Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000980.1 Hibiscus syriacus cultivar Beakdansim tig00001957_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: 105463
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3114 original size:8 final size:8
Alignment explanation
Indices: 3101--3125 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3091 GTTACCACCA
3101 CCTTCTCC
1 CCTTCTCC
3109 CCTTCTCC
1 CCTTCTCC
3117 CCTTCTCC
1 CCTTCTCC
3125 C
1 C
3126 GGAGGGTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (8 bp):
CCTTCTCC
Found at i:3309 original size:129 final size:132
Alignment explanation
Indices: 2993--3312 Score: 371
Period size: 134 Copynumber: 2.4 Consensus size: 132
2983 TATTCCCCCA
* * * *
2993 GAGGGACTAGAAAACCCAAAAAATTATGCGAAAATGTCATCAGCAGTCCTGGGGTTGACACCAGA
1 GAGGGACTAGAAAACCCGAAATACTATGAGAAAATGTCATCAGCAGTCCTGGGGTTGACACCAGA
* * * * * *
3058 GGGTGTTGACCTTGAACCACCATTCATTCCACTGTTACCACCACCTTCTCCCCTTCTCCCCTTCT
66 GGGTGTTGACCTTGAACCACCATTCATCCCACTGCTACCACCACC-TCACCAC-TCACCACTTCT
3123 CCCG
129 CCCG
* * * * *
3127 GAGGGTCTAGAAAACTCGAAATACTATGAAAAAATGTCATCAGCAGTCTTGGGGTTGAGACC-GA
1 GAGGGACTAGAAAACCCGAAATACTATGAGAAAATGTCATCAGCAGTCCTGGGGTTGACACCAG-
* * * *
3191 AGGGTTTTGGCCTTGAACCACC-TCTCATCCCACTGCTGCCTCCA-C-CACCAC-CACCACTTCT
65 AGGGTGTTGACCTTGAACCACCAT-TCATCCCACTGCTACCACCACCTCACCACTCACCACTTCT
*
3252 CCCT
129 CCCG
* *
3256 GAGGGACTAAAAAACCCGAAATACTCTGAGAAAATGTCATCAGCAGTCCTGGGGTTG
1 GAGGGACTAGAAAACCCGAAATACTATGAGAAAATGTCATCAGCAGTCCTGGGGTTG
3313 GACTTGGACC
Statistics
Matches: 158, Mismatches: 26, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
129 62 0.39
131 4 0.03
133 3 0.02
134 89 0.56
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (132 bp):
GAGGGACTAGAAAACCCGAAATACTATGAGAAAATGTCATCAGCAGTCCTGGGGTTGACACCAGA
GGGTGTTGACCTTGAACCACCATTCATCCCACTGCTACCACCACCTCACCACTCACCACTTCTCC
CG
Found at i:5939 original size:28 final size:26
Alignment explanation
Indices: 5884--5961 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 26
5874 AAATAAAAAT
5884 ATGATTATATTTTAAATATTTAAATAAA
1 ATGA-TAT-TTTTAAATATTTAAATAAA
*
5912 ATGATATCTTTTAAATATTTGAATTAAA
1 ATGATAT-TTTTAAATATTT-AAATAAA
5940 ATGATATTACTTTAAATATTTA
1 ATGATATT--TTTAAATATTTA
5962 TTTTTAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 16 0.36
28 18 0.40
29 11 0.24
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (26 bp):
ATGATATTTTTAAATATTTAAATAAA
Found at i:12602 original size:23 final size:24
Alignment explanation
Indices: 12556--12602 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
12546 TCATATTGGT
*
12556 AATTTCAAAAAGTAGTTCAGTAAA
1 AATTTCAAAAAGTAGTACAGTAAA
12580 AATTTCATAAAAGT-G-ACAGTAAA
1 AATTTCA-AAAAGTAGTACAGTAAA
12603 GTTTTCAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 8 0.38
25 6 0.29
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.28
Consensus pattern (24 bp):
AATTTCAAAAAGTAGTACAGTAAA
Found at i:13066 original size:18 final size:19
Alignment explanation
Indices: 13031--13068 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
13021 CACGGAATGT
13031 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-GAGAATAA
13051 AAGATTACCA-GAGAATAA
1 AAGATTACCAGGAGAATAA
13069 GATTACTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:17564 original size:14 final size:14
Alignment explanation
Indices: 17545--17575 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17535 CAATTTGAAA
