Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007152.1 Hibiscus syriacus cultivar Beakdansim tig00018711_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: 60725
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1370 original size:31 final size:31
Alignment explanation
Indices: 1330--1425 Score: 115
Period size: 31 Copynumber: 3.1 Consensus size: 31
1320 GTCCCGAAAG
* *
1330 ACCTATCCATATATTCCGAAGAACATAGGTA
1 ACCTGTCCATATGTTCCGAAGAACATAGGTA
*
1361 ACCTGTCCATATGTCCCGAATG-ACATAGGTA
1 ACCTGTCCATATGTTCCGAA-GAACATAGGTA
* *
1392 AACTGTCCATATGTTTCGAA-AGACATAGGTA
1 ACCTGTCCATATGTTCCGAAGA-ACATAGGTA
1423 ACC
1 ACC
1426 CTTGACTCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
31 54 0.98
32 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (31 bp):
ACCTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:5662 original size:31 final size:31
Alignment explanation
Indices: 5622--5717 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 31
5612 GTCCCGAAGG
* * *
5622 ACCTATCCATATATTCTGAAGAACATAGGTA
1 ACCTGTCCATATATCCCGAAGAACATAGGTA
* *
5653 ACCTGTCCATATGTCCCGAAGGACATAGGTA
1 ACCTGTCCATATATCCCGAAGAACATAGGTA
* * * * *
5684 AACTGTTCGTATGTCCC-AAAAGACATAGGTA
1 ACCTGTCCATATATCCCGAAGA-ACATAGGTA
5715 ACC
1 ACC
5718 CTCGACTCTT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
30 2 0.04
31 51 0.96
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (31 bp):
ACCTGTCCATATATCCCGAAGAACATAGGTA
Found at i:7878 original size:59 final size:59
Alignment explanation
Indices: 7810--7930 Score: 215
Period size: 59 Copynumber: 2.1 Consensus size: 59
7800 ATGTATTGAG
7810 TAAATAATAAAAGATGAGAATGATTTGTAATAGTGTTTAAACTAAAGTGTATCAATTAA
1 TAAATAATAAAAGATGAGAATGATTTGTAATAGTGTTTAAACTAAAGTGTATCAATTAA
* * *
7869 TAAATAATAAAAGATGAGAATGATTTGTAATAGTGTTTAGACTAAAGTGTATTAATTGA
1 TAAATAATAAAAGATGAGAATGATTTGTAATAGTGTTTAAACTAAAGTGTATCAATTAA
7928 TAA
1 TAA
7931 GGTAAAAGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.35
Consensus pattern (59 bp):
TAAATAATAAAAGATGAGAATGATTTGTAATAGTGTTTAAACTAAAGTGTATCAATTAA
Found at i:8176 original size:21 final size:21
Alignment explanation
Indices: 8137--8176 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
8127 TTGTAACCTT
*
8137 AAATGATATATAAGCTTAAGG
1 AAATGATATATAAGATTAAGG
* *
8158 AAATGTTATATAGGATTAA
1 AAATGATATATAAGATTAA
8177 AACTATGAAA
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:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (21 bp):
AAATGATATATAAGATTAAGG
Found at i:8547 original size:95 final size:95
Alignment explanation
Indices: 8407--8596 Score: 283
Period size: 95 Copynumber: 2.0 Consensus size: 95
8397 ATACCGACAA
* * * *
8407 GGTAGTATCGATACCATGGTAAGGGTATCGATATCAAGCATCATCGAATCTAAAATTGGTATCGA
1 GGTAATATCGATACCATGGTAAGGGTATCAATATCAAGCAACATCGAACCTAAAATTGGTATCGA
* *
8472 TATCGGAAGGGGGTATCGGTACCATAGTAT
66 TATAGGAAGGGGATATCGGTACCATAGTAT
*
8502 GGTAATATCGATACCATGGTAAGGGTATCAATA-CTAGGCAACATCGAACCTAAAATTGGTATCG
1 GGTAATATCGATACCATGGTAAGGGTATCAATATC-AAGCAACATCGAACCTAAAATTGGTATCG
* *
8566 ATATAGGAAGGGGATATTGGTACCGTAGTAT
65 ATATAGGAAGGGGATATCGGTACCATAGTAT
8597 AGAATTATCA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 1 0.01
95 84 0.99
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (95 bp):
GGTAATATCGATACCATGGTAAGGGTATCAATATCAAGCAACATCGAACCTAAAATTGGTATCGA
TATAGGAAGGGGATATCGGTACCATAGTAT
Found at i:8625 original size:95 final size:95
Alignment explanation
Indices: 8412--8632 Score: 252
Period size: 95 Copynumber: 2.3 Consensus size: 95
8402 GACAAGGTAG
* * * * * * *
8412 TATCGATACCATGGTAAGGGTATCGATA-TCAAGCATCATCGAATCTAAAATTGGTATCGATATC
1 TATCGATACCAGGGTAAGAGTATCAATACT-AGGCAACATCGAACCTAAAATTGGTATCGATATA
* *
8476 GGAAGGGGGTATCGGTACCATAGTATGGTAA
65 GGAAGGGGATATCGGTACCATAGTATAGTAA
* *
8507 TATCGATACCATGGTAAGGGTATCAATACTAGGCAACATCGAACCTAAAATTGGTATCGATATAG
1 TATCGATACCAGGGTAAGAGTATCAATACTAGGCAACATCGAACCTAAAATTGGTATCGATATAG
* *
8572 GAAGGGGATATTGGTACCGTAGTATAG-AA
66 GAAGGGGATATCGGTACCATAGTATAGTAA
*
