Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000057.1 Hibiscus syriacus cultivar Beakdansim tig00000086_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: 74031
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2506 original size:21 final size:21
Alignment explanation
Indices: 2482--2522 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2472 TAAAAAAGAG
*
2482 AAGTCTTTTAATCAAAAGGTT
1 AAGTCATTTAATCAAAAGGTT
*
2503 AAGTCATTTAATCGAAAGGT
1 AAGTCATTTAATCAAAAGGT
2523 CTTAACCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (21 bp):
AAGTCATTTAATCAAAAGGTT
Found at i:3742 original size:20 final size:20
Alignment explanation
Indices: 3717--3760 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3707 AACAATGAAT
3717 CCCTCAAAACTATGAAACCA
1 CCCTCAAAACTATGAAACCA
3737 CCCTCAAAACTATGAAACCA
1 CCCTCAAAACTATGAAACCA
3757 CCCT
1 CCCT
3761 GTAATCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.39, G:0.05, T:0.16
Consensus pattern (20 bp):
CCCTCAAAACTATGAAACCA
Found at i:6081 original size:24 final size:24
Alignment explanation
Indices: 6039--6084 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
6029 AATACTTTAA
*
6039 GTCATTATACTTTAGGGCATTTTG
1 GTCATTACACTTTAGGGCATTTTG
6063 GTCATTTACACTTTA-GGCATTT
1 GTCA-TTACACTTTAGGGCATTT
6085 CTATAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (24 bp):
GTCATTACACTTTAGGGCATTTTG
Found at i:7118 original size:14 final size:15
Alignment explanation
Indices: 7082--7140 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 15
7072 GGTCAAAGTC
*
7082 AACGGGTTGACTC-G
1 AACGAGTTGACTCAG
*
7096 AACAAGTTGACTCAG
1 AACGAGTTGACTCAG
*
7111 -ACGGGTTGACTCAG
1 AACGAGTTGACTCAG
**
7125 CCCGAGTTGACTCAG
1 AACGAGTTGACTCAG
7140 A
1 A
7141 CCAGACCAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (15 bp):
AACGAGTTGACTCAG
Found at i:7140 original size:29 final size:28
Alignment explanation
Indices: 7083--7141 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
7073 GTCAAAGTCA
7083 ACGGGTTGACTCGAACAAGTTGACTCAG
1 ACGGGTTGACTCGAACAAGTTGACTCAG
** *
7111 ACGGGTTGACTCAGCCCGAGTTGACTCAG
1 ACGGGTTGACTC-GAACAAGTTGACTCAG
7140 AC
1 AC
7142 CAGACCAGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.20
Consensus pattern (28 bp):
ACGGGTTGACTCGAACAAGTTGACTCAG
Found at i:10593 original size:25 final size:25
Alignment explanation
Indices: 10546--10593 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
10536 AATACTTTAA
*
10546 GTCATTACACTTTAGGGTTATTTTG
1 GTCATTACACTTTAGGGTCATTTTG
10571 GTCATTTACACTTTAGGG-CATTT
1 GTCA-TTACACTTTAGGGTCATTT
10594 CTCTAAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.46
Consensus pattern (25 bp):
GTCATTACACTTTAGGGTCATTTTG
Found at i:11627 original size:20 final size:20
Alignment explanation
Indices: 11564--11627 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
11554 GACTCTTTGG
*
11564 TCAAAGTCAACGGTTAACGA
1 TCAAAGTCAACGGTTAACAA
* *
11584 TCAAAGTCAAAGGTTAACAG
1 TCAAAGTCAACGGTTAACAA
* *
