Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000566.1 Hibiscus syriacus cultivar Beakdansim tig00001106_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: 100667
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:2107 original size:18 final size:15
Alignment explanation
Indices: 2072--2103 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2062 ATAGTTCGAG
2072 TGCTACACAAAATGA
1 TGCTACACAAAATGA
*
2087 TGCTACACAAGATGA
1 TGCTACACAAAATGA
2102 TG
1 TG
2104 ATGCACATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (15 bp):
TGCTACACAAAATGA
Found at i:4568 original size:101 final size:103
Alignment explanation
Indices: 4379--4581 Score: 304
Period size: 103 Copynumber: 2.0 Consensus size: 103
4369 TTTGGCTGCC
* ** *
4379 ATATATATATATATGTTTCGTTTTGCCAAATAATTGTTTTAATTTTTCATGTTCTTCTACATGTA
1 ATATATATACATACATTTCGTTTTGCCAAATAATTGTTTTAATTTTCCATGTTCTTCTACATGTA
4444 GGGGCAAGCTGTATGTTCTAGCTACACTATGTATGGAT
66 GGGGCAAGCTGTATGTTCTAGCTACACTATGTATGGAT
* *
4482 ATATATATACATACATTTCTTTTTGCCAAATAATTGTTTTAATTATTCCGTGTT-TT-TACATGT
1 ATATATATACATACATTTCGTTTTGCCAAATAATTGTTTTAATT-TTCCATGTTCTTCTACATGT
* *
4545 A-GGGCAAGCTTTATGTTCTAGCTACACTATTTATGGA
65 AGGGGCAAGCTGTATGTTCTAGCTACACTATGTATGGA
4582 CTGCAAATAT
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
101 34 0.37
102 8 0.09
103 42 0.46
104 7 0.08
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (103 bp):
ATATATATACATACATTTCGTTTTGCCAAATAATTGTTTTAATTTTCCATGTTCTTCTACATGTA
GGGGCAAGCTGTATGTTCTAGCTACACTATGTATGGAT
Found at i:6419 original size:12 final size:12
Alignment explanation
Indices: 6402--6427 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6392 TTAGTACTAT
6402 TTATAGACCGGC
1 TTATAGACCGGC
6414 TTATAGACCGGC
1 TTATAGACCGGC
6426 TT
1 TT
6428 GAATTAAATT
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:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (12 bp):
TTATAGACCGGC
Found at i:14374 original size:6 final size:6
Alignment explanation
Indices: 14363--14433 Score: 70
Period size: 6 Copynumber: 11.8 Consensus size: 6
14353 AGTACACGAT
* * * * *
14363 GGACAC GGACAC GGACAC GAACAC GGTCAC GGCCAC GGCCAC GAACAC
1 GGACAC GGACAC GGACAC GGACAC GGACAC GGACAC GGACAC GGACAC
* * *
14411 GGTCAC GGCCAC GGCCAC GGACA
1 GGACAC GGACAC GGACAC GGACA
14434 TGGGCATGGA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.28, C:0.38, G:0.31, T:0.03
Consensus pattern (6 bp):
GGACAC
Found at i:14399 original size:24 final size:24
Alignment explanation
Indices: 14366--14429 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
14356 ACACGATGGA
* *
14366 CACGGACACGGACACGAACACGGT
1 CACGGCCACGGCCACGAACACGGT
14390 CACGGCCACGGCCACGAACACGGT
1 CACGGCCACGGCCACGAACACGGT
14414 CACGGCCACGGCCACG
1 CACGGCCACGGCCACG
14430 GACATGGGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.27, C:0.41, G:0.30, T:0.03
Consensus pattern (24 bp):
CACGGCCACGGCCACGAACACGGT
Found at i:21787 original size:36 final size:37
Alignment explanation
Indices: 21742--21816 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 37
21732 CCACCGAAAG
21742 TGGCCTCCAAAATCCACCGAAAATT-CCCACCAATTT
1 TGGCCTCCAAAATCCACCGAAAATTGCCCACCAATTT
* *
21778 TGGCTTCCAAAATCCACCGAAAATTGGCCACCAATTT
1 TGGCCTCCAAAATCCACCGAAAATTGCCCACCAATTT
21815 TG
1 TG
21817 ACTTTTCCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 24 0.67
37 12 0.33
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.24
Consensus pattern (37 bp):
TGGCCTCCAAAATCCACCGAAAATTGCCCACCAATTT
Found at i:28427 original size:21 final size:21
Alignment explanation