8601 TTATC-AGTACCAGGGT-AGTAGTATCGATACTA
1 -TATCGA-TACCAGGGTAAG-AGTATCAATACTA
8633 TAGAGCCAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
94 5 0.05
95 104 0.95
96 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.27
Consensus pattern (95 bp):
TATCGATACCAGGGTAAGAGTATCAATACTAGGCAACATCGAACCTAAAATTGGTATCGATATAG
GAAGGGGATATCGGTACCATAGTATAGTAA
Found at i:9163 original size:79 final size:79
Alignment explanation
Indices: 9032--9598 Score: 875
Period size: 79 Copynumber: 7.1 Consensus size: 79
9022 TTGGAACGAA
*
9032 AGCATAAAGGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTAT
1 AGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTAT
9097 ATGGGTACATTGTC
66 ATGGGTACATTGTC
* * * * *
9111 AGCATAAAATAATAATGCATATAGGTACATTATTGGCATGAAAGTATGCCATAGCTAAAATGTAT
1 AGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATG---
9176 ATATATGGGTACATTGTC
63 -TATATGGGTACATTGTC
* *
9194 ACCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGTAT
1 AGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTAT
*
9259 ATGGGTACATTATTC
66 ATGGGTACATT-GTC
*
9274 -GCATAAAAGAATAATTCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTAT
1 AGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTAT
9338 ATGGGTACATTGTC
66 ATGGGTACATTGTC
* *
9352 AGCATAAAAAAATAATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGAAATGTAT
1 AGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTAT
9417 ATGGGTACATTGTC
66 ATGGGTACATTGTC
* *
9431 AGCATAAATGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGTAT
1 AGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTAT
9496 ATGGGTACATTGTC
66 ATGGGTACATTGTC
* * * * * *
9510 AGTATAAAAGAATAATGCATTTGGGTGCATTATTGGCATGAAAGGATACCATCGTTGAAATGCAT
1 AGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTAT
* *
9575 ATGGGTGCATTATC
66 ATGGGTACATTGTC
*
9589 ACCATAAAAG
1 AGCATAAAAG
9599 TATATTATAT
Statistics
Matches: 445, Mismatches: 37, Indels: 12
0.90 0.07 0.02
Matches are distributed among these distances:
78 2 0.00
79 369 0.83
80 2 0.00
83 72 0.16
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (79 bp):
AGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTAT
ATGGGTACATTGTC
Found at i:9697 original size:59 final size:59
Alignment explanation
Indices: 9623--9756 Score: 193
Period size: 59 Copynumber: 2.3 Consensus size: 59
9613 TGCATTACAA
* *
9623 ATATGAATTTCCGTATAGGGCACT-TCGTGTGCTAAAATGA-TAAGAAATTCATACTAAGT
1 ATATGAATTTTCGTATAGGGCACTAT-GTGTGCTAAAAT-ATTAAGAAAGTCATACTAAGT
9682 ATATGAATTTTCGTATAGGGCACTATGTGTGCTAAAATATTAAGAAAGTCATACTAAGT
1 ATATGAATTTTCGTATAGGGCACTATGTGTGCTAAAATATTAAGAAAGTCATACTAAGT
*
9741 GTATGAACTTTT-GTAT
1 ATATGAA-TTTTCGTAT
9757 GAGAAATATA
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
58 1 0.01
59 63 0.91
60 5 0.07
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (59 bp):
ATATGAATTTTCGTATAGGGCACTATGTGTGCTAAAATATTAAGAAAGTCATACTAAGT
Found at i:10328 original size:81 final size:81
Alignment explanation
Indices: 10091--10285 Score: 336
Period size: 81 Copynumber: 2.4 Consensus size: 81
10081 AGTTGTATAT
* * *
10091 ACGGTTAAATACCGTTGAGTAAAATAATAATGGCTTAATTGTGCAAATGACATAAAAGTGTAAAT
1 ACGGTTAAACACTGTTGAGTAAAAGAATAATGGCTTAATTGTGCAAATGACATAAAAGTGTAAAT
10156 GATGTCAGTTAGATGA
66 GATGTCAGTTAGATGA
* * *
10172 ACGGTTAAACACTGTTAAGTAAATGAATAATGGCTTAATTGTGCAAATGGCATAAAAGTGTAAAT
1 ACGGTTAAACACTGTTGAGTAAAAGAATAATGGCTTAATTGTGCAAATGACATAAAAGTGTAAAT
10237 GATGTCAGTTAGATGA
66 GATGTCAGTTAGATGA
10253 ACGGTTAAACACTGTTGAGTAAAAGAATAATGG
1 ACGGTTAAACACTGTTGAGTAAAAGAATAATGG
10286 ACTAGCAGTG
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 106 1.00
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (81 bp):
ACGGTTAAACACTGTTGAGTAAAAGAATAATGGCTTAATTGTGCAAATGACATAAAAGTGTAAAT
GATGTCAGTTAGATGA
Found at i:10401 original size:2 final size:2
Alignment explanation
Indices: 10394--10439 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
10384 ATATGAATGG
10394 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10435 TA TA T
1 TA TA T