11604 TCAAAGTCAACGGCTAAAAA
1 TCAAAGTCAACGGTTAACAA
11624 TCAA
1 TCAA
11628 CGGGTTGACT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (20 bp):
TCAAAGTCAACGGTTAACAA
Found at i:11648 original size:14 final size:14
Alignment explanation
Indices: 11631--11685 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
11621 AAATCAACGG
11631 GTTGACTCAGACGA
1 GTTGACTCAGACGA
* *
11645 GTTGACTTAGACGG
1 GTTGACTCAGACGA
*
11659 GTTGACTCATACCGA
1 GTTGACTCAGA-CGA
11674 GTTGACTCAGAC
1 GTTGACTCAGAC
11686 TAGACCATGC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:11667 original size:28 final size:29
Alignment explanation
Indices: 11627--11685 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
11617 CTAAAAATCA
*
11627 ACGGGTTGACTCAGA-CGAGTTGACTTAG
1 ACGGGTTGACTCAGACCGAGTTGACTCAG
*
11655 ACGGGTTGACTCATACCGAGTTGACTCAG
1 ACGGGTTGACTCAGACCGAGTTGACTCAG
11684 AC
1 AC
11686 TAGACCATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (29 bp):
ACGGGTTGACTCAGACCGAGTTGACTCAG
Found at i:15709 original size:41 final size:42
Alignment explanation
Indices: 15663--15743 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
15653 TCACGGATAG
* * *
15663 CCCTAAGGACTT-AACATCTTTCTCGAAAGACTGACAGATGA
1 CCCTAAGGACTTAAACATCATGCTCAAAAGACTGACAGATGA
* *
15704 CCCTAAGGATTTAAACATCATGCTCAAAAGACTGATAGAT
1 CCCTAAGGACTTAAACATCATGCTCAAAAGACTGACAGAT
15744 ACCTGAAGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 11 0.32
42 23 0.68
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (42 bp):
CCCTAAGGACTTAAACATCATGCTCAAAAGACTGACAGATGA
Found at i:15988 original size:42 final size:41
Alignment explanation
Indices: 15905--16005 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 41
15895 AGGTCTTATG
* * *
15905 GATGACCCAAAGGACTTAACATCTTGCTCAAAAGACTGACA
1 GATGACCCAAAGGATTTAACATCATGCTCAAAACACTGACA
*
15946 GATGACCCAAAGGATTTAAGCATCATGCTCGAAACACTGACA
1 GATGACCCAAAGGATTTAA-CATCATGCTCAAAACACTGACA
**
15988 GATGACCTTAAGGATTTA
1 GATGACCCAAAGGATTTA
16006 TATATTTGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 18 0.34
42 35 0.66
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (41 bp):
GATGACCCAAAGGATTTAACATCATGCTCAAAACACTGACA
Found at i:16196 original size:253 final size:253
Alignment explanation
Indices: 15381--16362 Score: 1247
Period size: 257 Copynumber: 3.9 Consensus size: 253
15371 GAGTAAAAAA
* * *
15381 ATCCTTCCCAAAGGTCTTACGGATAGCCCAAAGGACTTAACATCTT-CTCGAAAGACTGACAGAT
1 ATCCTACCTAAAGGTCTTACGGATAGCCCAAAGGACTTAACATCTTGCTCAAAAGACTGACAGAT
* *
15445 GACCCTAAGGATTTAAGCATCATGCTCAAAAGACTGACAGATGACCCGAATGATTTA-AAATTTG
66 GACCCTAAGGATTTAAGCATCATGCTCAAAAGACTGACAGATGACCTGAAGGATTTACAAATTTG
* *
15509 GGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTT
131 GGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTC-TACTTTTCAAGAATTTCATTTTC
* * * * *
15574 TGAACATTAATTGAGAATCTTTGGTAATCGCTTTCTCATTTTCATATGAAAATCATGTGTAAAC
195 TGAACATTAAATGAGAAACTTT-GAAATCAC-TTCT-ATTTTCATGTGAAAATCA--TGTAAAC
* * * *