17545 TGAGAATCATAATT
1 TGAGAATCATAATT
*
17559 TGAGAATCATAGTT
1 TGAGAATCATAATT
17573 TGA
1 TGA
17576 AGATATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (14 bp):
TGAGAATCATAATT
Found at i:27531 original size:15 final size:17
Alignment explanation
Indices: 27511--27542 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
27501 GATTTTTTTG
27511 TAAATT-CAA-ATAGAT
1 TAAATTGCAAGATAGAT
27526 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
27543 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:27802 original size:17 final size:17
Alignment explanation
Indices: 27789--27827 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
27779 AGTAGAGTTG
27789 GTGGTAATGTAGAGATA
1 GTGGTAATGTAGAGATA
27806 GTGGTAATGTAGAGATA
1 GTGGTAATGTAGAGATA
27823 GTGGT
1 GTGGT
27828 GGAGATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (17 bp):
GTGGTAATGTAGAGATA
Found at i:31661 original size:18 final size:18
Alignment explanation
Indices: 31638--31674 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31628 GGTATTGTTC
31638 TGTTATTTTAGTTTGACT
1 TGTTATTTTAGTTTGACT
31656 TGTTATTTTAGTTTGACT
1 TGTTATTTTAGTTTGACT
31674 T
1 T
31675 TATGTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.16, T:0.62
Consensus pattern (18 bp):
TGTTATTTTAGTTTGACT
Found at i:33434 original size:36 final size:36
Alignment explanation
Indices: 33393--33610 Score: 228
Period size: 37 Copynumber: 5.9 Consensus size: 36
33383 ATTTTTTTTA
* * *
33393 AAAATATATGTACTATATAG-TTTTGAAAACATTTCG
1 AAAATATATATAATATATAGTTTTTAAAAACATTT-G
* * *
33429 AAAATATATATAGTATATAGTTTTTAAAAAAAAATTG
1 AAAATATATATAATATATAGTTTTT-AAAAACATTTG
* * *
33466 AAAACATATATAATGTATAGTTTTTGAAAATGCATTTG
1 AAAATATATATAATATATAGTTTTT-AAAA-ACATTTG
* *
33504 AAAATATATATAATATATAG-TTTTGAAATCATTTTG
1 AAAATATATATAATATATAGTTTTTAAAAACA-TTTG
33540 AAAATATATATAATATATAGTTTTTAAAAAACATTTTTG
1 AAAATATATATAATATATAGTTTTT-AAAAACA--TTTG
33579 AAAA-ATTATATAATATATAG-TTTTAAAAACAT
1 AAAATA-TATATAATATATAGTTTTTAAAAACAT
33611 ATTTTTAAAT
Statistics
Matches: 156, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
35 3 0.02
36 45 0.29
37 46 0.29
38 39 0.25
39 23 0.15
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (36 bp):
AAAATATATATAATATATAGTTTTTAAAAACATTTG
Found at i:33523 original size:75 final size:72
Alignment explanation
Indices: 33406--33607 Score: 237
Period size: 75 Copynumber: 2.7 Consensus size: 72
33396 ATATATGTAC
*
33406 TATATAG-TTTTGAAAACATTTCGAAAATATATATAGTATATAGTTTTTAAAAAAAAATTGAAAA
1 TATATAGTTTTTGAAAACATTT-GAAAATATATATAATATATAG-TTTTAAAAAAAAATTGAAAA
33470 CATATATAA
64 CATATATAA
* * ** **
33479 TGTATAGTTTTTGAAAATGCATTTGAAAATATATATAATATATAGTTTTGAAATCATTTTGAAAA
1 TATATAGTTTTTGAAAA--CATTTGAAAATATATATAATATATAGTTTTAAAAAAAAATTGAAAA
*
33544 TATATATAA
64 CATATATAA
*
33553 TATATAGTTTTTAAAAAACATTTTTGAAAA-ATTATATAATATATAGTTTTAAAAA
1 TATATAGTTTTT-GAAAACA--TTTGAAAATA-TATATAATATATAGTTTTAAAAA
33608 CATATTTTTA
Statistics
Matches: 110, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
73 8 0.07
74 44 0.40
75 53 0.48
76 5 0.05
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (72 bp):
TATATAGTTTTTGAAAACATTTGAAAATATATATAATATATAGTTTTAAAAAAAAATTGAAAACA
TATATAA
Found at i:33569 original size:111 final size:112
Alignment explanation
Indices: 33393--33671 Score: 324
Period size: 111 Copynumber: 2.5 Consensus size: 112
33383 ATTTTTTTTA
* * * * *
33393 AAAATATATGTACTATATAGTTTTGAAAACATTTCGAAAATATATATAGTATATAGTTTTTAAAA
