Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000366.1 Hibiscus syriacus cultivar Beakdansim tig00000666_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: 70273
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:6617 original size:21 final size:20
Alignment explanation
Indices: 6569--6618 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
6559 TTTTTGGCTC
*
6569 AAAGGATCAATCCCTTAGCA
1 AAAGGATCAATCCCTGAGCA
*
6589 AAAGGATCAATCCCTCGAGGA
1 AAAGGATCAATCCCT-GAGCA
*
6610 AAATGATCA
1 AAAGGATCA
6619 TTTGCTTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAGGATCAATCCCTGAGCA
Found at i:7791 original size:12 final size:12
Alignment explanation
Indices: 7774--7802 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
7764 GAATAATTAG
7774 AAACATCCTTTA
1 AAACATCCTTTA
7786 AAACATCCTTTA
1 AAACATCCTTTA
7798 AAACA
1 AAACA
7803 AATTTAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (12 bp):
AAACATCCTTTA
Found at i:12790 original size:18 final size:18
Alignment explanation
Indices: 12763--12811 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 18
12753 ATTATCTATG
*
12763 TCCCGTAGGACCATTACA
1 TCCCGAAGGACCATTACA
12781 TCCCGAAGGA-C--TACA
1 TCCCGAAGGACCATTACA
* *
12796 TCTCGAAGGACTATTA
1 TCCCGAAGGACCATTA
12812 TACCCTCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
15 13 0.52
17 1 0.04
18 11 0.44
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (18 bp):
TCCCGAAGGACCATTACA
Found at i:12797 original size:15 final size:15
Alignment explanation
Indices: 12777--12808 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12767 GTAGGACCAT
12777 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
*
12792 TACATCTCGAAGGAC
1 TACATCCCGAAGGAC
12807 TA
1 TA
12809 TTATACCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:12957 original size:23 final size:26
Alignment explanation
Indices: 12920--12988 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
12910 TTCTCTTGTG
12920 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
12944 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
12969 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
12989 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:12970 original size:12 final size:12
Alignment explanation
Indices: 12953--12988 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
12943 TATCATGTTC
12953 TCATATCACATG
1 TCATATCACATG
*
12965 TCATATCACATA
1 TCATATCACATG
12977 TCATATCACATG
1 TCATATCACATG
12989 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:16835 original size:2 final size:2
Alignment explanation
Indices: 16828--16872 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
16818 AGTGCCCAAA
16828 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16870 AG A
1 AG A
16873 CTTGTCCCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18886 original size:20 final size:20
Alignment explanation
Indices: 18863--18959 Score: 83
Period size: 20 Copynumber: 4.8 Consensus size: 20
18853 ATTCGCGTTG
18863 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
18883 CATTTCGCGTTGCGATAGTCTA
1 CATTTCGCGTTGCGAT--TTTC
** *
18905 CGGTT-GTCGTTGCAATTTTC
1 CATTTCG-CGTTGCGATTTTC
*
18925 CAAATT--CGTTGCGATTTTC
1 C-ATTTCGCGTTGCGATTTTC
18944 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
18960 AGTCTACAGT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
18 3 0.05
19 13 0.22
20 28 0.47
21 3 0.05
22 13 0.22
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.41
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:18944 original size:61 final size:61
Alignment explanation
Indices: 18870--18997 Score: 238
Period size: 61 Copynumber: 2.1 Consensus size: 61
18860 TTGCATTTCG
*
18870 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACGGTTGTCGTTGCAATTTTCCAAATT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATT
*
18931 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATT
18992 CGTTGC
1 CGTTGC
18998 AATAGTCTAC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (61 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCAATTTTCCAAATT
Found at i:18979 original size:22 final size:22
Alignment explanation
Indices: 18951--19087 Score: 158
Period size: 22 Copynumber: 6.4 Consensus size: 22
18941 TTCCATTTCG
18951 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
18973 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
*
18992 CGTTGCAATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * *
19014 TGTTGCGATAGTTTACAAATT-T
1 CGTTGCGATAGTCTAC-AGTTGT
19036 -GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
19057 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
19079 CGTTGCGAT
1 CGTTGCGAT
19088 TTTCCAAATT
Statistics
Matches: 94, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
19 9 0.10
20 8 0.09
21 20 0.21
22 54 0.57
23 3 0.03
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:18996 original size:19 final size:19
