Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002603.1 Hibiscus syriacus cultivar Beakdansim tig00005263_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: 93015
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1292 original size:25 final size:25
Alignment explanation
Indices: 1264--1328 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
1254 TTATCATTAA
1264 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
1289 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
1314 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
1329 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:1653 original size:22 final size:22
Alignment explanation
Indices: 1608--1653 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1598 ATTACATAAC
*
1608 TTTTAAAAAAAGTATCGATCCT
1 TTTTAAAAAAAGTATCGAACCT
*
1630 TTTTATAAAAAGTAT-GAACACT
1 TTTTAAAAAAAGTATCGAAC-CT
1652 TT
1 TT
1654 CAATATATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTTAAAAAAAGTATCGAACCT
Found at i:1695 original size:23 final size:23
Alignment explanation
Indices: 1669--1731 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
1659 TATAGTAAAC
*
1669 ATATGATGTAATAGGT-TGCGCTT
1 ATATAATGTAATAGGTAT-CGCTT
*
1692 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGCTT
1715 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1732 GTGGTTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 36 0.97
24 1 0.03
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGCTT
Found at i:1739 original size:23 final size:23
Alignment explanation
Indices: 1669--1741 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1659 TATAGTAAAC
* * *
1669 ATATGATGTAATAGGTTGCGCTT
1 ATATAATGTAATAGGTAGTGCTT
*
1692 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
1715 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
1738 ATAT
1 ATAT
1742 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:2178 original size:18 final size:18
Alignment explanation
Indices: 2155--2190 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2145 GTAATTGGAG
2155 TTGAATTTAAATTTCAAT
1 TTGAATTTAAATTTCAAT
*
2173 TTGAATTTGAATTTCAAT
1 TTGAATTTAAATTTCAAT
2191 ATATATTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (18 bp):
TTGAATTTAAATTTCAAT
Found at i:2499 original size:34 final size:34
Alignment explanation
Indices: 2461--2526 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
2451 AAATCCAAAG
*
2461 CTCATATGGTGCCAAGCAAAAGGAAATCAAAAAT
1 CTCATATGATGCCAAGCAAAAGGAAATCAAAAAT
2495 CTCATATGATGCCAAGCAAAAGGAAATCAAAA
1 CTCATATGATGCCAAGCAAAAGGAAATCAAAA
2527 TCTACAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.48, C:0.18, G:0.17, T:0.17
Consensus pattern (34 bp):
CTCATATGATGCCAAGCAAAAGGAAATCAAAAAT
Found at i:2926 original size:21 final size:22
Alignment explanation
Indices: 2880--2926 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
2870 TAAATACATA
2880 ACTTTTAAAAAAAGTATCGATC
1 ACTTTTAAAAAAAGTATCGATC
* * *
2902 -CTTTTTATAAAAGTATGGA-C
1 ACTTTTAAAAAAAGTATCGATC
2922 ACTTT
1 ACTTT
2927 CATATAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (22 bp):
ACTTTTAAAAAAAGTATCGATC
Found at i:2995 original size:22 final size:23
Alignment explanation
Indices: 2943--3014 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
2933 ATAGGTAAAC
*
2943 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
2966 ATATAATGTAATATGTATCG-TT
1 ATATAATGTAATAGGTAGCGCTT
* * *
2988 TTATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
3011 ATAT
1 ATAT
3015 GTAAAGTGTC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 18 0.45
