Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004055.1 Hibiscus syriacus cultivar Beakdansim tig00008872_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: 64367
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3327 original size:107 final size:106
Alignment explanation
Indices: 3059--3426 Score: 628
Period size: 106 Copynumber: 3.5 Consensus size: 106
3049 ACGAAGGGGC
*
3059 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAATACAAGTT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
* *
3124 CAACTTCACAGCGGAGGGACGGCTGGTTGTCAACAAACAAT
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
*
3165 TTCCCAGATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
*
3230 CAACTTCACACCGAAGGGACGGCTGGTTGTCAACAAACAAT
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
*
3271 TTCCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGGACTCGAGACAACACAAGT
1 TT-CCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
*
3336 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAA
65 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
* * * *
3378 TTCCCAGTTCCAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
3427 TGGAACAGTA
Statistics
Matches: 250, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
106 148 0.59
107 102 0.41
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (106 bp):
TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
Found at i:7774 original size:2 final size:2
Alignment explanation
Indices: 7767--7791 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7757 CAAGAAAAGC
7767 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
7792 CTTTCTGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9715 original size:83 final size:81
Alignment explanation
Indices: 9616--9867 Score: 229
Period size: 81 Copynumber: 3.1 Consensus size: 81
9606 ATGCGTCATT
* *
9616 TTTCATCTAACTTGCATCAGTGGCACCTTTATGCCAAAATGCACAGTGAGGCATTTAGTCTTTTA
1 TTTCATCTAACTTGCATCAGTGGCACCTTTATGCC-AAATGCACAGTCAGGCATTTAATCTTTT-
*
9681 TCCCAAAGGCATTTAACC
64 GCCCAAAGGCATTTAACC
* * ** * *
9699 TTTCATCTAACTTGCATTATTGGCATTTTTCTTCCAAATGCACAGTCAGGCATTTAATCTTTTGC
1 TTTCATCTAACTTGCATCAGTGGCACCTTTATGCCAAATGCACAGTCAGGCATTTAATCTTTTGC
* * *
9764 TCAAAGGTATTTATCC
66 CCAAAGGCATTTAACC
* * * * * * * *
9780 TTTCATATAACTGGCATGATTGACACATTTCTGTCAAATGCACAG-CTAGG-AGTTTAATCTTTT
1 TTTCATCTAACTTGCATCAGTGGCACCTTTATGCCAAATGCACAGTC-AGGCA-TTTAATCTTTT
* * * * *
9843 ACTCAAAGGTACTTAATC
64 GCCCAAAGGCATTTAACC
9861 TTTCATC
1 TTTCATC
9868 AAGTTCTGTC
Statistics
Matches: 142, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
80 2 0.01
81 85 0.60
82 26 0.18
83 29 0.20
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (81 bp):
TTTCATCTAACTTGCATCAGTGGCACCTTTATGCCAAATGCACAGTCAGGCATTTAATCTTTTGC
CCAAAGGCATTTAACC
Found at i:9811 original size:81 final size:81
Alignment explanation
Indices: 9652--9866 Score: 240
Period size: 81 Copynumber: 2.6 Consensus size: 81
9642 CTTTATGCCA
* * * * * * * *
9652 AAATGCACAGTGAGGCATTTAGTCTTTTATCCCAAAGGCATTTAACCTTTCATCTAACTTGCATT
1 AAATGCACAGTCAGGCATTTAATCTTTTA-CTCAAAGGTATTTATCCTTTCATATAACTGGCATG
* **
9717 ATTGGCATTTTTCT-TCC
65 ATTGACACATTTCTGT-C
*
9734 AAATGCACAGTCAGGCATTTAATCTTTTGCTCAAAGGTATTTATCCTTTCATATAACTGGCATGA
1 AAATGCACAGTCAGGCATTTAATCTTTTACTCAAAGGTATTTATCCTTTCATATAACTGGCATGA
9799 TTGACACATTTCTGTC
66 TTGACACATTTCTGTC
*
9815 AAATGCACAG-CTAGG-AGTTTAATCTTTTACTCAAAGGTACTTAAT-CTTTCAT
1 AAATGCACAGTC-AGGCA-TTTAATCTTTTACTCAAAGGTA-TTTATCCTTTCAT
9867 CAAGTTCTGT
Statistics
Matches: 115, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
80 2 0.02
81 82 0.71
82 31 0.27
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (81 bp):