Alignment explanation
Indices: 18911--18997 Score: 68
Period size: 19 Copynumber: 4.4 Consensus size: 19
18901 TCTACGGTTG
*
18911 TCGTTGCAATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
*
18930 TCGTTGCGATTTTCC-ATT
1 TCGTTGCGATTTTCCAAAT
* * **
18948 TCGCGTTGCGATAGTCTACAGTT
1 T--CGTTGCGAT--TTTCCAAAT
18971 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
18991 TCGTTGC
1 TCGTTGC
18998 AATAGTCTAC
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
18 3 0.06
19 21 0.40
20 14 0.26
22 12 0.23
23 2 0.04
24 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:19047 original size:43 final size:43
Alignment explanation
Indices: 18951--19087 Score: 188
Period size: 43 Copynumber: 3.2 Consensus size: 43
18941 TTCCATTTCG
*
18951 CGTTGCGATAGTCTACAGTTGTCGTTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATAGTTTACAAATT
* *
18992 CGTTGCAATAGTCTACAGTTGTTGTTGCGATAGTTTACAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATAGTTTACAAATT
* * **
19035 TGTTGCGATAGTCTACAGTTGTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATAGTTTACAAAT-T
19079 CGTTGCGAT
1 CGTTGCGAT
19088 TTTCCAAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
41 29 0.35
43 45 0.54
44 9 0.11
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (43 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATAGTTTACAAATT
Found at i:19211 original size:6 final size:6
Alignment explanation
Indices: 19200--19232 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
19190 GACACGTATT
19200 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
19233 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:20244 original size:19 final size:19
Alignment explanation
Indices: 20220--20323 Score: 127
Period size: 19 Copynumber: 5.3 Consensus size: 19
20210 TTAACTATCA
20220 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
20239 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
*
20261 CAACAAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
20280 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
*
20299 CAACGAATTTGAAAAATCG
1 CAACGAATTTGGAAAATCG
20318 CAACGA
1 CAACGA
20324 CAACTGTAGA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 55 0.77
20 2 0.03
21 2 0.03
22 12 0.17
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.19
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:20308 original size:38 final size:39
Alignment explanation
Indices: 20220--20362 Score: 137
Period size: 41 Copynumber: 3.6 Consensus size: 39
20210 TTAACTATCA
**
20220 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
1 CAACGAATTTGGAAAATCGCAACG--AACTGTAGAAAATCG
* * *
20261 CAACAAATTTGGAAAATCGCAACGAA-TTTGGAAAATCG
1 CAACGAATTTGGAAAATCGCAACGAACTGTAGAAAATCG
* **
20299 CAACGAATTTGAAAAATCGCAACGACAACTGTAGACCATCG
1 CAACGAATTTGGAAAATCGCAACG--AACTGTAGAAAATCG
*
20340 CAACGTGAA-ATGGAAAATCGCAA
1 CAAC--GAATTTGGAAAATCGCAA
20363 TGCGATTTTC
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
38 30 0.36
39 2 0.02
40 2 0.02
41 35 0.42
42 12 0.14
43 3 0.04
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (39 bp):
CAACGAATTTGGAAAATCGCAACGAACTGTAGAAAATCG
Found at i:20378 original size:41 final size:41
Alignment explanation
Indices: 20333--20421 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
20323 ACAACTGTAG
* * *
20333 ACCATCGCAACGTGAAATGGAAAATCGCAATGCGATTTTCA
1 ACCATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
20374 ACCATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
1 ACCATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
*
20415 ACTATCG
1 ACCATCG
20422 TGGAGATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (41 bp):
ACCATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
Found at i:20402 original size:20 final size:20
Alignment explanation
Indices: 20336--20408 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
20326 ACTGTAGACC
* *
20336 ATCGCAACGTGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
* ** * **
20356 ATCGCAATGCGATTTTCAACC
1 ATCGCAACGCGA-AATGAAAA
20377 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
20397 ATCGCAACGCGA
1 ATCGCAACGCGA
20409 TTTTCAACTA
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 25 0.66
21 13 0.34
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:21361 original size:24 final size:24
Alignment explanation
Indices: 21309--21376 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
21299 TGAATAATAA
21309 TCTATG-TCCTTGTGACAC-ATTTT
1 TCTATGCT-CTTGTGACACGATTTT
21332 TCTATGCTCTTGTGACACGATTTT
1 TCTATGCTCTTGTGACACGATTTT
* *
21356 TTTATGCTCTTGTGGCACGAT
1 TCTATGCTCTTGTGACACGAT
21377 CCTTATGGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
23 16 0.39
24 25 0.61
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.46
Consensus pattern (24 bp):
TCTATGCTCTTGTGACACGATTTT
Found at i:36445 original size:2 final size:2
Alignment explanation