23 22 0.55
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:3216 original size:30 final size:28
Alignment explanation
Indices: 3157--3222 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 28
3147 ACGTACGTAT
* * *
3157 ATATTATTATTAAATTAAAAATTCTAATA
1 ATATT-TTATAAAATTAAAAAATCAAATA
3186 ATATTTTATAAAATATCAAAAAATCAAATA
1 ATATTTTATAAAAT-T-AAAAAATCAAATA
*
3216 ATTTTTT
1 ATATTTT
3223 GTGCAATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 8 0.26
29 6 0.19
30 17 0.55
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (28 bp):
ATATTTTATAAAATTAAAAAATCAAATA
Found at i:17051 original size:35 final size:35
Alignment explanation
Indices: 17007--17119 Score: 138
Period size: 35 Copynumber: 3.2 Consensus size: 35
16997 AAAATAGTCC
*
17007 TCAATTTCATTTTAAACCCCAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* **
17042 TCGATTTCATTCTAAACCTTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* ** *
17077 TCAATTAT-ATTCTAAAACCCAAATTTTAAAATACT
1 TCAATT-TCATTCTAAACCCCAAATTCCAAAATAAT
17112 TCAATTTC
1 TCAATTTC
17120 TGTCTTTTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 1 0.02
35 63 0.97
36 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:18229 original size:35 final size:35
Alignment explanation
Indices: 18181--18302 Score: 156
Period size: 35 Copynumber: 3.4 Consensus size: 35
18171 ATTCCTCCTT
*
18181 AAATTGAAGTATTTTAGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTTAGGGTTTAGAATG
* * *
18216 TAATTGAATTATTTTGGAATTTAAGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTTAGGGTTTAGAATG
* *
18251 AAATTGAATTA-CTTCGAAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTAG-AATTTAGGGTTTAGAATG
18286 AAATTGAGGATTATTTT
1 AAATTGA--ATTATTTT
18303 GTAAGTTTTA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
34 3 0.04
35 65 0.88
37 4 0.05
38 2 0.03
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTAGGGTTTAGAATG
Found at i:23943 original size:2 final size:2
Alignment explanation
Indices: 23936--23964 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23926 TTGTTCTTGA
23936 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 A
23965 ACAAATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24066 original size:2 final size:2
Alignment explanation
Indices: 24054--24105 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
24044 TATAGCACCC
24054 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24095 AT AT AT AT AT A
1 AT AT AT AT AT A
24106 AAATGTAATC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24454 original size:16 final size:16
Alignment explanation
Indices: 24417--24461 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
24407 AGTTGTTTGT
24417 AATTAGCGGTTAGAAA
1 AATTAGCGGTTAGAAA
** *
24433 GGTTAGCTGTTAGAAA
1 AATTAGCGGTTAGAAA
*
24449 AATTAGTGGTTAG
1 AATTAGCGGTTAG
24462 CAAAGTCCGA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.31
Consensus pattern (16 bp):
AATTAGCGGTTAGAAA
Found at i:24759 original size:125 final size:125
Alignment explanation
Indices: 24588--24833 Score: 343
Period size: 125 Copynumber: 2.0 Consensus size: 125
24578 GTTAGCTGAA
* * * *
24588 TCTGAACCATAATAATGTGGATCATACCCCGGATCGGGTTACCACAAGATCGATTCAAATATTAT
1 TCTGAACCATAATAATGTGGATCATACCCCAGATCGGGTCACCACAAGATCGAATCAAATATTAG
*
24653 AAACAATAAATAAATAAGCAACAGTTAGAA-TGCAATAAAAT-AAGTCAGTAGTTAATAGAG
66 AAACAATAAATAAATAA-CAACAGTTA-AAGTGCAATAAAATAAAGTCAATAGTTAATAGAG
* * * * *
24713 TCTGAATCATAATAATGTGGATCATATCCCAGATCTGGTCATCACAAGATCGAATCGAATATTAG
1 TCTGAACCATAATAATGTGGATCATACCCCAGATCGGGTCACCACAAGATCGAATCAAATATTAG
