Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006755.1 Hibiscus syriacus cultivar Beakdansim tig00017031_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: 79184
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:1542 original size:20 final size:20
Alignment explanation
Indices: 1517--1554 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1507 CAATTTATTC
1517 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
1537 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
1555 TCCTTCGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:10813 original size:21 final size:21
Alignment explanation
Indices: 10784--10827 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
10774 ACTCCGGGAG
* *
10784 CTAGTTCCTCTCGAGCTGCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
10805 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCTCGAGCTCCTC
10826 CT
1 CT
10828 CCTCCTCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.43, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCCTCTCGAGCTCCTC
Found at i:11564 original size:19 final size:19
Alignment explanation
Indices: 11518--11555 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
11508 AAAGGGGGAG
11518 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
11537 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
11556 GTTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (19 bp):
AAATGTTAAGTGTTGAAAT
Found at i:13686 original size:28 final size:28
Alignment explanation
Indices: 13646--13705 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
13636 GTTTGCCATC
13646 TTTTGTGAATTTGAGAGCAACTCCAATG
1 TTTTGTGAATTTGAGAGCAACTCCAATG
13674 TTTTGTGAATTTGAGAGCAACTCCAATG
1 TTTTGTGAATTTGAGAGCAACTCCAATG
13702 TTTT
1 TTTT
13706 TCTTCTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (28 bp):
TTTTGTGAATTTGAGAGCAACTCCAATG
Found at i:14741 original size:17 final size:17
Alignment explanation
Indices: 14728--14760 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
14718 CGAATGCATT
14728 CCATGCATCGATGCACA
1 CCATGCATCGATGCACA
*
14745 CCATGCACCGATGCAC
1 CCATGCATCGATGCAC
14761 TGAGGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.39, G:0.18, T:0.15
Consensus pattern (17 bp):
CCATGCATCGATGCACA
Found at i:14858 original size:64 final size:63
Alignment explanation
Indices: 14712--14870 Score: 209
Period size: 64 Copynumber: 2.5 Consensus size: 63
14702 GAATTAAATT
*
14712 GAACATCGAATGCATTCCATGCATCGATGCA-CACCATGCACCGATGCACTGAGGATTTTATAA
1 GAACATCGAATGCATT-GATGCATCGATGCACCACCATGCACCGATGCACTGAGGATTTTATAA
* *
14775 GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCG-GGCTATTT-T
1 GAACATCGAATGCA-TTGATGCATCGATGCACCA-CCATGCACCGATGCACT-GAGGAT-TTTAT
14838 AA
62 AA
14840 -AACATCGAATGCACTTGATGCATCGATGCAC
1 GAACATCGAATGCA-TTGATGCATCGATGCAC
14871 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
63 27 0.31
64 34 0.39
65 22 0.25
66 4 0.05
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (63 bp):
GAACATCGAATGCATTGATGCATCGATGCACCACCATGCACCGATGCACTGAGGATTTTATAA
Found at i:14870 original size:17 final size:19
Alignment explanation
Indices: 14842--14890 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
14832 TATTTTAAAA
14842 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
14860 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
14879 CACCGATGCACT
1 CATCGATGCACT
14891 AAGGTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:14886 original size:64 final size:61
Alignment explanation
Indices: 14712--14890 Score: 186
Period size: 64 Copynumber: 2.8 Consensus size: 61
14702 GAATTAAATT
*
14712 GAACATCGAATGCATTCCATGCATCGATGCACACCA-TGCACCGATGCACTGAGGATTTTATAA
1 GAACATCGAATGCATT-GATGCATCGATG--CACCAGTGCACCGATGCACTGAGGATTTTATAA
