Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006266.1 Hibiscus syriacus cultivar Beakdansim tig00014942_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: 58403
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3351 original size:95 final size:94
Alignment explanation
Indices: 3173--3352 Score: 256
Period size: 95 Copynumber: 1.9 Consensus size: 94
3163 TATAATATTA
*
3173 TATATATACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTGGTTAAACGCACCGACTTTATGGA
1 TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCACCGACTTTATGGA
* *
3238 TAATATTTAGCTAGCCTGATAAAGGTGAT
66 TAATATTCAGCTAACCTGATAAAGGTGAT
* * *
3267 TATACTATACAATAAAGCTTGAGCTGTCCCTCTA-AGGCAATTGGTTAAACGCTCCGGCTTTATG
1 TATA-TATACAATAAAGCTTGAGCTATCCCTCTAGA-GCAATTGGTTAAACGCACCGACTTTATG
*
3331 GATAAGT-TTCATCTAACCTGAT
64 GATAA-TATTCAGCTAACCTGAT
3353 TAAGCTATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
94 5 0.07
95 70 0.92
96 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCACCGACTTTATGGA
TAATATTCAGCTAACCTGATAAAGGTGAT
Found at i:4804 original size:36 final size:36
Alignment explanation
Indices: 4703--5060 Score: 308
Period size: 36 Copynumber: 10.1 Consensus size: 36
4693 CTGTGAATTC
* *
4703 GTTTTCCTTGAAACAAAGTGTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* * *
4740 GTTTCTCTTAAAACATA-TTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
4775 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
4811 GTTTCCCTTTAATCAAATTTGGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * * *
4847 GTTTCCCTTTAATCAAATTTGGTCTCTCTTGAGTCA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
4883 GTTTCCCTTGAAACAAA------ATC-ATTGA-ATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
** * * *
4911 TGTTTTTCTTTAAACAAATTTCGCCTCTC-T--GACA
1 -GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
** * * * *
4945 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGATATA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
* *
4982 ATTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* *
5019 ATTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
5056 GTTTC
1 GTTTC
5061 TCTTAAAGCA
Statistics
Matches: 264, Mismatches: 42, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.00
29 18 0.07
30 2 0.01
33 10 0.04
34 13 0.05
35 36 0.14
36 102 0.39
37 82 0.31
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:5002 original size:37 final size:37
Alignment explanation
Indices: 4960--5067 Score: 180
Period size: 37 Copynumber: 2.9 Consensus size: 37
4950 TTTTGGAACT
* *
4960 AAGTTTTGTCTCTCTTGATATAATTTCCCTTAAAACA
1 AAGTTTTGTCTCTCTTGAGACAATTTCCCTTAAAACA
4997 AAGTTTTGTCTCTCTTGAGACAATTTCCCTTAAAACA
1 AAGTTTTGTCTCTCTTGAGACAATTTCCCTTAAAACA
* *
5034 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAA
1 AAGTTTTGTCTCTCTTGAGACAATTTCCCTTAAA
5068 GCACCAATCT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (37 bp):
AAGTTTTGTCTCTCTTGAGACAATTTCCCTTAAAACA
Found at i:5090 original size:30 final size:29
Alignment explanation
Indices: 5056--5140 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 29
5046 TCTTGAGACA
* *
5056 GTTTCTCTTAAAGCACCAATCTTTGAAATT
1 GTTTCTCTTAAA-CACCAACCTTTGAAAAT
* **
5086 GTTTCTCATGAAACATAAAACCTTTGAAAAT
1 GTTTCTC-TTAAACA-CCAACCTTTGAAAAT
5117 GTTTCTCTTAAAACACCAAACCTT
1 GTTTCTCTT-AAACACC-AACCTT
5141 CGAGTTCAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
30 10 0.23
31 33 0.77
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.35
Consensus pattern (29 bp):
GTTTCTCTTAAACACCAACCTTTGAAAAT
Found at i:5131 original size:31 final size:31
Alignment explanation
Indices: 5076--5140 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
5066 AAGCACCAAT
* * *
5076 CTTTGAAATTGTTTCTCATGAAACATAAAAC
1 CTTTGAAAATGTTTCTCATAAAACACAAAAC
* *
5107 CTTTGAAAATGTTTCTCTTAAAACACCAAAC
1 CTTTGAAAATGTTTCTCATAAAACACAAAAC
5138 CTT
1 CTT
