Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007300.1 Hibiscus syriacus cultivar Beakdansim tig00019426_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: 101434
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3960 original size:67 final size:68
Alignment explanation
Indices: 3853--3988 Score: 249
Period size: 67 Copynumber: 2.0 Consensus size: 68
3843 TAATGTACTA
3853 AATACTATTTAATAGATACTTATTTGAATTTAATGAAAAAAATAAAACATGTG-TTATAATCTCA
1 AATACTATTTAATAGATACTTATTTGAATTTAATGAAAAAAATAAAACATGTGTTTATAATCTCA
3917 CTT
66 CTT
3920 AATACTATTTAATAGATACTTAATTTGAATTTAATG-AAAAAATAAAACATGTGTTTATAATCTC
1 AATACTATTTAATAGATACTT-ATTTGAATTTAATGAAAAAAATAAAACATGTGTTTATAATCTC
3984 ACTT
65 ACTT
3988 A
1 A
3989 TACCCGATTA
Statistics
Matches: 67, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
67 38 0.57
68 29 0.43
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (68 bp):
AATACTATTTAATAGATACTTATTTGAATTTAATGAAAAAAATAAAACATGTGTTTATAATCTCA
CTT
Found at i:5577 original size:33 final size:34
Alignment explanation
Indices: 5530--5593 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
5520 TATATTATAT
*
5530 TTTTTATACAATATCTAAAATAAAAGTATTTTAA
1 TTTTTATAAAATATCTAAAATAAAAGTATTTTAA
* *
5564 TTTTTA-AAAATATCTAAAGTTAAAGTATTT
1 TTTTTATAAAATATCTAAAATAAAAGTATTT
5594 GAGTTCTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (34 bp):
TTTTTATAAAATATCTAAAATAAAAGTATTTTAA
Found at i:7524 original size:31 final size:31
Alignment explanation
Indices: 7486--7547 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
7476 AAGTGTTCTA
7486 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
*
7517 TACGAGCTGTGGTGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
7548 ATGCGCCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.24
Consensus pattern (31 bp):
TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
Found at i:7580 original size:22 final size:22
Alignment explanation
Indices: 7551--7602 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
7541 GCTTTGCATG
*
7551 CGCCATGCACGTCGGAAGAGGT
1 CGCCATGCACATCGGAAGAGGT
*
7573 TGCCATGCACATCGGAAGAGGT
1 CGCCATGCACATCGGAAGAGGT
7595 CGCC-TGCA
1 CGCCATGCA
7603 TTCAGTGGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.23, C:0.29, G:0.33, T:0.15
Consensus pattern (22 bp):
CGCCATGCACATCGGAAGAGGT
Found at i:7685 original size:29 final size:29
Alignment explanation
Indices: 7648--7735 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
7638 AGGGCGCAGG
* *
7648 ACAAGGTCGCCCAGCGTGCATGGCGACCT
1 ACAAGGTCGCCCGGAGTGCATGGCGACCT
* * * *
7677 ACCATGTCGCCTGGAGTGCATGGCGATCT
1 ACAAGGTCGCCCGGAGTGCATGGCGACCT
*
7706 ACAAGGTCGCCCGGAGGGCATGGCGACCT
1 ACAAGGTCGCCCGGAGTGCATGGCGACCT
7735 A
1 A
7736 TGCTGGGAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.20, C:0.31, G:0.33, T:0.16
Consensus pattern (29 bp):
ACAAGGTCGCCCGGAGTGCATGGCGACCT
Found at i:14449 original size:55 final size:55
Alignment explanation
Indices: 14324--14613 Score: 374
Period size: 54 Copynumber: 5.3 Consensus size: 55
14314 TTCTTTGAGA
* * * *
14324 TGCACACGTATTGTCGATACAGTCATTCATAAACATATTA-GAATTATGTGG-GT
1 TGCACACTTAGTGTCGATACGGTCATTCATAAACATATTATGAATTATGTGGTTT
* * *
14377 TGCACACTTAGTGTCGATACGGTCGTTCATAAATATATTATGAATTTTGTGGTTT
1 TGCACACTTAGTGTCGATACGGTCATTCATAAACATATTATGAATTATGTGGTTT
* *
14432 TGCACACTTAGTTTCGATACAGTCATTCATAAACATA-TATGAATT-TCGTGGTTT
1 TGCACACTTAGTGTCGATACGGTCATTCATAAACATATTATGAATTAT-GTGGTTT
* * *
14486 TGCACACTTAGTGTCGATAAGGTCGTTCATAAACATATTATGAATTCTGTGGTTT
1 TGCACACTTAGTGTCGATACGGTCATTCATAAACATATTATGAATTATGTGGTTT
* * * *
14541 TGCACACTTAGTGCCCATACGGTCATTCATAAACAT-TAATGAATTACGTGGTTT
1 TGCACACTTAGTGTCGATACGGTCATTCATAAACATATTATGAATTATGTGGTTT
* *
14595 TGCACAGTTAGTGCCGATA
1 TGCACACTTAGTGTCGATA
14614 GTACACATAG