* *
14775 GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCG-GGCTATTT-T
1 GAACATCGAATGCA-TTGATGCATCGATGCACCAG---TGCACCGATGCACT-GAGGAT-TTTAT
14838 AA
60 AA
14840 -AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 GAACATCGAATGCA-TTGATGCATCGATGCAC-C--AGTGCACCGATGCACT
14891 AAGGTTCCAA
Statistics
Matches: 101, Mismatches: 5, Indels: 19
0.81 0.04 0.15
Matches are distributed among these distances:
61 5 0.05
63 25 0.25
64 45 0.45
65 20 0.20
66 4 0.04
67 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (61 bp):
GAACATCGAATGCATTGATGCATCGATGCACCAGTGCACCGATGCACTGAGGATTTTATAA
Found at i:17660 original size:12 final size:12
Alignment explanation
Indices: 17643--17667 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17633 ATGATGGTTC
17643 TCCAACGTCATG
1 TCCAACGTCATG
17655 TCCAACGTCATG
1 TCCAACGTCATG
17667 T
1 T
17668 ATATTTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCAACGTCATG
Found at i:20723 original size:65 final size:65
Alignment explanation
Indices: 20591--20750 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 65
20581 TGCACTAAGA
* * * *
20591 GTGCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGTCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGTCAT
*
20655 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGGT-
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCCTGAGTGCATCGATGCAT-GTC
20718 AT
64 AT
*
20720 GTGCATCTATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
20751 CAATTTATTC
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
64 27 0.31
65 55 0.63
66 5 0.06
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGTCAT
Found at i:22664 original size:28 final size:28
Alignment explanation
Indices: 22632--22693 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
22622 TATCCTTTTA
22632 CATTATGTCATCGAGCTAGTCCTTGAAG
1 CATTATGTCATCGAGCTAGTCCTTGAAG
* * *
22660 CATTACGTCATTGAGCTAGTTCTTGAAG
1 CATTATGTCATCGAGCTAGTCCTTGAAG
22688 CATTAT
1 CATTAT
22694 ATCAATGATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (28 bp):
CATTATGTCATCGAGCTAGTCCTTGAAG
Found at i:27549 original size:2 final size:2
Alignment explanation
Indices: 27542--27583 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
27532 AAAACAAATA
27542 AT 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 AT
27584 CCTTTAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38225 original size:19 final size:22
Alignment explanation
Indices: 38201--38256 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
38191 AATCTAATTT
38201 GGGTATCGGTACC-TAG-AT-G
1 GGGTATCGGTACCATAGCATAG
38220 GGGTATCGGTACCATAGCATAG
1 GGGTATCGGTACCATAGCATAG
*
38242 GGGTATCGATACCAT
1 GGGTATCGGTACCAT
38257 GGTGAGGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 13 0.39
20 3 0.09
21 2 0.06
22 15 0.45
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (22 bp):
GGGTATCGGTACCATAGCATAG
Found at i:38247 original size:22 final size:20
Alignment explanation
Indices: 38201--38275 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
38191 AATCTAATTT
38201 GGGTATCGGTACC-TAGATG
1 GGGTATCGGTACCATAGATG
38220 GGGTATCGGTACCATAGCATAG
1 GGGTATCGGTACCATAG-AT-G
* *
38242 GGGTATCGATACCAT-GGTG
1 GGGTATCGGTACCATAGATG
*
38261 AGGGTATCGATACCA
1 -GGGTATCGGTACCA
38276 GTCTATATCG
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
19 14 0.28
20 18 0.36
21 3 0.06
22 15 0.30
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.24
Consensus pattern (20 bp):
GGGTATCGGTACCATAGATG
Found at i:38328 original size:95 final size:94
Alignment explanation
Indices: 38146--38342 Score: 229
Period size: 95 Copynumber: 2.1 Consensus size: 94
38136 CCCAAGCAAT
