Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002149.1 Hibiscus syriacus cultivar Beakdansim tig00004390_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: 58788
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:878 original size:21 final size:20
Alignment explanation
Indices: 831--869 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
821 TGTAACTATT
831 AAATTTTCAAAATATATTCA
1 AAATTTTCAAAATATATTCA
851 AAATTTTCAAAA-ATATTCA
1 AAATTTTCAAAATATATTCA
870 CTAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTTTCAAAATATATTCA
Found at i:1066 original size:13 final size:13
Alignment explanation
Indices: 1052--1094 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1042 CTATATAATT
*
1052 AATTAATCAAATT
1 AATTAATCAAATC
** *
1065 AATTTTTTAAATC
1 AATTAATCAAATC
1078 AATTAATCAAATC
1 AATTAATCAAATC
1091 AATT
1 AATT
1095 GGTAAAATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (13 bp):
AATTAATCAAATC
Found at i:1102 original size:26 final size:26
Alignment explanation
Indices: 1052--1102 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1042 CTATATAATT
* ** *
1052 AATTAATCAAATTAATTTTTTAAATC
1 AATTAATCAAATCAATTGGTAAAATC
1078 AATTAATCAAATCAATTGGTAAAAT
1 AATTAATCAAATCAATTGGTAAAAT
1103 AAGCTACTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (26 bp):
AATTAATCAAATCAATTGGTAAAATC
Found at i:2434 original size:23 final size:23
Alignment explanation
Indices: 2365--2435 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 23
2355 CTGTTTATTT
*
2365 ATGTTTATGAACATTAAACGAAC
1 ATGTTCATGAACATTAAACGAAC
** ** **
2388 ACATTCATGAACGCTAAATAAAC
1 ATGTTCATGAACATTAAACGAAC
*
2411 ATGTTCATGAACATTAAGCGAAC
1 ATGTTCATGAACATTAAACGAAC
2434 AT
1 AT
2436 ATTTGTGAAC
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.27
Consensus pattern (23 bp):
ATGTTCATGAACATTAAACGAAC
Found at i:2452 original size:46 final size:46
Alignment explanation
Indices: 2365--2453 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
2355 CTGTTTATTT
* **
2365 ATGTTTATGAACATTAAACGAACACATTCATGAACGCTAAATAAAC
1 ATGTTCATGAACATTAAACGAACACATTCATGAACAATAAATAAAC
* * **
2411 ATGTTCATGAACATTAAGCGAACATATTTGTGAACAATAAATA
1 ATGTTCATGAACATTAAACGAACACATTCATGAACAATAAATA
2454 GACAAACACG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (46 bp):
ATGTTCATGAACATTAAACGAACACATTCATGAACAATAAATAAAC
Found at i:2478 original size:26 final size:24
Alignment explanation
Indices: 2449--2516 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
2439 TGTGAACAAT
*
2449 AAATAGACAAACACGAACACTTTTAA
1 AAATAAACAAACA--AACACTTTTAA
*
2475 AAATAAATAAACAAACACTTTTAA
1 AAATAAACAAACAAACACTTTTAA
* *
2499 AAATAAATAAATAAACAC
1 AAATAAACAAACAAACAC
2517 GAATACGATA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
24 28 0.72
26 11 0.28
ACGTcount: A:0.62, C:0.15, G:0.03, T:0.21
Consensus pattern (24 bp):
AAATAAACAAACAAACACTTTTAA
Found at i:2491 original size:24 final size:24
Alignment explanation
Indices: 2464--2516 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
2454 GACAAACACG
2464 AACACTTTTAAAAATAAATAAACA
1 AACACTTTTAAAAATAAATAAACA
*
2488 AACACTTTTAAAAATAAATAAATA
1 AACACTTTTAAAAATAAATAAACA
2512 AACAC
1 AACAC
2517 GAATACGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.25
Consensus pattern (24 bp):
AACACTTTTAAAAATAAATAAACA
Found at i:3040 original size:32 final size:31
Alignment explanation
Indices: 2973--3043 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 31
2963 AATTTTTTTG
* *
2973 AATATAATTTTATATATAAAAAGTTTAATTCA
1 AATATAATTTTAAATATAAAAAG-TTAATTAA
3005 AATATAATTTTAAATATAATAAA-TTAATATAA
1 AATATAATTTTAAATATAA-AAAGTTAAT-TAA
3037 AATATAA
1 AATATAA