Statistics
Matches: 208, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
53 36 0.17
54 90 0.43
55 81 0.39
56 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (55 bp):
TGCACACTTAGTGTCGATACGGTCATTCATAAACATATTATGAATTATGTGGTTT
Found at i:14524 original size:109 final size:109
Alignment explanation
Indices: 14324--14613 Score: 401
Period size: 109 Copynumber: 2.7 Consensus size: 109
14314 TTCTTTGAGA
* *
14324 TGCACACGTA-TTGTCGATACAGTCATTCATAAACATAT-TAGAATTAT-GTGG-GTTGCACACT
1 TGCACACTTAGTT-TCGATACAGTCATTCATAAACATATAT-GAATT-TCGTGGTTTTGCACACT
* * *
14385 TAGTGTCGATACGGTCGTTCATAAATATATTATGAATTTTGTGGTTT
63 TAGTGTCGATAAGGTCGTTCATAAACATATTATGAATTCTGTGGTTT
14432 TGCACACTTAGTTTCGATACAGTCATTCATAAACATATATGAATTTCGTGGTTTTGCACACTTAG
1 TGCACACTTAGTTTCGATACAGTCATTCATAAACATATATGAATTTCGTGGTTTTGCACACTTAG
14497 TGTCGATAAGGTCGTTCATAAACATATTATGAATTCTGTGGTTT
66 TGTCGATAAGGTCGTTCATAAACATATTATGAATTCTGTGGTTT
** * * * *
14541 TGCACACTTAGTGCCCATACGGTCATTCATAAACAT-TAATGAATTACGTGGTTTTGCACAGTTA
1 TGCACACTTAGTTTCGATACAGTCATTCATAAACATAT-ATGAATTTCGTGGTTTTGCACACTTA
*
14605 GTGCCGATA
65 GTGTCGATA
14614 GTACACATAG
Statistics
Matches: 165, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
107 1 0.01
108 44 0.27
109 120 0.73
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (109 bp):
TGCACACTTAGTTTCGATACAGTCATTCATAAACATATATGAATTTCGTGGTTTTGCACACTTAG
TGTCGATAAGGTCGTTCATAAACATATTATGAATTCTGTGGTTT
Found at i:20796 original size:18 final size:18
Alignment explanation
Indices: 20773--20807 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20763 ACTGAATATT
20773 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
20791 TGTCCCGAATGACCACT
1 TGTCCCGAATGACCACT
20808 GAAAATCCCT
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:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:22720 original size:55 final size:54
Alignment explanation
Indices: 22592--22884 Score: 336
Period size: 55 Copynumber: 5.4 Consensus size: 54
22582 TTTCTTTGGA
* * * * *
22592 TGCACACGTAGTACCGATACGGTCGTTCAGAAACATATTATGAATTCTGTGG-GT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATTC-GTGGTTT
* **
22646 TGCACACTTAGTACCGATACAATCATTCATAAACATATTATGAATTACGTGGTTT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATT-CGTGGTTT
* * * * *
22701 TGCATATTTAGTGTCGATACGGTCATTCATAAATATATTATGAATTGTGTGGTTT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATT-CGTGGTTT
* * * **
22756 TGCACACTTAGTGCTGATATGGTCGTTCATAAACATATTATGAATTTTATGGTTT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAA-TTCGTGGTTT
* * *
22811 TGTACACTTAGTACCGATACGGTCTTTCATAAACATATTATGAATTCTGTGGTTT
1 TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATTC-GTGGTTT
*
22866 TGCACACTTAGTGTCGATA
1 TGCACACTTAGTGCCGATA
22885 GTACACATAG
Statistics
Matches: 202, Mismatches: 33, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
54 47 0.23
55 153 0.76
56 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (54 bp):
TGCACACTTAGTGCCGATACGGTCATTCATAAACATATTATGAATTCGTGGTTT
Found at i:22798 original size:110 final size:110
Alignment explanation
Indices: 22592--22884 Score: 381
Period size: 110 Copynumber: 2.7 Consensus size: 110
22582 TTTCTTTGGA
* * * *
22592 TGCACACGTAGTACCGATACGGTCGTTCAGAAACATATTATGAATTCTGTGG-GTTGCACACTTA
1 TGCACACTTAGTACCGATACGGTCATTCATAAACATATTATGAATTCTGTGGTTTTGCACACTTA
* *
22656 GTACCGATACAATCATTCATAAACATATTATGAATTACGTGGTTT
66 GTGCCGATACAATCATTCATAAACATATTATGAATTACATGGTTT
* * ** * *
22701 TGCATATTTAGTGTCGATACGGTCATTCATAAATATATTATGAATTGTGTGGTTTTGCACACTTA
1 TGCACACTTAGTACCGATACGGTCATTCATAAACATATTATGAATTCTGTGGTTTTGCACACTTA
* *** * **
22766 GTGCTGATATGGTCGTTCATAAACATATTATGAATTTTATGGTTT
66 GTGCCGATACAATCATTCATAAACATATTATGAATTACATGGTTT
* *
22811 TGTACACTTAGTACCGATACGGTCTTTCATAAACATATTATGAATTCTGTGGTTTTGCACACTTA