** * * *
38146 GGGGTATCGATACTTTGGTAAGGGTATCGATACCAGTAAATATCAAATCTAATTTGGGTATCGGT
1 GGGGTATCGATACCATGGTAAGGGTATCGATACCAGTAAATATCAAAGCTAATTTCGGTATCGAT
*
38211 ACCTAGATGGGGTATCGGTACCAT-AGCATA
66 ACCTAGATGGGGTATCGATACCATAAG-A-A
* ** *
38241 GGGGTATCGATACCATGGTGAGGGTATCGATACCAGTCTATATCGAAGCTAATTTCGGTATCGAT
1 GGGGTATCGATACCATGGTAAGGGTATCGATACCAGTAAATATCAAAGCTAATTTCGGTATCGAT
* *
38306 ACATTA-A-GGGGATATTGATACCATAAGAA
66 AC-CTAGATGGGG-TATCGATACCATAAGAA
38335 GGGGTATC
1 GGGGTATC
38343 AAGACCAGAG
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
94 13 0.15
95 70 0.80
96 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (94 bp):
GGGGTATCGATACCATGGTAAGGGTATCGATACCAGTAAATATCAAAGCTAATTTCGGTATCGAT
ACCTAGATGGGGTATCGATACCATAAGAA
Found at i:38727 original size:57 final size:57
Alignment explanation
Indices: 38666--39093 Score: 642
Period size: 57 Copynumber: 7.5 Consensus size: 57
38656 GTGCAAAATA
* *
38666 TAAGAAATCATAGTAAGTGTATGAATTTCAGGTAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
38723 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
38780 TAAGAAATCATACTAAGGGTATGAATTTCAGATAGGGCATTTTGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
38837 TAAGAAATCATACTAAGTGTATGAATTTCAGGTAGGGCGTTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
38894 CAAGAAATCATACTAAGTGTATAAATTTCAGATAGTGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
38951 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* ** ** * **
39008 TAA-AAATCATACTAAGTGTATGAATTTTCAGATTGGGCACTTCGTGTGCTAACATAA
1 TAAGAAATCATACTAAGTGTATGAA-TTTCAGATAGGGCGTTTCGTACGCTAAAATGT
39065 TAAGAAATTCATACTAAGTGTATGAATTT
1 TAAGAAA-TCATACTAAGTGTATGAATTT
39094 TTGTATTAGA
Statistics
Matches: 340, Mismatches: 28, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
56 21 0.06
57 295 0.87
58 6 0.02
59 18 0.05
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:39116 original size:59 final size:58
Alignment explanation
Indices: 39014--39157 Score: 148
Period size: 59 Copynumber: 2.5 Consensus size: 58
39004 ATGTTAAAAA
* * * * * *
39014 TCATACTAAGTGTATGAATTTTCAG-ATTGGGCACTTCGTGTGCTAACATAATAAGAAAT
1 TCATACTAAGTGTATGAATTTT-TGTATTAGACACTTAGTGTGCTAA-AGAACAAGAAAT
* *
39073 TCATACTAAGTGTATGAATTTTTGTATTAGACATTTTAG-GTGCTAAAGGACAAGAAAT
1 TCATACTAAGTGTATGAATTTTTGTATTAGACA-CTTAGTGTGCTAAAGAACAAGAAAT
* * *
39131 TCATACTATGTGTATGAGTTTCTGTAT
1 TCATACTAAGTGTATGAATTTTTGTAT
39158 GGGAAACATA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
58 34 0.47
59 35 0.49
60 3 0.04
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.38
Consensus pattern (58 bp):
TCATACTAAGTGTATGAATTTTTGTATTAGACACTTAGTGTGCTAAAGAACAAGAAAT
Found at i:39587 original size:81 final size:81
Alignment explanation
Indices: 39441--39598 Score: 190
Period size: 81 Copynumber: 2.0 Consensus size: 81
39431 ATGTGTTGGC
* ** *
39441 CTAGCTGTGCAATTGACAGAAAAGTGTCAATTATGACAGTTAGATGAACAGTTAAGTACCGTTGA
1 CTAGCTGTGCAATTGACAGAAAAGTGTCAATTATGACAGTTAGATAAACAGTTAAACACCATTGA
39506 GTAAAAGAATAATGGT
66 GTAAAAGAATAATGGT
* * * ** ** *
39522 CTAGCTGTGCAATTGGCAGAAAGGTGTTAATTATTCCAGTTAGATAAAGGGTTAAACACTATTGA
1 CTAGCTGTGCAATTGACAGAAAAGTGTCAATTATGACAGTTAGATAAACAGTTAAACACCATTGA
**
39587 GTACGAGAATAA
66 GTAAAAGAATAA
39599 AGGAATTTTA
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 63 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28
Consensus pattern (81 bp):
CTAGCTGTGCAATTGACAGAAAAGTGTCAATTATGACAGTTAGATAAACAGTTAAACACCATTGA
GTAAAAGAATAATGGT
Found at i:43441 original size:19 final size:21
Alignment explanation
Indices: 43417--43470 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
43407 AATCTAATTT
43417 GGGTATCGGTACCTAG-AT-G
1 GGGTATCGGTACCTAGCATAG
* *
43436 GGGTATTGGTATCATAGCATAG
1 GGGTATCGGTA-CCTAGCATAG
*