**
24778 AAACAATAAATAAATAACAATTGTTAAAGTGCAATAAAATAAAAGTCAATAGTTAA
66 AAACAATAAATAAATAACAACAGTTAAAGTGCAATAAAAT-AAAGTCAATAGTTAA
24834 CTTTGAAATA
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
123 2 0.02
124 18 0.17
125 73 0.69
126 13 0.12
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (125 bp):
TCTGAACCATAATAATGTGGATCATACCCCAGATCGGGTCACCACAAGATCGAATCAAATATTAG
AAACAATAAATAAATAACAACAGTTAAAGTGCAATAAAATAAAGTCAATAGTTAATAGAG
Found at i:30159 original size:44 final size:44
Alignment explanation
Indices: 30099--30189 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
30089 ATATGTCACA
30099 TTAATATTTAAATTTATGTAAACTTACCCAACTAACAAGAAACG
1 TTAATATTTAAATTTATGTAAACTTACCCAACTAACAAGAAACG
* * *
30143 TTAACTATTT-AATTTATGTAAACTTACCCGATTAACAAGAAATG
1 TTAA-TATTTAAATTTATGTAAACTTACCCAACTAACAAGAAACG
30187 TTA
1 TTA
30190 TAAATGTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 38 0.88
45 5 0.12
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (44 bp):
TTAATATTTAAATTTATGTAAACTTACCCAACTAACAAGAAACG
Found at i:33357 original size:13 final size:13
Alignment explanation
Indices: 33339--33368 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
33329 GTTCAGGTTT
33339 CAATTATAGAAAG
1 CAATTATAGAAAG
33352 CAATTATAGAAAG
1 CAATTATAGAAAG
33365 CAAT
1 CAAT
33369 GTTGAATGGT
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:0.53, C:0.10, G:0.13, T:0.23
Consensus pattern (13 bp):
CAATTATAGAAAG
Found at i:34195 original size:2 final size:2
Alignment explanation
Indices: 34146--34177 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34136 CAAATTAAAG
34146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34178 TATTTGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41787 original size:4 final size:4
Alignment explanation
Indices: 41772--41804 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
41762 TTTTGTTTTA
41772 TATT TAATT TATT TATT TATT TATT TATT TATT
1 TATT T-ATT TATT TATT TATT TATT TATT TATT
41805 ACTACCACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:53689 original size:2 final size:2
Alignment explanation
Indices: 53682--53708 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53672 CAATTTTGTG
53682 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
53709 TTTGTGTGTA
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
Found at i:57531 original size:21 final size:21
Alignment explanation
Indices: 57507--57580 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
57497 TATCGTAAAT
*
57507 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
57528 TCGCATTGCGAT-TTTCTATT
1 TCGCGTTGCGATAGTTGAAAA
57548 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
57569 TCGCGTTGCGAT
1 TCGCGTTGCGAT
57581 TTTCCATTTC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:57554 original size:41 final size:41
Alignment explanation
Indices: 57506--57600 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
57496 CTATCGTAAA
* *
57506 TTCGCGTTGCGATAGTTGGAAATCGCATTGCGATTTTCTAT
1 TTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTCCAT
*
57547 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTCCAT
57588 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
57601 TTTCCATTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTCCAT
Found at i:57556 original size:20 final size:20
Alignment explanation
Indices: 57528--57620 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
57518 TAGTTGGAAA
* *
57528 TCGCATTGCGATTTTCTATT
1 TCGCGTTGCGATTTTCCATT
* ** **