15638 ATCCTACC-AAAGGTCTCACGGATAGCCCTAAGGACTTAACATCTTTCTCGAAAGACTGACAGAT
1 ATCCTACCTAAAGGTCTTACGGATAGCCCAAAGGACTTAACATCTTGCTCAAAAGACTGACAGAT
* * *
15702 GACCCTAAGGATTTAAACATCATGCTCAAAAGACTGATAGAT-ACCTGAAGGTTTTACAAATTTG
66 GACCCTAAGGATTTAAGCATCATGCTCAAAAGACTGACAGATGACCTGAAGGATTTACAAATTTG
* * * *
15766 GGAAATAATTCACTAGGTAACAAACTTTGGAAATTGCTTTCTTACTTTTCAAGAATTTCATTTTC
131 GGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTC-TACTTTTCAAGAATTTCATTTTC
*
15831 TGAACATTAAATGAGAAACTATGAAA--A--TC-ATTTTCATGTG-AAATCATGTAAAC
195 TGAACATTAAATGAGAAACTTTGAAATCACTTCTATTTTCATGTGAAAATCATGTAAAC
* * *
15884 ATCCCACCTGAAGGTCTTATGGAT-GACCCAAAGGACTTAACATCTTGCTCAAAAGACTGACAGA
1 ATCCTACCTAAAGGTCTTACGGATAG-CCCAAAGGACTTAACATCTTGCTCAAAAGACTGACAGA
* * * * * *
15948 TGACCCAAAGGATTTAAGCATCATGCTCGAAACACTGACAGATGACCTTAAGGATTTATATATTT
65 TGACCCTAAGGATTTAAGCATCATGCTCAAAAGACTGACAGATGACCTGAAGGATTTACAAATTT
*
16013 GGGAAATAATTTACT-CGTAAGAAACTTTGGAAATCGCTTTC-ACTTTTCAAGAATTTCATTTTC
130 GGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTACTTTTCAAGAATTTCATTTTC
* *
16076 TAAACTTTAAATG-GAAACTTTGAAAATCACTTCCTTATTTTCATGTGAAAATCATGTAAAC
195 TGAACATTAAATGAGAAACTTTG-AAATCACTT-C-TATTTTCATGTGAAAATCATGTAAAC
* * ** * * * *
16137 ATCCTGCCTAAAGGTCTTATGGAGGGCCCAATGGACTTAATATCTGGCTCAAAAGACTGATAGAT
1 ATCCTACCTAAAGGTCTTACGGATAGCCCAAAGGACTTAACATCTTGCTCAAAAGACTGACAGAT
* *
16202 GACCCTAAGGATTTAAGCATAATGCTCGAAAGACTGACAGATGA-CTCGAAGGATTTACAAATTT
66 GACCCTAAGGATTTAAGCATCATGCTCAAAAGACTGACAGATGACCT-GAAGGATTTACAAATTT
* * * *
16266 GGGAAATAGTTTACTGGGTAAGAAACTTTGAAAATTGCTTTCTTACTTTTCAATAATTTCATTTT
130 GGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTC-TACTTTTCAAGAATTTCATTTT
* *
16331 CAGAAAAGATTAAATGAGAAACTTTGGAAATC
194 CTG--AACATTAAATGAGAAACTTT-GAAATC
16363 GTTTTCTCAT
Statistics
Matches: 636, Mismatches: 66, Indels: 44
0.85 0.09 0.06
Matches are distributed among these distances:
244 8 0.01
245 36 0.06
246 15 0.02
247 109 0.17
248 37 0.06
249 11 0.02
250 1 0.00
251 2 0.00
252 13 0.02
253 137 0.22
254 24 0.04
256 70 0.11
257 150 0.24
258 9 0.01
259 13 0.02
260 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (253 bp):
ATCCTACCTAAAGGTCTTACGGATAGCCCAAAGGACTTAACATCTTGCTCAAAAGACTGACAGAT
GACCCTAAGGATTTAAGCATCATGCTCAAAAGACTGACAGATGACCTGAAGGATTTACAAATTTG
GGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTACTTTTCAAGAATTTCATTTTCT
GAACATTAAATGAGAAACTTTGAAATCACTTCTATTTTCATGTGAAAATCATGTAAAC
Found at i:17719 original size:39 final size:37
Alignment explanation
Indices: 17631--17770 Score: 128
Period size: 37 Copynumber: 3.8 Consensus size: 37
17621 TATTCCTGGA
**
17631 TGATATGGGCCTTCCAAAATGCCCCAACA----TTTGC
1 TGATATGAACCTT-CAAAATGCCCCAACATTTTTTTGC
* * **
17665 TGATACGAACGTTCAAAATGCGTTCAA-ATTGTTTCTTGC
1 TGATATGAACCTTCAAAATGC-CCCAACATT-TTT-TTGC
* *
17704 TGATATGAGCCTTCAAAATGCCCCAACATTTTTATGC
1 TGATATGAACCTTCAAAATGCCCCAACATTTTTTTGC
*
17741 TGATATGAACCTTCAAAATGTCCCAACATT
1 TGATATGAACCTTCAAAATGCCCCAACATT
17771 CCAAGTTGTA