5141 CGAGTTCAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (31 bp):
CTTTGAAAATGTTTCTCATAAAACACAAAAC
Found at i:6819 original size:9 final size:9
Alignment explanation
Indices: 6807--6872 Score: 66
Period size: 9 Copynumber: 7.2 Consensus size: 9
6797 ATTATCATTA
6807 TTTATATAT
1 TTTATATAT
6816 TTTATTACTAT
1 TTTA-TA-TAT
*
6827 TATTATATGT
1 T-TTATATAT
6837 TTTATATAT
1 TTTATATAT
6846 ATTTAT-TA-
1 -TTTATATAT
6854 -TTATATAT
1 TTTATATAT
6862 TTTATATAT
1 TTTATATAT
6871 TT
1 TT
6873 CATTTTATCT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
6 4 0.08
7 2 0.04
9 23 0.48
10 10 0.21
11 6 0.12
12 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTATATAT
Found at i:12608 original size:36 final size:36
Alignment explanation
Indices: 12518--12609 Score: 139
Period size: 36 Copynumber: 2.5 Consensus size: 36
12508 TAATTTACTC
*
12518 AAAACAATGTTTTGTCTCTCCTGAGACAGTTTCTCTT
1 AAAACAA-ATTTTGTCTCTCCTGAGACAGTTTCTCTT
* *
12555 AAAACAAATTTGGTCTCTCCTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCCTGAGACAGTTTCTCTT
*
12591 AAAACAAATTTTATCTCTC
1 AAAACAAATTTTGTCTCTC
12610 TTGAAACAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 43 0.86
37 7 0.14
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCCTGAGACAGTTTCTCTT
Found at i:12633 original size:21 final size:21
Alignment explanation
Indices: 12585--12634 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
12575 TGAGACATTT
*
12585 TCTCTTAAAACAAATTTTATC
1 TCTCTTGAAACAAATTTTATC
*
12606 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTATC
12627 TCTCTTGA
1 TCTCTTGA
12635 GACAGTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTATC
Found at i:12669 original size:57 final size:57
Alignment explanation
Indices: 12549--12670 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 57
12539 TGAGACAGTT
* * * *
12549 TCTCTTAAAACAAATTTGGTCTCTCCTGAGACATTTTCTCTTAAAACAAATTTTATC
1 TCTCTTGAAACAAATTTGGTCTCTCCTGAGACAGTTTCCCTTAAAACAAATTTGATC
* * * * *
12606 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTTAATCAAATTTGGTC
1 TCTCTTGAAACAAATTTGGTCTCTCCTGAGACAGTTTCCCTTAAAACAAATTTGATC
12663 TCTCTTGA
1 TCTCTTGA
12671 GACAGTTTCC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (57 bp):
TCTCTTGAAACAAATTTGGTCTCTCCTGAGACAGTTTCCCTTAAAACAAATTTGATC
Found at i:12788 original size:102 final size:99
Alignment explanation
Indices: 12527--12895 Score: 403
Period size: 102 Copynumber: 3.7 Consensus size: 99
12517 CAAAACAATG
* * * * * * *
12527 TTTTGTCTCTCCTGAGACAGTTTCTCTTAAAACAAATTTGGTCTCTCCTGAGACATTTTCTCTTA
1 TTTTGTCTCTCTTGAGACAGTTTCT-TTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
12592 AAAC-AAATT-T-TA-TC---TCTCTTGAAACAAA
65 AAACAAAATTGTGAATTCGTTTTTCTTGAAACAAA
* * *
12620 TTTTGTCTCTCTTGAGACAGTTTCCCTTTAATCAAATTTGGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTT-CTTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
12685 AAACAAAATCTTTGAATGT-GTTTTTCTTTAAACAAA
65 AAACAAAAT-TGTGAAT-TCGTTTTTCTTGAAACAAA
** * *
12721 TTTTGTCTCTCTCAAGACAGTTTCTTTTGGAACCAAATTTTGTCTCTCTTGAGACGGTTTCCCTT
1 TTTTGTCTCTCTTGAGACAGTTTCTTTT--AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
*
12786 GAAACAAAAATTGTGAATTCGTTTTCCTTGAAACAAA
64 GAAAC-AAAATTGTGAATTCGTTTTTCTTGAAACAAA
* * *
12823 GTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTT
1 -TTTTGTCTCTCTTGAGACAGTTTCT-TTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
12888 GAAACAAA
64 GAAACAAA
12896 TTTTGTCTCT
Statistics
Matches: 233, Mismatches: 27, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
93 59 0.25
94 5 0.02
95 1 0.00
96 1 0.00
97 1 0.00
99 1 0.00
100 4 0.02
101 37 0.16
102 94 0.40
103 28 0.12
104 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (99 bp):
TTTTGTCTCTCTTGAGACAGTTTCTTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAAATTGTGAATTCGTTTTTCTTGAAACAAA
Found at i:12866 original size:36 final size:36
Alignment explanation
Indices: 12704--13098 Score: 233