1 TGCACACTTAGTACCGATACGGTCATTCATAAACATATTATGAATTCTGTGGTTTTGCACACTTA
*
22876 GTGTCGATA
66 GTGCCGATA
22885 GTACACATAG
Statistics
Matches: 154, Mismatches: 29, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
109 43 0.28
110 111 0.72
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (110 bp):
TGCACACTTAGTACCGATACGGTCATTCATAAACATATTATGAATTCTGTGGTTTTGCACACTTA
GTGCCGATACAATCATTCATAAACATATTATGAATTACATGGTTT
Found at i:32784 original size:13 final size:13
Alignment explanation
Indices: 32766--32790 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32756 GTATGTACCT
32766 CCAGAAGTACCCC
1 CCAGAAGTACCCC
32779 CCAGAAGTACCC
1 CCAGAAGTACCC
32791 GTTGATGTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.44, G:0.16, T:0.08
Consensus pattern (13 bp):
CCAGAAGTACCCC
Found at i:44010 original size:17 final size:18
Alignment explanation
Indices: 43983--44021 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
43973 TGCTCGTGGA
43983 GTTACAACAGTTATTGTT
1 GTTACAACAGTTATTGTT
44001 GTTA-AACAGTTATTGTT
1 GTTACAACAGTTATTGTT
44018 GTTA
1 GTTA
44022 GGCAGTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (18 bp):
GTTACAACAGTTATTGTT
Found at i:45983 original size:16 final size:17
Alignment explanation
Indices: 45951--45984 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
45941 TGGCTTTAGA
45951 TTCTATATTTCTTTTGT
1 TTCTATATTTCTTTTGT
45968 TTCTATATTT-TTTTGT
1 TTCTATATTTCTTTTGT
45984 T
1 T
45985 GATGTTGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.74
Consensus pattern (17 bp):
TTCTATATTTCTTTTGT
Found at i:51997 original size:22 final size:22
Alignment explanation
Indices: 51971--52038 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
51961 CAATAAGTCT
51971 TTCGAGCATGATGATTAAATTC
1 TTCGAGCATGATGATTAAATTC
* * *
51993 TTCGAGC-T-ATCAGT-AAGTC
1 TTCGAGCATGATGATTAAATTC
*
52012 TTTCGAGCATGATGATTAAATCC
1 -TTCGAGCATGATGATTAAATTC
52035 TTCG
1 TTCG
52039 GGTAATTTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 4 0.11
20 11 0.31
21 2 0.06
22 15 0.43
23 3 0.09
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (22 bp):
TTCGAGCATGATGATTAAATTC
Found at i:52051 original size:42 final size:42
Alignment explanation
Indices: 51864--52040 Score: 273
Period size: 42 Copynumber: 4.2 Consensus size: 42
51854 ACTTAGTAAG
* *
51864 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
* **
51906 TCCTTTGGGCCATCAATAAGTCTTTCGAGCATGATTCTTAAA
1 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
51948 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
* * * *
51990 TTCTTCGAGCTATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
52032 TCCTTCGGG
1 TCCTTCGGG
52041 TAATTTGTAA
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 123 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (42 bp):
TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
Found at i:52097 original size:13 final size:13
Alignment explanation
Indices: 52079--52103 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52069 TGAAGTAATC
52079 CCATCAGTAAGTG
1 CCATCAGTAAGTG
52092 CCATCAGTAAGT
1 CCATCAGTAAGT
52104 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:52131 original size:22 final size:21
Alignment explanation
Indices: 52099--52173 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 21
52089 GTGCCATCAG
*
52099 TAAGTCTTTCGAGCATGATGA
1 TAAGTCCTTCGAGCATGATGA
* *
52120 TGAAGTCCTTCGGGCCATCA-G-
1 T-AAGTCCTTCGAG-CATGATGA
*
52141 TAAG-CCTTCCGAGCATGGTGA
1 TAAGTCCTT-CGAGCATGATGA
52162 TTAAGTCCTTCG
1 -TAAGTCCTTCG
52174 GGCCATCTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
19 7 0.17
20 7 0.17
21 2 0.05
22 17 0.41
23 8 0.20
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (21 bp):
TAAGTCCTTCGAGCATGATGA
Found at i:52154 original size:42 final size:42