57548 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
57569 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
57589 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
57609 TCGCATTGCGAT
1 TCGCGTTGCGAT
57621 AGTCTACAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 45 0.75
21 15 0.25
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:57610 original size:61 final size:61
Alignment explanation
Indices: 57528--57647 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 61
57518 TAGTTGGAAA
* *
57528 TCGCATTGCGATTTTCTATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCATT
1 TCGCATTGCGATTTTCCATTTCGCATTGCGATAGTCT-AAAAT-GTCGTTGCGATTTTCCATT
* *
57589 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCTACAATGTCGTTGCGATTTTCCA
1 TCGCATTGCGATTTTCCATTTCGCATTGCGATAGTCTAAAATGTCGTTGCGATTTTCCA
57648 AATTCGTTGC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
60 1 0.02
61 51 0.96
62 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.40
Consensus pattern (61 bp):
TCGCATTGCGATTTTCCATTTCGCATTGCGATAGTCTAAAATGTCGTTGCGATTTTCCATT
Found at i:57680 original size:22 final size:22
Alignment explanation
Indices: 57614--57704 Score: 91
Period size: 22 Copynumber: 4.3 Consensus size: 22
57604 CCATTTCGCA
*
57614 TTGCGATAGTCTACA-ATGTCG
1 TTGCGATAGTCTACAGTTGTCG
* * **
57635 TTGCGAT--TTTCCAAAT-TCG
1 TTGCGATAGTCTACAGTTGTCG
*
57654 TTGCGATAGTCTACAGTTGTTG
1 TTGCGATAGTCTACAGTTGTCG
*
57676 TTGCGAAAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGTTGTCG
57698 TTGCGAT
1 TTGCGAT
57705 TTTCCAAATT
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
19 14 0.25
20 2 0.04
21 12 0.21
22 28 0.50
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (22 bp):
TTGCGATAGTCTACAGTTGTCG
Found at i:57681 original size:41 final size:40
Alignment explanation
Indices: 57592--57668 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
57582 TTCCATTTCG
*
57592 CGTTGCGATTTTCCATTTCGCATTGCGATAGTCTACAATGT
1 CGTTGCGATTTTCCAATTCG-ATTGCGATAGTCTACAATGT
57633 CGTTGCGATTTTCCAAATTCG-TTGCGATAGTCTACA
1 CGTTGCGATTTTCC-AATTCGATTGCGATAGTCTACA
57669 GTTGTTGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
40 15 0.44
41 14 0.41
42 5 0.15
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTTCCAATTCGATTGCGATAGTCTACAATGT
Found at i:57815 original size:6 final size:6
Alignment explanation
Indices: 57804--57834 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
57794 ACACGTATGG
57804 CCACGA CCACGA CCACGA CCACGA CC-CGA CC
1 CCACGA CCACGA CCACGA CCACGA CCACGA CC
57835 CGAGACGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.29, C:0.55, G:0.16, T:0.00
Consensus pattern (6 bp):
CCACGA
Found at i:58355 original size:6 final size:6
Alignment explanation
Indices: 58344--58368 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58334 GTCGGGTCGG
58344 GTCCGT GTCCGT GTCCGT GTCCGT G
1 GTCCGT GTCCGT GTCCGT GTCCGT G
58369 GTCGTGGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.36, T:0.32
Consensus pattern (6 bp):
GTCCGT
Found at i:58374 original size:6 final size:6
Alignment explanation
Indices: 58365--58400 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
58355 TGTCCGTGTC
58365 CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT
1 CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT
58401 AATGGTAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
CGTGGT
Found at i:58374 original size:12 final size:11
Alignment explanation
Indices: 58333--58398 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 11
58323 TCTCGTCTCG
*
58333 GGTCGGGTCG-
