Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002785.1 Hibiscus syriacus cultivar Beakdansim tig00005740_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: 81140
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:535 original size:55 final size:55
Alignment explanation
Indices: 469--751 Score: 360
Period size: 51 Copynumber: 5.3 Consensus size: 55
459 AACTTCTCAC
*
469 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAATTCATTATGAA
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAA
* *
524 TTCTTAGTTTTTGCACACAAAGTGACCATATGGAAATTCAT-AACTC--T-TGAA
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAA
*
575 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAAATCATTATGAA
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAA
*
630 TTTCTTAGTTTTTGGCACA-AAAGTGCCCATATGG-AATTCA-AAACTCATTATGAA
1 -TTCTTAGTTTTT-GCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAA
* * * *
684 TTTCTTAGTTTTT--ACAC-AAGTGTCTATACGAAAATTC---AACTAATTATGAA
1 -TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAA
734 TTCTT-GTTTTTGCACACA
1 TTCTTAGTTTTTGCACACA
752 TATAGTGTCG
Statistics
Matches: 204, Mismatches: 13, Indels: 26
0.84 0.05 0.11
Matches are distributed among these distances:
48 6 0.03
49 5 0.02
50 16 0.08
51 56 0.27
52 10 0.05
54 31 0.15
55 49 0.24
56 26 0.13
57 5 0.02
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (55 bp):
TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAA
Found at i:629 original size:106 final size:108
Alignment explanation
Indices: 469--751 Score: 381
Period size: 106 Copynumber: 2.7 Consensus size: 108
459 AACTTCTCAC
*
469 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAATTCATTATGAATTCTTAGTTT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAAATCATTATGAATTCTTAGTTT
*
534 TTGCACACAAAGTGACCATATGGAAATTCATAACTC-T-TGAA-
66 TTGCACACAAAGTGACCATATGG-AATTCAAAACTCATATGAAT
575 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAAATCATTATGAATTTCTTAGTT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAAATCATTATGAA-TTCTTAGTT
*
640 TTTGGCACA-AAAGTGCCCATATGGAATTCAAAACTCATTATGAAT
65 TTT-GCACACAAAGTGACCATATGGAATTCAAAACTCA-TATGAAT
* * * * *
685 TTCTTAGTTTTT--ACAC-AAGTGTCTATACGAAAATTC---AACTAATTATGAATTCTT-GTTT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAAATCATTATGAATTCTTAGTTT
743 TTGCACACA
66 TTGCACACA
752 TATAGTGTCG
Statistics
Matches: 162, Mismatches: 8, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
101 5 0.03
102 7 0.04
103 5 0.03
104 11 0.07
106 65 0.40
107 43 0.27
108 10 0.06
109 4 0.02
110 12 0.07
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (108 bp):
TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAAATCATTATGAATTCTTAGTTT
TTGCACACAAAGTGACCATATGGAATTCAAAACTCATATGAAT
Found at i:904 original size:31 final size:32
Alignment explanation
Indices: 846--909 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
836 CACTCACCTG
846 GCTTGCCTCGCTTATATCCAAAACGTAACTCT
1 GCTTGCCTCGCTTATATCCAAAACGTAACTCT
878 GCTTGCCTCGC-TATTATCC-AAACGTAACTCT
1 GCTTGCCTCGCTTA-TATCCAAAACGTAACTCT
909 G
1 G
910 ATTACTCAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 15 0.48
32 16 0.52
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (32 bp):
GCTTGCCTCGCTTATATCCAAAACGTAACTCT