Statistics
Matches: 84, Mismatches: 14, Indels: 13
0.76 0.13 0.12
Matches are distributed among these distances:
33 9 0.11
34 12 0.14
37 31 0.37
38 7 0.08
39 25 0.30
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (37 bp):
TGATATGAACCTTCAAAATGCCCCAACATTTTTTTGC
Found at i:25099 original size:11 final size:12
Alignment explanation
Indices: 25073--25126 Score: 58
Period size: 11 Copynumber: 4.4 Consensus size: 12
25063 CAACATATTC
25073 TTTCTCTTCTTA
1 TTTCTCTTCTTA
25085 TTTCTCTTC-TA
1 TTTCTCTTCTTA
*
25096 TTTCTCTTCAACTA
1 TTTCTCTTC--TTA
25110 TTTTCTCTTCTT-
1 -TTTCTCTTCTTA
25122 TTTCT
1 TTTCT
25127 TGAATATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
11 16 0.43
12 9 0.24
13 1 0.03
14 2 0.05
15 9 0.24
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTCTCTTCTTA
Found at i:25114 original size:26 final size:23
Alignment explanation
Indices: 25085--25138 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 23
25075 TCTCTTCTTA
25085 TTTCTCTTCTATTTCTCTTCAACTAT
1 TTTCTCTTCT-TTT-TCTTCAA-TAT
*
25111 TTTCTCTTCTTTTTCTTGAATAT
1 TTTCTCTTCTTTTTCTTCAATAT
25134 TTTCT
1 TTTCT
25139 TCAGAGTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
24 6 0.22
25 3 0.11
26 10 0.37
ACGTcount: A:0.13, C:0.22, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTCTCTTCTTTTTCTTCAATAT
Found at i:29884 original size:36 final size:36
Alignment explanation
Indices: 29837--29913 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
29827 GAGGAGCTAT
29837 GAGAGTAGTCATTCCTTAGGAAAATACTTAGTGTTC
1 GAGAGTAGTCATTCCTTAGGAAAATACTTAGTGTTC
29873 GAGAGTAGTCATTCCTTAGGAAAATACTTAGTGTTC
1 GAGAGTAGTCATTCCTTAGGAAAATACTTAGTGTTC
29909 GAGAG
1 GAGAG
29914 AAACTAACTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (36 bp):
GAGAGTAGTCATTCCTTAGGAAAATACTTAGTGTTC
Found at i:29985 original size:32 final size:32
Alignment explanation
Indices: 29901--29985 Score: 143
Period size: 32 Copynumber: 2.7 Consensus size: 32
29891 GGAAAATACT
* *
29901 TAGTGTTCGAGAGAAACTAACTAGCTCATCTT
1 TAGTGTTCGAGAGAAACTAAGTAGCTCATCTA
*
29933 TAGTGTTCGAGAGAAACTAAGTAGTTCATCTA
1 TAGTGTTCGAGAGAAACTAAGTAGCTCATCTA
29965 TAGTGTTCGAGAGAAACTAAG
1 TAGTGTTCGAGAGAAACTAAG
29986 AAGGGTCAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (32 bp):
TAGTGTTCGAGAGAAACTAAGTAGCTCATCTA
Found at i:35631 original size:18 final size:17
Alignment explanation
Indices: 35600--35633 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
35590 AAATAATGAA
*
35600 TTTATTTTTCTTTTATC
1 TTTATTTTTATTTTATC
35617 TTTATTTTTTATTTTAT
1 TTTA-TTTTTATTTTAT
35634 TATTCGTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTTTATTTTATC
Found at i:43691 original size:20 final size:20
Alignment explanation
Indices: 43666--43708 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
43656 TACCAAAGTC
43666 ATAAAA-ATTCAAATAACCAA
1 ATAAAACATTCAAAT-ACCAA
*
43686 ATAAAACATTCAAGTACCAA
1 ATAAAACATTCAAATACCAA
43706 ATA
1 ATA
43709 CCAAAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.21