1 AAAATATATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGTTTTTAAAA
* **
33458 AA-A-AATTGAAAACA-TATATAATGTATAGTTTTTGAAA-ATGCATTTG
66 AACATAATTGAAAA-ATTATATAATATATAGTTTTAAAAACAT--ATTTG
33504 AAAATATATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGTTTTTAAAA
1 AAAATATATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGTTTTTAAAA
** *
33569 AACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATATTTT
66 AACATAATTGAAAAATTATATAATATATAGTTTTAAAAACATATTTG
* * * *
33616 TAAATCT-TAT-ATA-ATA-TTTTTAAATCATTTTTGAAAA-CTATATAATATATAGTTTT
1 AAAATATATATAATATATAGTTTTGAAATCA-TTTTGAAAATATATATAATATATAGTTTT
33672 GGAAATTTTT
Statistics
Matches: 148, Mismatches: 15, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
108 28 0.19
109 12 0.08
110 3 0.02
111 65 0.44
112 11 0.07
113 27 0.18
114 2 0.01
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (112 bp):
AAAATATATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGTTTTTAAAA
AACATAATTGAAAAATTATATAATATATAGTTTTAAAAACATATTTG
Found at i:33603 original size:38 final size:37
Alignment explanation
Indices: 33387--33743 Score: 255
Period size: 36 Copynumber: 9.8 Consensus size: 37
33377 TTTTTGATTT
* * * *
33387 TTTTTAAAAATATATGTACTATATAGTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTAAAAACA
* *
33424 -TTTCGAAAATATATATAGTATATAGTTTTTAAAAA-A
1 TTTTTGAAAATATATATAATATATAG-TTTTAAAAACA
*** * * *
33460 AAATTGAAAACATATATAATGTATAGTTTTTGAAAATGCA
1 TTTTTGAAAATATATATAATATATAG-TTTT-AAAA-ACA
* *
33500 --TTTGAAAATATATATAATATATAGTTTTGAAATCA
1 TTTTTGAAAATATATATAATATATAGTTTTAAAAACA
33535 -TTTTGAAAATATATATAATATATAGTTTTTAAAAAACA
1 TTTTTGAAAATATATATAATATATAG-TTTT-AAAAACA
33573 TTTTTGAAAA-ATTATATAATATATAGTTTTAAAAACA
1 TTTTTGAAAATA-TATATAATATATAGTTTTAAAAACA
* * * *
33610 TATTTT-TAAATCT-TAT-ATA-ATA-TTTTTAAATCA
1 T-TTTTGAAAATATATATAATATATAGTTTTAAAAACA
* **
33643 TTTTTGAAAA-CTATATAATATATAGTTTT-GGAA-A
1 TTTTTGAAAATATATATAATATATAGTTTTAAAAACA
* * *
33677 TTTTT---AAGA-ATATCATATATAGTTTTAAAAAATA
1 TTTTTGAAAATATATATAATATATAGTTTT-AAAAACA
33711 TTTTTGAAATATATATATTATATTATATAGTTT
1 TTTTTGAAA-ATATATA-TA-A-TATATAGTTT
33744 ATATTATATT
Statistics
Matches: 258, Mismatches: 33, Indels: 53
0.75 0.10 0.15
Matches are distributed among these distances:
31 18 0.07
32 6 0.02
33 18 0.07
34 18 0.07
35 9 0.03
36 56 0.22
37 53 0.21
38 41 0.16
39 26 0.10
40 2 0.01
41 1 0.00
42 10 0.04
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTAAAAACA
Found at i:33739 original size:14 final size:14
Alignment explanation
Indices: 33720--33758 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
33710 ATTTTTGAAA
33720 TATATATATTATAT
1 TATATATATTATAT
33734 TATATAGT-TTATAT
1 TATATA-TATTATAT
33748 TATAT-TATTAT
1 TATATATATTAT
33759 TAGTATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 4 0.17
14 17 0.74
15 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
TATATATATTATAT
Found at i:35166 original size:11 final size:11
Alignment explanation
Indices: 35152--35180 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
35142 TTTTTTCATG
35152 TTTTTATTTTA
1 TTTTTATTTTA
35163 TTTTTATTTTA
1 TTTTTATTTTA
35174 TTTTTAT
1 TTTTTAT
35181 CATATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:35186 original size:11 final size:11
Alignment explanation
Indices: 35131--35189 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
35121 TAACTTTTTA
35131 TTTATCATTATT
1 TTTATCA-TATT
