Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002857.1 Hibiscus syriacus cultivar Beakdansim tig00005883_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: 81097
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2813 original size:18 final size:17
Alignment explanation
Indices: 2775--2819 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2765 GCCGGTCACA
*
2775 ACCCGACCCAACCCGTT
1 ACCCGACCCGACCCGTT
*
2792 ACCCGACCCGACCCATTT
1 ACCCGACCCGACCC-GTT
2810 ACCCGACCCG
1 ACCCGACCCG
2820 TTGACCCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.22, C:0.53, G:0.13, T:0.11
Consensus pattern (17 bp):
ACCCGACCCGACCCGTT
Found at i:2834 original size:18 final size:18
Alignment explanation
Indices: 2813--2847 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2803 CCCATTTACC
2813 CGACCCGTTGACCCGACT
1 CGACCCGTTGACCCGACT
*
2831 CGACTCGTTGACCCGAC
1 CGACCCGTTGACCCGAC
2848 CCGTTGACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
CGACCCGTTGACCCGACT
Found at i:2845 original size:31 final size:31
Alignment explanation
Indices: 2779--2856 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
2769 GTCACAACCC
*
2779 GACCCAACCCGTT-ACCCGACCCGACCCATT
1 GACCCGACCCGTTGACCCGACCCGACCCATT
* * * *
2809 TACCCGACCCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCATT
2840 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
2857 GTTGACCGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 11 0.27
31 30 0.73
ACGTcount: A:0.19, C:0.46, G:0.18, T:0.17
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCATT
Found at i:2847 original size:13 final size:13
Alignment explanation
Indices: 2796--2856 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
2786 CCCGTTACCC
*
2796 GACCCGACCCATT
1 GACCCGACCCGTT
*
2809 TACCCGACCCGTT
1 GACCCGACCCGTT
2822 GACCCGACTCGACTCGTT
1 GACCCGA--C--C-CGTT
2840 GACCCGACCCGTT
1 GACCCGACCCGTT
2853 GACC
1 GACC
2857 GTTGACCGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 25 0.62
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 11 0.28
ACGTcount: A:0.18, C:0.44, G:0.20, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2860 original size:7 final size:7
Alignment explanation
Indices: 2848--2883 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
2838 TTGACCCGAC
2848 CCGTTGA
1 CCGTTGA
2855 CCGTTGA
1 CCGTTGA
2862 CCG-TGA
1 CCGTTGA
2868 CCCGTTGA
1 -CCGTTGA
2876 CCGTTGA
1 CCGTTGA
2883 C
1 C
2884 TACTGTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 3 0.11
7 21 0.78
8 3 0.11
ACGTcount: A:0.14, C:0.33, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:2871 original size:21 final size:20
Alignment explanation
Indices: 2836--2883 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
2826 CGACTCGACT
2836 CGTTGACCCGACCCGTTGAC
1 CGTTGACCCGACCCGTTGAC
*
2856 CGTTGACCGTGACCCGTTGAC
1 CGTTGACC-CGACCCGTTGAC
2877 CGTTGAC
1 CGTTGAC
2884 TACTGTTGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.15, C:0.35, G:0.27, T:0.23
Consensus pattern (20 bp):
CGTTGACCCGACCCGTTGAC
Found at i:4000 original size:18 final size:18
Alignment explanation
Indices: 3974--4008 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3964 TTCGAAGGAC
*
3974 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3992 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
4009 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:21591 original size:44 final size:44
Alignment explanation
Indices: 21528--21611 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
21518 CGTGTTCATT
*
21528 CGGTTAAAGTTAAACGAACGAACGTGAATATACTC-TCGTTCGTA
