Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005898.1 Hibiscus syriacus cultivar Beakdansim tig00013849_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: 105082
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:10159 original size:24 final size:24
Alignment explanation
Indices: 10127--10178 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
10117 GCAACATTGG
*
10127 CAGCTGCAGCTGCAGCCT-TTGCAA
1 CAGCAGCAGCTGCAG-CTATTGCAA
*
10151 CAGCAGCAGCTGCTGCTATTGCAA
1 CAGCAGCAGCTGCAGCTATTGCAA
10175 CAGC
1 CAGC
10179 TGCGGAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.19
Consensus pattern (24 bp):
CAGCAGCAGCTGCAGCTATTGCAA
Found at i:23290 original size:11 final size:11
Alignment explanation
Indices: 23274--23307 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
23264 ATAAAAAATA
23274 ATTTAATATTT
1 ATTTAATATTT
23285 ATTTAATATTT
1 ATTTAATATTT
23296 -TTTAAATATTT
1 ATTT-AATATTT
23307 A
1 A
23308 ACTATACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 18 0.86
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTAATATTT
Found at i:23699 original size:19 final size:19
Alignment explanation
Indices: 23660--23699 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
23650 TTAATTTTTT
**
23660 TAAAATAAAATAAAATTTA
1 TAAAATAAAATAAAAAATA
*
23679 TAAAATCAAATAAAAAATA
1 TAAAATAAAATAAAAAATA
23698 TA
1 TA
23700 TTTGATGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAATAAAATAAAAAATA
Found at i:26151 original size:19 final size:21
Alignment explanation
Indices: 26114--26156 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
26104 AGGTGACTAG
26114 TTTTATTAAATATTTTTTTTA
1 TTTTATTAAATATTTTTTTTA
26135 TTTTA-TAAATA-TTTTTTTA
1 TTTTATTAAATATTTTTTTTA
26154 TTT
1 TTT
26157 AAAAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.50
20 6 0.27
21 5 0.23
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTATTAAATATTTTTTTTA
Found at i:26163 original size:19 final size:20
Alignment explanation
Indices: 26121--26163 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
26111 TAGTTTTATT
* *
26121 AAATATTTTTTTTATTTTAT
1 AAATATTTTTTTTATTTAAA
26141 AAATA-TTTTTTTATTTAAA
1 AAATATTTTTTTTATTTAAA
26160 AAAT
1 AAAT
26164 TTAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
AAATATTTTTTTTATTTAAA
Found at i:29491 original size:3 final size:3
Alignment explanation
Indices: 29474--29531 Score: 82
Period size: 3 Copynumber: 19.3 Consensus size: 3
29464 TTGTAATATT
* *
29474 TAA TAAA TAA T-A TAA TAA TTA TAA TAA TAA TAC TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29519 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
29532 TTAAATGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:30552 original size:76 final size:76
Alignment explanation
Indices: 29656--30526 Score: 1683
Period size: 76 Copynumber: 11.5 Consensus size: 76
29646 GATGGAAATG
*
29656 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTG-AGGCTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAGC
29720 TCCCGAAGGCTT
65 TCCCGAAGGCTT
*
29732 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
29797 CCCGAAGGCTT
66 CCCGAAGGCTT
29808 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
29872 CTCGAAGGCTT
66 CCCGAAGGCTT
29883 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
29948 CCCGAAGGCTT
66 CCCGAAGGCTT
29959 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
30024 CCCGAAGGCTT
66 CCCGAAGGCTT
30035 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
30100 CTCGAAGGCTT
66 CCCGAAGGCTT
30111 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
30176 CCCGAAGGCTT
66 CCCGAAGGCTT
30187 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
30252 CCCGAAGGCTT
66 CCCGAAGGCTT