Indices: 28395--28448 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
28385 GTACGGTTAC
*
28395 GGTGGACATGGAAGTTACAGT
1 GGTGGACATGGAAGTAACAGT
* *
28416 GGTGGACGTGGAAGTAACGGT
1 GGTGGACATGGAAGTAACAGT
*
28437 GGTGGCCATGGA
1 GGTGGACATGGA
28449 GGGTACAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.11, G:0.44, T:0.20
Consensus pattern (21 bp):
GGTGGACATGGAAGTAACAGT
Found at i:28461 original size:21 final size:21
Alignment explanation
Indices: 28437--28589 Score: 279
Period size: 21 Copynumber: 7.3 Consensus size: 21
28427 AAGTAACGGT
*
28437 GGTGGCCATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
28458 GGTGGACATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
28479 GGTGGACATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
28500 GGTGGACATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
28521 GGTGGACATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
*
28542 GGTGGACATGGAGGATACAAA
1 GGTGGACATGGAGGGTACAAA
*
28563 GTTGGACATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
28584 GGTGGA
1 GGTGGA
28590 GAGCAGAACG
Statistics
Matches: 127, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 127 1.00
ACGTcount: A:0.33, C:0.10, G:0.42, T:0.15
Consensus pattern (21 bp):
GGTGGACATGGAGGGTACAAA
Found at i:30766 original size:21 final size:21
Alignment explanation
Indices: 30724--30808 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
30714 TCAAAACATT
*
30724 AAGTTACAGTGGTGGACGTGG
1 AAGTTACAGTGGTGGACATGG
* *
30745 AAGTTACGGTGGTGGCCATGG
1 AAGTTACAGTGGTGGACATGG
* * **
30766 AGGGTACAAAGGTGGACATGG
1 AAGTTACAGTGGTGGACATGG
* * **
30787 AGGGTACAAAGGTGGACATGG
1 AAGTTACAGTGGTGGACATGG
30808 A
1 A
30809 GGGTACAAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.28, C:0.11, G:0.42, T:0.19
Consensus pattern (21 bp):
AAGTTACAGTGGTGGACATGG
Found at i:30809 original size:21 final size:21
Alignment explanation
Indices: 30755--30865 Score: 186
Period size: 21 Copynumber: 5.3 Consensus size: 21
30745 AAGTTACGGT
*
30755 GGTGGCCATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
30776 GGTGGACATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
30797 GGTGGACATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
* *
30818 GGTCGACATGGAGGATACAAA
1 GGTGGACATGGAGGGTACAAA
*
30839 GTTGGACATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
30860 GGTGGA
1 GGTGGA
30866 GAGCAGAACG
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 83 1.00
ACGTcount: A:0.32, C:0.11, G:0.41, T:0.15
Consensus pattern (21 bp):
GGTGGACATGGAGGGTACAAA
Found at i:48022 original size:3 final size:3
Alignment explanation
Indices: 48014--48038 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
48004 CAATTATTCA
48014 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
48039 CAACATGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:50532 original size:20 final size:20
Alignment explanation
Indices: 50507--50546 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
50497 ATTATCTATT
50507 CATTCATTCAGGGTTTTGTA
1 CATTCATTCAGGGTTTTGTA
*
50527 CATTCATTTAGGGTTTTGTA
1 CATTCATTCAGGGTTTTGTA
50547 TTTGATGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (20 bp):
CATTCATTCAGGGTTTTGTA
Found at i:51041 original size:35 final size:37
Alignment explanation
Indices: 51002--51077 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
50992 GGTAAGGGAT
*
51002 TGGTGGTTA-TATAGGCGTG-AAATGGTGATAGAAGA
1 TGGTGGATATTATAGGCGTGAAAATGGTGATAGAAGA
*
51037 TGGT-GATATTATAGGCGTGAAAATGGTGATGGAAGA
1 TGGTGGATATTATAGGCGTGAAAATGGTGATAGAAGA
51073 TGGTG
1 TGGTG