10440 GTACATTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15891 original size:11 final size:11
Alignment explanation
Indices: 15877--15921 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
15867 TTGCAATTCA
15877 TTTATCTT-TT
1 TTTATCTTATT
*
15887 CTTTATCTTGTT
1 -TTTATCTTATT
*
15899 TTAATCTTATT
1 TTTATCTTATT
15910 TTTATCTTATT
1 TTTATCTTATT
15921 T
1 T
15922 CCAGCACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 28 0.93
12 2 0.07
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:22536 original size:22 final size:22
Alignment explanation
Indices: 22511--22552 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
22501 CAATTCATTT
22511 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
22533 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
22553 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:34126 original size:22 final size:24
Alignment explanation
Indices: 34099--34151 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
34089 AAAATCAGCA
* *
34099 AAGAAA-TTGAAGTACTC-AAAAG
1 AAGAAATTTCAAGCACTCAAAAAG
34121 AAGAAAATTTCAAGCACTCAAAAAG
1 AAG-AAATTTCAAGCACTCAAAAAG
34146 AAGAAA
1 AAGAAA
34152 AAGAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 3 0.12
23 3 0.12
24 12 0.46
25 8 0.31
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.15
Consensus pattern (24 bp):
AAGAAATTTCAAGCACTCAAAAAG
Found at i:36048 original size:23 final size:25
Alignment explanation
Indices: 36022--36076 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
36012 AAATCCAGCA
36022 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGCACTCAAAGAGG
* *
36045 AAGAAATTGAAAGCACTCAAAGAGG
1 AAGAAAATCAAAGCACTCAAAGAGG
36070 AAGAAAA
1 AAGAAAA
36077 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 19 0.70
24 1 0.04
25 7 0.26
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAGAGG
Found at i:38791 original size:22 final size:24
Alignment explanation
Indices: 38764--38816 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
38754 AAAATCAGCA
*
38764 AAGAAA-TTGAAGCACTC-AAAAG
1 AAGAAATTTCAAGCACTCAAAAAG
38786 AAGAAAATTTCAAGCACTCAAAAAG
1 AAG-AAATTTCAAGCACTCAAAAAG
38811 AAGAAA
1 AAGAAA
38817 AAGAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 3 0.11
23 3 0.11
24 13 0.48
25 8 0.30
ACGTcount: A:0.58, C:0.13, G:0.15, T:0.13
Consensus pattern (24 bp):
AAGAAATTTCAAGCACTCAAAAAG
Found at i:40713 original size:23 final size:25
Alignment explanation
Indices: 40687--40741 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
40677 AAATCCAGCA
40687 AAGAAAATCAAAGCACTCAAA-AG-
1 AAGAAAATCAAAGCACTCAAAGAGT
* *
40710 AAGAAATTGAAAGCACTCAAAGAGT
1 AAGAAAATCAAAGCACTCAAAGAGT
40735 AAGAAAA
1 AAGAAAA
40742 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 19 0.70
24 2 0.07
25 6 0.22
ACGTcount: A:0.60, C:0.13, G:0.16, T:0.11
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAGAGT
Found at i:43515 original size:25 final size:24
Alignment explanation
Indices: 43472--43521 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
43462 AGACAAAAAG
43472 AAGAAAAAAAATCAGAAAAGAAGAA
1 AAGAAAAAAAATCAGAAAAG-AGAA
*
43497 AAGAAAAAAAATTTA-AAAAGAGAA
1 AAGAAAAAAAA-TCAGAAAAGAGAA
43521 A
1 A
43522 GCAAGCCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 16 0.70
26 2 0.09
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.08
Consensus pattern (24 bp):
AAGAAAAAAAATCAGAAAAGAGAA
Found at i:48061 original size:21 final size:21
Alignment explanation
Indices: 48037--48076 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
48027 TCATAACATG
48037 TGCATTCATTCATT-ATATGGT
1 TGCA-TCATTCATTGATATGGT
*
48058 TGCATCATTGATTGATATG
1 TGCATCATTCATTGATATG
48077 CAAGCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.45
Consensus pattern (21 bp):
TGCATCATTCATTGATATGGT
Found at i:48840 original size:30 final size:31
Alignment explanation
Indices: 48806--48865 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
48796 CTTAGCTTTA
**
48806 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