30263 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
30328 CCCGAAGGCTT
66 CCCGAAGGCTT
30339 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
30404 CCCGAAGGCTT
66 CCCGAAGGCTT
30415 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
30480 CCCGAAGGCTT
66 CCCGAAGGCTT
30491 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
30527 GGGAAATAGC
Statistics
Matches: 788, Mismatches: 5, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
75 75 0.10
76 713 0.90
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:31241 original size:22 final size:22
Alignment explanation
Indices: 31216--31270 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
31206 CATAAAATTT
31216 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
31238 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
31260 TCATCTTTGAA
1 TCATCTTTGAA
31271 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:31719 original size:54 final size:54
Alignment explanation
Indices: 31637--31757 Score: 190
Period size: 54 Copynumber: 2.3 Consensus size: 54
31627 AGAATAACAG
**
31637 GTTCGTAAAACATTTGACAATGCATTCATCTTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAGAT
* **
31691 GTTCGTAAAACATTTGACAACACATTCATTTTTTTTTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAGAT
31745 GTTCGT-AAACATT
1 GTTCGTAAAACATT
31758 GAAGCTCTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
53 7 0.11
54 55 0.89
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGCTCAGAT
Found at i:34007 original size:115 final size:114
Alignment explanation
Indices: 33794--34033 Score: 345
Period size: 115 Copynumber: 2.1 Consensus size: 114
33784 GATCATGCAG
* * * * * *
33794 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTTAAAGA
1 TTCATCTTTCAAATCCAATGATCGATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
* * *
33859 ACACTTCCAGAAGATACTATTGGGCCTCGTTATTTCTACTATGAGCAAAA
66 ACACTTCCAGAAGATACTATTGAGCCTCCTTATTTCTACCATGAGC-AAA
* * *
33909 TTTATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
* *
33974 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACCATGAGCAAA
66 ACACTTCCAGAAGATACTATTGAGCCTCCTTATTTCTACCATGAGCAAA
34023 TTCATCTTTCA
1 TTCATCTTTCA
34034 GTTAATGTTT
Statistics
Matches: 110, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
114 13 0.12
115 97 0.88
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCGATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATACTATTGAGCCTCCTTATTTCTACCATGAGCAAA
Found at i:38694 original size:21 final size:21
Alignment explanation
Indices: 38670--38709 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38660 AAAAGTAAAA
38670 ATACAAAATGAAAATGCATAG
1 ATACAAAATGAAAATGCATAG
*
38691 ATACAAAATGTAAATGCAT
1 ATACAAAATGAAAATGCAT
38710 GTATGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
ATACAAAATGAAAATGCATAG
Found at i:40773 original size:15 final size:13
Alignment explanation
Indices: 40741--40778 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
40731 CAGAAAAAAA
40741 AAAT-AAATAATG
1 AAATAAAATAATG
40753 AAATAAAATAATTG
1 AAATAAAATAA-TG
40767 CAAATAAAATAA
1 -AAATAAAATAA
40779 AACATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 2 0.09
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (13 bp):
AAATAAAATAATG
Found at i:42972 original size:14 final size:14
Alignment explanation
Indices: 42953--43026 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 14
42943 TTGGGCTTTG
*
42953 TAATATTTAATAAA
1 TAATATATAATAAA
42967 TAATATATAATAATTA
1 TAATATATAATAA--A
42983 TAATA-ATAATACTAA
1 TAATATATAATA--AA
*
42998 TAATA-ATAATTTTAA
1 TAATATATAA--TAAA
43013 TAATA-ATAATAAA
1 TAATATATAATAAA
43026 T
1 T
43027 TTAAATGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