* *
35143 TTTTTCATGTT
1 TTTATCATATT
**
35154 TTTATTTTATT
1 TTTATCATATT
**
35165 TTTATTTTATT
1 TTTATCATATT
35176 TTTATCATATT
1 TTTATCATATT
35187 TTT
1 TTT
35190 TACTAGCTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
11 33 0.85
12 6 0.15
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTATCATATT
Found at i:44405 original size:19 final size:19
Alignment explanation
Indices: 44381--44426 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
44371 TTCGGGAAAG
44381 TTTCGCCAGTCGTCGGTGT
1 TTTCGCCAGTCGTCGGTGT
*
44400 TTTCGCCAGTCGTCGTTGT
1 TTTCGCCAGTCGTCGGTGT
44419 TTTCGCCA
1 TTTCGCCA
44427 ACGGCGTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.07, C:0.28, G:0.26, T:0.39
Consensus pattern (19 bp):
TTTCGCCAGTCGTCGGTGT
Found at i:44706 original size:25 final size:25
Alignment explanation
Indices: 44672--44731 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
44662 CACCCTACCA
44672 GTACGACACAATTAATCGATTTAAG
1 GTACGACACAATTAATCGATTTAAG
44697 GTACGACACAATTAATCGATTTAAG
1 GTACGACACAATTAATCGATTTAAG
*
44722 GTACTACACA
1 GTACGACACA
44732 GAATCACTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (25 bp):
GTACGACACAATTAATCGATTTAAG
Found at i:46945 original size:2 final size:2
Alignment explanation
Indices: 46938--46973 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
46928 TTCTTCGGAC
46938 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
46974 TGAAACTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47899 original size:51 final size:50
Alignment explanation
Indices: 47859--47971 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 50
47849 GTCTCCTGTT
**
47859 CCGCGTTATACGATGATTTGACGCCACGTGGGGTATAGCGCGCCCCCTGCA
1 CCGCGTTATACGATGAGCTGACGCCACGT-GGGTATAGCGCGCCCCCTGCA
* * * *
47910 CCGCGTTATACGGTGAGCTGGCGCCACGTGGGTATAGGGCGGCCCCTGCA
1 CCGCGTTATACGATGAGCTGACGCCACGTGGGTATAGCGCGCCCCCTGCA
* *
47960 GCGCGCTATACG
1 CCGCGTTATACG
47972 CCACGTAGGG
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
50 29 0.54
51 25 0.46
ACGTcount: A:0.16, C:0.31, G:0.34, T:0.19
Consensus pattern (50 bp):
CCGCGTTATACGATGAGCTGACGCCACGTGGGTATAGCGCGCCCCCTGCA
Found at i:48063 original size:51 final size:47
Alignment explanation
Indices: 47983--48094 Score: 115
Period size: 51 Copynumber: 2.3 Consensus size: 47
47973 CACGTAGGGG
* *
47983 TATAGCGC-GGATCAGGTACTGCGCTATACCTTTACTCCTGACATAATTTTA
1 TATAGCGCGGGATCAGGTACCGCGCTATACCTTTA-----AACATAATTTTA
*
48034 TATAGCGCGGGGT-AGGTACCGCGAC-ATACCTTTAAACATAATTTTA
1 TATAGCGCGGGATCAGGTACCGCG-CTATACCTTTAAACATAATTTTA
48080 TATAGCGC-GGATCAG
1 TATAGCGCGGGATCAG
48095 ATATCGCATT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
45 3 0.06
46 21 0.39
51 26 0.48
52 4 0.07
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (47 bp):
TATAGCGCGGGATCAGGTACCGCGCTATACCTTTAAACATAATTTTA
Found at i:49627 original size:20 final size:19
Alignment explanation
Indices: 49599--49637 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
49589 CTTTAAAAAG
*
49599 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGA-AAATTT
49619 AGAGAATTTGAGAAAATTT
1 AGAGAATTTGAGAAAATTT
49638 GGTGTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (19 bp):
AGAGAATTTGAGAAAATTT
Found at i:49864 original size:51 final size:50
Alignment explanation
Indices: 49769--49876 Score: 128
Period size: 51 Copynumber: 2.2 Consensus size: 50
49759 CGCGCTTCAG
* ** *
49769 GGGC-CGCGTTATACCCACGTGACGCCAGCTCACCGTACAGCGCGGTGCA
