Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006208.1 Hibiscus syriacus cultivar Beakdansim tig00014782_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: 84142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1703 original size:29 final size:28
Alignment explanation
Indices: 1661--1715 Score: 101
Period size: 29 Copynumber: 1.9 Consensus size: 28
1651 ATTCGCGTTG
1661 CATTTCGCGTTGCGATAGTTGAAAATCGC
1 CATTTCGCGTTGCGATAGTT-AAAATCGC
1690 CATTTCGCGTTGCGATAGTTAAAATC
1 CATTTCGCGTTGCGATAGTTAAAATC
1716 CGCACCGCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (28 bp):
CATTTCGCGTTGCGATAGTTAAAATCGC
Found at i:1772 original size:25 final size:25
Alignment explanation
Indices: 1739--1789 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1729 TCCATTTCGC
*
1739 GTTGCGATAGTCTACAGTTGTTGTT
1 GTTGCGATAGTCTACAGTTGTCGTT
*
1764 GTTGTGATAGTCTACAGTTGTCGTT
1 GTTGCGATAGTCTACAGTTGTCGTT
1789 G
1 G
1790 CGATTTTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.12, G:0.29, T:0.43
Consensus pattern (25 bp):
GTTGCGATAGTCTACAGTTGTCGTT
Found at i:1915 original size:6 final size:6
Alignment explanation
Indices: 1904--1938 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1894 GAAGACACGT
1904 ACGACC ACGACC ACGACC ACGACC ACGACC -CGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
1939 CGAGACGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.31, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:2461 original size:6 final size:6
Alignment explanation
Indices: 2421--2501 Score: 113
Period size: 6 Copynumber: 14.7 Consensus size: 6
2411 CCGTCTCTCG
2421 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTC-- GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2462 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
2502 ATACGTGTCT
Statistics
Matches: 74, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.05
5 24 0.32
6 46 0.62
ACGTcount: A:0.00, C:0.19, G:0.53, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:2665 original size:20 final size:20
Alignment explanation
Indices: 2640--2687 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2630 ATTTTCAACT
* *
2640 ATCGCAACACGAACTGGAAA
1 ATCGCAACACGAAATGAAAA
**
2660 ATCGCAATGCGAAATGAAAA
1 ATCGCAACACGAAATGAAAA
2680 ATCGCAAC
1 ATCGCAAC
2688 GCGCAACGCG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (20 bp):
ATCGCAACACGAAATGAAAA
Found at i:2704 original size:27 final size:27
Alignment explanation
Indices: 2662--2716 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
2652 ACTGGAAAAT
*
2662 CGCAATGCGAAATGAAAAATCGCAACG
1 CGCAACGCGAAATGAAAAATCGCAACG
*
2689 CGCAACGCGAACTGAAAAATCGCAACG
1 CGCAACGCGAAATGAAAAATCGCAACG
2716 C
1 C
2717 AAAATGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.27, G:0.22, T:0.09
Consensus pattern (27 bp):
CGCAACGCGAAATGAAAAATCGCAACG
Found at i:2714 original size:20 final size:20
Alignment explanation
Indices: 2689--2728 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2679 AATCGCAACG
* *
2689 CGCAACGCGAACTGAAAAAT
1 CGCAACGCAAAATGAAAAAT
2709 CGCAACGCAAAATGAAAAAT
1 CGCAACGCAAAATGAAAAAT
2729 TTAAATGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (20 bp):
CGCAACGCAAAATGAAAAAT
Found at i:21533 original size:32 final size:32
Alignment explanation
Indices: 21467--21581 Score: 151
Period size: 32 Copynumber: 3.6 Consensus size: 32
21457 CAATGTAATA
**
21467 ACGTGACATGTGCCATGTCA-CCAAGATGATG
1 ACGTGACATGTGCCACATCACCCAAGATGATG
* *
21498 ACGTGACATGTGCTACATCACCCAAAATGATG
1 ACGTGACATGTGCCACATCACCCAAGATGATG
* *
21530 ACGTGACATGTGCCACATCACCCAAGGTGACG
1 ACGTGACATGTGCCACATCACCCAAGATGATG
* *
21562 ACATGACATGTGACACATCA
1 ACGTGACATGTGCCACATCA
21582 ACTCTTAAGC
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
31 17 0.23
32 56 0.77
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (32 bp):
ACGTGACATGTGCCACATCACCCAAGATGATG
Found at i:24207 original size:14 final size:14
Alignment explanation
Indices: 24188--24215 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24178 TCGATTATAT
24188 GTTCATTTATGTTC
1 GTTCATTTATGTTC
24202 GTTCATTTATGTTC
1 GTTCATTTATGTTC
24216 ATTTATGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:24217 original size:24 final size:26
Alignment explanation
Indices: 24175--24225 Score: 88
Period size: 24 Copynumber: 2.0 Consensus size: 26
24165 CGTTCGTGAA
24175 CGTTCGATTATATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
24201 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
24225 C
1 C
24226 AAACAGATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTTATGTT
Found at i:28020 original size:22 final size:22
Alignment explanation
Indices: 27988--28049 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
27978 ACAGAACCCC
* *
27988 AGGGGGTATCGATTCCCCTGT-A