51078 ATGTTTAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
34 3 0.08
35 14 0.39
36 19 0.53
ACGTcount: A:0.30, C:0.03, G:0.38, T:0.29
Consensus pattern (37 bp):
TGGTGGATATTATAGGCGTGAAAATGGTGATAGAAGA
Found at i:51072 original size:36 final size:35
Alignment explanation
Indices: 51011--51079 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 35
51001 TTGGTGGTTA
51011 TATAGGCGTGAAATGGTGATAGAAGATGGTGATAT
1 TATAGGCGTGAAATGGTGATAGAAGATGGTGATAT
*
51046 TATAGGCGTGAAAATGGTGATGGAAGATGGTGAT
1 TATAGGCGTG-AAATGGTGATAGAAGATGGTGAT
51080 GTTTAGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 10 0.31
36 22 0.69
ACGTcount: A:0.33, C:0.03, G:0.36, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATAGAAGATGGTGATAT
Found at i:53018 original size:40 final size:41
Alignment explanation
Indices: 52970--53053 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 41
52960 GAAAATCGCA
*
52970 TTGCGATAGTCTA-CAATGTCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCTACCAATGTCGTTGCGATTTTCAAAATTCG
**
53010 TTGCGATAGTCTACCGTTGTCGTTGCGATTTTCAAAATTCG
1 TTGCGATAGTCTACCAATGTCGTTGCGATTTTCAAAATTCG
53051 TTG
1 TTG
53054 ATAGTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 13 0.32
41 27 0.68
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (41 bp):
TTGCGATAGTCTACCAATGTCGTTGCGATTTTCAAAATTCG
Found at i:53053 original size:19 final size:19
Alignment explanation
Indices: 52988--53053 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
52978 GTCTACAATG
*
52988 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCAAAAT
** ***
53007 TCGTTGCGATAGTCTACCGTT
1 TCGTTGCGATTTTC-A-AAAT
53028 GTCGTTGCGATTTTCAAAAT
1 -TCGTTGCGATTTTCAAAAT
53048 TCGTTG
1 TCGTTG
53054 ATAGTTAAAA
Statistics
Matches: 33, Mismatches: 11, Indels: 6
0.66 0.22 0.12
Matches are distributed among these distances:
19 18 0.55
20 1 0.03
21 2 0.06
22 12 0.36
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCAAAAT
Found at i:53698 original size:6 final size:5
Alignment explanation
Indices: 53640--53738 Score: 119
Period size: 6 Copynumber: 18.4 Consensus size: 5
53630 CCGTCTCGTC
53640 TCGGG TCGGG TCGGG TCGGG TCGGG TC-GG TCGGG TCGGG TCGGG TCGGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG
53689 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCG-GG TCG-GG TCG-GG TCG-GG TCG-GG TCG-GG TCG-GG TCG-GG TC
53739 ATACGTGTCT
Statistics
Matches: 92, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.04
5 42 0.46
6 46 0.50
ACGTcount: A:0.00, C:0.19, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:54158 original size:15 final size:13
Alignment explanation
Indices: 54131--54155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54121 GGTGCGTTTA
54131 TATTTTTTAAAAT
1 TATTTTTTAAAAT
54144 TATTTTTTAAAA
1 TATTTTTTAAAA
54156 AATAAAAGTT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTTTTAAAAT
Found at i:54409 original size:24 final size:24
Alignment explanation
Indices: 54377--54431 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
54367 AAATCGGTTG
54377 AACCGCTATTAGTGAACCGGCCAC
1 AACCGCTATTAGTGAACCGGCCAC
*
54401 AACCGCTATTAGTGAACCGGCCAG
1 AACCGCTATTAGTGAACCGGCCAC
54425 AACCGCT
1 AACCGCT
54432 GAACCGTTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.33, G:0.22, T:0.16
Consensus pattern (24 bp):
AACCGCTATTAGTGAACCGGCCAC
Found at i:56154 original size:17 final size:15
Alignment explanation
Indices: 56119--56157 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
56109 AAATTCTAAA
*
56119 TATTTAAATAAAAAT
1 TATTTATATAAAAAT
56134 TATTTATATAAAAAAT
1 TATTTATAT-AAAAAT
