33 final size:33
Alignment explanation
Indices: 18497--18574 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
18487 ACCATCCGAT
* * * *
18497 CGAGGCCATCCGACCGAGCTATGCGAGGGCATC
1 CGAGGGCAACCGAGCGAGCTATGCGAGGGAATC
18530 CGAGGGCAACCGAGCGAGCTATGCGAGGGAATC
1 CGAGGGCAACCGAGCGAGCTATGCGAGGGAATC
18563 CGA--GCAACCGAG
1 CGAGGGCAACCGAG
18575 TGCACTCCGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 9 0.22
33 32 0.78
ACGTcount: A:0.26, C:0.29, G:0.36, T:0.09
Consensus pattern (33 bp):
CGAGGGCAACCGAGCGAGCTATGCGAGGGAATC
Found at i:18659 original size:24 final size:22
Alignment explanation
Indices: 18631--18705 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 22
18621 CATAGCTCGG
18631 TCGGATGGCCTCGATCGGATGGTC
1 TCGGATGG-CTCG-TCGGATGGTC
* *
18655 TCGGATGGC-C-TCGGATGCTT
1 TCGGATGGCTCGTCGGATGGTC
*
18675 TCGGATGGTCTCGGTCAGATGGTC
1 TCGGATGG-CTC-GTCGGATGGTC
18699 TCGGATG
1 TCGGATG
18706 CCCAGCGTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 16 0.38
21 1 0.02
22 2 0.05
23 1 0.02
24 22 0.52
ACGTcount: A:0.12, C:0.23, G:0.37, T:0.28
Consensus pattern (22 bp):
TCGGATGGCTCGTCGGATGGTC
Found at i:18705 original size:10 final size:10
Alignment explanation
Indices: 18645--18688 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
18635 ATGGCCTCGA
18645 TCGGATGGTC
1 TCGGATGGTC
*
18655 TCGGATGGCC
1 TCGGATGGTC
* *
18665 TCGGATGCTT
1 TCGGATGGTC
18675 TCGGATGGTC
1 TCGGATGGTC
18685 TCGG
1 TCGG
18689 TCAGATGGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.09, C:0.23, G:0.39, T:0.30
Consensus pattern (10 bp):
TCGGATGGTC
Found at i:18808 original size:29 final size:29
Alignment explanation
Indices: 18768--18850 Score: 166
Period size: 29 Copynumber: 2.9 Consensus size: 29
18758 GTGACCTACC
18768 TAGGTCGCTGGGCGTGCATGGCGACCTGG
1 TAGGTCGCTGGGCGTGCATGGCGACCTGG
18797 TAGGTCGCTGGGCGTGCATGGCGACCTGG
1 TAGGTCGCTGGGCGTGCATGGCGACCTGG
18826 TAGGTCGCTGGGCGTGCATGGCGAC
1 TAGGTCGCTGGGCGTGCATGGCGAC
18851 TTATATGGGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.11, C:0.24, G:0.45, T:0.20
Consensus pattern (29 bp):
TAGGTCGCTGGGCGTGCATGGCGACCTGG
Found at i:30388 original size:2 final size:2
Alignment explanation
Indices: 30381--30419 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
30371 ACTCGACATG
30381 AT AT AT AT AT AT AT A- 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
30420 TAAGAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42358 original size:53 final size:53
Alignment explanation
Indices: 42273--42419 Score: 251
Period size: 53 Copynumber: 2.8 Consensus size: 53
42263 TGATGGGTCT
* * *
42273 GCTCCCTCTTG-TTCAGGGAGTAGAATTTGAATAATCTTCTGCTTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCCTACGGGTTC
42325 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCCTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCCTACGGGTTC
*
42378 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTG
42420 GTGTGATTCT
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 11 0.12
53 79 0.88
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (53 bp):
GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCCTACGGGTTC
Found at i:42846 original size:41 final size:41
Alignment explanation
Indices: 42785--42877 Score: 111
Period size: 40 Copynumber: 2.3 Consensus size: 41
42775 CACTATTCCG
* *
42785 AAAAGGCTTA-AAATGGCCCGAAGGACTTATCATC-TCA-CTC
1 AAAAGACTTACAAATGACCCGAAGGA-TT-TCATCATCAGCTC
42825 AAAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTC
1 AAAAGACTTACAAATGACCCGAAGGATTTCATCATCA-GCTC
*
42867 GAAAGACTTAC
1 AAAAGACTTAC
42878 TGATGAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
39 5 0.11
40 14 0.30
41 14 0.30
42 13 0.28
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.23
Consensus pattern (41 bp):
AAAAGACTTACAAATGACCCGAAGGATTTCATCATCAGCTC
Found at i:42872 original size:42 final size:42
Alignment explanation
Indices: 42786--42999 Score: 146
Period size: 42 Copynumber: 5.2 Consensus size: 42
42776 ACTATTCCGA
* * *
42786 AAAGGCTTA-AAATGGCCCGAAGGACTTATCATC-TCA--CTCA
1 AAAGACTTACAAATGACCCGAAGGA-TT-TCATCATCATGCTCG
42826 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
1 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
* ** * * *
42868 AAAGACTTAC---TGA--TGAATTTACTTCA-CTACTCTTCGGT-G
1 AAAGACTTACAAATGACCCGAA-GGATTTCATC-A-TCAT-GCTCG
* * * *
42907 -AAGGCTTACAAATTATCCGAAGGATTTAATCATCATGCTCG
1 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
** *
42948 AAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCG
1 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
42990 AAAGACTTAC
1 AAAGACTTAC
43000 TGATGGACCG
Statistics
Matches: 133, Mismatches: 25, Indels: 30
0.71 0.13 0.16
Matches are distributed among these distances:
37 4 0.03
38 14 0.11
39 12 0.09
40 17 0.13
41 20 0.15
42 62 0.47
43 4 0.03
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (42 bp):
AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
Found at i:43000 original size:42 final size:42
Alignment explanation
Indices: 42923--43014 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
42913 TACAAATTAT
*
42923 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
1 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGA
*
42965 CCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGA
1 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGA
43007 CCGAAGGA
1 CCGAAGGA
43015 CTTATAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (42 bp):
CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGA
Found at i:43182 original size:41 final size:41
Alignment explanation