Found at i:10411 original size:34 final size:33
Alignment explanation
Indices: 10369--10439 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 33
10359 CCTTAAGGAG
10369 TTTATATCTTTTG-AATATTAAA-ATTAAAAGATA
1 TTTATATCTTTTGAAAT-TTAAATATT-AAAGATA
* *
10402 TTTATTATCTTTTTAAATTTAAATATTAAAGTTA
1 TTTA-TATCTTTTGAAATTTAAATATTAAAGATA
10436 TTTA
1 TTTA
10440 AAAGATATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
33 4 0.12
34 23 0.70
35 6 0.18
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (33 bp):
TTTATATCTTTTGAAATTTAAATATTAAAGATA
Found at i:10851 original size:2 final size:2
Alignment explanation
Indices: 10846--11102 Score: 243
Period size: 2 Copynumber: 128.0 Consensus size: 2
10836 ATATATATAT
10846 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10888 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* ** * * ** * *
10930 AG AG AG AG AG AG AG AG AG AG AG AG A- ACT TC ATT ATT TT CG ATC
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG A-G A-G AG AG A-G
** * * * * * * * * * * *
10973 TC A- AG ATC A- AG AT AT AT AT AT A- AT AT AT AT AT AG AG AG AG
1 AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
11013 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
11055 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
11097 AG AG AG
1 AG AG AG
11103 GCATGTACGT
Statistics
Matches: 233, Mismatches: 14, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
1 4 0.02
2 225 0.97
3 4 0.02
ACGTcount: A:0.48, C:0.02, G:0.41, T:0.08
Consensus pattern (2 bp):
AG
Found at i:12415 original size:22 final size:21
Alignment explanation
Indices: 12390--12430 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
12380 TTTAAAAAAT
12390 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
12412 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
12431 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:13059 original size:2 final size:2
Alignment explanation
Indices: 13054--13083 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13044 CGTGTGTGTG
13054 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13084 ACAACTACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14616 original size:43 final size:43
Alignment explanation
Indices: 14394--14744 Score: 227
Period size: 43 Copynumber: 8.2 Consensus size: 43
14384 TTTCAAGAAA
*
14394 AAACGCCGCAATAGGTGTTGATATTTAGCGGCG-TTTGATAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTGAT-CAC
* * * * **
14437 AAATGCCACAATAGATGTTGATATTTAGCGGCGTTTGGAAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTGATCAC
* * * * **
14480 AAACGTCGCAATAGATGTTGATATTTAGCGGCATTTGGAAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTGATCAC
* * * ** *
14523 AAACGCCACAGTAGGT-TTCGAT-TTATAGCAGCGTTTTTCTCAG
1 AAACGCCGCAATAGGTGTT-GATATT-TAGCGGCGTTTTGATCAC
* * * *
14566 AAACGCCGCAGTAGGTGTTGATTTTTAGTGGCGTTTTTATCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTGATCAC
* * ** * * **
14609 AAACGCCGCAATAAGTGTTAAGGTTTAGCGGCGTTTTTAGCTT
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTGATCAC
* * *
14652 AAACGCCGCAATATGTGTT--TGATTTGGCGGCGTCTTTAAT-AC
1 AAACGCCGCAATAGGTGTTGAT-ATTTAGCGGCGT-TTTGATCAC
* * *
14694 AAACGCCGCTAA-A-GAG-AGATATATAGCGGCGTTTTAGAAT-AC
1 AAACGCCGC-AATAGGTGTTGATATTTAGCGGCGTTTT-G-ATCAC
14736 AAACGCCGC
1 AAACGCCGC