AAATGCACAGTCAGGCATTTAATCTTTTACTCAAAGGTATTTATCCTTTCATATAACTGGCATGA
TTGACACATTTCTGTC
Found at i:9907 original size:63 final size:63
Alignment explanation
Indices: 9808--9930 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
9798 ATTGACACAT
* *
9808 TTCTGTCAAATGCACAGCTAGGAGTTTAATCTTTTACTCAAAGGTACTTAATCTTTCATCAAG
1 TTCTGTCAAATGCACAACTAGGAGTTTAATCTTTTACTCAAAGGTACTTAACCTTTCATCAAG
*
9871 TTCTGTCAAATGCACAACTAGGCA-TTTAATCTTTTACTCAAAGGTATTTAACCTTTCATC
1 TTCTGTCAAATGCACAACTAGG-AGTTTAATCTTTTACTCAAAGGTACTTAACCTTTCATC
9931 TAACTGGCAT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 55 0.98
64 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (63 bp):
TTCTGTCAAATGCACAACTAGGAGTTTAATCTTTTACTCAAAGGTACTTAACCTTTCATCAAG
Found at i:13997 original size:7 final size:7
Alignment explanation
Indices: 13985--14034 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
13975 CTTTTATAGT
13985 TAAACCC
1 TAAACCC
13992 TAAACCC
1 TAAACCC
13999 TAAACCC
1 TAAACCC
14006 TAAACCC
1 TAAACCC
14013 TAAACCC
1 TAAACCC
14020 TAAACCC
1 TAAACCC
14027 TAAACCC
1 TAAACCC
14034 T
1 T
14035 CGGTATTTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:16815 original size:12 final size:12
Alignment explanation
Indices: 16798--16823 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16788 AACAAGGAAC
16798 AAAAACAATCAT
1 AAAAACAATCAT
16810 AAAAACAATCAT
1 AAAAACAATCAT
16822 AA
1 AA
16824 TTCATCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAACAATCAT
Found at i:23381 original size:30 final size:30
Alignment explanation
Indices: 23347--23412 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
23337 ATATCAAAAA
* *
23347 TCGGATATATGATATTTGAATATATGTTAT
1 TCGGATATATGATATTCGAACATATGTTAT
* * *
23377 TCGGACATATGTTATTCGGACATATGTTAT
1 TCGGATATATGATATTCGAACATATGTTAT
23407 TCGGAT
1 TCGGAT
23413 CGGATCAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (30 bp):
TCGGATATATGATATTCGAACATATGTTAT
Found at i:23386 original size:15 final size:15
Alignment explanation
Indices: 23368--23411 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
23358 ATATTTGAAT
23368 ATATGTTATTCGGAC
1 ATATGTTATTCGGAC
23383 ATATGTTATTCGGAC
1 ATATGTTATTCGGAC
23398 ATATGTTATTCGGA
1 ATATGTTATTCGGA
23412 TCGGATCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.41
Consensus pattern (15 bp):
ATATGTTATTCGGAC
Found at i:28902 original size:35 final size:35
Alignment explanation
Indices: 28852--28941 Score: 144
Period size: 35 Copynumber: 2.5 Consensus size: 35
28842 TATAATCTTT
*
28852 GATCGAAATAAAACTTAAACCACATGATATTGAAAC
1 GATCG-AACAAAACTTAAACCACATGATATTGAAAC
*
28888 GATCGAACAAAACTTAAACCACGTGATATTGAAAC
1 GATCGAACAAAACTTAAACCACATGATATTGAAAC
*
28923 TATCGAACAAAACTTAAAC
1 GATCGAACAAAACTTAAAC
28942 TACTTGACAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 46 0.90
36 5 0.10
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.21
Consensus pattern (35 bp):
GATCGAACAAAACTTAAACCACATGATATTGAAAC
Found at i:32805 original size:16 final size:16
Alignment explanation
Indices: 32784--32838 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
32774 ATAAATGAAC
32784 ATAAACGAACACGAAA
1 ATAAACGAACACGAAA
*
32800 ATAAACGAACACGAAC
1 ATAAACGAACACGAAA
*
32816 ATAAATGAACAC-AAA
1 ATAAACGAACACGAAA
32831 CATAAACG
1 -ATAAACG
32839 TTGGAGACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 2 0.06
16 32 0.94
ACGTcount: A:0.60, C:0.20, G:0.11, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACGAAA
Found at i:34416 original size:14 final size:14
Alignment explanation
Indices: 34399--34429 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
34389 AGCGCACATA