3044 AATAATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 5 0.14
32 27 0.77
33 3 0.09
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (31 bp):
AATATAATTTTAAATATAAAAAGTTAATTAA
Found at i:3086 original size:117 final size:117
Alignment explanation
Indices: 2965--3191 Score: 454
Period size: 117 Copynumber: 1.9 Consensus size: 117
2955 TATAACATAA
2965 TTTTTTTGAATATAATTTTATATATAAAAAGTTTAATTCAAATATAATTTTAAATATAATAAATT
1 TTTTTTTGAATATAATTTTATATATAAAAAGTTTAATTCAAATATAATTTTAAATATAATAAATT
3030 AATATAAAATATAAAATAATATAAACTAATGATGTCTTCTTCGTTCATAATT
66 AATATAAAATATAAAATAATATAAACTAATGATGTCTTCTTCGTTCATAATT
3082 TTTTTTTGAATATAATTTTATATATAAAAAGTTTAATTCAAATATAATTTTAAATATAATAAATT
1 TTTTTTTGAATATAATTTTATATATAAAAAGTTTAATTCAAATATAATTTTAAATATAATAAATT
3147 AATATAAAATATAAAATAATATAAACTAATGATGTCTTCTTCGTT
66 AATATAAAATATAAAATAATATAAACTAATGATGTCTTCTTCGTT
3192 ATTGTGTTCC
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 110 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (117 bp):
TTTTTTTGAATATAATTTTATATATAAAAAGTTTAATTCAAATATAATTTTAAATATAATAAATT
AATATAAAATATAAAATAATATAAACTAATGATGTCTTCTTCGTTCATAATT
Found at i:3157 original size:32 final size:31
Alignment explanation
Indices: 3090--3160 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 31
3080 TTTTTTTTTG
* *
3090 AATATAATTTTATATATAAAAAGTTTAATTCA
1 AATATAATTTTAAATATAAAAAG-TTAATTAA
3122 AATATAATTTTAAATATAATAAA-TTAATATAA
1 AATATAATTTTAAATATAA-AAAGTTAAT-TAA
3154 AATATAA
1 AATATAA
3161 AATAATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 5 0.14
32 27 0.77
33 3 0.09
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (31 bp):
AATATAATTTTAAATATAAAAAGTTAATTAA
Found at i:6673 original size:18 final size:18
Alignment explanation
Indices: 6650--6684 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6640 CGAGGGTTAC
*
6650 AGTGGTCCTACGGGATAT
1 AGTGGTCATACGGGATAT
*
6668 AGTGGTCATTCGGGATA
1 AGTGGTCATACGGGATA
6685 AATTTCAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.14, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCATACGGGATAT
Found at i:12059 original size:42 final size:42
Alignment explanation
Indices: 11994--12077 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
11984 ATATATCCCA
* *
11994 ATGGGTTTGACATAAAAATTTATGAGCTAGACATATAAATCG
1 ATGGGTTTGACATAAAAACTTATGAGATAGACATATAAATCG
* * * * * *
12036 ATGGGTTTGATATATAACCTTATGGGATCGACATGTAAATCG
1 ATGGGTTTGACATAAAAACTTATGAGATAGACATATAAATCG
12078 TCGGGCTTGG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (42 bp):
ATGGGTTTGACATAAAAACTTATGAGATAGACATATAAATCG
Found at i:26293 original size:20 final size:20
Alignment explanation
Indices: 26252--26293 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
26242 CGATCATGAC
*
26252 ATTTCAATATGCATGTACAT
1 ATTTCAATATGCATATACAT
*
26272 ATTTC-ATATGACATATATAT
1 ATTTCAATATG-CATATACAT
26292 AT
1 AT
26294 AACTATGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (20 bp):
ATTTCAATATGCATATACAT
Found at i:26474 original size:17 final size:17
Alignment explanation
Indices: 26452--26492 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
26442 ATAAATTGTG
26452 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
26469 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
26486 TCCCGAA
1 TCCCGAA
26493 TGATGTCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.29, C:0.37, G:0.17, T:0.17
Consensus pattern (17 bp):
TCCCGAAGGACCTATCA
Found at i:26512 original size:21 final size:19
Alignment explanation
Indices: 26486--26549 Score: 53
Period size: 21 Copynumber: 3.3 Consensus size: 19
26476 GGACCTATCA
26486 TCCCGAATGATGTCATCTGTG
1 TCCCGAA-GATGT-ATCTGTG
*