13 4 0.08
14 12 0.24
15 27 0.53
16 6 0.12
17 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATATATAATAAA
Found at i:42979 original size:3 final size:3
Alignment explanation
Indices: 42960--43024 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
42950 TTGTAATATT
* *
42960 TAA TAAA TAA TATA TAA TAA TTA TAA TAA TAA TAC TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
43007 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
43025 ATTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:43029 original size:18 final size:18
Alignment explanation
Indices: 42995--43030 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
42985 ATAATAATAC
*
42995 TAATAATAATAATTTTAA
1 TAATAATAATAAATTTAA
43013 TAATAATAATAAATTTAA
1 TAATAATAATAAATTTAA
43031 ATGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATAAATTTAA
Found at i:52898 original size:41 final size:41
Alignment explanation
Indices: 52852--52943 Score: 166
Period size: 41 Copynumber: 2.2 Consensus size: 41
52842 TGAGTATTGT
52852 ATAATGCTCATTCAACTAGCATTGTAAATTGTCATTTCTTG
1 ATAATGCTCATTCAACTAGCATTGTAAATTGTCATTTCTTG
* *
52893 ATAATGTTAATTCAACTAGCATTGTAAATTGTCATTTCTTG
1 ATAATGCTCATTCAACTAGCATTGTAAATTGTCATTTCTTG
52934 ATAATGCTCA
1 ATAATGCTCA
52944 ATTTTGATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (41 bp):
ATAATGCTCATTCAACTAGCATTGTAAATTGTCATTTCTTG
Found at i:52967 original size:63 final size:63
Alignment explanation
Indices: 52891--53028 Score: 249
Period size: 63 Copynumber: 2.2 Consensus size: 63
52881 TGTCATTTCT
*
52891 TGATAATGTTAATTCAACTAGCATTGTAAATTGTCATTTCTTGATAATGCTCAATTTTGATAA
1 TGATAATGCTAATTCAACTAGCATTGTAAATTGTCATTTCTTGATAATGCTCAATTTTGATAA
* *
52954 TGCTAATGCTAATTCAACTAGCATTGTAAATTGTCATTTCTTGATAATGCTCAATTTTTATAA
1 TGATAATGCTAATTCAACTAGCATTGTAAATTGTCATTTCTTGATAATGCTCAATTTTGATAA
53017 TGATAATGCTAA
1 TGATAATGCTAA
53029 AATTAGGTTA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (63 bp):
TGATAATGCTAATTCAACTAGCATTGTAAATTGTCATTTCTTGATAATGCTCAATTTTGATAA
Found at i:58403 original size:41 final size:41
Alignment explanation
Indices: 58357--58530 Score: 312
Period size: 41 Copynumber: 4.2 Consensus size: 41
58347 TGAGTGTTGT
*
58357 ATAATGCTCATTCAACTAGCATTGTAAATTGCCATTTCTTG
1 ATAATGCTCATTCAACTAGCATTGTAAATTGTCATTTCTTG
*
58398 ATAATGCTCAGTCAACTAGCATTGTAAATTGTCATTTCTTG
1 ATAATGCTCATTCAACTAGCATTGTAAATTGTCATTTCTTG
58439 ATAATGCTCATTCAACTAGCATTGTAAATTGTCATTTCTTG
1 ATAATGCTCATTCAACTAGCATTGTAAATTGTCATTTCTTG
* *
58480 ATAATGTTAATTCAACTAGCATTGTAAATTGTCATTTCTTG
1 ATAATGCTCATTCAACTAGCATTGTAAATTGTCATTTCTTG
58521 ATAATGCTCA
1 ATAATGCTCA
58531 ATTTTGATAA
Statistics
Matches: 126, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 126 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATAATGCTCATTCAACTAGCATTGTAAATTGTCATTTCTTG
Found at i:60135 original size:30 final size:29
Alignment explanation
Indices: 60100--60211 Score: 179
Period size: 30 Copynumber: 3.8 Consensus size: 29
60090 TAAAATCAGA
60100 AGGTATTAAAGGGAAAATAAGTGCCCGAG
1 AGGTATTAAAGGGAAAATAAGTGCCCGAG
60129 ATGGTATTAAAGGGAAAATAAGTGCCCGAG
1 A-GGTATTAAAGGGAAAATAAGTGCCCGAG
*
60159 AAGGTATTAAAGGGAAAATAAGTGCCAGAGG
1 -AGGTATTAAAGGGAAAATAAGTGCCCGA-G
*
60190 AGATATTAAAGGGAAAATAAGT
1 AGGTATTAAAGGGAAAATAAGT
60212 AGCAACAGCA
Statistics
Matches: 78, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
29 1 0.01
30 75 0.96
31 2 0.03
ACGTcount: A:0.45, C:0.07, G:0.29, T:0.19
Consensus pattern (29 bp):
AGGTATTAAAGGGAAAATAAGTGCCCGAG
Found at i:62593 original size:2 final size:2
Alignment explanation
Indices: 62586--62613 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62576 TAGCAGTAGA
62586 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
