Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004480.1 Hibiscus syriacus cultivar Beakdansim tig00009874_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: 66572
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8900 original size:2 final size:2
Alignment explanation
Indices: 8893--8922 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8883 ATAAATCAGC
8893 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
8923 TAATAAATCT
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):
AT
Found at i:15110 original size:12 final size:12
Alignment explanation
Indices: 15093--15119 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15083 TTAATCGCAA
15093 AAATTGAAATTT
1 AAATTGAAATTT
15105 AAATTGAAATTT
1 AAATTGAAATTT
15117 AAA
1 AAA
15120 AACTTGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATTGAAATTT
Found at i:15416 original size:17 final size:17
Alignment explanation
Indices: 15373--15415 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
15363 TAAATTAAAT
15373 ATAAGAAAAAGAAAAAA
1 ATAAGAAAAAGAAAAAA
* *
15390 ATTAGAAAAAGAAAGAA
1 ATAAGAAAAAGAAAAAA
15407 ATAA-AAAAA
1 ATAAGAAAAA
15416 ACTTTAAGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (17 bp):
ATAAGAAAAAGAAAAAA
Found at i:16479 original size:14 final size:13
Alignment explanation
Indices: 16460--16526 Score: 50
Period size: 12 Copynumber: 5.2 Consensus size: 13
16450 TGAAAAAAGG
16460 AAAAAATAATAATT
1 AAAAAATAATAA-T
* *
16474 AAAAAAAGAATAAGG
1 -AAAAAATAATAA-T
*
16489 AAAAAAGAATAA-
1 AAAAAATAATAAT
16501 AAAAAATAAT-AT
1 AAAAAATAATAAT
*
16513 AAATAAT-ATAAT
1 AAAAAATAATAAT
16525 AA
1 AA
16527 TTTTCGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
11 3 0.07
12 19 0.42
14 12 0.27
15 11 0.24
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:16492 original size:15 final size:14
Alignment explanation
Indices: 16456--16500 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
16446 ACCCTGAAAA
*
16456 AAGGAAAAAATAAT
1 AAGGAAAAAAGAAT
**
16470 AATTAAAAAAAGAAT
1 AA-GGAAAAAAGAAT
16485 AAGGAAAAAAGAAT
1 AAGGAAAAAAGAAT
16499 AA
1 AA
16501 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (14 bp):
AAGGAAAAAAGAAT
Found at i:16638 original size:63 final size:62
Alignment explanation
Indices: 16567--16686 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 62
16557 TATTATACGT
*
16567 TTTCAAAAAAAAATTCAAAATTATATATTATATATATTTTTTAAAAATGTTTTCAAAATAATA
1 TTTCAAAAAAAAATTCAAAATAATATATTATATATA-TTTTTAAAAATGTTTTCAAAATAATA
**** *
16630 TTTCAAAAACGTTTTCAAAATAATATATTATATATATTTTTGAAAATGTTTTCAAAA
1 TTTCAAAAAAAAATTCAAAATAATATATTATATATATTTTTAAAAATGTTTTCAAAA
16687 AAACTATATA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
62 20 0.39
63 31 0.61
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (62 bp):
TTTCAAAAAAAAATTCAAAATAATATATTATATATATTTTTAAAAATGTTTTCAAAATAATA
Found at i:16686 original size:37 final size:36
Alignment explanation
Indices: 16635--16923 Score: 184
Period size: 38 Copynumber: 8.1 Consensus size: 36
16625 TAATATTTCA
*
16635 AAAACGTTTTCAAAATAATATATTATATATATTTTT
1 AAAATGTTTTCAAAATAATATATTATATATATTTTT
*
16671 GAAAATGTTTTCAAAAAAACTATATATATATATATATTTT
1 -AAAATGTTTTCAAAATAA-TATAT-TATATATAT-TTTT
* * *
16711 AACATGTTTTCAAAACT-ATATAATATATATATTTTCA
1 AAAATGTTTTCAAAA-TAATATATTATATATATTTT-T
16748 AAAATTGTTTTC-AAA-AAT-TA-TATAT-TA----T
1 AAAA-TGTTTTCAAAATAATATATTATATATATTTTT
* * * *
16776 -ATATATTTTCAAAACT-ATATAATATATATATTTTCA