26507 TCCCGAA-A-G-ATCTGTCA
1 TCCCGAAGATGTATCTGT-G
26524 TCCCGAAGGATGTAATCTGTG
1 TCCCGAA-GATGT-ATCTGTG
26545 TCCCG
1 TCCCG
26550 TAGGACCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
16 6 0.17
17 7 0.20
18 1 0.03
19 2 0.06
20 1 0.03
21 12 0.34
22 6 0.17
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (19 bp):
TCCCGAAGATGTATCTGTG
Found at i:26513 original size:38 final size:38
Alignment explanation
Indices: 26469--26562 Score: 134
Period size: 38 Copynumber: 2.5 Consensus size: 38
26459 GGACCTATCA
* *
26469 TCCCGAAGGACCTATCATCCCGAATGATGTCATCTGTG
1 TCCCGAAGGACCTATCATCCCGAAGGATGTAATCTGTG
* * *
26507 TCCCGAAAGATCTGTCATCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGACCTATCATCCCGAAGGATGTAATCTGTG
*
26545 TCCCGTAGGACCTATCAT
1 TCCCGAAGGACCTATCAT
26563 ATGTCTTATA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (38 bp):
TCCCGAAGGACCTATCATCCCGAAGGATGTAATCTGTG
Found at i:32008 original size:23 final size:23
Alignment explanation
Indices: 31963--32011 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
31953 ATTTTCTGTT
* *
31963 TTTATGACACGTTTATCTTTGTC
1 TTTATGACACATTTATCTATGTC
* *
31986 TTTATGGCACATTTTTCTATGTC
1 TTTATGACACATTTATCTATGTC
32009 TTT
1 TTT
32012 TGGTAGATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.16, C:0.16, G:0.12, T:0.55
Consensus pattern (23 bp):
TTTATGACACATTTATCTATGTC
Found at i:34980 original size:19 final size:19
Alignment explanation
Indices: 34956--35191 Score: 79
Period size: 20 Copynumber: 11.8 Consensus size: 19
34946 ATGACCAACA
* * *
34956 AAATCGTAATGCGATCTCT
1 AAATCGCAACGCGATATCT
34975 AAATCGCAACGCGATATCT
1 AAATCGCAACGCGATATCT
* ** * *
34994 AGTATCGCAAATC-AGTTTCC
1 A-AATCGCAACGCGA-TATCT
* *
35014 AGATTCGCAACGCGAT-TTT
1 A-AATCGCAACGCGATATCT
* * *
35033 GACTATCGCAATGCGAATATGT
1 -A-AATCGCAACGCG-ATATCT
*
35055 AAATCACAACGCGAT-TCT
1 AAATCGCAACGCGATATCT
* * * *
35073 GACTATCGCAATGTGAATATGT
1 -A-AATCGCAACGCG-ATATCT
*
35095 AAATTGCAACGCGAT-TCT
1 AAATCGCAACGCGATATCT
* *
35113 GACTATCGCAACGCGATAATACA
1 -A-AATCGCAACGCGAT-AT-CT
35136 AAATCGCAACGCGAT-TCT
1 AAATCGCAACGCGATATCT
35154 AACTATCGCAACGCGAT-TCT
1 AA--ATCGCAACGCGATATCT
*
35174 GACTATCGCAACGCGATA
1 -A-AATCGCAACGCGATA
35192 ATACAAAATC
Statistics
Matches: 158, Mismatches: 39, Indels: 38
0.67 0.17 0.16
Matches are distributed among these distances:
18 7 0.04
19 26 0.16
20 97 0.61
21 21 0.13
22 6 0.04
23 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (19 bp):
AAATCGCAACGCGATATCT
Found at i:35041 original size:20 final size:20
Alignment explanation
Indices: 35018--35190 Score: 145
Period size: 20 Copynumber: 8.6 Consensus size: 20
35008 GTTTCCAGAT
*
35018 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* * * *
35038 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
*
35058 TCACAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* * * * *
35078 TCGCAATGTGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
*
35098 TTGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
** *
35118 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATTCTGAC--TA
*
35139 TCGCAACGCGATTCTAACTA
1 TCGCAACGCGATTCTGACTA
35159 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
35179 TCGCAACGCGAT
1 TCGCAACGCGAT
35191 AATACAAAAT
Statistics
Matches: 117, Mismatches: 29, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.03
20 95 0.81
21 16 0.14
22 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:35170 original size:41 final size:40
Alignment explanation
Indices: 35018--35169 Score: 198
Period size: 40 Copynumber: 3.8 Consensus size: 40
35008 GTTTCCAGAT
* *