Indices: 36438--36468 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
36428 ATAATATTCC
36438 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 A
36469 GGAGTAGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39909 original size:23 final size:23
Alignment explanation
Indices: 39883--39931 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
39873 AATAACATAT
39883 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
39906 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
39929 TAG
1 TAG
39932 ACATTTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:39992 original size:87 final size:87
Alignment explanation
Indices: 39846--40008 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
39836 AATGTTAAAT
*
39846 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
*
39911 AGCGCTTATATAATGTAATAGA
66 AACGCTTATATAATGTAATAGA
* *
39933 CATTTAATCAGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGT
1 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
39998 AACGCTTATAT
66 AACGCTTATAT
40009 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (87 bp):
CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AACGCTTATATAATGTAATAGA
Found at i:40455 original size:73 final size:72
Alignment explanation
Indices: 40329--40486 Score: 198
Period size: 73 Copynumber: 2.2 Consensus size: 72
40319 TATAAATGTA
* *
40329 TCGACACTTTATGGTTGCACCCTTTTTGGTATTCATTCTGGACCAAAAATATCGACACAAATTTA
1 TCGACACTTTATGGTTGCACCCTTTTTGGCATTCATCCTGGACCAAAAATATCGACACAAA-TTA
40394 -TCAAGTG
65 CTCAAGTG
*
40401 TCGACACTTTATGCG-TGCA-CCTTGTTTGTGCATTCATCCTGGA-CAATAAGTATCGACACAAA
1 TCGACACTTTATG-GTTGCACCCTT-TTTG-GCATTCATCCTGGACCAA-AAATATCGACACAAA
40463 TTACTCAAGTG
62 TTACTCAAGTG
* *
40474 TCGATACATTATG
1 TCGACACTTTATG
40487 TTGACTTGTT
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
71 4 0.05
72 27 0.36
73 45 0.59
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (72 bp):
TCGACACTTTATGGTTGCACCCTTTTTGGCATTCATCCTGGACCAAAAATATCGACACAAATTAC
TCAAGTG
Found at i:44993 original size:3 final size:3
Alignment explanation
Indices: 44985--45028 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
44975 ACTTGTTTGG
* * * *
44985 ATC ATC ATC ATC ATC ATC ATC GTC ATC GTC ATC TTC ATC TTC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
45029 TGACCGCTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (3 bp):
ATC
Found at i:45504 original size:34 final size:32
Alignment explanation
Indices: 45451--45520 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
45441 CCTTACAAAC
*
45451 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
45483 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
45517 TCCC
1 TCCC
45521 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:45826 original size:21 final size:21
Alignment explanation
Indices: 45800--45841 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
45790 CCAGAATGGG
*
45800 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
45821 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
45842 ATATTCAAAT
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:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:45971 original size:19 final size:19
Alignment explanation
Indices: 45947--46013 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
45937 GAGCCTCGGG
*
45947 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
45966 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* * *
45985 TTGCTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
46004 TTACTATTCA
1 TTACTGTTCA
46014 TAAAAACATT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:46126 original size:30 final size:31
Alignment explanation
Indices: 46079--46169 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
46069 AAATTTTGAA
46079 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
46108 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
46139 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
46170 CCTTAAATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:46360 original size:22 final size:22
Alignment explanation
Indices: 46328--46375 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
46318 TAAGCTCCCC
46328 TTTTTTCATTAAGAAATTGAAT
1 TTTTTTCATTAAGAAATTGAAT
*
46350 TTTTTTTATTAAGAAATTGAAT
1 TTTTTTCATTAAGAAATTGAAT
46372 TTTT
1 TTTT
46376 CAAACTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.56
Consensus pattern (22 bp):
TTTTTTCATTAAGAAATTGAAT
Found at i:46910 original size:19 final size:19
Alignment explanation
Indices: 46886--46925 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
46876 CAATTTTGAC
* *
46886 CAAATAGTAATTTACTGTT
1 CAAATAGTAAATTACTATT
46905 CAAATAGTAAATTACTATT
1 CAAATAGTAAATTACTATT
46924 CA
1 CA
46926 TAAAAACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (19 bp):
CAAATAGTAAATTACTATT
Found at i:47038 original size:30 final size:31
Alignment explanation