Indices: 43127--43233 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 41
43117 CCCGAAGGTT
* * * *
43127 TTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
* * *
43168 TTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGAC
*
43210 TTACTGATGGCCCGAAGGACTTAT
1 TTACAGATGGCCCGAAGGACTTAT
43234 AAATTGTGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 20 0.37
42 34 0.63
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.25
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
Found at i:43215 original size:214 final size:214
Alignment explanation
Indices: 42923--43564 Score: 1070
Period size: 214 Copynumber: 3.0 Consensus size: 214
42913 TACAAATTAT
* * * * * * * *
42923 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCT
1 CCGAAGGACTT-ATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCT
* * *
42988 CGAAAGACTTACTGATGGACCGAAGGACTTATAAATTGTGAAATTTTGAAAATCGCATTATTTGT
65 CGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGT
* * ** *
43053 TTTCAAAAATTTCATATTCTCAAAACATCGTTTTTCATTTTCAAATTCTTTTGAAAACATCTTAC
130 TTTCAAAAATTTCATCTTCTTAAAACATTATTTTTTATTTTCAAATTCTTTTGAAAACATCTTAC
43118 CCGAAGGTTTTACGGATGGC
195 CCGAAGGTTTTACGGATGGC
43138 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTC
1 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTC
*
43203 GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTT
66 GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTT
*
43268 TTCAAAAATTCCATCTTCTTAAAACATTATTTTTTATTTTCAAATTCTTTTGAAAACATCTTACC
131 TTCAAAAATTTCATCTTCTTAAAACATTATTTTTTATTTTCAAATTCTTTTGAAAACATCTTACC
43333 CGAAGGTTTTACGGATGGC
196 CGAAGGTTTTACGGATGGC
*
43352 CCGAAGGACTTATCATCTTGCTCTAAAGGCTCACAGATGACCCGAAGGATTTAAGCATCATGCTC
1 CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTC
43417 GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTT
66 GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTT
43482 TTCAAAAA-TTCTATCTTCTTAAAACATTATTTTTTATTTTCAAATTCTTTTGAAAACATCTTAC
131 TTCAAAAATTTC-ATCTTCTTAAAACATTATTTTTTATTTTCAAATTCTTTTGAAAACATCTTAC
* *
43546 CCGAAGGTCTTATGGATGG
195 CCGAAGGTTTTACGGATGG
43565 TTTGCTTCAC
Statistics
Matches: 403, Mismatches: 23, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
213 2 0.00
214 391 0.97
215 10 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (214 bp):
CCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTC
GAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTT
TTCAAAAATTTCATCTTCTTAAAACATTATTTTTTATTTTCAAATTCTTTTGAAAACATCTTACC
CGAAGGTTTTACGGATGGC
Found at i:43396 original size:41 final size:41
Alignment explanation
Indices: 43346--43447 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
43336 AGGTTTTACG
* * *
43346 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTCACA
1 GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTCACA
* * * * *
43387 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTCACA
43429 GATGGCCCGAAGGACTTAT
1 GATGGCCCGAAGGACTTAT
43448 AAATTGTGAA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTCACA
Found at i:46002 original size:720 final size:720
Alignment explanation
Indices: 44624--46063 Score: 2880
Period size: 720 Copynumber: 2.0 Consensus size: 720
44614 ATTGACAACG
44624 TCATAAGGAAATTTTATAAGTTTCATTCTTCATTCATTCTGTTCTCTTGGACCATCTACTTCAAG
1 TCATAAGGAAATTTTATAAGTTTCATTCTTCATTCATTCTGTTCTCTTGGACCATCTACTTCAAG
44689 ATCGTGGAATACTTCATGTTCTGGCATTGCTTATTCCTTTTCTCCAATAGAGGCATAATGAGTCT
66 ATCGTGGAATACTTCATGTTCTGGCATTGCTTATTCCTTTTCTCCAATAGAGGCATAATGAGTCT
44754 CACAAGCTTCAAGGACCTTTCACACTTGAAACTGTCATGTTTGAAAATGTTTTTCCCTTTTCTCT
131 CACAAGCTTCAAGGACCTTTCACACTTGAAACTGTCATGTTTGAAAATGTTTTTCCCTTTTCTCT
44819 TATTATAGGGATCAAAGAATGAAAGAATTTTATAAAATATTGCCCCTTAATTCAGGCTCACAATC
196 TATTATAGGGATCAAAGAATGAAAGAATTTTATAAAATATTGCCCCTTAATTCAGGCTCACAATC
44884 AAATCAAATCATAAACATGAGTTCAAAGAATATCAAAAGAATCAATAACTATTTAATTTTTCAGA
261 AAATCAAATCATAAACATGAGTTCAAAGAATATCAAAAGAATCAATAACTATTTAATTTTTCAGA
44949 GTTATAACTCTTTGACAAGTGTCAAAATTGATGAGTTGGCTTCAGGTTGTCTTCCTATTTTTTAA
326 GTTATAACTCTTTGACAAGTGTCAAAATTGATGAGTTGGCTTCAGGTTGTCTTCCTATTTTTTAA
45014 GGTTTCGGCCAACAAACTTACATTTCTTTCTCGGTCCTTGTGAACATCACAACATACCCCTCCTT
391 GGTTTCGGCCAACAAACTTACATTTCTTTCTCGGTCCTTGTGAACATCACAACATACCCCTCCTT
45079 CTGGCTTGGTATTTTTAATCGGATACGGACAAAATGGCGCAACTAGCATAATCAATTACTAGATT
456 CTGGCTTGGTATTTTTAATCGGATACGGACAAAATGGCGCAACTAGCATAATCAATTACTAGATT
45144 TTCTAGAAAACTTCTATTTCAGTTCTCTACAATCTTCCATTTGTTCAAGCTTCATAGACTCCTCT
521 TTCTAGAAAACTTCTATTTCAGTTCTCTACAATCTTCCATTTGTTCAAGCTTCATAGACTCCTCT
45209 AACAAAGGCAGTGCAGAAATATCGGTCTAAAAATGAAATTTCTGAGTGCTCGTGTGAAATTTACT
586 AACAAAGGCAGTGCAGAAATATCGGTCTAAAAATGAAATTTCTGAGTGCTCGTGTGAAATTTACT
45274 ATAACAGGTGTTCCTTAACTCCCTTAGTCCATCTTTACCGAAACTCCTTATTCATAAAATTTGCC
651 ATAACAGGTGTTCCTTAACTCCCTTAGTCCATCTTTACCGAAACTCCTTATTCATAAAATTTGCC
45339 ATTGT
716 ATTGT
45344 TCATAAGGAAATTTTATAAGTTTCATTCTTCATTCATTCTGTTCTCTTGGACCATCTACTTCAAG
1 TCATAAGGAAATTTTATAAGTTTCATTCTTCATTCATTCTGTTCTCTTGGACCATCTACTTCAAG
45409 ATCGTGGAATACTTCATGTTCTGGCATTGCTTATTCCTTTTCTCCAATAGAGGCATAATGAGTCT
66 ATCGTGGAATACTTCATGTTCTGGCATTGCTTATTCCTTTTCTCCAATAGAGGCATAATGAGTCT
45474 CACAAGCTTCAAGGACCTTTCACACTTGAAACTGTCATGTTTGAAAATGTTTTTCCCTTTTCTCT
131 CACAAGCTTCAAGGACCTTTCACACTTGAAACTGTCATGTTTGAAAATGTTTTTCCCTTTTCTCT
45539 TATTATAGGGATCAAAGAATGAAAGAATTTTATAAAATATTGCCCCTTAATTCAGGCTCACAATC
196 TATTATAGGGATCAAAGAATGAAAGAATTTTATAAAATATTGCCCCTTAATTCAGGCTCACAATC
45604 AAATCAAATCATAAACATGAGTTCAAAGAATATCAAAAGAATCAATAACTATTTAATTTTTCAGA
261 AAATCAAATCATAAACATGAGTTCAAAGAATATCAAAAGAATCAATAACTATTTAATTTTTCAGA