1 AGGGGGAATCGATTCCCAT-TAA
* *
28010 GGGGGGAATCGGTTCCCATTCAA
1 AGGGGGAATCGATTCCCATT-AA
28033 AGGGGGAATCGATTCCC
1 AGGGGGAATCGATTCCC
28050 TCATGGGGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 1 0.03
22 15 0.47
23 16 0.50
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCATTAA
Found at i:28067 original size:20 final size:20
Alignment explanation
Indices: 28034--28071 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28024 CCCATTCAAA
*
28034 GGGGGAATCGATTCCCTCAT
1 GGGGGAATCAATTCCCTCAT
*
28054 GGGGGGATCAATTCCCTC
1 GGGGGAATCAATTCCCTC
28072 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (20 bp):
GGGGGAATCAATTCCCTCAT
Found at i:39953 original size:3 final size:3
Alignment explanation
Indices: 39945--40051 Score: 160
Period size: 3 Copynumber: 34.7 Consensus size: 3
39935 TTTATCCATT
*
39945 TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
39993 TTA TTA GTA TTCA TTA TTA TTA TTA ATA TTA TATA TTA TTA TTA TATA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA
40041 TTA TTA TTA TT
1 TTA TTA TTA TT
40052 TAATAAATAA
Statistics
Matches: 95, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
3 86 0.91
4 9 0.09
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:41294 original size:20 final size:20
Alignment explanation
Indices: 41269--41306 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41259 TAATTAGTAA
* *
41269 TTAGTTTTTATTTTTATAAT
1 TTAGTTATTAATTTTATAAT
41289 TTAGTTATTAATTTTATA
1 TTAGTTATTAATTTTATA
41307 TGTCTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
TTAGTTATTAATTTTATAAT
Found at i:42163 original size:13 final size:15
Alignment explanation
Indices: 42132--42168 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
42122 TATATGGTTT
42132 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
42147 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
42160 TA-TTTATTT
1 TATTTTATTT
42169 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:45486 original size:14 final size:15
Alignment explanation
Indices: 45457--45489 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
45447 TTATTATTTT
45457 ATTTATTAAGTTAAA
1 ATTTATTAAGTTAAA
45472 ATTTATTAA-TTAAA
1 ATTTATTAAGTTAAA
45486 ATTT
1 ATTT
45490 GAAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTAAGTTAAA
Found at i:52766 original size:17 final size:17
Alignment explanation
Indices: 52744--52809 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
52734 TGCTTGAAGA
52744 GAAAAAAGAAGAAAAAT
1 GAAAAAAGAAGAAAAAT
*
52761 GAAAAAA-AATAGAAAAT
1 GAAAAAAGAAGA-AAAAT
* * *
52778 GAAAAAAAAAAAAAAAA
1 GAAAAAAGAAGAAAAAT
*
52795 AAAAAAAG-AGAAAAA
1 GAAAAAAGAAGAAAAA
52810 GGGGGTCAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
16 9 0.22
17 29 0.71
18 3 0.07
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (17 bp):
GAAAAAAGAAGAAAAAT
Found at i:53828 original size:52 final size:52
Alignment explanation
Indices: 53750--54515 Score: 1381
Period size: 52 Copynumber: 14.7 Consensus size: 52
53740 TATGTGTTCA
*
53750 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
53802 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGATATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
53854 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
53906 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
53958 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGATATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
54010 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
54062 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
54114 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGATATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
54166 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGATATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
54218 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
54270 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
54322 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
54374 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
54426 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
* *
54478 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATTTGATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
54516 CGAAAAAGTG
Statistics
Matches: 692, Mismatches: 21, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
51 5 0.01
52 687 0.99
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:55276 original size:113 final size:113
Alignment explanation
Indices: 55078--55407 Score: 579
Period size: 113 Copynumber: 2.9 Consensus size: 113
55068 GATTCAAATT
*
55078 CATCATTTGATGGATCATCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
55143 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
* * *
55191 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