1 AAAATGTTTTCAAAA-TAATATATTATATATATTTT-T
*
16812 AAAATCGTTTTCAAAACT-ATATATTATATATATTTTCAA
1 AAAAT-GTTTTCAAAA-TAATATATTATATATATTTT--T
16851 AAAATGTTTTCAAAAT--TATA-TA-ATATATTTTT
1 AAAATGTTTTCAAAATAATATATTATATATATTTTT
* * *
16883 TAAATCGTATTTTC-AAA-ACTATATTATATATATATTT
1 AAAAT-G--TTTTCAAAATAATATATTATATATATTTTT
16920 AAAA
1 AAAA
16924 ACCGTTTTTT
Statistics
Matches: 205, Mismatches: 19, Indels: 56
0.73 0.07 0.20
Matches are distributed among these distances:
26 6 0.03
27 5 0.02
28 2 0.01
29 2 0.01
30 5 0.02
31 2 0.01
32 4 0.02
33 3 0.01
34 17 0.08
35 13 0.06
36 11 0.05
37 47 0.23
38 54 0.26
39 30 0.15
40 4 0.02
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (36 bp):
AAAATGTTTTCAAAATAATATATTATATATATTTTT
Found at i:16718 original size:39 final size:38
Alignment explanation
Indices: 16627--16924 Score: 209
Period size: 39 Copynumber: 8.3 Consensus size: 38
16617 TTTCAAAATA
* * *
16627 ATATTTCAAAAACGTTTTCAAAATAATATAT-TATATAT
1 ATATTTTAAAAATGTTTTCAAAA-ACTATATATATATAT
*
16665 AT-TTTTGAAAATGTTTTCAAAAAAACTATATATATATAT
1 ATATTTTAAAAATGTTTTC--AAAAACTATATATATATAT
*
16704 ATATTTT-AACATGTTTTC-AAAACTATATA-ATATAT
1 ATATTTTAAAAATGTTTTCAAAAACTATATATATATAT
*
16739 ATATTTTCAAAAATTGTTTTCAAAAATTATATAT-TATAT
1 ATATTTT-AAAAA-TGTTTTCAAAAACTATATATATATAT
* *
16778 ATATTTTCAAAA------C---TA-TATA-ATATATAT
1 ATATTTTAAAAATGTTTTCAAAAACTATATATATATAT
*
16805 AT-TTTCAAAAATCGTTTTC-AAAACTATATAT-TATAT
1 ATATTTTAAAAAT-GTTTTCAAAAACTATATATATATAT
16841 ATATTTTCAAAAAATGTTTTC-AAAA-T-TATATA-ATAT
1 ATATTTT--AAAAATGTTTTCAAAAACTATATATATATAT
* ** *
16877 ATTTTTTAAATCGTATTTTC-AAAACTATAT-TATATAT
1 ATATTTTAAA-AATGTTTTCAAAAACTATATATATATAT
16914 ATA-TTTAAAAA
1 ATATTTTAAAAA
16925 CCGTTTTTTT
Statistics
Matches: 211, Mismatches: 20, Indels: 61
0.72 0.07 0.21
Matches are distributed among these distances:
26 9 0.04
27 11 0.05
28 1 0.00
31 1 0.00
33 1 0.00
34 3 0.01
35 24 0.11
36 46 0.22
37 31 0.15
38 29 0.14
39 51 0.24
40 4 0.02
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (38 bp):
ATATTTTAAAAATGTTTTCAAAAACTATATATATATAT
Found at i:16724 original size:76 final size:74
Alignment explanation
Indices: 16640--16919 Score: 263
Period size: 76 Copynumber: 3.9 Consensus size: 74
16630 TTTCAAAAAC
* **
16640 GTTTTCAAAA-TAATATATTATATATATTTTTGAAAA-TGTTTTCAAAAAAACTATATATATATA
1 GTTTTCAAAACT-ATATAATATATATATTTTCAAAAATTGTTTTC--AAAAACTATATAT-TATA
16703 TATATTTTAACAT
62 TATATTTTAACAT
16716 GTTTTCAAAACTATATAATATATATATTTTCAAAAATTGTTTTCAAAAA-T-TATA-TAT-TATA
1 GTTTTCAAAACTATATAATATATATATTTTCAAAAATTGTTTTCAAAAACTATATATTATATATA
16777 ---T---AT
66 TTTTAACAT
* *
16780 ATTTTCAAAACTATATAATATATATATTTTCAAAAATCGTTTTC-AAAACTATATATTATATATA
1 GTTTTCAAAACTATATAATATATATATTTTCAAAAATTGTTTTCAAAAACTATATATTATATATA
*
16844 TTTTCAAAAAAT
66 TTTT---AACAT
* *** *
16856 GTTTTCAAAATTATATAATATAT-T-TTTT-AAATCGTATTTTC-AAAACTATAT-TATATATAT
1 GTTTTCAAAACTATATAATATATATATTTTCAAAAATTGTTTTCAAAAACTATATAT-TATATAT
16916 ATTT
65 ATTT
16920 AAAAACCGTT
Statistics
Matches: 176, Mismatches: 12, Indels: 35
0.79 0.05 0.16
Matches are distributed among these distances:
63 4 0.02
64 45 0.26
65 4 0.02
66 3 0.02
67 5 0.03
70 5 0.03
71 3 0.02
72 1 0.01
73 33 0.19
74 5 0.03
75 6 0.03
76 54 0.31
77 8 0.05
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (74 bp):
GTTTTCAAAACTATATAATATATATATTTTCAAAAATTGTTTTCAAAAACTATATATTATATATA
TTTTAACAT
Found at i:16760 original size:13 final size:13