62614 TCCAACCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70857 original size:34 final size:32
Alignment explanation
Indices: 70804--70873 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
70794 CCTTACAAAC
*
70804 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
70836 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
70870 TCCC
1 TCCC
70874 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:71182 original size:21 final size:21
Alignment explanation
Indices: 71156--71197 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
71146 CCAGAATGGG
*
71156 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
71177 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
71198 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:71327 original size:19 final size:19
Alignment explanation
Indices: 71303--71369 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
71293 GAGCCTCGGG
*
71303 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
71322 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* * *
71341 TTATTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
71360 TTACTATTCA
1 TTACTGTTCA
71370 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:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:71481 original size:30 final size:31
Alignment explanation
Indices: 71434--71524 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
71424 AAATTTTGAA
71434 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
71463 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
71494 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
71525 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:71714 original size:22 final size:22
Alignment explanation
Indices: 71683--71729 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
71673 AAGCTCCCCA
71683 TTTTTCATTAAGAAATTGAATT
1 TTTTTCATTAAGAAATTGAATT
*
71705 TTTTTTATTAAGAAATTGAATT
1 TTTTTCATTAAGAAATTGAATT
71727 TTT
1 TTT
71730 CAAACTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (22 bp):
TTTTTCATTAAGAAATTGAATT
Found at i:73756 original size:34 final size:32
Alignment explanation
Indices: 73703--73772 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
73693 CCTTACAAAC
*
73703 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
73735 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
73769 TCCC
1 TCCC
73773 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:74081 original size:21 final size:21
Alignment explanation
Indices: 74055--74096 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
74045 CCAGAATGGG
*
74055 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
74076 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
74097 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:74207 original size:19 final size:19
Alignment explanation
Indices: 74185--74235 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
74175 TACAAACTGG
74185 AATTTACTGTTCAAATAGT
1 AATTTACTGTTCAAATAGT
74204 AATTTACTGTTCAAATAGT
1 AATTTACTGTTCAAATAGT
* *
74223 AAATTACTATTCA
1 AATTTACTGTTCA
74236 TAAAAACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (19 bp):
AATTTACTGTTCAAATAGT
Found at i:74347 original size:30 final size:31
Alignment explanation
Indices: 74300--74390 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
74290 AAATTTTGAA
74300 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
74329 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
74360 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
74391 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:75238 original size:101 final size:100
Alignment explanation
Indices: 75055--75239 Score: 214