56150 CTATTTAT
1 -TATTTAT
56158 TGATAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 6 0.29
17 7 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
TATTTATATAAAAAT
Found at i:63955 original size:26 final size:27
Alignment explanation
Indices: 63926--63983 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 27
63916 CTGCTTAATT
63926 TAAAATTTATAA-AATTTTAGAG-AAAA
1 TAAAATTTA-AAGAATTTTAGAGAAAAA
* *
63952 T-AAACTTAAAGAATTTTATAGAAAAA
1 TAAAATTTAAAGAATTTTAGAGAAAAA
63978 TAAAAT
1 TAAAAT
63984 AAATTACCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
24 2 0.08
25 15 0.58
26 6 0.23
27 3 0.12
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (27 bp):
TAAAATTTAAAGAATTTTAGAGAAAAA
Found at i:66740 original size:3 final size:3
Alignment explanation
Indices: 66732--66756 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
66722 AGCCGAGTAG
66732 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
66757 CAAAACCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:67531 original size:28 final size:29
Alignment explanation
Indices: 67491--67550 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
67481 TTAAAATGAA
* *
67491 GATCATAGATTTG-GGATTAAATTGAAAT
1 GATCATAGATTTGAGGACTAAATTAAAAT
*
67519 GATCATA-AGTTTGAGGACTAATTTAAAAT
1 GATCATAGA-TTTGAGGACTAAATTAAAAT
67548 GAT
1 GAT
67551 AATCTTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.04
28 11 0.41
29 15 0.56
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (29 bp):
GATCATAGATTTGAGGACTAAATTAAAAT
Found at i:67573 original size:60 final size:60
Alignment explanation
Indices: 67465--67578 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
67455 AATGTTTAAA
* * *
67465 AAGTTTGGGGACCAATTTAAAATGAAGATCATAGATTTGGGATTAAATTGAAATGATCAT
1 AAGTTTGAGGACCAATTTAAAATGAAGATCATAGATTTGGGATGAAATTAAAATGATCAT
* * *
67525 AAGTTTGAGGACTAATTTAAAATGATA-ATCTTAG-TTTATGGATGAAATTAAAAT
1 AAGTTTGAGGACCAATTTAAAATGA-AGATCATAGATTT-GGGATGAAATTAAAAT
67579 ATTTAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 3 0.07
60 42 0.91
61 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.34
Consensus pattern (60 bp):
AAGTTTGAGGACCAATTTAAAATGAAGATCATAGATTTGGGATGAAATTAAAATGATCAT
Found at i:68222 original size:20 final size:20
Alignment explanation
Indices: 68197--68244 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
68187 CTTCCGTACA
68197 TCTTTCATCAAAGATGCGTG
1 TCTTTCATCAAAGATGCGTG
68217 TCTTTCATCAAAGATGCGTG
1 TCTTTCATCAAAGATGCGTG
68237 TCTTTCAT
1 TCTTTCAT
68245 ATGTCTTCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TCTTTCATCAAAGATGCGTG
Found at i:69764 original size:20 final size:20
Alignment explanation
Indices: 69739--69776 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
69729 TTGAATATTT
69739 TTTGTT-TTAAATAAAAATAA
1 TTTGTTATTAAA-AAAAATAA
69759 TTTGTTATTAAAAAAAAT
1 TTTGTTATTAAAAAAAAT
69777 CAAGTCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTGTTATTAAAAAAAATAA
Found at i:69984 original size:2 final size:2
Alignment explanation
Indices: 69977--70011 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
69967 TTCAATTCGA
69977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
70012 GTGCTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76146 original size:21 final size:21
Alignment explanation
Indices: 76122--76166 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
76112 GATTTCTGGG
* *
76122 CAAGGGAAATCGGTACCCATT
1 CAAGGGAAACCGATACCCATT
* *
76143 CAAGGGGAACCGATACCCCTT
1 CAAGGGAAACCGATACCCATT
76164 CAA
1 CAA
76167 ACGAACAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGAAACCGATACCCATT
Found at i:76886 original size:31 final size:31
Alignment explanation
Indices: 76848--76935 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 31
76838 TCGAGGGTTT
76848 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTTT-GAGACATATGGACAGTA
** *
76879 TACCTATGTTCTAAG-GAACATATGGACAGTT
1 TACCTATGTTCTTTGAG-ACATATGGACAGTA
* *
76910 TACCTAGGTTCTTTGGGACATATGGA
1 TACCTATGTTCTTTGAGACATATGGA
76936 TAGTTGCCGA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.90
32 4 0.08
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTTTGAGACATATGGACAGTA
Found at i:76951 original size:30 final size:31
Alignment explanation
Indices: 76864--76953 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
76854 TGTCTTTCGA
* * * **
76864 GACATATGGACAGTATACCTATGTTCTAAGG
1 GACATATGGACAGTTTACCGAGGTTCTTTGG
* *
76895 AACATATGGACAGTTTACCTAGGTTCTTTGG
1 GACATATGGACAGTTTACCGAGGTTCTTTGG
* *
76926 GACATATGGATAG-TTGCCGAGGTTCTTT
1 GACATATGGACAGTTTACCGAGGTTCTTT
76954 ATGACCTCTG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 13 0.26
31 37 0.74
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (31 bp):
GACATATGGACAGTTTACCGAGGTTCTTTGG
Found at i:76992 original size:29 final size:30
Alignment explanation
Indices: 76932--76996 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
76922 TTGGGACATA
* * *
76932 TGGATAGTTGCCGAGGTTCTTTATGACCTC
1 TGGATAGTTACCGAGGGTCTGTATGACCTC
*
76962 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGATAGTTACCGAGGGTCTGTATGACCTC
76991 TGGATA
1 TGGATA
76997 AGTCCTTCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.17, C:0.18, G:0.31, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGGTCTGTATGACCTC
Found at i:80314 original size:21 final size:21
Alignment explanation
Indices: 80288--80332 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
80278 GATTTCTGGG
*
80288 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
80309 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
80330 CAA
1 CAA
80333 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:81106 original size:31 final size:31
Alignment explanation
Indices: 81012--81119 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
81002 AGTCGAGGGT
* *
81012 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
81043 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
81074 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
81105 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
81120 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.21
31 47 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:81126 original size:30 final size:30
Alignment explanation
Indices: 81034--81140 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
81024 TTTCGAGACA
* * * *
81034 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGT-TACCGAGGTTCTTTAGG-ACC
* *
81065 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
81096 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
81126 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
81141 GGGTCTGTGT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 29 0.46
31 30 0.48
32 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:82603 original size:41 final size:41
Alignment explanation
Indices: 82540--82730 Score: 122
Period size: 41 Copynumber: 4.6 Consensus size: 41
82530 GTACATTAGC
*
82540 GGCA-TTTTTATACAAACACCGCAATAGGTGTAATATATAGT
1 GGCATTTTTTA-ACAAACGCCGCAATAGGTGTAATATATAGT
* ** *
82581 GGCTTTTTTTAACAAACGCCGCAACATATTTGTACT-T-TAGT
1 GGCATTTTTTAACAAACGCCGC-A-ATAGGTGTAATATATAGT
* * ** * *