45669 GTTATAACTCTTTGACAAGTGTCAAAATTGATGAGTTGGCTTCAGGTTGTCTTCCTATTTTTTAA
326 GTTATAACTCTTTGACAAGTGTCAAAATTGATGAGTTGGCTTCAGGTTGTCTTCCTATTTTTTAA
45734 GGTTTCGGCCAACAAACTTACATTTCTTTCTCGGTCCTTGTGAACATCACAACATACCCCTCCTT
391 GGTTTCGGCCAACAAACTTACATTTCTTTCTCGGTCCTTGTGAACATCACAACATACCCCTCCTT
45799 CTGGCTTGGTATTTTTAATCGGATACGGACAAAATGGCGCAACTAGCATAATCAATTACTAGATT
456 CTGGCTTGGTATTTTTAATCGGATACGGACAAAATGGCGCAACTAGCATAATCAATTACTAGATT
45864 TTCTAGAAAACTTCTATTTCAGTTCTCTACAATCTTCCATTTGTTCAAGCTTCATAGACTCCTCT
521 TTCTAGAAAACTTCTATTTCAGTTCTCTACAATCTTCCATTTGTTCAAGCTTCATAGACTCCTCT
45929 AACAAAGGCAGTGCAGAAATATCGGTCTAAAAATGAAATTTCTGAGTGCTCGTGTGAAATTTACT
586 AACAAAGGCAGTGCAGAAATATCGGTCTAAAAATGAAATTTCTGAGTGCTCGTGTGAAATTTACT
45994 ATAACAGGTGTTCCTTAACTCCCTTAGTCCATCTTTACCGAAACTCCTTATTCATAAAATTTGCC
651 ATAACAGGTGTTCCTTAACTCCCTTAGTCCATCTTTACCGAAACTCCTTATTCATAAAATTTGCC
46059 ATTGT
716 ATTGT
46064 CTGGCTAGCT
Statistics
Matches: 720, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
720 720 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (720 bp):
TCATAAGGAAATTTTATAAGTTTCATTCTTCATTCATTCTGTTCTCTTGGACCATCTACTTCAAG
ATCGTGGAATACTTCATGTTCTGGCATTGCTTATTCCTTTTCTCCAATAGAGGCATAATGAGTCT
CACAAGCTTCAAGGACCTTTCACACTTGAAACTGTCATGTTTGAAAATGTTTTTCCCTTTTCTCT
TATTATAGGGATCAAAGAATGAAAGAATTTTATAAAATATTGCCCCTTAATTCAGGCTCACAATC
AAATCAAATCATAAACATGAGTTCAAAGAATATCAAAAGAATCAATAACTATTTAATTTTTCAGA
GTTATAACTCTTTGACAAGTGTCAAAATTGATGAGTTGGCTTCAGGTTGTCTTCCTATTTTTTAA
GGTTTCGGCCAACAAACTTACATTTCTTTCTCGGTCCTTGTGAACATCACAACATACCCCTCCTT
CTGGCTTGGTATTTTTAATCGGATACGGACAAAATGGCGCAACTAGCATAATCAATTACTAGATT
TTCTAGAAAACTTCTATTTCAGTTCTCTACAATCTTCCATTTGTTCAAGCTTCATAGACTCCTCT
AACAAAGGCAGTGCAGAAATATCGGTCTAAAAATGAAATTTCTGAGTGCTCGTGTGAAATTTACT
ATAACAGGTGTTCCTTAACTCCCTTAGTCCATCTTTACCGAAACTCCTTATTCATAAAATTTGCC
ATTGT
Found at i:56753 original size:24 final size:25
Alignment explanation
Indices: 56712--56758 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
56702 TGAACTAAAA
56712 AAAATTAGAAGCTCGATTGAAGTCT
1 AAAATTAGAAGCTCGATTGAAGTCT
* *
56737 AAAATTCG-AGCTTGATTGAAGT
1 AAAATTAGAAGCTCGATTGAAGT
56759 AAAAGAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (25 bp):
AAAATTAGAAGCTCGATTGAAGTCT
Found at i:60379 original size:69 final size:69
Alignment explanation
Indices: 60292--60434 Score: 214
Period size: 69 Copynumber: 2.1 Consensus size: 69
60282 GCCACGGCAC
* * * *
60292 TATCACCAACCAAAGCATGACGTATATTCTCAACAGAATCATTAATATTCAAGACATGGCCATGA
1 TATCACCAACCAAAGCATGACGCATATTCTCAACAGAATCATTAATACTCAAAACATGACCATGA
*
60357 GAAT
66 GAAA
* * *
60361 TATCACCCACCAAAGCATGACGCATATTCTCAACAGAATCATTAATGCTCAAAACATGATCATGA
1 TATCACCAACCAAAGCATGACGCATATTCTCAACAGAATCATTAATACTCAAAACATGACCATGA
60426 GAAA
66 GAAA
60430 TATCA
1 TATCA