Period size: 36 Copynumber: 11.2 Consensus size: 36
12694 CTTTGAATGT
* *
12704 GTTTTTCTTTAAACAAATTTTGTCTCTCTCAAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTCAAGACA
* * ** *
12740 GTTTCTTTTGGAACCAAATTTTGTCTCTCTTGAGACG
1 GTTTCTCTT-GAAACAAATTTTGTCTCTCTCAAGACA
* ** ***
12777 GTTTCCCTTGAAACAAAAATTGTGAAT-TC--G---
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTCAAGACA
* **
12807 TTTTC-CTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAA-TTTTGTCTCTCTCAAGACA
* ** *
12843 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTCAAGACA
**
12879 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTCAAGACA
* * * * **
12915 GTTTCCCTTTAATCAAATTTGGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTCAAGACA
* * * ***
12951 GTTTCCCTTGAAACAAA----ATCT-T-TGAA-TTT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTCAAGACA
* * * *
12980 GTTTTTCTTTAAACAAATTTCGTCTCTCTCTAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTCAAGACA
* * * **
13016 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAAC-AAATTTTGTCTCTCTCAAGACA
* * **
13053 GTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAA-TTTTGTCTCTCTCAAGACA
13090 GTTTCTCTT
1 GTTTCTCTT
13099 AAAGCACCAA
Statistics
Matches: 278, Mismatches: 63, Indels: 35
0.74 0.17 0.09
Matches are distributed among these distances:
29 25 0.09
30 11 0.04
31 2 0.01
32 3 0.01
33 5 0.02
34 1 0.00
35 3 0.01
36 134 0.48
37 94 0.34
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTCAAGACA
Found at i:12946 original size:174 final size:175
Alignment explanation
Indices: 12704--13094 Score: 522
Period size: 174 Copynumber: 2.2 Consensus size: 175
12694 CTTTGAATGT
* * ** * *
12704 GTTTTTCTTTAAACAAATTTTGTCTCTCTCAAGACAGTTT-CTTTTGGAACCAAATTTTGTCTCT
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTT-GAACCAAATTTGGTCTCT
* *
12768 CTTGAGACGGTTTCCCTTGAAACAAAAAT-TGTGAATTCGTTTTCCTTGAAACAAAGTTTTGTCT
65 CTTGAGACAGTTTCCCTTGAAAC-AAAATCTGTGAATTCGTTTTCCTTGAAACAAA-TTTCGTCT
*
12832 CTCT-TGAGACAGTTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGATA
128 CTCTCT-AGACAGTTTCTCTTAAAACTAAATTTTGTCTCTCTTGAGACA
* *
12879 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTT-AATCAAATTTGGTCTCTC
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTTGAACCAAATTTGGTCTCTC
* * * *
12943 TTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTGTTTTTCTTTAAACAAATTTCGTCTCTC
66 TTGAGACAGTTTCCCTTGAAACAAAATCTGTGAATTCGTTTTCCTTGAAACAAATTTCGTCTCTC
* ** *
13008 TCTAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
131 TCTAGACAGTTTCTCTTAAAACTAAATTTTGTCTCTCTTGAGACA
*
13053 GTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACAGTTTC
1 GTTTCTCTTAAAACAAA-TTTTGTCTCTCTTGAGACAGTTTC
13095 TCTTAAAGCA
Statistics
Matches: 191, Mismatches: 20, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
173 32 0.17
174 95 0.50
175 60 0.31
176 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (175 bp):
GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTTGAACCAAATTTGGTCTCTC
TTGAGACAGTTTCCCTTGAAACAAAATCTGTGAATTCGTTTTCCTTGAAACAAATTTCGTCTCTC
TCTAGACAGTTTCTCTTAAAACTAAATTTTGTCTCTCTTGAGACA
Found at i:12961 original size:72 final size:72
Alignment explanation
Indices: 12806--13094 Score: 308
Period size: 72 Copynumber: 4.1 Consensus size: 72
12796 TTGTGAATTC
* *
12806 GTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTC
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTTGTCTCTC
*
12871 TTGAGATA
65 TTGAGACA
* * * *
12879 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTTAATCAAATTTGGTCTCTCT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTTGTCTCTCT
12944 TGAGACA
66 TGAGACA
* ** ** * *
12951 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATTTGTTTTTCTTTAAACAAATTTCGTCTCTC
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA-CAGTTTCCCTTAAAACAAATTTTGTCTCTC
13008 TCT-AGACA
65 T-TGAGACA
** * *
13016 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAGTTTTGTCTCT
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA-TTTTGTCTCT
13081 CTTGAGACA
64 CTTGAGACA
13090 GTTTC
1 GTTTC
13095 TCTTAAAGCA
Statistics
Matches: 177, Mismatches: 26, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
64 1 0.01
65 45 0.25
66 6 0.03
72 69 0.39
73 34 0.19
74 22 0.12
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (72 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTTGTCTCTCT
TGAGACA
Found at i:13044 original size:37 final size:37
Alignment explanation
Indices: 12980--13101 Score: 149
Period size: 37 Copynumber: 3.3 Consensus size: 37
12970 CTTTGAATTT
* * *
12980 GTTTTTCTTTAAACAAA-TTTCGTCTCTCTCT-AGACA
1 GTTTCTCTTAAAACAAAGTTTTGTCTCTCT-TGAGACA
* ** *
13016 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
*
13053 GTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
13090 GTTTCTCTTAAA
1 GTTTCTCTTAAA
13102 GCACCAATCT
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
36 13 0.18
37 59 0.82
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (37 bp):
GTTTCTCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
Found at i:13148 original size:31 final size:31
Alignment explanation
Indices: 13090--13174 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 31
13080 TCTTGAGACA
* * * *
13090 GTTTCTCTTAAAGCAC-CAATCTTTGAAATT
1 GTTTCTCTTAAAACACAAAACCTTTGAAAAT
*
13120 GTTTCTCTTGAAACACAAAACCTTTGAAAAT
1 GTTTCTCTTAAAACACAAAACCTTTGAAAAT
*
13151 GTTTCTCTTAAAACACCAAACCTT
1 GTTTCTCTTAAAACACAAAACCTT
13175 CGAGTTTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 14 0.30
31 33 0.70
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.35
Consensus pattern (31 bp):
GTTTCTCTTAAAACACAAAACCTTTGAAAAT
Found at i:13545 original size:20 final size:19
Alignment explanation
Indices: 13509--13547 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
13499 TTGATTAATA
*
13509 TTATTATATAATATATATT
1 TTATTATATAAGATATATT
*
13528 TTATTATTATAAGGTATATT
1 TTATTA-TATAAGATATATT
13548 ACATAATACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTATTATATAAGATATATT
Found at i:14757 original size:25 final size:24
Alignment explanation
Indices: 14715--14767 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
14705 ACTTTTCTAT
14715 TTTTATTTTTATTATACTATTATTA
1 TTTTATTTTTATTATACTA-TATTA
* *
14740 TTTTATTTCTT-TTTTACTATATTT
1 TTTTATTT-TTATTATACTATATTA
14764 TTTT
1 TTTT
14768 CATTATTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.32
25 15 0.60
26 2 0.08
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTATTTTTATTATACTATATTA
Found at i:14863 original size:14 final size:14
Alignment explanation
Indices: 14787--14855 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 14
14777 TTTGACTTTA
*
14787 TTATCATTAT-TAT
1 TTATTATTATATAT
14800 TTATATATT-T-TAT
1 TTAT-TATTATATAT
*
14813 TACTATTATTATAT-G
1 T--TATTATTATATAT
14828 TT-TTA-TATATAT
1 TTATTATTATATAT
14840 TTATTATTATATAT
1 TTATTATTATATAT
14854 TT
1 TT
14856 CATTTTATCT
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
11 5 0.11
12 5 0.11
13 13 0.29
14 16 0.36
15 5 0.11
16 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (14 bp):
TTATTATTATATAT
Found at i:16773 original size:37 final size:37
Alignment explanation
Indices: 16723--16804 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
16713 TATTTTCTAG
*
16723 TCGAGTCGAGTTTATGAAATTACAGCTCAAAATCAAT
1 TCGAGTCGAGTTTATGAAATTACAACTCAAAATCAAT
* *
16760 TCGAGTCGAGTTTATGAAATTACAATTCAAAGTCAAT
1 TCGAGTCGAGTTTATGAAATTACAACTCAAAATCAAT
*
16797 TTGAGTCG
1 TCGAGTCG
16805 TGTTGTTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (37 bp):
TCGAGTCGAGTTTATGAAATTACAACTCAAAATCAAT
Found at i:19662 original size:24 final size:24
Alignment explanation
Indices: 19635--19681 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
19625 AAGTGGTCAA
19635 GTGATTGATTTGAGCTTCATCTGC
1 GTGATTGATTTGAGCTTCATCTGC