43458 GGGTATCGATACC
1 GGGTATCGGTACC
43471 AGTCTATATC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 10 0.37
20 4 0.15
21 3 0.11
22 10 0.37
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (21 bp):
GGGTATCGGTACCTAGCATAG
Found at i:43945 original size:57 final size:57
Alignment explanation
Indices: 43884--44654 Score: 1224
Period size: 57 Copynumber: 13.5 Consensus size: 57
43874 GTGCAAAATA
* *
43884 TAAGAAATCATAGTAAGTGTATGAATTTCAGATAGGGCGTTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
43941 TAAGAAATCATACTAAGTGTATGAATTTCATATAGGGCGTTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
43998 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCATACGTTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
44055 TAAGAAATCATACTAAGTGTATGGATTTCAGATAGGGCATTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
44112 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
44169 TAAGAAATTATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* **
44226 TAAGAAATCATACTAAGTGTATGAATTTC-GTATAGGGCATTTCACACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAG-ATAGGGCGTTTCGTACGCTAAAATGT
* *
44283 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGTTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
44340 TAAGAAATCATACTAAGTGTATCG-ATTTCAGATAGGGCGTTTCGTACGCTAAAATGA
1 TAAGAAATCATACTAAGTGTAT-GAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* **
44397 TAAGAAATCATACTAAGTGTATGAATTTTAGATACAGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
44454 TAAGAAATTATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
44511 TAAGAAATCATACTATGTGTATGAATTTCAGATAGGGCGTTTAGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * ** * *
44568 TAAGAAATCATTCTAAGTGTATGAATTTTCAGATAGGGCACTTT-GTGTGCTAACATGA
1 TAAGAAATCATACTAAGTGTATGAA-TTTCAGATAGGGC-GTTTCGTACGCTAAAATGT
44626 TAAGAAATTCATACTAAGTGTATGAATTT
1 TAAGAAA-TCATACTAAGTGTATGAATTT
44655 TTGTATTGGA
Statistics
Matches: 667, Mismatches: 40, Indels: 13
0.93 0.06 0.02
Matches are distributed among these distances:
56 2 0.00
57 610 0.91
58 35 0.05
59 20 0.03
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:44677 original size:59 final size:58
Alignment explanation
Indices: 44562--44722 Score: 173
Period size: 58 Copynumber: 2.8 Consensus size: 58
44552 TAGTACGCTA
* * * * * *
44562 AAATGTTAAGAAA-TCATTCTAAGTGTATGAATTTTCAG-ATAGGGCACTTTGTGTGCT
1 AAATGATAAGAAATTCATACTAAGTGTATGAATTTT-TGTATTGGACACTTTGGGTGCT
*
44619 AACATGATAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGACATTTTGGGTGCT
1 AA-ATGATAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGACACTTTGGGTGCT
* * * * * *
44678 AAAGGACAAGAAATTCATACTATGTGTATGAGTTTCTATATTGGA
1 AAATGATAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGA
44723 AACAGAAGGG
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
57 2 0.02
58 48 0.55
59 38 0.43
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (58 bp):
AAATGATAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGACACTTTGGGTGCT
Found at i:47648 original size:16 final size:16
Alignment explanation
Indices: 47622--47663 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
47612 ATGAATTAAG
*
47622 AAAAGATGAAA-GAATA
1 AAAAAATGAAATG-ATA
*
47638 AAGAAATGAAATGATA
1 AAAAAATGAAATGATA
47654 AAAAAATGAA
1 AAAAAATGAA
47664 GATAACTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (16 bp):
AAAAAATGAAATGATA
Found at i:57383 original size:17 final size:17
Alignment explanation
Indices: 57335--57384 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
57325 TAAGAGTTTA
*
57335 TTTAATAAATGAACTAG
1 TTTAATGAATGAACTAG
* *
57352 TTTGATGAATAAACTAG
1 TTTAATGAATGAACTAG
* *
57369 TTTAATTACTGAACTA
1 TTTAATGAATGAACTA