Alignment explanation
Indices: 16742--16766 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16732 AATATATATA
16742 TTTTCAAAAATTG
1 TTTTCAAAAATTG
16755 TTTTCAAAAATT
1 TTTTCAAAAATT
16767 ATATATTATA
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:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTTCAAAAATTG
Found at i:16785 original size:64 final size:63
Alignment explanation
Indices: 16717--16852 Score: 245
Period size: 64 Copynumber: 2.1 Consensus size: 63
16707 TTTTAACATG
* *
16717 TTTTCAAAACTATATAATATATATATTTTCAAAAATTGTTTTCAAAAATTATATATTATATATA
1 TTTTCAAAACTATATAATATATATATTTTCAAAAATCGTTTTC-AAAACTATATATTATATATA
16781 TTTTCAAAACTATATAATATATATATTTTCAAAAATCGTTTTCAAAACTATATATTATATATA
1 TTTTCAAAACTATATAATATATATATTTTCAAAAATCGTTTTCAAAACTATATATTATATATA
16844 TTTTCAAAA
1 TTTTCAAAA
16853 AATGTTTTCA
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
63 28 0.40
64 42 0.60
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (63 bp):
TTTTCAAAACTATATAATATATATATTTTCAAAAATCGTTTTCAAAACTATATATTATATATA
Found at i:16800 original size:23 final size:25
Alignment explanation
Indices: 16755--16814 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
16745 TCAAAAATTG
* *
16755 TTTTCAAAAATTATATATTATATATA
1 TTTTC-AAAACTATATAATATATATA
16781 TTTTCAAAACTATATAATATATATA
1 TTTTCAAAACTATATAATATATATA
16806 TTTTCAAAA
1 TTTTCAAAA
16815 ATCGTTTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 27 0.84
26 5 0.16
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTTCAAAACTATATAATATATATA
Found at i:16831 original size:102 final size:99
Alignment explanation
Indices: 16686--16878 Score: 307
Period size: 102 Copynumber: 1.9 Consensus size: 99
16676 TGTTTTCAAA
*
16686 AAAACTATATATATATATATATTTTAACATGTTTTCAAAACTATATAATATATATATTTTCAAAA
1 AAAACTATATATATATATATATTTTAAAATGTTTTCAAAACTATATAATATATATATTTTCAAAA
* *
16751 ATTGTTTTCAAAAATTATATATTATATATATTTTC
66 AATGTTTTC-AAAATTATATAATATATATATTTTC
*
16786 AAAACTATATA-ATATATATATTTTCAAAAATCGTTTTCAAAACTATATATTATATATATTTTCA
1 AAAACTATATATATATATATATTTT--AAAAT-GTTTTCAAAACTATATAATATATATATTTTCA
16850 AAAAATGTTTTCAAAATTATATAATATAT
63 AAAAATGTTTTCAAAATTATATAATATAT
16879 TTTTTAAATC
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
99 13 0.15
100 11 0.13
101 20 0.23
102 42 0.49
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (99 bp):
AAAACTATATATATATATATATTTTAAAATGTTTTCAAAACTATATAATATATATATTTTCAAAA
AATGTTTTCAAAATTATATAATATATATATTTTC
Found at i:16919 original size:73 final size:74
Alignment explanation
Indices: 16781--16919 Score: 196
Period size: 73 Copynumber: 1.9 Consensus size: 74
16771 ATTATATATA
16781 TTTTCAAAACTATATAATATATATATTTTCAAAAATCGTTTTCAAAACTATATATTATATATATT
1 TTTTCAAAACTATATAATATATATATTTT--AAAATCGTTTTCAAAACTATATATTATATATATT
16846 TTCAAAAAATG
64 TTCAAAAAATG
*
16857 TTTTCAAAATTATATAATATAT-T-TTTT-AAATCGTATTTTCAAAACTATAT-TATATATATAT
1 TTTTCAAAACTATATAATATATATATTTTAAAATCG--TTTTCAAAACTATATAT-TATATATAT
16918 TT
63 TT
16920 AAAAACCGTT
Statistics
Matches: 59, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
71 6 0.10
72 1 0.02
73 26 0.44
74 4 0.07
75 1 0.02
76 21 0.36
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.47
Consensus pattern (74 bp):
TTTTCAAAACTATATAATATATATATTTTAAAATCGTTTTCAAAACTATATATTATATATATTTT
CAAAAAATG
Found at i:16931 original size:71 final size:74
Alignment explanation
Indices: 16781--16931 Score: 188
Period size: 71 Copynumber: 2.1 Consensus size: 74