82622 GGCATTTTTAAACTCAAACGCCGCAAAAAATTTAGATA-GTAGT
1 GGCATTTTTTAA--CAAACGCCGCAATAGGTGTA-ATATATAGT
* * * **
82665 GGC-GTTTATAACAAATGCCGCAATAGGTGTACCATATAGT
1 GGCATTTTTTAACAAACGCCGCAATAGGTGTAATATATAGT
* * *
82705 GGCATTTTTCACCAAACACCGCAATA
1 GGCATTTTTTAACAAACGCCGCAATA
82731 TATTTGAATT
Statistics
Matches: 111, Mismatches: 29, Indels: 20
0.69 0.18 0.12
Matches are distributed among these distances:
39 1 0.01
40 22 0.20
41 48 0.43
42 15 0.14
43 25 0.23
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (41 bp):
GGCATTTTTTAACAAACGCCGCAATAGGTGTAATATATAGT
Found at i:82794 original size:124 final size:124
Alignment explanation
Indices: 82558--82813 Score: 275
Period size: 124 Copynumber: 2.1 Consensus size: 124
82548 TATACAAACA
* * * * * *
82558 CCGCAATAGGTGTAATATATAGTGGCTTTTTTTAACAAACGCCGCAACATATTTGTACTTTAGTG
1 CCGCAATAGGTGTAACATATAGTGGCATTTTTCAACAAACACCGCAACATATTTGTAATTTAGCG
* * * *
82623 GCATTTTTAAACTCAAACGCCGCAAAAAATTTAGATAGTAGTGGCGTTTA-TAACAAATG
66 GCATTTCTAAACACAAACGCCGCAAAAAATATAGACAGTAGTGGCGTTTATTAA-AAATG
* * *
82682 CCGCAATAGGTGTACCATATAGTGGCATTTTTCACCAAACACCGCAATATATTTG-AATTGTCA-
1 CCGCAATAGGTGTAACATATAGTGGCATTTTTCAACAAACACCGCAACATATTTGTAATT-T-AG
* * * * * * *
82745 CGGCGTTTCTAGACACAAACGCCGCAATATATATGGACATTAGTTGCGTTTATTAAAAATG
64 CGGCATTTCTAAACACAAACGCCGCAAAAAATATAGACAGTAGTGGCGTTTATTAAAAATG
*
82806 CCACAATA
1 CCGCAATA
82814 TAGTATAACT
Statistics
Matches: 108, Mismatches: 21, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
123 3 0.03
124 101 0.94
125 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (124 bp):
CCGCAATAGGTGTAACATATAGTGGCATTTTTCAACAAACACCGCAACATATTTGTAATTTAGCG
GCATTTCTAAACACAAACGCCGCAAAAAATATAGACAGTAGTGGCGTTTATTAAAAATG
Found at i:83201 original size:81 final size:81
Alignment explanation
Indices: 83056--83217 Score: 227
Period size: 81 Copynumber: 2.0 Consensus size: 81
83046 GTATGCTTTA
*
83056 ACACCGTCGCTGCCCGGTACTCAACTGCTGCTGCTCGTCGCCGCTTGAAGCCTTCAATCCTGCTG
1 ACACCGTCGCTGCCCGGTACTCAACTGCTGATGCTCGTCGCCGCTTGAAGCCTTCAATCCTGCTG
*
83121 CTGCTCGTCATCACCT
66 CTGCTCATCATCACCT
* * * ** *
83137 ACACCGTCGCTGCCCGGTACTCAACTGCTGATGCTCGTTGGCGCTTGAAGTCGTT-GTTCTTGCT
1 ACACCGTCGCTGCCCGGTACTCAACTGCTGATGCTCGTCGCCGCTTGAAG-CCTTCAATCCTGCT
*
83201 GCTGCTCATTATCACCT
65 GCTGCTCATCATCACCT
83218 CCATTGTTAC
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 68 0.96
82 3 0.04
ACGTcount: A:0.14, C:0.35, G:0.22, T:0.29
Consensus pattern (81 bp):
ACACCGTCGCTGCCCGGTACTCAACTGCTGATGCTCGTCGCCGCTTGAAGCCTTCAATCCTGCTG
CTGCTCATCATCACCT
Found at i:85889 original size:17 final size:17
Alignment explanation
Indices: 85864--85897 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
85854 TGTAACTTAC
*
85864 AAAACAAAATATTTATT
1 AAAACAAAATAATTATT
*
85881 AAAATAAAATAATTATT
1 AAAACAAAATAATTATT
85898 TTATCATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAACAAAATAATTATT
Found at i:86185 original size:31 final size:30
Alignment explanation
Indices: 86053--86185 Score: 77
Period size: 34 Copynumber: 4.1 Consensus size: 30
86043 CTGTGACTAG
* * *
86053 ATAATTTTGTTACAATTTGTTATTGTGAAAGA
1 ATAAATTTGTCACAATTT-TTATTTTGAAA-A
* * **
86085 ATATTATTTGTCACATTTTTTTATAAATGAGAAA
1 ATA-AATTTGTCACA-ATTTTTAT-TTTGA-AAA
* * * *
86119 TTAATATTTGTTACAAATTGTTATTTTGATTAA
1 ATAA-ATTTGTCAC-AATTTTTATTTTGA-AAA
86152 ATAAATTTGTCACAATTTTTATTTTGACAAA
1 ATAAATTTGTCACAATTTTTATTTTGA-AAA
86183 ATA
1 ATA
86186 TTGAGACGAA
Statistics
Matches: 75, Mismatches: 20, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
31 18 0.24
32 11 0.15
33 20 0.27
34 23 0.31
35 3 0.04