14745 TAAATTACAC
Statistics
Matches: 248, Mismatches: 48, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
40 3 0.01
41 12 0.05
42 38 0.15
43 187 0.75
44 8 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTGATCAC
Found at i:14698 original size:42 final size:44
Alignment explanation
Indices: 14607--14744 Score: 112
Period size: 42 Copynumber: 3.2 Consensus size: 44
14597 CGTTTTTATC
* * *
14607 ACAAACGCCGCAATAAGTGTTAAGGTTTAGCGGCGTTTTTAGCT
1 ACAAACGCCGCAATAAGTGTTAAGATTTAGCGGCGTCTTTAGAT
* * * *
14651 -TAAACGCCGCAATATGTGTT-TGATTTGGCGGCGTCTTTA-AT
1 ACAAACGCCGCAATAAGTGTTAAGATTTAGCGGCGTCTTTAGAT
* *
14692 ACAAACGCCGCTA-AAGAG---AGATATATAGCGGCGT-TTTAGAAT
1 ACAAACGCCGCAATAAGTGTTAAGAT-T-TAGCGGCGTCTTTAG-AT
14734 ACAAACGCCGC
1 ACAAACGCCGC
14745 TAAATTACAC
Statistics
Matches: 76, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
39 3 0.04
40 5 0.07
41 12 0.16
42 38 0.50
43 18 0.24
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
ACAAACGCCGCAATAAGTGTTAAGATTTAGCGGCGTCTTTAGAT
Found at i:15096 original size:21 final size:21
Alignment explanation
Indices: 15071--15127 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
15061 ATATGTTGCT
15071 TCTCTTTGTGCTGCCGCTGCC
1 TCTCTTTGTGCTGCCGCTGCC
15092 TCTCTTTGTGCTGCCGCTGCC
1 TCTCTTTGTGCTGCCGCTGCC
*
15113 TCTCTCTGTGCTGCC
1 TCTCTTTGTGCTGCC
15128 ACTGTTTCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.00, C:0.39, G:0.23, T:0.39
Consensus pattern (21 bp):
TCTCTTTGTGCTGCCGCTGCC
Found at i:15137 original size:21 final size:21
Alignment explanation
Indices: 15071--15153 Score: 103
Period size: 21 Copynumber: 4.0 Consensus size: 21
15061 ATATGTTGCT
*
15071 TCTCTTTGTGCTGCCGCTGCC
1 TCTCTCTGTGCTGCCGCTGCC
*
15092 TCTCTTTGTGCTGCCGCTGCC
1 TCTCTCTGTGCTGCCGCTGCC
* **
15113 TCTCTCTGTGCTGCCACTGTT
1 TCTCTCTGTGCTGCCGCTGCC
* *
15134 TCTCTCTCTGCTTCCGCTGC
1 TCTCTCTGTGCTGCCGCTGC
15154 TGCTCTGGCT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.01, C:0.39, G:0.20, T:0.40
Consensus pattern (21 bp):
TCTCTCTGTGCTGCCGCTGCC
Found at i:15196 original size:21 final size:21
Alignment explanation
Indices: 15100--15190 Score: 94
Period size: 21 Copynumber: 4.3 Consensus size: 21
15090 CCTCTCTTTG
* *
15100 TGCTGCCGCTGCCT-CTCTCTG
1 TGCTTCCGCTG-CTGCTCTCTC
* * * *
15121 TGCTGCCACTGTTTCTCTCTC
1 TGCTTCCGCTGCTGCTCTCTC
**
15142 TGCTTCCGCTGCTGCTCTGGC
1 TGCTTCCGCTGCTGCTCTCTC
15163 TGCTTCCGCTGCTGCTCTCTC
1 TGCTTCCGCTGCTGCTCTCTC
15184 TGCTTCC
1 TGCTTCC
15191 CTTGCTTCAT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 1 0.02
21 57 0.98
ACGTcount: A:0.01, C:0.41, G:0.21, T:0.37
Consensus pattern (21 bp):
TGCTTCCGCTGCTGCTCTCTC
Found at i:17192 original size:60 final size:59
Alignment explanation
Indices: 17125--17249 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 59
17115 CACATACGAA
* * * *
17125 TTTTATCTTGGCGTACCAAGTAACATAGTTGAGCCTTAGCTCTTTATCATTCACATGGT
1 TTTTATCTTGGCGTACCAAGTAACATAGTTGAGCATTAACTCCTTATCATTCACATAGT
* *
17184 TTCTTATCTTGGCTTACCTAGTAACATAGTTGAGCATTAACTCCTTATCATTCACATAGT
1 TT-TTATCTTGGCGTACCAAGTAACATAGTTGAGCATTAACTCCTTATCATTCACATAGT
17244 TTTTAT
1 TTTTAT
17250 TCATGGATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 6 0.10
60 53 0.90
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.42
Consensus pattern (59 bp):