16771 ATTATATATA
16781 TTTTCAAAACTATATAATATATATATTTTCAAAAATCGTTTTCAAAACTATATATTATATATATT
1 TTTTCAAAACTATATAATATATATATTTT--AAAATCGTTTTCAAAACTATATATTATATATATT
*
16846 TTCAAAAAATG
64 TTCAAAAAACG
*
16857 TTTTCAAAATTATATAATATAT-T-TTTT-AAATCGTATTTTCAAAAC--TATATTATATATATA
1 TTTTCAAAACTATATAATATATATATTTTAAAATCG--TTTTCAAAACTATATATTATATATAT-
*
16917 TTT-AAAAACCG
63 TTTCAAAAAACG
16928 TTTT
1 TTTT
16932 TTTTTTAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
71 30 0.43
72 3 0.04
73 10 0.14
74 4 0.06
75 1 0.01
76 21 0.30
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (74 bp):
TTTTCAAAACTATATAATATATATATTTTAAAATCGTTTTCAAAACTATATATTATATATATTTT
CAAAAAACG
Found at i:16975 original size:109 final size:110
Alignment explanation
Indices: 16779--16979 Score: 252
Period size: 111 Copynumber: 1.8 Consensus size: 110
16769 ATATTATATA
*
16779 TATTTTCAAAACTATATAATATATATATTTTCAAAAATCGTTTTCAAAACTATATATTATATATA
1 TATTTTCAAAACTATATAATATATATATTTTCAAAAACCGTTTTCAAAAC-ATATATTATATATA
* *
16844 TTTTCAAAAAATGTTTTCAAAATTATATAATATATTTTTTAAATCG
65 TTTTCAAAAAATATTTTAAAAATTATATAATATATTTTTTAAATCG
* *
16890 TATTTTCAAAACTATATTATATATATA-TTT-AAAAACCGTTTTTTTTTTAAAAC-TATA-TAT-
1 TATTTTCAAAACTATATAATATATATATTTTCAAAAACCG-----TTTTCAAAACATATATTATA
*
16950 TATATTTTC-AAAAGTATTTTAAAAATTATA
61 TATATTTTCAAAAAATATTTTAAAAATTATA
16980 CTATATTAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
109 25 0.32
110 12 0.15
111 29 0.37
112 4 0.05
114 9 0.11
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.47
Consensus pattern (110 bp):
TATTTTCAAAACTATATAATATATATATTTTCAAAAACCGTTTTCAAAACATATATTATATATAT
TTTCAAAAAATATTTTAAAAATTATATAATATATTTTTTAAATCG
Found at i:22839 original size:6 final size:6
Alignment explanation
Indices: 22828--22856 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
22818 CTCCGAGGGA
22828 GCCATT GCCATT GCCATT GCCATT GCCAT
1 GCCATT GCCATT GCCATT GCCATT GCCAT
22857 GGCTTTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.17, T:0.31
Consensus pattern (6 bp):
GCCATT
Found at i:29803 original size:17 final size:18
Alignment explanation
Indices: 29762--29810 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
29752 ATATATTTTT
29762 AAAAATATTATAAATAAA
1 AAAAATATTATAAATAAA
29780 AATAAAT-TTA-AAATAAA
1 AA-AAATATTATAAATAAA
29797 CAAAAATATATATA
1 -AAAAATAT-TATA
29811 TAATTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 11 0.42
18 8 0.31
19 6 0.23
20 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATATTATAAATAAA
Found at i:36691 original size:21 final size:21
Alignment explanation
Indices: 36667--36711 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
36657 AATATTGCAG
36667 TGTCAAAATTAGGTGCAACAA
1 TGTCAAAATTAGGTGCAACAA
*
36688 TGTCAAAATTAGGTGCAATAA
1 TGTCAAAATTAGGTGCAACAA
36709 TGT
1 TGT
36712 TTGAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (21 bp):
TGTCAAAATTAGGTGCAACAA
Found at i:37902 original size:17 final size:18
Alignment explanation
Indices: 37870--37903 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37860 CCGGTTTCGA
*
37870 TTTTAAAAAACCCGGTTT
1 TTTTAAAAAACACGGTTT
37888 TTTTAAAAAA-ACGGTT
1 TTTTAAAAAACACGGTT
37904 ATAAAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
TTTTAAAAAACACGGTTT
Found at i:38372 original size:21 final size:21
Alignment explanation
Indices: 38346--38402 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
38336 TTTTACACTT