Indices: 46991--47081 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
46981 AAATTTTGAA
46991 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
47020 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
47051 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
47082 CCTTAAATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:48738 original size:201 final size:201
Alignment explanation
Indices: 48387--48925 Score: 963
Period size: 201 Copynumber: 2.7 Consensus size: 201
48377 TATTTAAATT
* *
48387 AGTATCGACACAAAATTAAACAAGTGTTGATATATGTTGTAGACCTATTGTCTCATAAAACTGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTGTCTCATAAAACTGGT
*
48452 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTTTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
48517 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCAC-TCTTTTTGGCATACATTCTG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACAT-TTTTTGGCATACATTCTG
48581 GACCAAA
195 GACCAAA
* *
48588 AGTATTGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTGTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTGTCTCATAAAACTGGT
*
48653 ATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* *
48718 GGATCGACATTTTTTGAAAATGTATCGACACTTTATGCGTTCACATTTTTTGGCATCCATTCTGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACATTTTTTGGCATACATTCTGG
48783 ACCAAA
196 ACCAAA
* *
48789 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGAGCTATTCTCTCATAAAACTGGT
1 AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTGTCTCATAAAACTGGT
*
48854 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATAGATGCATATGTTTCTG
66 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
48919 GGATCGA
131 GGATCGA
48926 TAAATTTTAC
Statistics
Matches: 323, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
201 322 1.00
202 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (201 bp):
AGTATCGACACAAAATTAAACAAGTGTCGATACATGTTGTAGACCTATTGTCTCATAAAACTGGT
ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACATTTTTTGGCATACATTCTGG
ACCAAA
Found at i:51109 original size:21 final size:21
Alignment explanation
Indices: 51084--51144 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
51074 CCCCTTATGC
* *
51084 CTCTCAAGTGTATCTTCGAAT
1 CTCTCAAGTTTCTCTTCGAAT
51105 CTCTCAAGTTTCTCTTCGAAT
1 CTCTCAAGTTTCTCTTCGAAT
51126 CTCTCAAGTTTCTCTTCGA
1 CTCTCAAGTTTCTCTTCGA
51145 CTCTTGATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.28, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGAAT
Found at i:53437 original size:21 final size:20
Alignment explanation
Indices: 53385--53440 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
53375 GGTAGCGTTT
53385 TACCGGTTTTATCATTTTGA
1 TACCGGTTTTATCATTTTGA
*
53405 TATCGGTTTTATCATTTTGA
1 TACCGGTTTTATCATTTTGA
53425 TACCGGTTTTTATCAT
1 TACCGG-TTTTATCAT
53441 ATTTTTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 24 0.73
21 9 0.27
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.52
Consensus pattern (20 bp):
TACCGGTTTTATCATTTTGA
Found at i:58019 original size:18 final size:19
Alignment explanation
Indices: 57996--58036 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
57986 TTTTTATTCA
57996 AAAT-AAAAA-TATAATTTT
1 AAATAAAAAATTAT-ATTTT
58014 AAATAAAAAATTATATTTT
1 AAATAAAAAATTATATTTT
58033 AAAT
1 AAAT
58037 CTTAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 14 0.67
20 3 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATAAAAAATTATATTTT
Found at i:60772 original size:16 final size:16
Alignment explanation
Indices: 60751--60790 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
60741 AACTGGTCAA
60751 AGTCAACGGTCAGACC
1 AGTCAACGGTCAGACC
*
60767 AGTCAACGGTCATACC
1 AGTCAACGGTCAGACC
*
60783 AATCAACG
1 AGTCAACG
60791 ATCAACGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (16 bp):
AGTCAACGGTCAGACC
Found at i:62825 original size:24 final size:24
Alignment explanation
Indices: 62782--62872 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 24
62772 TTACAAATGT
*
62782 TAAACAAACATGTT-GATGAATAAA
1 TAAACAAATATGTTCG-TGAATAAA
* * *
62806 TGAACAAATATGTTCGTGAA-CAT
1 TAAACAAATATGTTCGTGAATAAA
** * * *
62829 TAAATTAATATATTTGTGAATATA
1 TAAACAAATATGTTCGTGAATAAA
62853 TAAACAAATATGTTCGTGAA
1 TAAACAAATATGTTCGTGAA
62873 CGCTAAATAA
Statistics
Matches: 49, Mismatches: 16, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
23 16 0.33
24 32 0.65
25 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (24 bp):
TAAACAAATATGTTCGTGAATAAA
Found at i:62967 original size:25 final size:26
Alignment explanation
Indices: 62925--62973 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
62915 AAACACAATA
* *
62925 TTAAAAATGAACTAAACATTAACACC
1 TTAAAAATAAACTAAACATAAACACC
*
62951 TTAAAAATAAAC-GAACATAAACA
1 TTAAAAATAAACTAAACATAAACA
62974 TAATTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.59, C:0.16, G:0.04, T:0.20
Consensus pattern (26 bp):
TTAAAAATAAACTAAACATAAACACC
Done.