Alignment explanation
Indices: 52091--52190 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
52081 ATCAGTAAGT
* *
52091 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
1 GCCATCAGTAAGCCTTCCGAGCATGATGATGAAGTCCTTCGG
* *
52133 GCCATCAGTAAGCCTTCCGAGCATGGTGATTAAGTCCTTCGG
1 GCCATCAGTAAGCCTTCCGAGCATGATGATGAAGTCCTTCGG
*
52175 GCCATC-TTAAGCCTTC
1 GCCATCAGTAAGCCTTC
52191 ACAAAAGAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 9 0.17
42 44 0.83
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (42 bp):
GCCATCAGTAAGCCTTCCGAGCATGATGATGAAGTCCTTCGG
Found at i:52286 original size:53 final size:53
Alignment explanation
Indices: 52219--52390 Score: 274
Period size: 53 Copynumber: 3.2 Consensus size: 53
52209 AGAATCACAC
* *
52219 CAGAAGATTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGG
* *
52272 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACCCATAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGG
* *
52325 CAGAAGACTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATTAGT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCA-TAGG
52379 C-GAAGATTGTTC
1 CAGAAGATTGTTC
52391 AAAGAAGAGG
Statistics
Matches: 109, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
53 105 0.96
54 4 0.04
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGG
Found at i:56034 original size:33 final size:33
Alignment explanation
Indices: 55992--56054 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
55982 ACGGTGACCG
55992 GCGGTGGTCATCGGTGCAGGAGTTTGGTTTTTA
1 GCGGTGGTCATCGGTGCAGGAGTTTGGTTTTTA
*
56025 GCGGTGGTCATCGGTGCCGGAGTTTGGTTT
1 GCGGTGGTCATCGGTGCAGGAGTTTGGTTT
56055 CCTGCGATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.10, C:0.14, G:0.41, T:0.35
Consensus pattern (33 bp):
GCGGTGGTCATCGGTGCAGGAGTTTGGTTTTTA
Found at i:56066 original size:33 final size:33
Alignment explanation
Indices: 55996--56066 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
55986 TGACCGGCGG
* *
55996 TGGTCATCGGTGCAGGAGTTTGGTTTTTAGCGG
1 TGGTCATCGGTGCAGGAGTTTGGTTTCTAGCGA
*
56029 TGGTCATCGGTGCCGGAGTTTGGTTTCCT-GCGA
1 TGGTCATCGGTGCAGGAGTTTGGTTT-CTAGCGA
56062 TGGTC
1 TGGTC
56067 GAATTTCTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.10, C:0.17, G:0.38, T:0.35
Consensus pattern (33 bp):
TGGTCATCGGTGCAGGAGTTTGGTTTCTAGCGA
Found at i:57445 original size:21 final size:21
Alignment explanation
Indices: 57419--57491 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
57409 TAAATAGTAT
*
57419 ATCGATGCACTACTACAGTGC
1 ATCGATGCACTACTATAGTGC
* * * *
57440 ATCGATGCAGTCATTGTAGTGT
1 ATCGATGCACT-ACTATAGTGC
* *
57462 ACCGATGCACTGCTATAGTGC
1 ATCGATGCACTACTATAGTGC
57483 ATCGATGCA
1 ATCGATGCA
57492 GTTACTGTTC
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
21 24 0.62
22 15 0.38
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (21 bp):
ATCGATGCACTACTATAGTGC
Found at i:57897 original size:34 final size:32
Alignment explanation
Indices: 57858--57927 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
57848 TTTTGTGAAG
* *
57858 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
57892 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
57924 GGGA
1 GGGA
57928 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:60993 original size:21 final size:21
Alignment explanation
Indices: 60964--61003 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
60954 TTTGAGTAGA
60964 AAAATCATCTCCAAACGGCTCC
1 AAAATCATC-CCAAACGGCTCC
*
60986 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCAAACGGCT
61004 ATATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTCC
Found at i:61257 original size:34 final size:32
Alignment explanation
Indices: 61218--61287 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
61208 TTTTGTAAAG