Period size: 101 Copynumber: 1.8 Consensus size: 100
75045 AATATATTGT
* ** * *
75055 ACCAAGTCACTCCACCTTGTGAACCATTAAAGCACCCGAGTCAGACCCCAAGTAACCCATCTTGG
1 ACCAAATCACTCCACCTCATGAACCACTAAAGCACCCGAGTCAGACCACAAGTAACCCATCTTGG
* *
75120 TGTCATATAATACACATATAAAGCTAGTCAAATAC
66 TATCATATAATAAACATATAAAGCTAGTCAAATAC
* * * *
75155 ACCAAATCACTCCACCTCATGCACCACTAAGGTACGCCGAGTCAGACCACGAGTAATCCACA-C-
1 ACCAAATCACTCCACCTCATGAACCACTAAAGCAC-CCGAGTCAGACCACAAGTAA-CC-CATCT
75218 TGGTATCATATCAA-AAACATAT
63 TGGTATCATAT-AATAAACATAT
75240 TCAGATTCAC
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
100 28 0.40
101 35 0.50
102 5 0.07
103 2 0.03
ACGTcount: A:0.36, C:0.30, G:0.13, T:0.21
Consensus pattern (100 bp):
ACCAAATCACTCCACCTCATGAACCACTAAAGCACCCGAGTCAGACCACAAGTAACCCATCTTGG
TATCATATAATAAACATATAAAGCTAGTCAAATAC
Found at i:78384 original size:5 final size:5
Alignment explanation
Indices: 78363--78400 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
78353 TATATAAAGT
78363 TAAAA -AAAA TCAAAA TAAAA TAAAA TAAAA TAACAA TA
1 TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAA-AA TA
78401 CACACCGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.13
5 17 0.57
6 9 0.30
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:78557 original size:22 final size:20
Alignment explanation
Indices: 78495--78536 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
78485 TGATGTCATC
78495 AAAAATATT-T-AA-AAATA
1 AAAAATATTATAAATAAATA
78512 AAAAATATTATAAATAAATA
1 AAAAATATTATAAATAAATA
78532 AAAAA
1 AAAAA
78537 ATAATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.41
18 1 0.05
19 2 0.09
20 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATATTATAAATAAATA
Found at i:78557 original size:23 final size:21
Alignment explanation
Indices: 78495--78549 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 21
78485 TGATGTCATC
78495 AAAAATATT-T-AA-AAAT-A
1 AAAAATATTATAAATAAATAA
78512 AAAAATATTATAAATAAATAA
1 AAAAATATTATAAATAAATAA
78533 AAAAATAATTATTAAAT
1 AAAAAT-ATTA-TAAAT
78550 TTATAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.28
18 1 0.03
19 2 0.06
20 4 0.12
21 7 0.22
22 4 0.12
23 5 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAATATTATAAATAAATAA
Found at i:84694 original size:202 final size:202
Alignment explanation
Indices: 84348--84751 Score: 772
Period size: 202 Copynumber: 2.0 Consensus size: 202
84338 TTGGAACTTC
84348 ATTTAAGGATGTTCATATTCCTTTCGATTCTTTGATGGGGGATTTAAAACTAGCAGACTTGAATG
1 ATTTAAGGATGTTCATATTCCTTTCGATTCTTTGATGGGGGATTTAAAACTAGCAGACTTGAATG
* **
84413 GCAATCTGAAAAAGAGGTCTCCACCTTCTTCTAGGTGGAGTCCTCCTCTGGAAGGGTTCTTAAAA
66 ACAATCTGAAAAAGAGGTCTCCACCTTCTTCTAGGTGGAGTCCTCCTCCAGAAGGGTTCTTAAAA
84478 GTAAACGTAGATGGTGCAATGGTCAAAGGTTGGGATAAGGGTGGAATAGGTGGATTGATTAGAGA
131 GTAAACGTAGATGGTGCAATGGTCAAAGGTTGGGATAAGGGTGGAATAGGTGGATTGATTAGAGA
84543 TGGCAGT
196 TGGCAGT
84550 ATTTAAGGATGTTCATATTCCTTTCGATTCTTTGATGGGGGATTTAAAACTAGCAGACTTGAATG
1 ATTTAAGGATGTTCATATTCCTTTCGATTCTTTGATGGGGGATTTAAAACTAGCAGACTTGAATG
84615 ACAATCTGAAAAAGAGGTCTCCACCTTCTTCTAGGTGGAGTCCTCCTCCAGAAGGGTTCTTAAAA
66 ACAATCTGAAAAAGAGGTCTCCACCTTCTTCTAGGTGGAGTCCTCCTCCAGAAGGGTTCTTAAAA
*
84680 GTAAACGTAGATGGTGCAATGGTCAAAGGTTGGGATAAGGGTGGAATAGGTGGATTGATTAGGGA
131 GTAAACGTAGATGGTGCAATGGTCAAAGGTTGGGATAAGGGTGGAATAGGTGGATTGATTAGAGA
84745 TGGCAGT
196 TGGCAGT
84752 GGTTCGGTGC
Statistics
Matches: 198, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
202 198 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (202 bp):
ATTTAAGGATGTTCATATTCCTTTCGATTCTTTGATGGGGGATTTAAAACTAGCAGACTTGAATG
ACAATCTGAAAAAGAGGTCTCCACCTTCTTCTAGGTGGAGTCCTCCTCCAGAAGGGTTCTTAAAA
GTAAACGTAGATGGTGCAATGGTCAAAGGTTGGGATAAGGGTGGAATAGGTGGATTGATTAGAGA
TGGCAGT
Done.