1 CGGTTAAAGTTAAACGAACGAACATGAATATA-TCATCGTTCGTA
21572 CGGTTAAAGTTAAACGAACGAACATGAATATATCATCGTT
1 CGGTTAAAGTTAAACGAACGAACATGAATATATCATCGTT
21612 TTCTTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 2 0.05
44 36 0.95
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (44 bp):
CGGTTAAAGTTAAACGAACGAACATGAATATATCATCGTTCGTA
Found at i:22525 original size:2 final size:2
Alignment explanation
Indices: 22518--22551 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22508 TAACATACAA
22518 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
22552 GTGGACATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23128 original size:2 final size:2
Alignment explanation
Indices: 23121--23165 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
23111 ATTAAATCCC
23121 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23163 TA T
1 TA T
23166 CCTTGTTGTG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25986 original size:39 final size:39
Alignment explanation
Indices: 25930--26058 Score: 222
Period size: 39 Copynumber: 3.3 Consensus size: 39
25920 TATTGTCCCT
* *
25930 ACAATTATCCAACCAAAATATCACCATGTAGCGCTTTCC
1 ACAATTATCCAACCAAAATATCACCATGTTGCACTTTCC
*
25969 AAAATTATCCAACCAAAATATCACCATGTTGCACTTTCC
1 ACAATTATCCAACCAAAATATCACCATGTTGCACTTTCC
*
26008 GCAATTATCCAACCAAAATATCACCATGTTGCACTTTCC
1 ACAATTATCCAACCAAAATATCACCATGTTGCACTTTCC
26047 ACAATTATCCAA
1 ACAATTATCCAA
26059 AAAAACTACG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 84 1.00
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.27
Consensus pattern (39 bp):
ACAATTATCCAACCAAAATATCACCATGTTGCACTTTCC
Found at i:28830 original size:13 final size:12
Alignment explanation
Indices: 28796--28838 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
28786 CAGCAGCCGC
28796 CTTTTTCTCTTTTT
1 CTTTTTC-C-TTTT
*
28810 CCTTTTCCTTCTT
1 CTTTTTCCTT-TT
28823 CTTTTTCCTTTT
1 CTTTTTCCTTTT
28835 CTTT
1 CTTT
28839 GCAGCAGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 8 0.31
13 12 0.46
14 6 0.23
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCCTTTT
Found at i:29055 original size:12 final size:12
Alignment explanation
Indices: 29035--29069 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
29025 GTCCTTTCAC
29035 TCTTGTTCTTCT
1 TCTTGTTCTTCT
*
29047 TCTTATTCTTCT
1 TCTTGTTCTTCT
29059 TCTTGTTCTTC
1 TCTTGTTCTTC
29070 GAAGTTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.03, C:0.26, G:0.06, T:0.66
Consensus pattern (12 bp):
TCTTGTTCTTCT
Found at i:29561 original size:126 final size:126
Alignment explanation
Indices: 29415--29660 Score: 332
Period size: 126 Copynumber: 2.0 Consensus size: 126
29405 TGATAAAGAC
* * * * * * *
29415 AATGAACGAACATCTTCTTCCTCATCTTCTTTTACA-CTCTCTTCATTTTCTAGTTCGTCATCTA
1 AATGAACGAACATCTTCTTCCTCATCTTCTTTCACAGC-ATCTTCATTTTCAAGCTCATCACCCA
* *
29479 AGGCTGCAAATGTAGCACTGTTTTTCTTCTTAGATGACTTCTTCTTATGACCTGAAGATCCA
65 AGGCTGCAAATGCAGCACTGCTTTTCTTCTTAGATGACTTCTTCTTATGACCTGAAGATCCA
* * *
29541 AATGAAGGAGCATCTTCTTCCTCATCTTCTTTCACAGCATCTTCGTTTTCAAGCTCATCACCCAA
1 AATGAACGAACATCTTCTTCCTCATCTTCTTTCACAGCATCTTCATTTTCAAGCTCATCACCCAA
* * * *
29606 GGCTGCAAATGCAGCAGTGCTTTTCTTCTTAGATGTCTTCTTCTTCTTACCTGAA
66 GGCTGCAAATGCAGCACTGCTTTTCTTCTTAGATGACTTCTTCTTATGACCTGAA
29661 AATGCAATCA
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
126 102 0.99
127 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (126 bp):
AATGAACGAACATCTTCTTCCTCATCTTCTTTCACAGCATCTTCATTTTCAAGCTCATCACCCAA
GGCTGCAAATGCAGCACTGCTTTTCTTCTTAGATGACTTCTTCTTATGACCTGAAGATCCA