19659 GTGATTGATTTGAGCTTCATCTG
1 GTGATTGATTTGAGCTTCATCTG
19682 TGGTCTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.43
Consensus pattern (24 bp):
GTGATTGATTTGAGCTTCATCTGC
Found at i:22027 original size:92 final size:92
Alignment explanation
Indices: 21864--22049 Score: 302
Period size: 92 Copynumber: 2.0 Consensus size: 92
21854 TTTTTATGTT
* *
21864 TGAATAAATTTTAAAATTAGTAATTAAGTTCAGTAGTTATTTTTTTATCAAATATAATTATAAAT
1 TGAATAAATTTTAAAATTAGTAATTAAGTTCAATAGTTATTTTTTTATCAAATATAATTATAAAA
*
21929 ATTCAATTCCTAATTGATTTAATGGGA
66 AATCAATTCCTAATTGATTTAATGGGA
* *
21956 TGAATACATTTTAAAATTAGTAATTAAGTTTAATAGTTA-TTTTTTATCAAATATAATTATAAAA
1 TGAATAAATTTTAAAATTAGTAATTAAGTTCAATAGTTATTTTTTTATCAAATATAATTAT-AAA
*
22020 AAATCAATTCCTAATTTATTTAATGGGA
65 AAATCAATTCCTAATTGATTTAATGGGA
22048 TG
1 TG
22050 GATTCAGTAA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
91 21 0.24
92 66 0.76
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.44
Consensus pattern (92 bp):
TGAATAAATTTTAAAATTAGTAATTAAGTTCAATAGTTATTTTTTTATCAAATATAATTATAAAA
AATCAATTCCTAATTGATTTAATGGGA
Found at i:22768 original size:12 final size:12
Alignment explanation
Indices: 22751--22790 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
22741 TATCAATATC
*
22751 AACATCTCTGAT
1 AACATCTCTAAT
22763 AACATCTCTAAT
1 AACATCTCTAAT
22775 AACATCTCTAAT
1 AACATCTCTAAT
22787 AACA
1 AACA
22791 AGGACTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.30
Consensus pattern (12 bp):
AACATCTCTAAT
Found at i:22963 original size:2 final size:2
Alignment explanation
Indices: 22956--23046 Score: 175
Period size: 2 Copynumber: 46.0 Consensus size: 2
22946 CCCCAAACTC
22956 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
22998 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
23040 AT A- AT AT
1 AT AT AT AT
23047 GCATTTCAAG
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 87 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25362 original size:3 final size:3
Alignment explanation
Indices: 25342--25378 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
25332 AAATTTTAAA
25342 TAT TAT T-T TAT T-T ATAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
25379 ATAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 3 0.10
3 27 0.87
4 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:27537 original size:2 final size:2
Alignment explanation
Indices: 27530--27557 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27520 TATTTTCATA
27530 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
27558 TATTTTATTA
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:30881 original size:15 final size:15
Alignment explanation
Indices: 30861--30892 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30851 GATCAATACC
30861 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
30876 TTTTGCATACATTCA
1 TTTTGCATACATGCA
30891 TT
1 TT
30893 ATTCATTGCA
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:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:34965 original size:124 final size:124
Alignment explanation
Indices: 34727--35765 Score: 1719
Period size: 124 Copynumber: 8.4 Consensus size: 124
34717 CATTCGATGG
* * * *
34727 ATCAACATTTCC-GGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
34791 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAATGAGATAGATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
34850 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
34915 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCCATCACAGAAGGAGATAGATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
* *
34974 ATCAACTTTTCCAGAAAATGTTTATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
35039 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
* * *
35098 ATCAACTTTTCCAAAAAAAGTTCATAATAGGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
35163 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