* * *
61218 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCG-G-AAAAACTA
*
61252 GGGAAAAGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
61284 GGGA
1 GGGA
61288 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:72685 original size:80 final size:80
Alignment explanation
Indices: 72552--72715 Score: 301
Period size: 80 Copynumber: 2.0 Consensus size: 80
72542 TTGAATGATT
*
72552 AAACAAAGTGACATACCTGCTAATACCTCACCTTGTTCAGCTCAAACTGCAATGTATTTTAGGAA
1 AAACAAAGTGACATACCTGCTAACACCTCACCTTGTTCAGCTCAAACTGCAATGTATTTTAGGAA
72617 ATCAATTCAGAATCA
66 ATCAATTCAGAATCA
* *
72632 AAACAAAGTGACATACCTGCTCACACCTCACCTTGTTCAGCTCAACCTGCAATGTATTTTAGGAA
1 AAACAAAGTGACATACCTGCTAACACCTCACCTTGTTCAGCTCAAACTGCAATGTATTTTAGGAA
72697 ATCAATTCAGAATCA
66 ATCAATTCAGAATCA
72712 AAAC
1 AAAC
72716 GTTCATGATC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.26
Consensus pattern (80 bp):
AAACAAAGTGACATACCTGCTAACACCTCACCTTGTTCAGCTCAAACTGCAATGTATTTTAGGAA
ATCAATTCAGAATCA
Found at i:77151 original size:17 final size:17
Alignment explanation
Indices: 77129--77163 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
77119 AATATGTCTG
77129 TCTGATGCGAGTATGTA
1 TCTGATGCGAGTATGTA
*
77146 TCTGATGCGGGTATGTA
1 TCTGATGCGAGTATGTA
77163 T
1 T
77164 ATTTTTTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.37
Consensus pattern (17 bp):
TCTGATGCGAGTATGTA
Found at i:91943 original size:62 final size:62
Alignment explanation
Indices: 91855--91972 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 62
91845 AATAAAGAAA
* * * * * *
91855 ACATCGAATGCAATTAGTGTATCGATACACAGTTAGTGTATCGATACTCCCCTTAAAATGAT
1 ACATCGAATGAAATTAGGGTACCGATACACAGGTAGTGTATCGATACACCCATTAAAATGAT
*
91917 ACATCGAATGTAAATT-GGGTACCGATACACAGGTGGTGTATCGATACACCCATTAA
1 ACATCGAATG-AAATTAGGGTACCGATACACAGGTAGTGTATCGATACACCCATTAA
91973 GGAATGTATC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 44 0.92
63 4 0.08
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (62 bp):
ACATCGAATGAAATTAGGGTACCGATACACAGGTAGTGTATCGATACACCCATTAAAATGAT
Found at i:92571 original size:18 final size:18
Alignment explanation
Indices: 92548--92582 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
92538 AGGGATTATC
*
92548 AGTGGTCCTTCGAGACAT
1 AGTGGTCATTCGAGACAT
92566 AGTGGTCATTCGAGACA
1 AGTGGTCATTCGAGACA
92583 AATATTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGAGACAT
Found at i:94033 original size:14 final size:14
Alignment explanation
Indices: 94014--94040 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
94004 TTTTTTTAAA
94014 TTTTTTAAAAATAT
1 TTTTTTAAAAATAT
94028 TTTTTTAAAAATA
1 TTTTTTAAAAATA
94041 AAAATGTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTTTAAAAATAT
Found at i:95161 original size:20 final size:21
Alignment explanation
Indices: 95124--95164 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
95114 TGAAGAGATT
*
95124 TCATCCCCAAACGGCTAAAAA
1 TCATCCCCAAACGCCTAAAAA
95145 TCATCCCC-AACGCCTAAAAA
1 TCATCCCCAAACGCCTAAAAA
95165 CGACCACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.41, C:0.37, G:0.07, T:0.15
Consensus pattern (21 bp):
TCATCCCCAAACGCCTAAAAA
Found at i:97404 original size:16 final size:17
Alignment explanation
Indices: 97373--97405 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
97363 GAAAAAACAT
*
97373 AAAAGTTTAAATACTAA
1 AAAAGATTAAATACTAA
97390 AAAAGATTAAA-ACTAA
1 AAAAGATTAAATACTAA
97406 TAGTTTAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAAGATTAAATACTAA
Found at i:97442 original size:2 final size:2
Alignment explanation
Indices: 97435--97472 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
97425 TAATTTACCC
97435 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
97473 GTGTGTGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.