Found at i:29686 original size:126 final size:126
Alignment explanation
Indices: 29426--29689 Score: 309
Period size: 126 Copynumber: 2.1 Consensus size: 126
29416 ATGAACGAAC
* * * * * * *
29426 ATCTTCTTCCTCATCTTCTTTTACACTCTCTTCATTTTCTAGTTCGTCATCTAAGGCTGCAAATG
1 ATCTTCTTCCTCATCTTCTTTCACACTATCTTCATTTTCAAGCTCATCACCCAAGGCTGCAAATG
* * * * *
29491 TAGCACTGTTTTTCTTCTTAGATGACTTCTTCTTATGACCTGAAGATCCAAATGAAGGAGC
66 CAGCACTGCTTTTCTTCTTAGATGACTTCTTCTTATGACCTGAAAATCCAAATCAAGGAGA
*
29552 ATCTTCTTCCTCATCTTCTTTCACAGC-ATCTTCGTTTTCAAGCTCATCACCCAAGGCTGCAAAT
1 ATCTTCTTCCTCATCTTCTTTCACA-CTATCTTCATTTTCAAGCTCATCACCCAAGGCTGCAAAT
* * * * * *
29616 GCAGCAGTGCTTTTCTTCTTAGATGTCTTCTTCTTCTTACCTGAAAATGC-AATCATGGCAGA
65 GCAGCACTGCTTTTCTTCTTAGATGACTTCTTCTTATGACCTGAAAATCCAAATCAAGG-AGA
29678 AT-TATCTTCCTC
1 ATCT-TCTTCCTC
29690 GTCATCAACA
Statistics
Matches: 116, Mismatches: 19, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
125 7 0.06
126 108 0.93
127 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (126 bp):
ATCTTCTTCCTCATCTTCTTTCACACTATCTTCATTTTCAAGCTCATCACCCAAGGCTGCAAATG
CAGCACTGCTTTTCTTCTTAGATGACTTCTTCTTATGACCTGAAAATCCAAATCAAGGAGA
Found at i:37604 original size:3 final size:3
Alignment explanation
Indices: 37596--37647 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
37586 CTTTTTTGTA
** *
37596 TAT TAT TAT TAT CGT TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
37644 TAT T
1 TAT T
37648 TAATTTACAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40873 original size:30 final size:31
Alignment explanation
Indices: 40834--40902 Score: 122
Period size: 31 Copynumber: 2.2 Consensus size: 31
40824 TTATTGAAAT
40834 TTTTAATTGCTTTG-TTTTTTTCGTACTAACA
1 TTTT-ATTGCTTTGTTTTTTTTCGTACTAACA
40865 TTTTATTGCTTTGTTTTTTTTCGTACTAACA
1 TTTTATTGCTTTGTTTTTTTTCGTACTAACA
40896 TTTTATT
1 TTTTATT
40903 TTTGGCTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 9 0.24
31 28 0.76
ACGTcount: A:0.17, C:0.12, G:0.09, T:0.62
Consensus pattern (31 bp):
TTTTATTGCTTTGTTTTTTTTCGTACTAACA
Found at i:41660 original size:31 final size:32
Alignment explanation
Indices: 41624--41685 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
41614 ATTTTACATG
41624 TACTAACTTA-TTTTTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTTTTCTCTTTTGTTTGTGTA
41655 TACTAACTTATTTTTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTTTTCTCTTTTGTTTGTGT
41686 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 10 0.33
32 20 0.67
ACGTcount: A:0.15, C:0.13, G:0.10, T:0.63
Consensus pattern (32 bp):
TACTAACTTATTTTTTCTCTTTTGTTTGTGTA
Found at i:44832 original size:11 final size:11
Alignment explanation
Indices: 44804--44841 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
44794 AAGAGCAAAG
44804 AGAAAAATCAA
1 AGAAAAATCAA
44815 AGCAAAAATCAA
1 AG-AAAAATCAA
*
44827 AGAAAAAGCAA
1 AGAAAAATCAA
44838 AGAA
1 AGAA
44842 TAAAAGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:44834 original size:18 final size:19
Alignment explanation
Indices: 44813--44848 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
44803 GAGAAAAATC
*
44813 AAAGCAAA-AATCAAAGAA
1 AAAGCAAAGAATAAAAGAA
44831 AAAGCAAAGAATAAAAGA
1 AAAGCAAAGAATAAAAGA
44849 GGACAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.72, C:0.08, G:0.14, T:0.06
Consensus pattern (19 bp):
AAAGCAAAGAATAAAAGAA
Found at i:46022 original size:4 final size:4
Alignment explanation
Indices: 46013--46046 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
46003 AAAAGTATAC
46013 ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