*
35222 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
35287 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAAGAGATAGATCATC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
* * *
35346 ATCAACTTTTCTAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAATAATAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
35411 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
35470 ATCAACTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 ATCAACTTTTCCAG-AAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* *
35535 TAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
65 TAATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
* * *
35595 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAAAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * * *
35659 AACGAGAAGAACTTGTTCAACCTTTTGTATGA-TCTATCACAGAAGAAGATAGATTAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
** * *
35717 ATCAACATTTT-CAG-AAGTGTTTATAATGAGAAGAACTCATCTGAAGAAG
1 ATCAAC-TTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAG
35766 AAGGAGCAGA
Statistics
Matches: 869, Mismatches: 43, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
121 30 0.03
122 32 0.04
123 58 0.07
124 629 0.72
125 120 0.14
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (124 bp):
ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
Found at i:36024 original size:3 final size:3
Alignment explanation
Indices: 36004--36040 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
35994 TAATTTTAAA
36004 TAT TAT T-T TAT T-T ATAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
36041 ATAAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 3 0.10
3 27 0.87
4 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:37384 original size:2 final size:2
Alignment explanation
Indices: 37357--37402 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
37347 TTTATTTGCA
37357 AT AT AT -T AT -T AT AT -T AT CAT -T 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
37396 AT AT AT A
1 AT AT AT A
37403 AAATAAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.10
2 33 0.85
3 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:38307 original size:77 final size:78
Alignment explanation
Indices: 38226--38383 Score: 185
Period size: 77 Copynumber: 2.0 Consensus size: 78
38216 AGAAATACGT
* * * * * ** *
38226 TTGCGCCCAATAATGTTAT-AGTTCACTAAGAAACATGTTGTGATATGTAATGTTAATA-TTTTT
1 TTGCGCCCAAGAATGTCATGA-TTCACTAAGAAACAGGTTGCGATATGGAAACTTAAAATTTTTT
*
38289 ATTAATAAAATAGG
65 AATAATAAAATAGG
* *
38303 TTGCGCCCAAGAATGTCATGATTCACTAATAAATAGGTTGCGATATGGAAACTTAAAATTTTTTA
1 TTGCGCCCAAGAATGTCATGATTCACTAAGAAACAGGTTGCGATATGGAAACTTAAAATTTTTTA
*
38368 ATAATAAAATGGG
66 ATAATAAAATAGG
38381 TTG
1 TTG
38384 TGACTAAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
77 46 0.69
78 21 0.31
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (78 bp):
TTGCGCCCAAGAATGTCATGATTCACTAAGAAACAGGTTGCGATATGGAAACTTAAAATTTTTTA
ATAATAAAATAGG
Found at i:42594 original size:17 final size:18
Alignment explanation
Indices: 42553--42597 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
42543 ATTCATGCAT
42553 CTAGTTCATTGAATAAAG
1 CTAGTTCATTGAATAAAG
*
42571 TTAGTTCATT-AATTAAA-
1 CTAGTTCATTGAA-TAAAG
42588 CTAGTTCATT
1 CTAGTTCATT
42598 CATCATTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (18 bp):
CTAGTTCATTGAATAAAG
Found at i:47905 original size:42 final size:43
Alignment explanation
Indices: 47850--48073 Score: 143
Period size: 42 Copynumber: 5.2 Consensus size: 43
47840 TTTTTTGTTA
*
47850 AAAAACGCCGCAATAGGTTTTGATATTTAGCAGCGTTTTTCAG
1 AAAAACGCCGCAATAGGTTTTGATATTTAGCGGCGTTTTTCAG
* *
47893 -AAAACGCTGCAATA-GTTGTTGATATTTAGTGGCGTTTGTT-AG
1 AAAAACGCCGCAATAGGTT-TTGATATTTAGCGGCGTTT-TTCAG
* * * * **
47935 AAAAAATGCCGTAATAGGTTATGATGTTTAGCGGCGTTTTTCTC
1 -AAAAACGCCGCAATAGGTTTTGATATTTAGCGGCGTTTTTCAG
* * * * * * * * *