55256 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
55304 CATCATTTGATGGATCATCATTACCAGAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATCATCATTACCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGG
* **
55369 AAGAAGAAGTTCATAATAAGAAGAGCTTGTTCAACCTTT
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
55408 GTTTGATATC
Statistics
Matches: 205, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
113 143 0.70
114 62 0.30
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
CATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
Found at i:55433 original size:61 final size:62
Alignment explanation
Indices: 55355--55473 Score: 195
Period size: 61 Copynumber: 1.9 Consensus size: 62
55345 TGAGAAGAAC
* *
55355 TCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAGCTTGTTCAAC-CTTTGTTTGATA
1 TCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTCTTTGTTTGATA
* *
55416 TCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
1 TCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTCTTTGTTT
55474 AAATTCATCA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
61 46 0.87
62 7 0.13
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (62 bp):
TCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTCTTTGTTTGATA
Found at i:55532 original size:175 final size:175
Alignment explanation
Indices: 55241--55582 Score: 549
Period size: 175 Copynumber: 2.0 Consensus size: 175
55231 TGAGAAGAAC
* * *
55241 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCA
1 TCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTAAATCCA
* * *
55306 TCATTTGATGGATCATCATTACCAGAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAA
66 TCATTTGATGGATCAACATGACCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAA
*
55371 GAAGAAGTTCATAATAAGAAGAGCTTGTTCAACCTTTGTTTGATA
131 GAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTGTTTGATA
* *** *
55416 TCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCA
1 TCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTAAATCCA
*
55481 TCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAA
66 TCATTTGATGGATCAACATGACCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAA
* *
55546 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
131 GAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTT
55583 TACCTGAATC
Statistics
Matches: 152, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
175 152 1.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (175 bp):
TCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTAAATCCA
TCATTTGATGGATCAACATGACCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTGTTTGATA
Found at i:55687 original size:113 final size:114
Alignment explanation
Indices: 55416--55813 Score: 629
Period size: 114 Copynumber: 3.5 Consensus size: 114
55406 TTGTTTGATA
* *
55416 TCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCA
55481 TCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAAC
66 TCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAAC
* *** * *
55530 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCA
* * * ** *
55595 TCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCAT-AATGAGAAGAAC
66 TCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAAC
*
55643 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCA
*
55708 TCATTTGATGGATCAACAGGGCCAAAGAAAGTTCATGAATGAGAAGAAC
66 TCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAAC
*
55757 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC-TTTGTTT
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
55814 GATATCATCT
Statistics
Matches: 253, Mismatches: 30, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
113 106 0.42
114 147 0.58
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (114 bp):
TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCA
TCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAAC
Found at i:56114 original size:3 final size:3
Alignment explanation
Indices: 56106--56206 Score: 148
Period size: 3 Copynumber: 32.7 Consensus size: 3
56096 TTTATCCATT
*
56106 TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
56154 GTA TTCA TTA TTA TTA TTA ATA TTA TATA TTA TTA TTA TATA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA
56202 TTA TT
1 TTA TT
56207 TAATAAATAA
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
3 80 0.90
4 9 0.10
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:67248 original size:23 final size:23
Alignment explanation
Indices: 67222--67288 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
67212 CACCACAGCT
*
67222 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
67245 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
67268 CGTAGAAATGCACCGAAGTGC
1 CGTAGAAATGCACCGAAGTGC