46047 GATACATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 26 0.93
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:46037 original size:22 final size:21
Alignment explanation
Indices: 46009--46054 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
45999 CGAGAAAAGT
46009 ATACACATACATACATACATAC
1 ATACACATACATACAT-CATAC
*
46031 ATACACATACATACATGATAC
1 ATACACATACATACATCATAC
46052 ATA
1 ATA
46055 AAATTTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
ATACACATACATACATCATAC
Found at i:46661 original size:105 final size:102
Alignment explanation
Indices: 46520--46758 Score: 286
Period size: 105 Copynumber: 2.3 Consensus size: 102
46510 TGAGAATTTT
* * *
46520 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATCTGATTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATCTGATTCACA
*
46584 TAAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 T-AAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * * *
46625 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATCTGATTCACA
* * *
46690 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
*
46727 AAAACAAACTTCGTCTCGCTTGAGACAATTTT
1 AAAACAAATTTCGTCTCGCTTGAGAC-ATTTT
46759 TCTAAAAACA
Statistics
Matches: 117, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
101 2 0.02
102 25 0.21
103 8 0.07
104 4 0.03
105 77 0.66
106 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATCTGATTCACA
TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:46766 original size:36 final size:35
Alignment explanation
Indices: 46719--46824 Score: 108
Period size: 34 Copynumber: 3.0 Consensus size: 35
46709 CTTGAGATCG
46719 TTTTCTCAAAAACAAACTTCGTCTCGCTTGAGACAAT
1 TTTTCT-AAAAACAAACTTCGTCTCGCTTGAGAC-AT
**
46756 TTTTCTAAAAACAAATCTT-GTCTCATTTGAGAC-T
1 TTTTCTAAAAACAAA-CTTCGTCTCGCTTGAGACAT
* * * * *
46790 ATATCTTAAAGCAAATTTCGTCTCGCTTGAGACAT
1 TTTTCTAAAAACAAACTTCGTCTCGCTTGAGACAT
46825 CATTTTTTCT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
33 2 0.04
34 24 0.42
35 1 0.02
36 21 0.37
37 9 0.16
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (35 bp):
TTTTCTAAAAACAAACTTCGTCTCGCTTGAGACAT
Found at i:47106 original size:25 final size:26
Alignment explanation
Indices: 47077--47131 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
47067 TTTTGAGGAA
*
47077 AAAAATCTTTGAGTTTGCTCCTCTTG
1 AAAATTCTTTGAGTTTGCTCCTCTTG
* * *
47103 AAAATTTTTTTGAGTTTGTTCCTTTTG
1 AAAA-TTCTTTGAGTTTGCTCCTCTTG
47130 AA
1 AA
47132 TAAAAATCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.49
Consensus pattern (26 bp):
AAAATTCTTTGAGTTTGCTCCTCTTG
Found at i:47151 original size:29 final size:29
Alignment explanation
Indices: 47077--47202 Score: 152
Period size: 29 Copynumber: 4.5 Consensus size: 29
47067 TTTTGAGGAA
* *
47077 AAAAATCTTTGAGTTTGCTCCTCTTG-A-
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
** *
47104 AAATTTTTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
*
47133 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
* *
47162 AAAAATCTTTAAG-TTGTTTCTTTTGAA-
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
47189 AAAAATCTTTGAGT
1 AAAAATCTTTGAGT
47203 CTATTTATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
27 33 0.40
28 14 0.17
29 36 0.43
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTGTTCCTTTTGAAT
Found at i:47193 original size:56 final size:55
Alignment explanation
Indices: 47074--47202 Score: 152
Period size: 56 Copynumber: 2.3 Consensus size: 55
47064 TTCTTTTGAG
** * *
47074 GAAAAAAATCTTTGAGTTTGCTCCTCTTGAAAATTTTTTTGAGTTTGTTCCTTTT