47979 TAAAACGTCGCAGTAGGTGTTGTTGTTTTGCGGTG-TTTTCAC
1 AAAAACGCCGCAATAGGTTTTGATATTTAGCGGCGTTTTTCAG
* * * * * ** *
48021 ACAAACGTCGTAGTAGGTTTTGATGTTTTTCGGCGTTTTTGC-T
1 AAAAACGCCGCAATAGGTTTTGATATTTAGCGGCGTTTTT-CAG
48064 AAAAACGCCG
1 AAAAACGCCG
48074 GTAAAGGTCT
Statistics
Matches: 141, Mismatches: 32, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
41 3 0.02
42 66 0.47
43 41 0.29
44 28 0.20
45 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.37
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTTTTGATATTTAGCGGCGTTTTTCAG
Found at i:48530 original size:21 final size:21
Alignment explanation
Indices: 48505--48544 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
48495 TGTTTCTTCT
48505 CTGCTTCCGCTACTGCTCTGG
1 CTGCTTCCGCTACTGCTCTGG
* *
48526 CTGCTTCTGCTGCTGCTCT
1 CTGCTTCCGCTACTGCTCT
48545 CTCTACTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.38, G:0.23, T:0.38
Consensus pattern (21 bp):
CTGCTTCCGCTACTGCTCTGG
Found at i:48553 original size:21 final size:21
Alignment explanation
Indices: 48502--48554 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
48492 CGCTGTTTCT
48502 TCTCTGCTTCCGCTACTGCTC
1 TCTCTGCTTCCGCTACTGCTC
** * *
48523 TGGCTGCTTCTGCTGCTGCTC
1 TCTCTGCTTCCGCTACTGCTC
*
48544 TCTCTACTTCC
1 TCTCTGCTTCC
48555 CTTTCTTCAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.04, C:0.40, G:0.17, T:0.40
Consensus pattern (21 bp):
TCTCTGCTTCCGCTACTGCTC
Found at i:56341 original size:17 final size:17
Alignment explanation
Indices: 56290--56341 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
56280 TGCTGGTGGT
56290 GGTTGCGCTGGTGGAGAA
1 GGTTGCGCTGGTGGAG-A
* * *
56308 GCTTGCACTGCTGGAGA
1 GGTTGCGCTGGTGGAGA
*
56325 GGTTGCGCTGGTAGAGA
1 GGTTGCGCTGGTGGAGA
56342 ATGTTAGGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.17, C:0.15, G:0.44, T:0.23
Consensus pattern (17 bp):
GGTTGCGCTGGTGGAGA
Found at i:57394 original size:40 final size:40
Alignment explanation
Indices: 57351--57543 Score: 152
Period size: 39 Copynumber: 4.9 Consensus size: 40
57341 GTTTATACAA
*
57351 AAAAATACCACTATTGATTACACTATT-CTGGCATTTGT-T
1 AAAAACACCACTATTGATTACACTATTGC-GGCATTTGTCT
* * * *
57390 AAAAACGCCACTATTAATTAACATTATTGCGGCGTTTGTCT
1 AAAAACACCACTATTGATT-ACACTATTGCGGCATTTGTCT
* ** *
57431 AAAAACACCACTATTGATTAAAAGGATTGCGGCATTTTTCT
1 AAAAACACCACTATTGATT-ACACTATTGCGGCATTTGTCT
* * **
57472 -AAAACTCCATTA-TGATTAACACTATTGCGGTGTTT-TCT
1 AAAAACACCACTATTGATT-ACACTATTGCGGCATTTGTCT
*
57510 AAAAACGCCACTATAT-ATT--ACTATTGCGGC-TTTG
1 AAAAACACCACTAT-TGATTACACTATTGCGGCATTTG
57544 AGGAATAAAC
Statistics
Matches: 125, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
36 3 0.02
37 10 0.08
38 3 0.02
39 44 0.35
40 28 0.22
41 37 0.30
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (40 bp):
AAAAACACCACTATTGATTACACTATTGCGGCATTTGTCT
Found at i:57434 original size:41 final size:41
Alignment explanation
Indices: 57358--57523 Score: 173
Period size: 39 Copynumber: 4.2 Consensus size: 41
57348 CAAAAAAATA
57358 CCACTATTGATT-ACACTATT-CTGGCATTTGT-TAAAAACG
1 CCACTATTGATTAACACTATTGC-GGCATTTGTCTAAAAACG
* * * *
57397 CCACTATTAATTAACATTATTGCGGCGTTTGTCTAAAAACA
1 CCACTATTGATTAACACTATTGCGGCATTTGTCTAAAAACG
* ** * *
57438 CCACTATTGATTAAAAGGATTGCGGCATTTTTCT-AAAACT
1 CCACTATTGATTAACACTATTGCGGCATTTGTCTAAAAACG
* **
57478 CCATTA-TGATTAACACTATTGCGGTGTTT-TCTAAAAACG
1 CCACTATTGATTAACACTATTGCGGCATTTGTCTAAAAACG
57517 CCACTAT
1 CCACTAT
57524 ATATTACTAT
Statistics
Matches: 103, Mismatches: 19, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
38 3 0.03
39 39 0.38
40 25 0.24
41 36 0.35
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (41 bp):
CCACTATTGATTAACACTATTGCGGCATTTGTCTAAAAACG
Found at i:57444 original size:80 final size:79
Alignment explanation
Indices: 57351--57523 Score: 190
Period size: 80 Copynumber: 2.2 Consensus size: 79
57341 GTTTATACAA
* * *