*
34399 AACGAACATAATTG
1 AACGAACATAAATG
34413 AACGAACATAAATG
1 AACGAACATAAATG
34427 AAC
1 AAC
34430 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (14 bp):
AACGAACATAAATG
Found at i:34421 original size:24 final size:24
Alignment explanation
Indices: 34379--34433 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
34369 TATTGGGTTA
* *
34379 AACATAAATGAGCGCACATAAACG
1 AACATAAATGAACGAACATAAACG
* *
34403 AACATAATTGAACGAACATAAATG
1 AACATAAATGAACGAACATAAACG
34427 AACATAA
1 AACATAA
34434 CCGAACGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:34439 original size:24 final size:24
Alignment explanation
Indices: 34394--34440 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
34384 AAATGAGCGC
**
34394 ACATAAACGAACATAATTGAACGA
1 ACATAAACGAACATAACCGAACGA
*
34418 ACATAAATGAACATAACCGAACG
1 ACATAAACGAACATAACCGAACG
34441 TTCACGAACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.19, G:0.13, T:0.15
Consensus pattern (24 bp):
ACATAAACGAACATAACCGAACGA
Found at i:36677 original size:23 final size:23
Alignment explanation
Indices: 36647--36695 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
36637 GGAAGACTTG
36647 CAATAAGTCGACCTTGTTTATAT
1 CAATAAGTCGACCTTGTTTATAT
36670 CAATAAGTCGACCTTGTTTATAT
1 CAATAAGTCGACCTTGTTTATAT
36693 CAA
1 CAA
36696 CATGATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (23 bp):
CAATAAGTCGACCTTGTTTATAT
Found at i:37290 original size:45 final size:45
Alignment explanation
Indices: 37223--37379 Score: 210
Period size: 45 Copynumber: 3.5 Consensus size: 45
37213 TACGAGCTTA
* *
37223 AGCTTATGGAAT-AATGGCAAGTATATTGGTAAAATAAGCTTATG
1 AGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACG
* * *
37267 AACTTATGGAACAAATGGTAAGTATGA-TGGTAAGATAAGCTTACG
1 AGCTTATGGAATAAATGGTAAGTAT-ATTGGTAAAATAAGCTTACG
* *
37312 AGCTTATGGGATAAATGGTAAGTATTTTGGTAAAATAAGCTTACG
1 AGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACG
37357 AGCTTATGGTTAATAAATGGTAA
1 AGCTTATGG--AATAAATGGTAA
37380 AATATTGAAT
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
44 10 0.10
45 75 0.77
46 1 0.01
47 11 0.11
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (45 bp):
AGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACG
Found at i:40346 original size:21 final size:21
Alignment explanation
Indices: 40320--40359 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40310 ATGTGAGATC
40320 TATTCCAG-TTAAGAAATTGGA
1 TATTCC-GCTTAAGAAATTGGA
*
40341 TATTCCGCTTAAGAGATTG
1 TATTCCGCTTAAGAAATTG
40360 TGTTGCCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (21 bp):
TATTCCGCTTAAGAAATTGGA
Found at i:42699 original size:28 final size:28
Alignment explanation
Indices: 42659--42714 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
42649 ATAGTTCAGA
42659 TTGGTGTCTGGGCTAATTCGAATTGGCC
1 TTGGTGTCTGGGCTAATTCGAATTGGCC
42687 TTGGTGTCTGGGCTAATTCGAATTGGCC
1 TTGGTGTCTGGGCTAATTCGAATTGGCC
42715 ACTGCTGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.18, G:0.32, T:0.36
Consensus pattern (28 bp):
TTGGTGTCTGGGCTAATTCGAATTGGCC
Found at i:43263 original size:15 final size:16
Alignment explanation
Indices: 43239--43273 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
43229 TGTGGTGGTT
43239 GTTTTAAAGTTT-ATG
1 GTTTTAAAGTTTAATG
*
43254 GTTTTTAAGTTTAATG
1 GTTTTAAAGTTTAATG
43270 GTTT
1 GTTT
43274 AAGTCATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (16 bp):
GTTTTAAAGTTTAATG
Found at i:44854 original size:29 final size:29
Alignment explanation
Indices: 44812--44922 Score: 179
Period size: 29 Copynumber: 3.8 Consensus size: 29
44802 GACCGTTGAC
44812 TGGTGCTATTCTGGTAAATAATTCTGTTT
1 TGGTGCTATTCTGGTAAATAATTCTGTTT