60435 TCTTGCTGCT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.24
Consensus pattern (69 bp):
TATCACCAACCAAAGCATGACGCATATTCTCAACAGAATCATTAATACTCAAAACATGACCATGA
GAAA
Found at i:61058 original size:211 final size:211
Alignment explanation
Indices: 60694--61114 Score: 842
Period size: 211 Copynumber: 2.0 Consensus size: 211
60684 CGGATTGTTA
60694 TAGCCTTAGGAGCTTTGGTAGCCACTTTCGATTTTCCTTTGGATTTAGACTTGGGATTTAGTCGG
1 TAGCCTTAGGAGCTTTGGTAGCCACTTTCGATTTTCCTTTGGATTTAGACTTGGGATTTAGTCGG
60759 GGAGGATCAGCAATCGTTTGAGGGTGAACAGGAGCAGGCTGTTCAGTCGCATCATTGGTATCCAT
66 GGAGGATCAGCAATCGTTTGAGGGTGAACAGGAGCAGGCTGTTCAGTCGCATCATTGGTATCCAT
60824 ATCAATTATCGGGTTGAATCGGGAGCTCTGAACCATGTTATTATTAGGGTTGGCTGCTGCCTCCT
131 ATCAATTATCGGGTTGAATCGGGAGCTCTGAACCATGTTATTATTAGGGTTGGCTGCTGCCTCCT
60889 GTTTTGATTATCCGGG
196 GTTTTGATTATCCGGG
60905 TAGCCTTAGGAGCTTTGGTAGCCACTTTCGATTTTCCTTTGGATTTAGACTTGGGATTTAGTCGG
1 TAGCCTTAGGAGCTTTGGTAGCCACTTTCGATTTTCCTTTGGATTTAGACTTGGGATTTAGTCGG
60970 GGAGGATCAGCAATCGTTTGAGGGTGAACAGGAGCAGGCTGTTCAGTCGCATCATTGGTATCCAT
66 GGAGGATCAGCAATCGTTTGAGGGTGAACAGGAGCAGGCTGTTCAGTCGCATCATTGGTATCCAT
61035 ATCAATTATCGGGTTGAATCGGGAGCTCTGAACCATGTTATTATTAGGGTTGGCTGCTGCCTCCT
131 ATCAATTATCGGGTTGAATCGGGAGCTCTGAACCATGTTATTATTAGGGTTGGCTGCTGCCTCCT
61100 GTTTTGATTATCCGG
196 GTTTTGATTATCCGG
61115 CGAGGACGAC
Statistics
Matches: 210, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
211 210 1.00
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (211 bp):
TAGCCTTAGGAGCTTTGGTAGCCACTTTCGATTTTCCTTTGGATTTAGACTTGGGATTTAGTCGG
GGAGGATCAGCAATCGTTTGAGGGTGAACAGGAGCAGGCTGTTCAGTCGCATCATTGGTATCCAT
ATCAATTATCGGGTTGAATCGGGAGCTCTGAACCATGTTATTATTAGGGTTGGCTGCTGCCTCCT
GTTTTGATTATCCGGG
Found at i:66087 original size:3 final size:3
Alignment explanation
Indices: 66079--66106 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
66069 CGTTAACCCA
66079 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
66107 CTCCTAATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:72354 original size:6 final size:6
Alignment explanation
Indices: 72343--72376 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
72333 TCCTGCTCAA
* *
72343 CATCAT CATCAT CATCAC CATCAC CATCAC CATC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATC
72377 GGTGATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (6 bp):
CATCAC
Found at i:73567 original size:23 final size:22
Alignment explanation
Indices: 73524--73567 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
73514 CGAAATAATA
* *
73524 TATTCATTAAAAATATTATTTT
1 TATTCAATAAAAATATGATTTT
73546 TATTCAATAAAAATATGGATTT
1 TATTCAATAAAAATAT-GATTT
73568 AATCGAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (22 bp):
TATTCAATAAAAATATGATTTT
Found at i:74015 original size:102 final size:102
Alignment explanation