57351 AAAAATACCACTATTGATT-ACACTATT-CTGGCATTTGTT-AAAAACGCCACTATTAATTAACA
1 AAAAACACCACTATTGATTAAAACGATTGC-GGCATTT-TTCAAAAACGCCACTA-TAATTAACA
*
57413 TTATTGCGGCGTTTGTCT
63 CTATTGCGGCGTTT-TCT
* * * * *
57431 AAAAACACCACTATTGATTAAAAGGATTGCGGCATTTTTCTAAAACTCCATTATGATTAACACTA
1 AAAAACACCACTATTGATTAAAACGATTGCGGCATTTTTCAAAAACGCCACTATAATTAACACTA
*
57496 TTGCGGTGTTTTCT
66 TTGCGGCGTTTTCT
*
57510 AAAAACGCCACTAT
1 AAAAACACCACTAT
57524 ATATTACTAT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
79 16 0.20
80 40 0.51
81 22 0.28
82 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (79 bp):
AAAAACACCACTATTGATTAAAACGATTGCGGCATTTTTCAAAAACGCCACTATAATTAACACTA
TTGCGGCGTTTTCT
Found at i:57646 original size:41 final size:39
Alignment explanation
Indices: 57600--57741 Score: 110
Period size: 41 Copynumber: 3.5 Consensus size: 39
57590 CTAATTTACC
*
57600 ACTCTATTGCGGCATTTTGACTCAATCGCTGCAAAATTTAT
1 ACTCTATTGCGGCGTTTTGACT-AATCG-TGCAAAATTTAT
** * *
57641 ACTCTATTATGGCGTTTGTGGTA-TAAACGTTGC-TAATTTACT
1 ACTCTATTGCGGCGTTT-T-G-ACTAATCG-TGCAAAATTTA-T
* *
57683 ACTCTATTGCGGCGTTTTGGCTAAATCGTCGTAAAATTTAT
1 ACTCTATTGCGGCGTTTTGACT-AATCGT-GCAAAATTTAT
*
57724 ACTCTATTGTGGC-TTTTG
1 ACTCTATTGCGGCGTTTTG
57742 TGGTATAAAC
Statistics
Matches: 80, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
40 8 0.10
41 39 0.49
42 30 0.38
43 2 0.03
44 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (39 bp):
ACTCTATTGCGGCGTTTTGACTAATCGTGCAAAATTTAT
Found at i:57697 original size:42 final size:41
Alignment explanation
Indices: 57634--57778 Score: 143
Period size: 42 Copynumber: 3.5 Consensus size: 41
57624 ATCGCTGCAA
** *
57634 AATTTATACTCTATTATGGCGTTTGTGGTATAAACGTTGCT
1 AATTTATACTCTATTGCGGCGTTTGTGGTATAAACGTCGCT
*
57675 AATTTACTACTCTATTGCGGCGTTT-TGGCTA-AATCGTCG-T
1 AATTTA-TACTCTATTGCGGCGTTTGTGG-TATAAACGTCGCT
* * *
57715 AAAATTTATACTCTATTGTGGCTTTTGTGGTATAAACGCCGCT
1 --AATTTATACTCTATTGCGGCGTTTGTGGTATAAACGTCGCT
* *
57758 AATTTACCACCCTATTGCGGC
1 AATTTA-TACTCTATTGCGGC
57779 ATTTTTTATA
Statistics
Matches: 85, Mismatches: 11, Indels: 15
0.77 0.10 0.14
Matches are distributed among these distances:
40 1 0.01
41 39 0.46
42 44 0.52
43 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (41 bp):
AATTTATACTCTATTGCGGCGTTTGTGGTATAAACGTCGCT
Found at i:57720 original size:83 final size:83
Alignment explanation
Indices: 57581--57783 Score: 300
Period size: 83 Copynumber: 2.4 Consensus size: 83
57571 ATTACGGTTT
*
57581 TAAACGCCGCTAATTTACCACTCTATTGCGGCATTTTGACTCAATCGCTGCAAAATTTATACTCT
1 TAAACGCCGCTAATTTACCACTCTATTGCGGCATTTTGACTAAATCGCTGCAAAATTTATACTCT
57646 ATTATGGCGTTTGTGGTA
66 ATTATGGCGTTTGTGGTA
** * * * *
57664 TAAACGTTGCTAATTTACTACTCTATTGCGGCGTTTTGGCTAAATCG-TCGTAAAATTTATACTC
1 TAAACGCCGCTAATTTACCACTCTATTGCGGCATTTTGACTAAATCGCT-GCAAAATTTATACTC
* *
57728 TATTGTGGCTTTTGTGGTA
65 TATTATGGCGTTTGTGGTA
*
57747 TAAACGCCGCTAATTTACCACCCTATTGCGGCATTTT
1 TAAACGCCGCTAATTTACCACTCTATTGCGGCATTTT
57784 TTATAAAAAC
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
82 1 0.01
83 104 0.99
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (83 bp):
TAAACGCCGCTAATTTACCACTCTATTGCGGCATTTTGACTAAATCGCTGCAAAATTTATACTCT
ATTATGGCGTTTGTGGTA
Found at i:57762 original size:41 final size:41
Alignment explanation
Indices: 57634--57763 Score: 140
Period size: 41 Copynumber: 3.1 Consensus size: 41
57624 ATCGCTGCAA
* * *
57634 AATTTATACTCTATTATGGCGTTTGTGGTATAAACGTTGCT
1 AATTTATACTCTATTGTGGCTTTTGTGGTATAAACGTCGCT
* * *
57675 AATTTACTACTCTATTGCGGCGTTTTG-GCTA-AATCGTCG-T
1 AATTTA-TACTCTATTGTGGC-TTTTGTGGTATAAACGTCGCT
*
57715 AAAATTTATACTCTATTGTGGCTTTTGTGGTATAAACGCCGCT
1 --AATTTATACTCTATTGTGGCTTTTGTGGTATAAACGTCGCT
57758 AATTTA
1 AATTTA
57764 CCACCCTATT
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
40 6 0.08
41 34 0.47
42 27 0.38
43 5 0.07
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (41 bp):
AATTTATACTCTATTGTGGCTTTTGTGGTATAAACGTCGCT
Done.