TTTTATCTTGGCGTACCAAGTAACATAGTTGAGCATTAACTCCTTATCATTCACATAGT
Found at i:18445 original size:42 final size:42
Alignment explanation
Indices: 18399--18502 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 42
18389 GTTTTTAATT
* *
18399 AAAAACGCAACTAAAGTACGCAT-CATTTGCGGCGTTTGTTA-G
1 AAAAACGCAACTAAAGTACGAATAC-TTTGCGGCGTTT-CTACG
** * *
18441 AAAAACGCTGCTAAATTACTAATACTTTGCGGCGTTTCTACG
1 AAAAACGCAACTAAAGTACGAATACTTTGCGGCGTTTCTACG
*
18483 -AAAACGCCACTAAAGTACGA
1 AAAAACGCAACTAAAGTACGA
18503 GGCTATAGCG
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 18 0.36
42 31 0.62
43 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (42 bp):
AAAAACGCAACTAAAGTACGAATACTTTGCGGCGTTTCTACG
Found at i:19062 original size:57 final size:57
Alignment explanation
Indices: 18843--19030 Score: 358
Period size: 57 Copynumber: 3.3 Consensus size: 57
18833 ATTAAAACAG
*
18843 AAGTACTTATGCATAAAACTAATTAACAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
18900 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
*
18957 AAGTACTTATGCATAAAACTACTTAAAAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
19014 AAGTACTTATGCATAAA
1 AAGTACTTATGCATAAA
19031 CAGTCTTCAC
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 129 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.30
Consensus pattern (57 bp):
AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
Found at i:20141 original size:41 final size:40
Alignment explanation
Indices: 20096--20203 Score: 105
Period size: 41 Copynumber: 2.6 Consensus size: 40
20086 TCACATATTT
* *
20096 TTGCGGCGTTTATACAATAAGCGTCGCTATAT-TAC-ACTATA
1 TTGCGGCGTTT-TACAATAA-CGCCGCTAAATGT-CTACTATA
20137 TTGCGGCGTTTTTAGCTAA-AACGCCGCTAAATGTCTACTATA
1 TTGCGGCG-TTTTA-C-AATAACGCCGCTAAATGTCTACTATA
*
20179 TTGCGGCGTTTTACTATAAACGCCG
1 TTGCGGCGTTTTACAAT-AACGCCG
20204 TTATTGTTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
39 1 0.02
40 1 0.02
41 32 0.56
42 21 0.37
43 2 0.04
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (40 bp):
TTGCGGCGTTTTACAATAACGCCGCTAAATGTCTACTATA
Found at i:33803 original size:13 final size:13
Alignment explanation
Indices: 33785--33812 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33775 TTTAATTCTC
33785 AAACCCTAACCCT
1 AAACCCTAACCCT
33798 AAACCCTAACCCT
1 AAACCCTAACCCT
33811 AA
1 AA
33813 TTTTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (13 bp):
AAACCCTAACCCT
Found at i:33875 original size:21 final size:20
Alignment explanation
Indices: 33836--33887 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 20
33826 CCAATTATAG
* *
33836 AACCCTAATTCTCAAATTAA
1 AACCATAATTCCCAAATTAA
* *
33856 ATACCATAATTCCCACATTAG
1 A-ACCATAATTCCCAAATTAA
33877 AACCA-AATTCC
1 AACCATAATTCC
33888 AACAATTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 6 0.22
20 5 0.19
21 16 0.59
ACGTcount: A:0.42, C:0.29, G:0.02, T:0.27
Consensus pattern (20 bp):
AACCATAATTCCCAAATTAA
Found at i:33898 original size:19 final size:20
Alignment explanation
Indices: 33833--33905 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
33823 AGGCCAATTA
*
33833 TAGAACCCTAATTCTCAA-AT
1 TAGAACCATAATTC-CAACAT
* *
33853 TAAATACCATAATTCCCACAT
1 TAGA-ACCATAATTCCAACAT
33874 TAGAACCA-AATTCCAACAAT
1 TAGAACCATAATTCCAAC-AT
*
33894 T-GAACCCTAATT