*
44841 TGGTGCTATTCTGGTAAATAATT-TGGATT
1 TGGTGCTATTCTGGTAAATAATTCT-GTTT
*
44870 TGGTGCTATTATGGTAAATAATTCTGTTT
1 TGGTGCTATTCTGGTAAATAATTCTGTTT
*
44899 TGGTGCTATTCTGGTAATTAATTC
1 TGGTGCTATTCTGGTAAATAATTC
44923 GAAATGTGTA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
28 1 0.01
29 73 0.97
30 1 0.01
ACGTcount: A:0.23, C:0.09, G:0.22, T:0.47
Consensus pattern (29 bp):
TGGTGCTATTCTGGTAAATAATTCTGTTT
Found at i:44902 original size:58 final size:58
Alignment explanation
Indices: 44812--44921 Score: 202
Period size: 58 Copynumber: 1.9 Consensus size: 58
44802 GACCGTTGAC
*
44812 TGGTGCTATTCTGGTAAATAATTCTGTTTTGGTGCTATTCTGGTAAATAATTTGGATT
1 TGGTGCTATTATGGTAAATAATTCTGTTTTGGTGCTATTCTGGTAAATAATTTGGATT
*
44870 TGGTGCTATTATGGTAAATAATTCTGTTTTGGTGCTATTCTGGTAATTAATT
1 TGGTGCTATTATGGTAAATAATTCTGTTTTGGTGCTATTCTGGTAAATAATT
44922 CGAAATGTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.23, C:0.08, G:0.22, T:0.47
Consensus pattern (58 bp):
TGGTGCTATTATGGTAAATAATTCTGTTTTGGTGCTATTCTGGTAAATAATTTGGATT
Found at i:44937 original size:58 final size:58
Alignment explanation
Indices: 44812--44937 Score: 173
Period size: 58 Copynumber: 2.2 Consensus size: 58
44802 GACCGTTGAC
* * * * *
44812 TGGTGCTATTCTGGTAAATAATTCTGTTTTGGTGCTATTCTGGTAAATAATTTGGATT
1 TGGTACTATTATGGTAAATAATTCTGTTTTGGTGCTATTCTGGTAAATAATTCGAATG
* *
44870 TGGTGCTATTATGGTAAATAATTCTGTTTTGGTGCTATTCTGGTAATTAATTCGAAATG
1 TGGTACTATTATGGTAAATAATTCTGTTTTGGTGCTATTCTGGTAAATAATTCG-AATG
44929 T-GTACTATT
1 TGGTACTATT
44938 TTTGGTAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 58 0.95
59 3 0.05
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.46
Consensus pattern (58 bp):
TGGTACTATTATGGTAAATAATTCTGTTTTGGTGCTATTCTGGTAAATAATTCGAATG
Found at i:45028 original size:10 final size:10
Alignment explanation
Indices: 45013--45042 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
45003 GACCAAAACG
45013 TTGACCGGCT
1 TTGACCGGCT
45023 TTGACCGGCT
1 TTGACCGGCT
45033 TTGACCGGCT
1 TTGACCGGCT
45043 ATTAAACGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.10, C:0.30, G:0.30, T:0.30
Consensus pattern (10 bp):
TTGACCGGCT
Found at i:45821 original size:13 final size:13
Alignment explanation
Indices: 45803--45827 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45793 GTCACGGTGC
45803 AATTGAATTTTGG
1 AATTGAATTTTGG
45816 AATTGAATTTTG
1 AATTGAATTTTG
45828 ATGGAATAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
AATTGAATTTTGG
Found at i:47441 original size:19 final size:19
Alignment explanation
Indices: 47417--47467 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
47407 GAAAATATTC
47417 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
47436 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
47455 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
47468 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:47443 original size:65 final size:65
Alignment explanation
Indices: 47311--47469 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 65
47301 GCACTAAGGA
* ***
47311 TGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGAG
* **
47375 TGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATGGAGA
47439 G
65 G
* **
47440 TGCATCGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCATAAAATGCATTCGATGTT
47470 CAATTAATTC
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
64 35 0.42
65 48 0.58
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGAG
Found at i:47886 original size:31 final size:31
Alignment explanation
Indices: 47848--47927 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
47838 ATTGATTTTG
47848 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