Indices: 73887--74098 Score: 316
Period size: 102 Copynumber: 2.1 Consensus size: 102
73877 GTAATCGACT
* * * * * * *
73887 CCGATCGAGTTTTATTCACTCTTATATATAGCGGCGCAACACCTTAAGAGGCTGATTCCCCTAGC
1 CCGATCGAGTTCTATTCACCCCTATATATAGCGGCGCAACACCATAACAGGCCGATTCCCCCAGC
*
73952 AAAGAAACGCTGCTATTGATAATGCTTCCGGTCGGCC
66 AAAGAAACGCTGCTATCGATAATGCTTCCGGTCGGCC
*
73989 CCGATTGAGTTCTATTCACCCCTATATATAGCGGCGCAACACCATAACAGGCCGATTCCCCCAGC
1 CCGATCGAGTTCTATTCACCCCTATATATAGCGGCGCAACACCATAACAGGCCGATTCCCCCAGC
* * *
74054 AAAGAAACGCTGCTGTCGATGATGCTTCTGGTCGGCC
66 AAAGAAACGCTGCTATCGATAATGCTTCCGGTCGGCC
74091 CCGATCGA
1 CCGATCGA
74099 TGATTCACCG
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 97 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (102 bp):
CCGATCGAGTTCTATTCACCCCTATATATAGCGGCGCAACACCATAACAGGCCGATTCCCCCAGC
AAAGAAACGCTGCTATCGATAATGCTTCCGGTCGGCC
Found at i:74946 original size:37 final size:37
Alignment explanation
Indices: 74864--74986 Score: 92
Period size: 37 Copynumber: 3.4 Consensus size: 37
74854 ATGTTTGGTC
* * * * *
74864 GACCC-ACCCGAAAATATATATCTTCTACCCGAAGTC-
1 GACCCGACCCAAAAATATATATCATCCA-CCTAACTCT
* * *
74900 GACCTGACCCAAAAATTATGTATCATCCA-TTCAA-TCT
1 GACCCGACCCAAAAA-TATATATCATCCACCT-AACTCT
* * *
74937 GATCCGACCCGAAAATATATATCTTCCACCTAACTCT
1 GACCCGACCCAAAAATATATATCATCCACCTAACTCT
74974 GACCCGACCCAAA
1 GACCCGACCCAAA
74987 TTTTTAGACT
Statistics
Matches: 66, Mismatches: 15, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
36 19 0.29
37 37 0.56
38 10 0.15
ACGTcount: A:0.34, C:0.33, G:0.10, T:0.24
Consensus pattern (37 bp):
GACCCGACCCAAAAATATATATCATCCACCTAACTCT
Found at i:79527 original size:3 final size:3
Alignment explanation
Indices: 79519--79598 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
79509 AGAAATGGGT
79519 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
79567 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
79599 GTGAACACGG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:86736 original size:31 final size:31
Alignment explanation
Indices: 86698--86763 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
86688 GCTTATGTAA
* *
86698 TAAAACATACCAAAGCTGATAGTTTAGGTAC
1 TAAAACATACCAAAACTAATAGTTTAGGTAC
86729 TAAAACATACCAAAACTAATAGTTTAGGTAC
1 TAAAACATACCAAAACTAATAGTTTAGGTAC
86760 TAAA
1 TAAA
86764 CGTGTTAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (31 bp):
TAAAACATACCAAAACTAATAGTTTAGGTAC
Found at i:95668 original size:20 final size:20
Alignment explanation
Indices: 95640--95677 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
95630 ATATTGTAGT
*
95640 TCACTGTACTAACATGACAA
1 TCACAGTACTAACATGACAA
*
95660 TCACAGTACTAACGTGAC
1 TCACAGTACTAACATGAC
95678 TGATCGTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (20 bp):
TCACAGTACTAACATGACAA
Done.