67289 TATATAAGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:67525 original size:16 final size:16
Alignment explanation
Indices: 67506--67544 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
67496 TATCATACAT
*
67506 TCACATATACATATAG
1 TCACATATACACATAG
67522 TCACATATACACATAG
1 TCACATATACACATAG
67538 TCACATA
1 TCACATA
67545 GTTCTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.23, G:0.05, T:0.28
Consensus pattern (16 bp):
TCACATATACACATAG
Found at i:68525 original size:9 final size:9
Alignment explanation
Indices: 68497--68548 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
68487 TTAGTCATGC
68497 ATACATATA
1 ATACATATA
*
68506 ATTA-ATGTA
1 A-TACATATA
68515 ATACATATA
1 ATACATATA
68524 ATCACATATA
1 AT-ACATATA
*
68534 ACACATATA
1 ATACATATA
68543 AT-CATA
1 ATACATA
68549 ACAACCACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
8 6 0.17
9 20 0.56
10 10 0.28
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (9 bp):
ATACATATA
Found at i:68541 original size:19 final size:18
Alignment explanation
Indices: 68499--68546 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
68489 AGTCATGCAT
* * *
68499 ACATATAATTAATGTAAT
1 ACATATAATCAATATAAC
68517 ACATATAATCACATATAAC
1 ACATATAATCA-ATATAAC
68536 ACATATAATCA
1 ACATATAATCA
68547 TAACAACCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (18 bp):
ACATATAATCAATATAAC
Found at i:68557 original size:19 final size:19
Alignment explanation
Indices: 68517--68563 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
68507 TTAATGTAAT
*
68517 ACATATAATCACATATAAC
1 ACATATAATCACATACAAC
*
68536 ACATATAATCATA-ACAAC
1 ACATATAATCACATACAAC
*
68554 -CACATAATCA
1 ACATATAATCA
68564 TGTTCATGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 9 0.36
18 4 0.16
19 12 0.48
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (19 bp):
ACATATAATCACATACAAC
Found at i:68894 original size:19 final size:19
Alignment explanation
Indices: 68829--68897 Score: 57
Period size: 23 Copynumber: 3.4 Consensus size: 19
68819 AATAAATGTA
* *
68829 TGCATCGATGCACTATACAG
1 TGCATCGATGCACTA-CCTG
* *
68849 TGTATCGATGCATCCTTAACGTG
1 TGCATCGATGCA--C-T-ACCTG
68872 TGCATCGATGCACTACCTG
1 TGCATCGATGCACTACCTG
68891 TGCATCG
1 TGCATCG
68898 GTACACAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
19 11 0.28
20 12 0.31
21 1 0.03
22 1 0.03
23 13 0.33
24 1 0.03
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (19 bp):
TGCATCGATGCACTACCTG
Found at i:68959 original size:19 final size:19
Alignment explanation
Indices: 68935--68987 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
68925 TCTTAAGGGG
68935 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
68954 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
68973 ATGCATCGATGCACT
1 ATGCATCGATGCACT
68988 AATTGCATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:70461 original size:201 final size:201
Alignment explanation
Indices: 70116--70513 Score: 778
Period size: 201 Copynumber: 2.0 Consensus size: 201
70106 TTTGTTCAAA
*
70116 GAATAATCATTCATTCTCGTTCTTTTAATAATTGAAAATTGTATCATTTCATTATCAAACTTATA
1 GAATAATCATTCATTCTCGTTCTTTTAATAATTGAAAATTGTATCATTTCAATATCAAACTTATA
70181 ACTTATATCTCAATATACCTCTTGTCATACTTGATCTTTTAAACTCCATCTTTGACTTTTCCTAT
66 ACTTATATCTCAATATACCTCTTGTCATACTTGATCTTTTAAACTCCATCTTTGACTTTTCCTAT
*
70246 CCCTTTATTTTTTTCATTCCTTCAAAATCAAAATCTTTTTATACACATATCATATCTTTTCTTTA
131 CCCTTTATTTTTTTCATTCCTTCAAAATCAAAATCTTCTTATACACATATCATATCTTTTCTTTA
70311 ATAATT
196 ATAATT
70317 GAATAATCATTCATTCTCGTTCTTTTAATAATTGAAAATTGTATCATTTCAATATCAAACTTATA
1 GAATAATCATTCATTCTCGTTCTTTTAATAATTGAAAATTGTATCATTTCAATATCAAACTTATA
70382 ACTTATATCTCAATATACCTCTTGTCATACTTGATCTTTTAAACTCCATCTTTGACTTTTCCTAT
66 ACTTATATCTCAATATACCTCTTGTCATACTTGATCTTTTAAACTCCATCTTTGACTTTTCCTAT
70447 CCCTTTATTTTTTTCATTCCTTCAAAATCAAAATCTTCTTATACACATATCATATCTTTTCTTTA
131 CCCTTTATTTTTTTCATTCCTTCAAAATCAAAATCTTCTTATACACATATCATATCTTTTCTTTA
70512 AT
196 AT
70514 GTTCACATAT
Statistics
Matches: 195, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
201 195 1.00
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.47
Consensus pattern (201 bp):
GAATAATCATTCATTCTCGTTCTTTTAATAATTGAAAATTGTATCATTTCAATATCAAACTTATA
ACTTATATCTCAATATACCTCTTGTCATACTTGATCTTTTAAACTCCATCTTTGACTTTTCCTAT
CCCTTTATTTTTTTCATTCCTTCAAAATCAAAATCTTCTTATACACATATCATATCTTTTCTTTA
ATAATT
Found at i:71314 original size:26 final size:26
Alignment explanation
Indices: 71298--71349 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
71288 CCTTAGCTTT
71298 ACTCAAACATACGAATCCTAACCTTC
1 ACTCAAACATACGAATCCTAACCTTC
71324 ACTCAAACATACGAATCCTAACCTTC
1 ACTCAAACATACGAATCCTAACCTTC
71350 TTCACCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.35, G:0.04, T:0.23
Consensus pattern (26 bp):
ACTCAAACATACGAATCCTAACCTTC
Done.