38346 AGGGAACCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
38367 AGGGAACCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
*
38388 AGGGTACCGATTCCC
1 AGGGAACCGATTCCC
38403 CCACGCTCCA
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:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (21 bp):
AGGGAACCGATTCCCTATGAG
Found at i:38619 original size:13 final size:13
Alignment explanation
Indices: 38598--38652 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
38588 AAGTTCGATA
*
38598 AATTCAAATACTT
1 AATTGAAATACTT
38611 AATTGAAATACTT
1 AATTGAAATACTT
* *
38624 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
38638 AATTGAAATACTT
1 AATTGAAATACTT
38651 AA
1 AA
38653 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:38734 original size:32 final size:33
Alignment explanation
Indices: 38638--38736 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
38628 AACTCAACAT
* * **
38638 AATTGAAATACTTAAATACTTCCAAGTTTTATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
38671 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
38704 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
38736 A
1 A
38737 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 12 0.19
33 50 0.81
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:38755 original size:21 final size:21
Alignment explanation
Indices: 38731--38772 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
38721 ACTTCAAGTT
38731 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
38752 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
38773 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:55256 original size:2 final size:2
Alignment explanation
Indices: 55251--55279 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55241 ATTAATTAAT
55251 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 T
55280 TCGTTTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58957 original size:37 final size:37
Alignment explanation
Indices: 58908--58981 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
58898 ATGGACGAAC
*
58908 CAACAACATGACATTACACATCAATTAATTCATCACA
1 CAACAACATGACATTACACATCAATTAAGTCATCACA
58945 CAACAACATGACATTACACATCAATTAAGTCATCACA
1 CAACAACATGACATTACACATCAATTAAGTCATCACA
58982 TGCTTTAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.46, C:0.27, G:0.04, T:0.23
Consensus pattern (37 bp):
CAACAACATGACATTACACATCAATTAAGTCATCACA
Found at i:61943 original size:30 final size:30
Alignment explanation
Indices: 61907--61979 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
61897 ATCTGGCGAG
61907 TGAGTGCTGACCCTAGTTGCTGCTGCCTAC
1 TGAGTGCTGACCCTAGTTGCTGCTGCCTAC
61937 TGAGTGCTGACCCTAGTTGCTGCTGCCTAC
1 TGAGTGCTGACCCTAGTTGCTGCTGCCTAC
61967 TGAGTGCTGACCC
1 TGAGTGCTGACCC
61980 ATCAAGTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.14, C:0.30, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGTGCTGACCCTAGTTGCTGCTGCCTAC
Found at i:61960 original size:16 final size:16
Alignment explanation
Indices: 61911--61961 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
61901 GGCGAGTGAG
61911 TGCTGACCCTAGTTGC
1 TGCTGACCCTAGTTGC
* *
61927 TGCTG--CCTA-CTGAG
1 TGCTGACCCTAGTTG-C
61941 TGCTGACCCTAGTTGC
1 TGCTGACCCTAGTTGC
61957 TGCTG
1 TGCTG
61962 CCTACTGAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 2 0.07
14 9 0.33
16 14 0.52
17 2 0.07
ACGTcount: A:0.12, C:0.29, G:0.27, T:0.31
Consensus pattern (16 bp):
TGCTGACCCTAGTTGC
Done.