47879 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
** * *
47910 TTAAATTTTCTCCCCCTT
1 AAAAACTTACTCCCCCTT
47928 TTTATTAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (31 bp):
AAAAACTTACTCCCCCTTACTATAGCACATC
Found at i:53985 original size:22 final size:21
Alignment explanation
Indices: 53943--53982 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53933 GAGTTTGTTT
*
53943 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
53964 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
53983 ACAGTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:56045 original size:19 final size:19
Alignment explanation
Indices: 56021--56071 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
56011 GAAAATATTC
56021 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
* *
56040 AGAGTGTATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
56059 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
56072 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 3 0.11
18 6 0.22
19 18 0.67
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:56056 original size:65 final size:65
Alignment explanation
Indices: 55915--56073 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 65
55905 GCACTAAGGA
* ***
55915 TGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGAG
* **
55979 TGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATGGAGA
56043 G
65 G
* * **
56044 TGTATCGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCATAAAATGCATTCGATGTT
56074 CAATTAATTC
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
64 35 0.43
65 47 0.57
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGAG
Found at i:62005 original size:13 final size:13
Alignment explanation
Indices: 61987--62016 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
61977 GACCGGTCAC
61987 GACCCGACCCGTT
1 GACCCGACCCGTT
62000 GACCCGACCCGTT
1 GACCCGACCCGTT
62013 GACC
1 GACC
62017 GTTTACCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:62177 original size:29 final size:29
Alignment explanation
Indices: 62029--62184 Score: 179
Period size: 29 Copynumber: 5.4 Consensus size: 29
62019 TTACCAGTGT
*
62029 TATTCTGGTAAATAATTC-AGTTTTGGTAC
1 TATTCTGGTAAATAATTCGA-TTTTGGTGC
* *
62058 TATTCTGGTAAATAATTCGGTTTTGGTGA
1 TATTCTGGTAAATAATTCGATTTTGGTGC
* * *
62087 TATTCTGGTAAATATTTCGGTTTTAGTGC
1 TATTCTGGTAAATAATTCGATTTTGGTGC
* *
62116 TATTCTGGTAAATAATTCTATTTTTGTGC
1 TATTCTGGTAAATAATTCGATTTTGGTGC
* ** *
62145 TATTCTGGTAATTAATTCGAAATTGGTGT
1 TATTCTGGTAAATAATTCGATTTTGGTGC
*
62174 TATTTTGGTAA
1 TATTCTGGTAA
62185 TTTTTTTTAA
Statistics
Matches: 109, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
29 109 1.00
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.47
Consensus pattern (29 bp):
TATTCTGGTAAATAATTCGATTTTGGTGC
Found at i:62183 original size:87 final size:87
Alignment explanation
Indices: 62024--62184 Score: 225
Period size: 87 Copynumber: 1.9 Consensus size: 87
62014 ACCGTTTACC
* ***
62024 AGTGTTATTCTGGTAAATAATTCAGTTTTGGTACTATTCTGGTAAATAATTCGGTTTTGGTGATA
1 AGTGCTATTCTGGTAAATAATTCAGTTTTGGTACTATTCTGGTAAATAATTCGAAATTGGTGATA
62089 TTCTGGTAAATATTTCGGTTTT
66 TTCTGGTAAATATTTCGGTTTT
* * * *
62111 AGTGCTATTCTGGTAAATAATTCTA-TTTTTGTGCTATTCTGGTAATTAATTCGAAATTGGTGTT
1 AGTGCTATTCTGGTAAATAATTC-AGTTTTGGTACTATTCTGGTAAATAATTCGAAATTGGTGAT
*
62175 ATTTTGGTAA
65 ATTCTGGTAA
62185 TTTTTTTTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
87 63 0.98
88 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.47
Consensus pattern (87 bp):
AGTGCTATTCTGGTAAATAATTCAGTTTTGGTACTATTCTGGTAAATAATTCGAAATTGGTGATA
TTCTGGTAAATATTTCGGTTTT
Done.