1 GGTCGTGTCGT
58343 GGTCCGTGTCCGT
1 GGT-CGTGT-CGT
58356 -GTCCGTGTCCGT
1 GGT-CGTGT-CGT
58368 GGTCGTGGTCGT
1 GGTCGT-GTCGT
58380 GGTCGTGGTCGT
1 GGTCGT-GTCGT
58392 GGTCGTG
1 GGTCGTG
58399 GTAATGGTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
10 3 0.06
11 5 0.10
12 38 0.76
13 4 0.08
ACGTcount: A:0.00, C:0.23, G:0.47, T:0.30
Consensus pattern (11 bp):
GGTCGTGTCGT
Found at i:58374 original size:18 final size:18
Alignment explanation
Indices: 58333--58400 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
58323 TCTCGTCTCG
*
58333 GGTCGGGTCG-GGTCCGT
1 GGTCGTGTCGTGGTCCGT
58350 -GTCCGTGTCCGT-GTCCGT
1 GGT-CGTGT-CGTGGTCCGT
58368 GGTCGTGGTCGTGGT-CGT
1 GGTCGT-GTCGTGGTCCGT
58386 GGTCGTGGTCGTGGT
1 GGTCGT-GTCGTGGT
58401 AATGGTAATG
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
16 2 0.05
17 4 0.09
18 32 0.73
19 6 0.14
ACGTcount: A:0.00, C:0.22, G:0.47, T:0.31
Consensus pattern (18 bp):
GGTCGTGTCGTGGTCCGT
Found at i:58406 original size:18 final size:18
Alignment explanation
Indices: 58367--58406 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
58357 TCCGTGTCCG
**
58367 TGGTCGTGGTCGTGGTCG
1 TGGTCGTGGTCGTGGTAA
58385 TGGTCGTGGTCGTGGTAA
1 TGGTCGTGGTCGTGGTAA
58403 TGGT
1 TGGT
58407 AATGGTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.12, G:0.47, T:0.35
Consensus pattern (18 bp):
TGGTCGTGGTCGTGGTAA
Found at i:62641 original size:2 final size:2
Alignment explanation
Indices: 62634--62673 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
62624 ATGTACTTTG
62634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62674 GTTTTGTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67343 original size:4 final size:4
Alignment explanation
Indices: 67334--67370 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
67324 ATGATGAGTG
* *
67334 ACAT ACAT ACAT GCAT ACAT ACAT TCAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
67371 ATTTTTGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.46, C:0.24, G:0.03, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:69309 original size:2 final size:2
Alignment explanation
Indices: 69302--69338 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
69292 TTCTAAATCA
69302 AT 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 AT A
69339 ATTTTTTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:70611 original size:14 final size:13
Alignment explanation
Indices: 70588--70629 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
70578 AAATAATTGT
70588 ATTTTTATATTTA
1 ATTTTTATATTTA
*
70601 ATTTTTAATATTTT
1 ATTTTT-ATATTTA
70615 ATATTTTATATTTA
1 AT-TTTTATATTTA
70629 A
1 A
70630 AATTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.24
14 15 0.60
15 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTTATATTTA
Found at i:70616 original size:21 final size:21
Alignment explanation
Indices: 70590--70634 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
70580 ATAATTGTAT
* *
70590 TTTTATATTTAATTTTTAATA
1 TTTTATATTTAATATTTAAAA
*
70611 TTTTATATTTTATATTTAAAA
1 TTTTATATTTAATATTTAAAA
70632 TTT
1 TTT
70635 AAAATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATATTTAATATTTAAAA
Found at i:70622 original size:7 final size:7
Alignment explanation
Indices: 70590--70627 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
70580 ATAATTGTAT
70590 TTTTATA
1 TTTTATA
*
70597 TTTAAT-
1 TTTTATA
70603 TTTTAATA
1 TTTT-ATA
70611 TTTTATA
1 TTTTATA
70618 TTTTATA
1 TTTTATA
70625 TTT
1 TTT
70628 AAAATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 3 0.11
7 20 0.74