1 GAAAAAAATCTTTGAGTTTGCTCCTCTTGAAAAAATCTTTAAGTTTGTTCCTTTT
* * * *
47129 GAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAAAATCTTTAAG-TTGTTTCTTTT
1 GAA-AAAAATCTTTGAGTTTGCTCCTCTTG-A-AAAAATCTTTAAGTTTGTTCCTTTT
47186 GAAAAAAATCTTTGAGT
1 GAAAAAAATCTTTGAGT
47203 CTATTTATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
55 3 0.05
56 36 0.58
57 14 0.23
58 9 0.15
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (55 bp):
GAAAAAAATCTTTGAGTTTGCTCCTCTTGAAAAAATCTTTAAGTTTGTTCCTTTT
Found at i:47217 original size:28 final size:28
Alignment explanation
Indices: 47111--47216 Score: 124
Period size: 29 Copynumber: 3.7 Consensus size: 28
47101 TGAAAATTTT
*
47111 TTTGAGTTTGTTCCTTTTGAATAAAAATC
1 TTTGAG-TTGTTTCTTTTGAATAAAAATC
* *
47140 TTGGAGTTTGTTCCTTTTGAATAAAAATC
1 TTTGAG-TTGTTTCTTTTGAATAAAAATC
*
47169 TTTAAGTTGTTTCTTTTGAA-AAAAATC
1 TTTGAGTTGTTTCTTTTGAATAAAAATC
* *
47196 TTTGAGTCTATTTATTTTGAA
1 TTTGAGT-TGTTTCTTTTGAA
47217 ACGAAGTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
27 13 0.19
28 24 0.35
29 32 0.46
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.49
Consensus pattern (28 bp):
TTTGAGTTGTTTCTTTTGAATAAAAATC
Found at i:47262 original size:61 final size:61
Alignment explanation
Indices: 47189--47326 Score: 267
Period size: 61 Copynumber: 2.3 Consensus size: 61
47179 TTCTTTTGAA
*
47189 AAAAATCTTTGAGTCTATTTATTTTGAAACGAAGTTTTGTCTCTCTTGAGACAATTTCGTG
1 AAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG
47250 AAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG
1 AAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG
47311 AAAAATCTTTGAGTCT
1 AAAAATCTTTGAGTCT
47327 GAAACAAAGT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 76 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (61 bp):
AAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG
Found at i:47432 original size:29 final size:30
Alignment explanation
Indices: 47368--47431 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
47358 TTGTAAAAAA
*
47368 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
47398 AAAAATCTTTGAG-TTGGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATT-GTTTCTTTGGAAAC
47428 AAAA
1 AAAA
47432 TTTTGTCTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:47606 original size:64 final size:64
Alignment explanation
Indices: 47385--47630 Score: 205
Period size: 64 Copynumber: 3.8 Consensus size: 64
47375 TTTGAGATTG
* * * * *
47385 TTTCTTTTGAAACAAAAATCTTTGAGTTGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTG-AACAAAAATCTTTGAGTTTGTTTCTCTGGAAACAAGA-TTT-TCTCCCTTAACAT
47450 AA
63 AA
* * * * * *
47452 TTTCTTTTGGA-AAAAATCTTTGAATATGTTTCTCT-TAAA-ATGAATTTTGTCCCTTGAAACAT
1 TTTCTTTTGAACAAAAATCTTTGAGTTTGTTTCTCTGGAAACAAG-ATTTTCTCCCTT--AACAT
47514 --
63 AA
* ** *
47514 TTTCCCTTAAAACAAGAACATCTTTGAGTTTGTTTCTCTGGAAACAAGGTTTTCTCCCTTAACAT
1 TTT-CTTTTGAACAA-AA-ATCTTTGAGTTTGTTTCTCTGGAAACAAGATTTTCTCCCTTAACAT
47579 AA
63 AA
* * * *
47581 TTTCTTTTGAAGAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTT
1 TTTCTTTTGAACAAAAATCTTTGAGTTTGTTTCTCTGGAAACAAGATTTT
47631 GTCTCACTAA
Statistics
Matches: 139, Mismatches: 29, Indels: 25
0.72 0.15 0.13
Matches are distributed among these distances:
62 9 0.06
63 8 0.06
64 40 0.29
65 29 0.21
66 26 0.19
67 25 0.18
68 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (64 bp):
TTTCTTTTGAACAAAAATCTTTGAGTTTGTTTCTCTGGAAACAAGATTTTCTCCCTTAACATAA
Found at i:47850 original size:35 final size:35
Alignment explanation
Indices: 47804--47899 Score: 167
Period size: 35 Copynumber: 2.7 Consensus size: 35