48836 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
48866 GGAAACTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:49772 original size:19 final size:21
Alignment explanation
Indices: 49748--49799 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
49738 CGGCCAAGAG
*
49748 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
49767 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
49788 CATGTATTTTCA
1 CATGTATTTTCA
49800 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:50250 original size:18 final size:19
Alignment explanation
Indices: 50209--50247 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
50199 TATCCTTTCT
50209 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTCTTA
50228 TTATTTC-TTTCATTACTTA
1 TTATTTCATTTCATT-CTTA
50247 T
1 T
50248 ATTATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTCATTTCATTCTTA
Found at i:53862 original size:18 final size:20
Alignment explanation
Indices: 53833--53878 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
53823 CGGCCAAGAG
53833 CATGTA-TTCA-TT-AAAAT
1 CATGTATTTCATTTAAAAAT
53850 CATGTATTTCATTTAAAAAT
1 CATGTATTTCATTTAAAAAT
*
53870 CATATATTT
1 CATGTATTT
53879 TCAAAGGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 6 0.24
18 4 0.16
19 2 0.08
20 13 0.52
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (20 bp):
CATGTATTTCATTTAAAAAT
Found at i:54318 original size:18 final size:18
Alignment explanation
Indices: 54274--54310 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54264 ATCTCTATCC
54274 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
*
54291 TTCTTATATTTCTTTTCA
1 TTCTTATATTTCATTTCA
54309 TT
1 TT
54311 ACTATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (18 bp):
TTCTTATATTTCATTTCA
Found at i:56279 original size:15 final size:15
Alignment explanation
Indices: 56245--56282 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
56235 GAAATGGAAG
56245 AAGAAATGAAATGAT
1 AAGAAATGAAATGAT
*
56260 AAGAATTGAAATGGAT
1 AAGAAATGAAAT-GAT
56276 -AGAAATG
1 AAGAAATG
56283 TTATCAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (15 bp):
AAGAAATGAAATGAT
Found at i:56907 original size:20 final size:20
Alignment explanation
Indices: 56870--56907 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56860 AAGGAAGATT
*
56870 AATGAATGATAAAGATAAGG
1 AATGAATGATAAAAATAAGG
56890 AATGAATGA-AATAAATAA
1 AATGAATGATAA-AAATAA
56908 AGGCTAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (20 bp):
AATGAATGATAAAAATAAGG
Found at i:56956 original size:22 final size:21
Alignment explanation
Indices: 56930--56970 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
56920 GCTATGGAAT
56930 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
56952 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
56971 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:58214 original size:10 final size:10
Alignment explanation
Indices: 58192--58238 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
58182 AAGTTATCAT
*
58192 TATA-ATAAC
1 TATATATAAA
*
58201 TATAGATAAA
1 TATATATAAA
*
58211 TATATATATA
1 TATATATAAA
*
58221 TATATATATA
1 TATATATAAA
58231 TATATATA
1 TATATATA
58239 TGAAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 4 0.12
10 30 0.88
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (10 bp):
TATATATAAA
Found at i:58217 original size:2 final size:2
Alignment explanation
Indices: 58210--58239 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
58200 CTATAGATAA
58210 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
58240 GAAAATAATT
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:60016 original size:18 final size:17
Alignment explanation
Indices: 59989--60023 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
59979 CATCTCCGTT
59989 TCATCATCAACACCATC
1 TCATCATCAACACCATC
*
60006 TCATCCATCAAGACCATC
1 TCAT-CATCAACACCATC
60024 AATTCTGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.34, C:0.40, G:0.03, T:0.23
Consensus pattern (17 bp):
TCATCATCAACACCATC
Done.