1 GGGCGCGCGCTATACCCACGTGACGCCAAATCACCGTACAACGCGGTGCA
* * *
49818 GGGCGCGCGCTATACCCCACGTGGCGCCAAATCATCGTATAACGCGGTGCA
1 GGGCGCGCGCTATA-CCCACGTGACGCCAAATCACCGTACAACGCGGTGCA
*
49869 GGGGGCGC
1 GGGCGCGC
49877 TTTACTGCTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 4 0.08
50 8 0.16
51 37 0.76
ACGTcount: A:0.19, C:0.34, G:0.33, T:0.14
Consensus pattern (50 bp):
GGGCGCGCGCTATACCCACGTGACGCCAAATCACCGTACAACGCGGTGCA
Found at i:51496 original size:20 final size:20
Alignment explanation
Indices: 51473--51516 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
51463 AATAATCACA
* *
51473 CAAAATATAACAATTAAACT
1 CAAAATAAAACAACTAAACT
*
51493 CAAAATAAAATAACTAAACT
1 CAAAATAAAACAACTAAACT
51513 CAAA
1 CAAA
51517 TAACGAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (20 bp):
CAAAATAAAACAACTAAACT
Found at i:51902 original size:2 final size:2
Alignment explanation
Indices: 51895--51934 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
51885 AATGCAATGC
51895 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
51935 CACTTTCGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52273 original size:21 final size:21
Alignment explanation
Indices: 52240--52279 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52230 TTCTAACATG
**
52240 AAATATTTTGATCGAAAATTA
1 AAATATTAAGATCGAAAATTA
*
52261 AAATATTAAGATCTAAAAT
1 AAATATTAAGATCGAAAAT
52280 GTTAAAAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (21 bp):
AAATATTAAGATCGAAAATTA
Found at i:52445 original size:13 final size:13
Alignment explanation
Indices: 52401--52450 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
52391 AAAAAAAGTT
52401 AAAAATAATTTT-
1 AAAAATAATTTTA
*
52413 AAAAAT-A-TTAA
1 AAAAATAATTTTA
52424 AACAAATAATTTTA
1 AA-AAATAATTTTA
52438 AAAAATAATTTTA
1 AAAAATAATTTTA
52451 TAATATTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 10 0.31
13 12 0.38
14 5 0.16
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:53492 original size:23 final size:23
Alignment explanation
Indices: 53466--53554 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 23
53456 GTATAAATGT
53466 ACCGAAGTGCCACGTAGAATTGC
1 ACCGAAGTGCCACGTAGAATTGC
* * *
53489 ACCGTAGTGCCGCGTAGAAATGC
1 ACCGAAGTGCCACGTAGAATTGC
* *
53512 ACTGAAGTGCCGCGTAGAATTGC
1 ACCGAAGTGCCACGTAGAATTGC
*
53535 ACCCTAAG-GACCACGTAGAA
1 A-CCGAAGTG-CCACGTAGAA
53555 AATTCCTTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
23 42 0.76
24 13 0.24
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.17
Consensus pattern (23 bp):
ACCGAAGTGCCACGTAGAATTGC
Found at i:58204 original size:31 final size:31
Alignment explanation
Indices: 58128--58189 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
58118 ATTGATTTTG
58128 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
58159 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
58190 TTAAATTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.35, G:0.03, T:0.26
Consensus pattern (31 bp):
AAAAACTTACTCCCCCTTACTATAGCACATC
Found at i:67817 original size:30 final size:31
Alignment explanation
Indices: 67752--67818 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
67742 ATGATGGTAG
* * *
67752 AGTGATCATTTTGTTACAAATTCGTAACGTC
1 AGTGACCATTTTGTTACAAATTCATAACATC
*
67783 AGTGACCATTTTG-TACAAA-TCTATAACATT
1 AGTGACCATTTTGTTACAAATTC-ATAACATC
67813 AGTGAC
1 AGTGAC
67819 TAATTTATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 2 0.06