1 TAGAACCATAATT
33906 TTTTTATTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 13 0.30
20 16 0.37
21 14 0.33
ACGTcount: A:0.42, C:0.26, G:0.04, T:0.27
Consensus pattern (20 bp):
TAGAACCATAATTCCAACAT
Found at i:34519 original size:21 final size:21
Alignment explanation
Indices: 34478--34554 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
34468 ATTGGAAAAA
**
34478 AATTTGATAAAA-TAAGTGGTC
1 AATTTGA-AAAATTAAAAGGTC
**
34499 AATTCAAAAAATTAAAAGGTC
1 AATTTGAAAAATTAAAAGGTC
* *
34520 AATTTGAAAAATTAAATGATC
1 AATTTGAAAAATTAAAAGGTC
34541 AATTTGAAAAATTA
1 AATTTGAAAAATTA
34555 GTGAACATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 4 0.09
21 43 0.91
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.31
Consensus pattern (21 bp):
AATTTGAAAAATTAAAAGGTC
Found at i:37557 original size:56 final size:56
Alignment explanation
Indices: 37496--37794 Score: 481
Period size: 56 Copynumber: 5.3 Consensus size: 56
37486 AACTTCTCAC
*
37496 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAATTCATTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
* *
37552 TTCTTAGTTTTTGCACACAAAGTGACCATATGGAAATTCATAAACTCATTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
*
37608 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAAATCATTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
* * *
37664 TTCTTAGTTTTTGCACATAAAGTTCCCATATGGAAATTCATAAACTCATTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
* * * * *
37720 TTCTTAGTTTTTACACACAAAGTGTCTATACGAAAATTCATAAACTAATTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
*
37776 TTCTTTGTTTTTGCACACA
1 TTCTTAGTTTTTGCACACA
37795 TATAGTGTCG
Statistics
Matches: 223, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 223 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (56 bp):
TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
Found at i:38402 original size:26 final size:26
Alignment explanation
Indices: 38372--38425 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
38362 TTTCCATTTT
38372 TCTACCCGATTCTTACCCAAATTTAA
1 TCTACCCGATTCTTACCCAAATTTAA
38398 TCTACCCGATTCTTACCCAAATTTAA
1 TCTACCCGATTCTTACCCAAATTTAA
38424 TC
1 TC
38426 AAATTTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.31, G:0.04, T:0.35
Consensus pattern (26 bp):
TCTACCCGATTCTTACCCAAATTTAA
Found at i:46780 original size:22 final size:21
Alignment explanation
Indices: 46734--46788 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
46724 CCAGGGAGGT
*
46734 ATCGATTCCC-CTGTGGGGGGA
1 ATCGATTCCCTC-ATGGGGGGA
*
46755 ATCGGTTCCCTCATGGGGGGA
1 ATCGATTCCCTCATGGGGGGA
46776 GATCGATTCCCTC
1 -ATCGATTCCCTC
46789 TGCACCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.15, C:0.27, G:0.33, T:0.25
Consensus pattern (21 bp):
ATCGATTCCCTCATGGGGGGA
Found at i:54003 original size:56 final size:56
Alignment explanation
Indices: 53942--54175 Score: 342
Period size: 56 Copynumber: 4.3 Consensus size: 56
53932 AACTTCTTAC
* * *
53942 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGGAATTCATAAACTCATTACGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTCATTATGAAT
53998 TTCTTAGTTTTTGCACACAAAGTG------C---AATTCATAAACTCATTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTCATTATGAAT
54045 TTCTTAGTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTCATTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTCATTATGAAT
** * *
54101 TTCTTAGTTTTTGCACACAAAGTGCCTGTATAGAAATTCATAAACTCGTTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTCATTATGAAT
54157 TTCTTAGTTTTTGCACACA
1 TTCTTAGTTTTTGCACACA
54176 TATGTGTCAT
Statistics
Matches: 164, Mismatches: 5, Indels: 18
0.88 0.03 0.10
Matches are distributed among these distances:
47 45 0.27
50 1 0.01
53 1 0.01
56 117 0.71
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (56 bp):
TTCTTAGTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTCATTATGAAT
Found at i:54101 original size:103 final size:105
Alignment explanation
Indices: 53942--54175 Score: 355
Period size: 103 Copynumber: 2.2 Consensus size: 105
53932 AACTTCTTAC
* *
53942 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGGAATTCATAAACTCATTACGAATTTCTTAGTT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTCATTACGAATTTCTTAGTT
54007 TTTGCACACAAAGTG-C-AATTCATAAACTCATTATGAAT
66 TTTGCACACAAAGTGCCAAATTCATAAACTCATTATGAAT
*
54045 TTCTTAGTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTCATTATGAATTTCTTAGTT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTCATTACGAATTTCTTAGTT
*
54110 TTTGCACACAAAGTGCCTGTATAGAAATTCATAAACTCGTTATGAAT
66 TTTGCACACAAAGTGCC-------AAATTCATAAACTCATTATGAAT
54157 TTCTTAGTTTTTGCACACA
1 TTCTTAGTTTTTGCACACA
54176 TATGTGTCAT
Statistics
Matches: 118, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
103 77 0.65
104 1 0.01
112 40 0.34
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (105 bp):
TTCTTAGTTTTTGCACACAAAGTGCCCATACAGAAATTCATAAACTCATTACGAATTTCTTAGTT
TTTGCACACAAAGTGCCAAATTCATAAACTCATTATGAAT
Found at i:54636 original size:18 final size:18
Alignment explanation
Indices: 54613--54647 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
54603 CGATGCCTTC
54613 CTCATAGAATCGATACCA
1 CTCATAGAATCGATACCA
54631 CTCATAGAATCGATACC
1 CTCATAGAATCGATACC
54648 CCCTGGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (18 bp):
CTCATAGAATCGATACCA
Found at i:61609 original size:11 final size:11
Alignment explanation
Indices: 61590--61624 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
61580 GAGGACATTA
*
61590 TGGAGTAAAAT
1 TGGAATAAAAT
61601 TGGAATAAAAT
1 TGGAATAAAAT
*
61612 TGGAACAAAAT
1 TGGAATAAAAT
61623 TG
1 TG
61625 CTATTCTCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.49, C:0.03, G:0.23, T:0.26
Consensus pattern (11 bp):
TGGAATAAAAT
Found at i:63593 original size:24 final size:25
Alignment explanation
Indices: 63548--63599 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
63538 GTTTGAGATA
* **
63548 CAACATCACCACCATCTTCCAT-TT
1 CAACATCAACACCATCAACCATCTT
63572 CAACATCAACACCATCAACCATCTT
1 CAACATCAACACCATCAACCATCTT
63597 CAA
1 CAA
63600 TCAAGGCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (25 bp):
CAACATCAACACCATCAACCATCTT
Found at i:66400 original size:18 final size:18
Alignment explanation
Indices: 66368--66405 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
66358 AGTATCATTG
*
66368 ACACTCTAGGATCATGTA
1 ACACTCTAGGATCATCTA
66386 ACACTCTATGG-TCATCTA
1 ACACTCTA-GGATCATCTA
66404 AC
1 AC
66406 TATGCATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (18 bp):
ACACTCTAGGATCATCTA
Found at i:67651 original size:19 final size:20