35018 TCGCAACGCGATTTTGACTATCGCAATGCGAATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGAATATGTAAA
* * *
35058 TCACAACGCGATTCTGACTATCGCAATGTGAATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGAATATGTAAA
* **
35098 TTGCAACGCGATTCTGACTATCGCAACGCG-ATAATACAAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGAAT-AT-GTAAA
*
35139 TCGCAACGCGATTCTAACTATCGCAACGCGA
1 TCGCAACGCGATTCTGACTATCGCAACGCGA
35170 TTCTGACTAT
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
39 2 0.02
40 65 0.66
41 31 0.32
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (40 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGAATATGTAAA
Found at i:35382 original size:22 final size:22
Alignment explanation
Indices: 35357--35407 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
35347 CTACGGCGAC
35357 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
35379 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
*
35401 ATTCGTC
1 ATCCGTC
35408 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:35812 original size:19 final size:19
Alignment explanation
Indices: 35788--35831 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
35778 AAATCGCAAC
* *
35788 GCGATTTTAGTTTCGTGTT
1 GCGATTTTAATTTCGCGTT
35807 GCGATTTTAATTTCGCGTT
1 GCGATTTTAATTTCGCGTT
35826 GCGATT
1 GCGATT
35832 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.25, T:0.48
Consensus pattern (19 bp):
GCGATTTTAATTTCGCGTT
Found at i:35861 original size:20 final size:20
Alignment explanation
Indices: 35836--35884 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
35826 GCGATTATCT
35836 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
35856 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
35876 TGTTGCGAT
1 CGTTGCGAT
35885 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:43873 original size:24 final size:23
Alignment explanation
Indices: 43831--43877 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
43821 AAGAATTTTC
43831 AAAAAAAATTTAATTTTTCGAAAT
1 AAAAAAAATTTAATTTTTC-AAAT
43855 AAAAAAAATGTTAA-TTTTCAAAT
1 AAAAAAAAT-TTAATTTTTCAAAT
43878 TATTGTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.18
24 14 0.64
25 4 0.18
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (23 bp):
AAAAAAAATTTAATTTTTCAAAT
Found at i:47403 original size:20 final size:20
Alignment explanation
Indices: 47380--47448 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
47370 GAAACTTAAA
47380 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
47400 ATCGCAACGCGGAACTGACT
1 ATCGCAACGCGAAAATGACT
**
47420 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
47440 ATCGCAACG
1 ATCGCAACG
47449 GGATAACCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:47554 original size:34 final size:34
Alignment explanation
Indices: 47511--47606 Score: 149
Period size: 34 Copynumber: 2.8 Consensus size: 34
47501 GTCAATTCGT
* * *
47511 GTTGCGATAGTCTAATACGCTTTGCGATTTTCT-C
1 GTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGC
47545 GTTGCGATAGTCAAATTCGCGTTGCGATTTTTGC
1 GTTGCGATAGTCAAATTCGCGTTGCGATTTTTGC
47579 GTTGCGATAGTCAAATTCGCGTTGCGAT
1 GTTGCGATAGTCAAATTCGCGTTGCGAT
47607 ATTCAAATGA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 1 0.02
34 57 0.98
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (34 bp):
GTTGCGATAGTCAAATTCGCGTTGCGATTTTTGC
Found at i:47569 original size:20 final size:20
Alignment explanation
Indices: 47544--47614 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
47534 GCGATTTTCT
47544 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
47564 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
47578 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