30 17 0.55
31 12 0.39
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (31 bp):
AGTGACCATTTTGTTACAAATTCATAACATC
Found at i:69211 original size:21 final size:23
Alignment explanation
Indices: 69185--69227 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
69175 CATTCTCCTT
69185 AATTTTTAA-TTTT-ATTATACA
1 AATTTTTAATTTTTAATTATACA
69206 AATTTTTAATTTTTAATTATAC
1 AATTTTTAATTTTTAATTATAC
69228 TCTATATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (23 bp):
AATTTTTAATTTTTAATTATACA
Found at i:69275 original size:34 final size:32
Alignment explanation
Indices: 69176--69263 Score: 96
Period size: 28 Copynumber: 2.8 Consensus size: 32
69166 TCCCCGAAAC
69176 ATTCTCCTTAATTTTTAATTTTATTAT-A-CAA
1 ATTCT-CTTAATTTTTAATTTTATTATAATCAA
*
69207 ATT-T-TTAATTTTTAATTATACTCTAT-ATGCAA
1 ATTCTCTTAATTTTTAATTTTA-T-TATAAT-CAA
69239 ATTCTCTTAATTTTTAATTTTATTA
1 ATTCTCTTAATTTTTAATTTTATTA
69264 ATAAATTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
28 15 0.31
29 1 0.02
30 5 0.10
31 3 0.06
32 8 0.16
33 2 0.04
34 15 0.31
ACGTcount: A:0.32, C:0.10, G:0.01, T:0.57
Consensus pattern (32 bp):
ATTCTCTTAATTTTTAATTTTATTATAATCAA
Found at i:76427 original size:31 final size:32
Alignment explanation
Indices: 76389--76453 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 32
76379 TATACATACA
76389 CTTTTATTTT-AACTTGATAATATTCTAACGG
1 CTTTTATTTTAAACTTGATAATATTCTAACGG
76420 CTTTTATTTTAACAACTTGATAATATTCTAACGG
1 CTTTTATTTT-A-AACTTGATAATATTCTAACGG
76454 TGATGAATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 10 0.32
34 21 0.68
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (32 bp):
CTTTTATTTTAAACTTGATAATATTCTAACGG
Found at i:76451 original size:19 final size:19
Alignment explanation
Indices: 76399--76451 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 19
76389 CTTTTATTTT
76399 AACTTGATAATATTCTAAC
1 AACTTGATAATATTCTAAC
** *
76418 GGCTT--T--TATTTTAAC
1 AACTTGATAATATTCTAAC
76433 AACTTGATAATATTCTAAC
1 AACTTGATAATATTCTAAC
76452 GGTGATGAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 8
0.63 0.16 0.21
Matches are distributed among these distances:
15 11 0.46
17 2 0.08
19 11 0.46
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (19 bp):
AACTTGATAATATTCTAAC
Found at i:88309 original size:2 final size:2
Alignment explanation
Indices: 88302--88378 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
88292 CCACGTACAA
88302 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
88344 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
88379 CGTACGTACA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:102253 original size:11 final size:12
Alignment explanation
Indices: 102237--102290 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 12
102227 CAGTGTAGTA
102237 AGTAATA-ATAT
1 AGTAATATATAT
102248 AGTAATATATAT
1 AGTAATATATAT
102260 A-T-ATATATAT
1 AGTAATATATAT
102270 A-T-ATATATAT
1 AGTAATATATAT
102280 A-T-ATATATAT
1 AGTAATATATAT
102290 A
1 A
102291 TTCTTAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
10 29 0.69
11 8 0.19
12 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (12 bp):
AGTAATATATAT
Found at i:102259 original size:2 final size:2
Alignment explanation
Indices: 102252--102291 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
102242 TAATATAGTA
102252 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
102292 TCTTAAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.