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (30 bp):
ATAAATTTGTCACAATTTTTATTTTGAAAA
Found at i:86398 original size:198 final size:195
Alignment explanation
Indices: 86048--86550 Score: 704
Period size: 198 Copynumber: 2.5 Consensus size: 195
86038 TTTTACTGTG
* *
86048 ACTAGATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACATTTTTTTATAAAT
1 ACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT--AT
*
86113 GAGAAATTAATATTTGTTACAAATTGTTATTTTGATTAAATAAATTTGTCACAATTTTTATTTTG
64 GAGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCACAATTTTTATTTTG
* * * *
86178 ACAAAATATTGAGACGAAATAAATTTGACATAACTGTTTACTTTGACTAAATTTA-ACGTGTTAT
129 AAAAAATATTGAGACAAAATAAATTTGACACAACTGTTTACTTTGAATAAATTTATAC--GTTAT
86242 TGTGA
192 TGT-A
* * *
86247 A-TAAATCATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTCTTTATGATG
1 ACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT-ATG
* *
86311 AGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCAGAATTTTTTATTTTG
65 AGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCACAA-TTTTTATTTTG
* * * *
86376 AAAAAATATTGTGACAAAATAAATTTGACACAATTTTTTATTTTGAATAAATTTATTACGTTATT
129 AAAAAATATTGAGACAAAATAAATTTGACACAACTGTTTACTTTGAATAAATTTA-TACGTTATT
86441 GTA
193 GTA
* * * *
86444 ACTAAATAAATTTGTTACAATTTGTTATTATGAAAGAATATTTTTTGTCATAATTTTTTATATTG
1 ACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTATA-TG
* * *
86509 AGAAATTAATAATTGTTATAAATTGTTATTATGACTAAATAA
65 AGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAA
86551 TATCGAAATC
Statistics
Matches: 271, Mismatches: 28, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
197 56 0.21
198 212 0.78
199 1 0.00
200 2 0.01
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.46
Consensus pattern (195 bp):
ACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTATATGA
GAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCACAATTTTTATTTTGAA
AAAATATTGAGACAAAATAAATTTGACACAACTGTTTACTTTGAATAAATTTATACGTTATTGTA
Found at i:91203 original size:66 final size:65
Alignment explanation
Indices: 91081--91211 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 65
91071 ATTAGAAATC
*
91081 ATACTATTGCCTTCTCTCATCTTATTATAAATCCATGTACGATTTCTAATCAAGGTCTTGTTAAT
1 ATACTATTGCCTTCTCTCATCTTATTAAAAATCCATGTACGATTTCTAATCAAGGTCTTGTTAAT
* *
91146 ATACTATTGCCTTCTCTCATCTTATTACAAAATCCATGTATGATTTTTAATCAAGGTCTTGTTAA
1 ATACTATTGCCTTCTCTCATCTTATTA-AAAATCCATGTACGATTTCTAATCAAGGTCTTGTTAA
91211 T
65 T
91212 GATGATGACA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
65 27 0.44
66 35 0.56
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (65 bp):
ATACTATTGCCTTCTCTCATCTTATTAAAAATCCATGTACGATTTCTAATCAAGGTCTTGTTAAT
Found at i:92029 original size:43 final size:43
Alignment explanation
Indices: 91933--92048 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
91923 CTTTTGCATA
* * * * * *
91933 AAAAACGCCACTAAATCTCAACACTTATTGCGACGTTTGTGAT
1 AAAAACGCCGCTAAATCTCAACACCTATTGCGACATTTATAAG
91976 AAAAACGCCGCTAAATCTCAACACCTATTGCGACATTTATAAG
1 AAAAACGCCGCTAAATCTCAACACCTATTGCGACATTTATAAG
* * * **
92019 ACAAATGCCGCTAAATATCAGTACCTATTG
1 AAAAACGCCGCTAAATCTCAACACCTATTG
92049 TGGCGTTTGT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (43 bp):
AAAAACGCCGCTAAATCTCAACACCTATTGCGACATTTATAAG
Found at i:94084 original size:2 final size:2
Alignment explanation
Indices: 94077--94103 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
94067 GTTATTAAAT
94077 TA 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 TA T
94104 TTGCTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.