47598 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
47615 GAATGTGTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 12 0.29
16 1 0.02
18 1 0.02
20 28 0.67
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:47800 original size:12 final size:12
Alignment explanation
Indices: 47785--47827 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
47775 AAGCCGGTTG
*
47785 TGATTGGGATTT
1 TGATTGCGATTT
**
47797 TGATTTTGATTT
1 TGATTGCGATTT
47809 TGATTGCGATTT
1 TGATTGCGATTT
47821 TGATTGC
1 TGATTGC
47828 CTTTTGCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.16, C:0.05, G:0.26, T:0.53
Consensus pattern (12 bp):
TGATTGCGATTT
Found at i:47801 original size:6 final size:6
Alignment explanation
Indices: 47792--47825 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
47782 TTGTGATTGG
**
47792 GATTTT GATTTT GATTTT GATTGC GATTTT GATT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATT
47826 GCCTTTTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.18, C:0.03, G:0.21, T:0.59
Consensus pattern (6 bp):
GATTTT
Found at i:50119 original size:24 final size:24
Alignment explanation
Indices: 50085--50138 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
50075 CTGAAACATC
*
50085 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
50109 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
50133 ATCAAA
1 ATCAAA
50139 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:50821 original size:17 final size:17
Alignment explanation
Indices: 50795--50829 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
50785 ATGGGGAATA
*
50795 ATGTCGTTGGATATAGG
1 ATGTCATTGGATATAGG
*
50812 ATGTCATTGGATGTAGG
1 ATGTCATTGGATATAGG
50829 A
1 A
50830 ACAGATGTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.34, T:0.34
Consensus pattern (17 bp):
ATGTCATTGGATATAGG
Found at i:51001 original size:41 final size:41
Alignment explanation
Indices: 50955--51043 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 41
50945 ACTAAAACCT
50955 GTTGCGAATTTGAAAT-TCAGTATTGCGATAGTCAGAATCGC
1 GTTGCGAATTTGAAATATC-GTATTGCGATAGTCAGAATCGC
* * * *
50996 GTTGCGATTTTGTATTATCGTGTTGCGATAGTCAGAATCGC
1 GTTGCGAATTTGAAATATCGTATTGCGATAGTCAGAATCGC
51037 GTTGCGA
1 GTTGCGA
51044 TTTACATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 41 0.95
42 2 0.05
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.35
Consensus pattern (41 bp):
GTTGCGAATTTGAAATATCGTATTGCGATAGTCAGAATCGC
Found at i:51002 original size:20 final size:20
Alignment explanation
Indices: 50977--51044 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
50967 AAATTCAGTA
50977 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* ** *
50997 TTGCGATTTTGT-ATTATCGTG
1 TTGCGA--TAGTCAGAATCGCG
51018 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
51038 TTGCGAT
1 TTGCGAT
51045 TTACATATTC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 3 0.08
20 19 0.51
21 12 0.32
22 3 0.08
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:51608 original size:4 final size:4
Alignment explanation
Indices: 51601--51628 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
51591 TAGATATCTG
51601 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
51629 TTGATCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:58248 original size:23 final size:23
Alignment explanation
Indices: 58222--58269 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
58212 AATCTTCATA
*
58222 TAAC-TTTAAATTATTATAAAATT
1 TAACTTTTAAATT-TAATAAAATT
*
58245 TAACTTTTATATTTAATAAAATT
1 TAACTTTTAAATTTAATAAAATT
58268 TA
1 TA
58270 TTAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
TAACTTTTAAATTTAATAAAATT
Done.