57385 CTTCCCTAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:63714 original size:17 final size:17
Alignment explanation
Indices: 63685--63734 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
63675 TAAGAATTAA
*
63685 TTTAATAAATGAACTAG
1 TTTAATGAATGAACTAG
*
63702 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
*
63719 TTTAATTAATGAACTA
1 TTTAATGAATGAACTA
63735 CTTTCCCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:69710 original size:15 final size:15
Alignment explanation
Indices: 69690--69748 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
69680 TTTCTATCGT
*
69690 ATTTCATGTCGTTGC
1 ATTTCATGTCATTGC
69705 ATTTCAT-TGCATTGC
1 ATTTCATGT-CATTGC
*
69720 ATGTCATTGTCATTGC
1 ATTTCA-TGTCATTGC
69736 ATTTGCATGTCAT
1 ATTT-CATGTCAT
69749 CATGTTACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 1 0.03
15 17 0.46
16 16 0.43
17 3 0.08
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.46
Consensus pattern (15 bp):
ATTTCATGTCATTGC
Found at i:72616 original size:30 final size:31
Alignment explanation
Indices: 72559--72626 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
72549 ATGATCAAAA
72559 CACTTAATTAAGGCACATAACAACATTTGGT
1 CACTTAATTAAGGCACATAACAACATTTGGT
* *
72590 CACTTAATTGATGCACATAA-AACATTTGGT
1 CACTTAATTAAGGCACATAACAACATTTGGT
72620 CACTTAA
1 CACTTAA
72627 GGTATACTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 17 0.49
31 18 0.51
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (31 bp):
CACTTAATTAAGGCACATAACAACATTTGGT
Found at i:73562 original size:17 final size:18
Alignment explanation
Indices: 73526--73573 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
73516 CGCGCTTGCG
* *
73526 CGCACGCGCACACGCACA
1 CGCACACGCACACGCGCA
*
73544 CGC-CACGCGCACGCGCA
1 CGCACACGCACACGCGCA
73561 CGCACACGCACAC
1 CGCACACGCACAC
73574 ACACACACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.25, C:0.52, G:0.23, T:0.00
Consensus pattern (18 bp):
CGCACACGCACACGCGCA
Found at i:73566 original size:23 final size:24
Alignment explanation
Indices: 73524--73569 Score: 76
Period size: 23 Copynumber: 1.9 Consensus size: 24
73514 CGCGCGCTTG
73524 CGCGCACGCGCACACGCACACGCCA
1 CGCGCACGCG-ACACGCACACGCCA
73549 CGCGCACGCG-CACGCACACGC
1 CGCGCACGCGACACGCACACGC
73570 ACACACACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 11 0.52
25 10 0.48
ACGTcount: A:0.22, C:0.52, G:0.26, T:0.00
Consensus pattern (24 bp):
CGCGCACGCGACACGCACACGCCA
Found at i:73570 original size:6 final size:6
Alignment explanation
Indices: 73526--73590 Score: 69
Period size: 6 Copynumber: 11.0 Consensus size: 6
73516 CGCGCTTGCG
* * *
73526 CGCACG CGCACA CGCACA CGC-CA CGCGCA CGCGCA CGCACA CGCACA
1 CGCACA CGCACA CGCACA CGCACA CGCACA CGCACA CGCACA CGCACA
* * *
73573 CACACA CACACA CACACA
1 CGCACA CGCACA CGCACA
73591 TATACATATA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
5 5 0.09
6 50 0.91
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
CGCACA
Found at i:73597 original size:6 final size:6
Alignment explanation
Indices: 73588--73659 Score: 119
Period size: 6 Copynumber: 12.2 Consensus size: 6
73578 ACACACACAC
* *
73588 ACATAT ACATAT ACATAT ATATGT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
73636 AC-TAT ACATAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT A
73660 TGTACATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.08
6 56 0.92
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (6 bp):
ACATAT
Found at i:78562 original size:2 final size:2
Alignment explanation
Indices: 78557--78592 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
78547 TATATATATA
*
78557 TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
78593 GGAAAACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Done.