Consensus pattern (20 bp):
ATAAAACATTCAAATACCAA
Found at i:48407 original size:21 final size:21
Alignment explanation
Indices: 48353--48408 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
48343 GTAAGAAATA
*
48353 GATCGATCATTTAAATGAAAG
1 GATCGATCATTTTAATGAAAG
** * *
48374 GATCGATTTTTTTAGTGAATG
1 GATCGATCATTTTAATGAAAG
48395 GATCGATCATTTTA
1 GATCGATCATTTTA
48409 CTCGAGGGAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (21 bp):
GATCGATCATTTTAATGAAAG
Found at i:51246 original size:39 final size:38
Alignment explanation
Indices: 51141--51251 Score: 107
Period size: 39 Copynumber: 2.8 Consensus size: 38
51131 ATTTTAAAAT
* * *
51141 AATTTAGAATGTTAATGCTAAAGAATTTAAGAAATTAAT
1 AATTTAGAATGTTAGTG-TAAAAAATTTAAGAAATTAAG
* * *
51180 AATTTAGAATGTT-GTGGTGATAAAATTTAATAAATTAGG
1 AATTTAGAATGTTAGT-GT-AAAAAATTTAAGAAATTAAG
* *
51219 AATTTTGAATGTTAGTGTAAAATAATTTGAGAA
1 AATTTAGAATGTTAGTGTAAAA-AATTTAAGAA
51252 TTATAAATAA
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
38 5 0.09
39 51 0.88
40 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.17, T:0.38
Consensus pattern (38 bp):
AATTTAGAATGTTAGTGTAAAAAATTTAAGAAATTAAG
Found at i:56980 original size:21 final size:20
Alignment explanation
Indices: 56936--56989 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
56926 ACCAATGGTG
*
56936 AGTATCGATACTCAAGGGTT
1 AGTATCGATACTAAAGGGTT
*
56956 AGTACCGATACTAAAGGGCTT
1 AGTATCGATACTAAAGGG-TT
*
56977 AGTATTGATACTA
1 AGTATCGATACTA
56990 GCTTATAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTAAAGGGTT
Found at i:60917 original size:36 final size:36
Alignment explanation
Indices: 60860--60932 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
60850 GCATTAACCC
*
60860 AAGTTGCTTCTACTGCAGTGTCTGCTACGCTGTGAT
1 AAGTTACTTCTACTGCAGTGTCTGCTACGCTGTGAT
* *
60896 AAGTTACTTCTGCTGCGGTGTCTGCTACGCTGTGAT
1 AAGTTACTTCTACTGCAGTGTCTGCTACGCTGTGAT
60932 A
1 A
60933 CTCAGCTTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (36 bp):
AAGTTACTTCTACTGCAGTGTCTGCTACGCTGTGAT
Found at i:62392 original size:50 final size:51
Alignment explanation
Indices: 62317--62412 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 51
62307 TGAGTGGCTG
* *
62317 AATTTTCATTGTCATCAACTGAAGCAGG-CTTGCGACTCTCGATGCGGCAA
1 AATTTTCATCGTCATCAACCGAAGCAGGACTTGCGACTCTCGATGCGGCAA
* *
62367 AATTTTCATCGTCATCAGCCGAAGCAGGATTTGCGACTCTCGATGC
1 AATTTTCATCGTCATCAACCGAAGCAGGACTTGCGACTCTCGATGC
62413 ATCAACATGC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 25 0.61
51 16 0.39
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (51 bp):
AATTTTCATCGTCATCAACCGAAGCAGGACTTGCGACTCTCGATGCGGCAA
Found at i:72995 original size:3 final size:3
Alignment explanation
Indices: 72989--73018 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
72979 AGAAATAATA
*
72989 AAG AAG AAG ATG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
73019 GGGTTTATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AAG
Done.