8 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTATA
Found at i:70635 original size:28 final size:28
Alignment explanation
Indices: 70590--70650 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
70580 ATAATTGTAT
* *
70590 TTTTATATTT-AATTTTTAATATTTTATA
1 TTTTATATTTAAAATTTAAATATTTT-TA
70618 TTTTATATTTAAAATTTAAAATATTTTTA
1 TTTTATATTTAAAATTT-AAATATTTTTA
70647 TTTT
1 TTTT
70651 TAAAAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 10 0.34
29 11 0.38
30 8 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTATATTTAAAATTTAAATATTTTTA
Found at i:71841 original size:2 final size:2
Alignment explanation
Indices: 71834--71859 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71824 GATTTTCTTT
71834 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
71860 CCATTTCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72433 original size:84 final size:85
Alignment explanation
Indices: 72292--72467 Score: 291
Period size: 84 Copynumber: 2.1 Consensus size: 85
72282 TTCATTGACT
* * * *
72292 AGTCTTGCTTGAAATTGTCTATATGGTTATATGTATCTGCAAATTTCTTCCCTTGGAACTATTCA
1 AGTCTTGCATGAAATTGTCTACATGGTTATATGTACCTGAAAATTTCTTCCCTTGGAACTATTCA
72357 TTC-CAGGTCACTATTAATC
66 TTCACAGGTCACTATTAATC
72376 AGTCTTGCATGAAATTGTCTACATGGTTATATGTACCTGAAAATTTCTTCCCTTGGAACTATTCA
1 AGTCTTGCATGAAATTGTCTACATGGTTATATGTACCTGAAAATTTCTTCCCTTGGAACTATTCA
* *
72441 TTCATAGGTCAGTATTAATC
66 TTCACAGGTCACTATTAATC
72461 AGTCTTG
1 AGTCTTG
72468 ATTGTTTGAA
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 64 0.75
85 21 0.25
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (85 bp):
AGTCTTGCATGAAATTGTCTACATGGTTATATGTACCTGAAAATTTCTTCCCTTGGAACTATTCA
TTCACAGGTCACTATTAATC
Found at i:80488 original size:22 final size:21
Alignment explanation
Indices: 80463--80505 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
80453 TAAAAAATTT
*
80463 CCTAAAACATTATTTATTTTTA
1 CCTAAAACATTAATT-TTTTTA
80485 CCTAAAACATTAATTTTTTTA
1 CCTAAAACATTAATTTTTTTA
80506 ACATTTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (21 bp):
CCTAAAACATTAATTTTTTTA
Found at i:80531 original size:25 final size:27
Alignment explanation
Indices: 80503--80563 Score: 108
Period size: 25 Copynumber: 2.3 Consensus size: 27
80493 ATTAATTTTT
80503 TTAACATTTCTGGTAAAGT-T-GAATA
1 TTAACATTTCTGGTAAAGTGTCGAATA
80528 TTAACATTTCTGGTAAAGTGTCGAATA
1 TTAACATTTCTGGTAAAGTGTCGAATA
80555 TTAACATTT
1 TTAACATTT
80564 TCGATAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 19 0.56
26 1 0.03
27 14 0.41
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (27 bp):
TTAACATTTCTGGTAAAGTGTCGAATA
Found at i:82793 original size:30 final size:31
Alignment explanation
Indices: 82747--82815 Score: 104
Period size: 30 Copynumber: 2.2 Consensus size: 31
82737 ACCTTTTTCT
*
82747 CTTCTCTCTTAATTATCTCCATGACTCTCTTA
1 CTTCTC-CTTAATTATCTCCAGGACTCTCTTA
*
82779 CTTCTCCTT-ATTATCTCCAGGCCTCTCTTA
1 CTTCTCCTTAATTATCTCCAGGACTCTCTTA
82809 CTTCTCC
1 CTTCTCC
82816 CCTAAAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 26 0.74
31 3 0.09
32 6 0.17
ACGTcount: A:0.14, C:0.36, G:0.04, T:0.45
Consensus pattern (31 bp):
CTTCTCCTTAATTATCTCCAGGACTCTCTTA
Found at i:91283 original size:17 final size:18
Alignment explanation
Indices: 91238--91286 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
91228 TATTTCTGAG
*
91238 GGAATTGGAAACTGTGAA
1 GGAATTGGAATCTGTGAA
* * *
91256 TGAATTAGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
91273 GGAATTGGAATCTG
1 GGAATTGGAATCTG
91287 AAACCTGTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Done.