Alignment explanation
Indices: 67606--67654 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
67596 CTCTGCCAGT
* *
67606 AGTATCGATGCTGACCCATG
1 AGTATCGATACTCACCCATG
*
67626 GGTATCGATACTCACCC-TG
1 AGTATCGATACTCACCCATG
67645 AGTATCGATA
1 AGTATCGATA
67655 GCAAAAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (20 bp):
AGTATCGATACTCACCCATG
Found at i:69580 original size:5 final size:5
Alignment explanation
Indices: 69570--69643 Score: 84
Period size: 5 Copynumber: 15.2 Consensus size: 5
69560 AATATTTATA
* *
69570 ATAAT ATAAT ATAAT ATAAT ATAAT AATAA- ATAAA ATTAT ATAAT AT--T
1 ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT
69618 ATAA- ATAAT ATATAT ATAAT ATAAT A
1 ATAAT ATAAT ATA-AT ATAAT ATAAT A
69644 CGTACACTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
3 3 0.05
4 8 0.13
5 40 0.67
6 9 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:69580 original size:20 final size:21
Alignment explanation
Indices: 69556--69641 Score: 97
Period size: 20 Copynumber: 4.1 Consensus size: 21
69546 AATAAATCAA
*
69556 AAATAATATTTATAATAATAT
1 AAATAATATATATAATAATAT
69577 AATATAATATA-AT-ATAATAAT
1 AA-ATAATATATATAATAAT-AT
* *
69598 AAATAAAATTATATAATATTAT
1 AAATAATA-TATATAATAATAT
69620 AAATAATATATAT-ATAATAT
1 AAATAATATATATAATAATAT
69640 AA
1 AA
69642 TACGTACACT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
20 18 0.33
21 15 0.27
22 18 0.33
23 4 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATAATATATATAATAATAT
Found at i:69603 original size:25 final size:25
Alignment explanation
Indices: 69558--69643 Score: 97
Period size: 25 Copynumber: 3.4 Consensus size: 25
69548 TAAATCAAAA
*
69558 ATAATATTTATAATAATATAATATAAT
1 ATAATA-TAATAATAA-ATAATATAAT
* *
69585 ATAATATAATAATAAATAAAATTAT
1 ATAATATAATAATAAATAATATAAT
69610 ATAATAT--T-ATAAATAATATATAT
1 ATAATATAATAATAAATAATATA-AT
69633 ATAATATAATA
1 ATAATATAATA
69644 CGTACACTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
22 10 0.20
23 10 0.20
25 16 0.32
26 8 0.16
27 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAATATAATAATAAATAATATAAT
Found at i:69672 original size:18 final size:20
Alignment explanation
Indices: 69649--69777 Score: 85
Period size: 22 Copynumber: 6.4 Consensus size: 20
69639 TAATACGTAC
69649 ACTATATT-TATTTT-AAAA
1 ACTATATTATATTTTCAAAA
69667 ACTATATTATATTTTCAAAA
1 ACTATATTATATTTTCAAAA
*
69687 ACTATATATATGCGTTTTCAAAA
1 ACTATAT-TAT--ATTTTCAAAA
69710 AC-AT-TT-T-TTTT--AAA
1 ACTATATTATATTTTCAAAA
*
69724 ACTATATATTATACGTTTTCAAGA
1 AC--TATATTATA--TTTTCAAAA
* *
69748 CCTATACTATATACTTTCAAAA
1 ACTATA-T-TATATTTTCAAAA
69770 ACTATATT
1 ACTATATT
69778 TGAAATTATC
Statistics
Matches: 88, Mismatches: 6, Indels: 32
0.70 0.05 0.25
Matches are distributed among these distances:
14 5 0.06
16 4 0.05
17 2 0.02
18 10 0.11
19 8 0.09
20 13 0.15
21 5 0.06
22 22 0.25
23 12 0.14
24 7 0.08
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.44
Consensus pattern (20 bp):
ACTATATTATATTTTCAAAA
Found at i:71360 original size:2 final size:2
Alignment explanation
Indices: 71353--71387 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
71343 CTTTAAACGT
71353 TA TA TA TA 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 TA TA TA TA T
71388 TTGAAATTAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.