47794 AAAAATTTAC
47804 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
1 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
47839 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
1 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
*
47874 CATCTTTGAGATC-ATTTCCCTTGAAA
1 CATCTTTGA-ATCTGTTTCCCTTGAAA
47900 TGAATTTTGT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
35 56 0.95
36 3 0.05
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.33
Consensus pattern (35 bp):
CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
Found at i:47960 original size:66 final size:63
Alignment explanation
Indices: 47874--48052 Score: 180
Period size: 66 Copynumber: 2.8 Consensus size: 63
47864 ACAAAACAAA
* *
47874 CATCTTTGAGATCATTTCCCTTGAAATGAATTTTGTCTCATTTGAGACAATTTCCCATGAAACGC
1 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTC-TTTGAGACAA-TTCCCATGAAACGC
* * * * * * *
47939 CGATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGCTTGAGACAATTCCCTTTAAATG
1 C-ATCTTTGAGATCGTTTCCCTT-GAAACGAATTTTGTCTC-TTTGAGACAATTCCCATGAAACG
48004 C
63 C
* * * *
48005 CATCTTTG-GGTTGTTTCCTTTGAAACGAATCTTGTCTCTTTCGAGACA
1 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTT-GAGACA
48053 GTTGCTGTGG
Statistics
Matches: 93, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
62 2 0.02
63 20 0.22
64 9 0.10
65 8 0.09
66 31 0.33
67 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (63 bp):
CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTGAGACAATTCCCATGAAACGC
Found at i:48221 original size:28 final size:28
Alignment explanation
Indices: 48171--48224 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
48161 TCAAAATCCA
* * *
48171 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTCTCCATTGAAACAC
*
48199 ATCTTTGAGTTGGTCTCCCTTGAAAC
1 ATCTTTGAGTTGGTCTCCATTGAAAC
48225 CATTATCCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.43
Consensus pattern (28 bp):
ATCTTTGAGTTGGTCTCCATTGAAACAC
Found at i:48306 original size:46 final size:46
Alignment explanation
Indices: 48250--48576 Score: 219
Period size: 46 Copynumber: 7.5 Consensus size: 46
48240 TAACCAGCCG
* *
48250 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 TCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGGCCAGATC
* * ** *
48296 TCTTCATCACGTAAGAACCGTGCCATC-CC--TCGA---CCAGATC
1 TCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGGCCAGATC
* * * ** * *
48336 TCTTCATCACGTAGGAGCCGTG---TCACCCATAGATAACCAGCTG
1 TCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGGCCAGATC
* *
48379 TCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAG-CC
1 TCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGGCCAGATC
** *
48424 GTCCTCATCACGTAGGAACCGTGCCATC-CC--TCGA---CCAGATC
1 -TCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGGCCAGATC
* * ** ** *
48465 TCTTCATCACGTAGGAGCCGTG---TCACCCCTAGATAACCA-ACC
1 TCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGGCCAGATC
* * *
48507 GTCCTCATCACGTAGGAACTGTGTTATCACCTAAAGATGGCTAG-TC
1 -TCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGGCCAGATC
48553 GTCCTCATCACGTAGGAACCGTGT
1 -TCCTCATCACGTAGGAACCGTGT
48577 CAACCCTCGA
Statistics
Matches: 220, Mismatches: 39, Indels: 44
0.73 0.13 0.15
Matches are distributed among these distances:
37 4 0.02
38 4 0.02
40 56 0.25
41 1 0.00
42 2 0.01
43 52 0.24
45 4 0.02
46 97 0.44
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.24
Consensus pattern (46 bp):
TCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGGCCAGATC
Found at i:48344 original size:40 final size:40
Alignment explanation
Indices: 48253--48612 Score: 170
Period size: 40 Copynumber: 8.4 Consensus size: 40
48243 CCAGCCGTCC
** *
48253 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGCCATC-CC--TAGA---CCAGATCTCT
* *
48299 TCATCACGTAAGAACCGTGCCATCCCTCGACCAGATCTCT
1 TCATCACGTAGGAACCGTGCCATCCCTAGACCAGATCTCT
* * * * *
48339 TCATCACGTAGGAGCCGTGTCA-CCCATAGATAACCAGCTGTCC
1 TCATCACGTAGGAACCGTGCCATCCC-TAG---ACCAGATCTCT
** * *
48382 TCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAG-CCGTCC
1 TCATCACGTAGGAACCGTGCCATC-CCT--AGA---CCAGATC-TCT
*
48428 TCATCACGTAGGAACCGTGCCATCCCTCGACCAGATCTCT
1 TCATCACGTAGGAACCGTGCCATCCCTAGACCAGATCTCT
* * * * *
48468 TCATCACGTAGGAGCCGTGTCACCCCTAGATAACCA-ACCGTCC
1 TCATCACGTAGGAACCGTGCCATCCCTAG---ACCAGATC-TCT
* ** * *
48511 TCATCACGTAGGAACTGTGTTATCACCTAAAGATGGCTAG-TCGTCC
1 TCATCACGTAGGAACCGTGCCATC-CCT--AGA---CCAGATC-TCT
* * * * *
48557 TCATCACGTAGGAACCGTGTCAACCCTCGACCAGATTTCC
1 TCATCACGTAGGAACCGTGCCATCCCTAGACCAGATCTCT
48597 TCATCACGTAGGAACC
1 TCATCACGTAGGAACC
48613 ATGTCACCCT
Statistics
Matches: 250, Mismatches: 39, Indels: 56
0.72 0.11 0.16
Matches are distributed among these distances:
39 3 0.01
40 83 0.33
41 2 0.01
42 2 0.01
43 63 0.25
44 5 0.02
45 10 0.04
46 82 0.33
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (40 bp):
TCATCACGTAGGAACCGTGCCATCCCTAGACCAGATCTCT
Found at i:48467 original size:129 final size:129
Alignment explanation
Indices: 48237--48626 Score: 602
Period size: 129 Copynumber: 3.0 Consensus size: 129
48227 TTATCCCTAG
** *
48237 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC-TCTTC
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAG-ACGTCCTC
*
48301 ATCACGTAAGAACCGTGCCATCCCTCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCCAT
65 ATCACGTAGGAACCGTGCCATCCCTCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCCAT
* *
48366 AGATAACCAGCTGTCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAGCCGTCCTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAGACGTCCTCA
*
48431 TCACGTAGGAACCGTGCCATCCCTCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCCCT
66 TCACGTAGGAACCGTGCCATCCCTCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCCAT
* * * *
48495 AGATAACCAACCGTCCTCATCACGTAGGAACTGTGTTATCACCTAAAGATGGCTAGTCGTCCTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAGACGTCCTCA
* * * * * * *
48560 TCACGTAGGAACCGTGTCAACCCTCGACCAGATTTCCTCATCACGTAGGAACCATGTCACCCTT
66 TCACGTAGGAACCGTGCCATCCCTCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCCAT
48624 AGA
1 AGA
48627 CGACCCGAAC
Statistics
Matches: 241, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
128 1 0.00
129 240 1.00
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGGCCAGACGTCCTCA
TCACGTAGGAACCGTGCCATCCCTCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCCAT
Found at i:48824 original size:3 final size:3
Alignment explanation
Indices: 48816--48867 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
48806 CTTTTTTGTA
**
48816 TAT TAT TAT TAT CGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
48864 TAT T
1 TAT T
48868 TAATTTACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:55920 original size:13 final size:13
Alignment explanation
Indices: 55902--55930 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
55892 CATCTCATTT
55902 TATGTTTAGATGA
1 TATGTTTAGATGA
55915 TATGTTTAGATGA
1 TATGTTTAGATGA
55928 TAT
1 TAT
55931 TATACTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (13 bp):
TATGTTTAGATGA
Found at i:56498 original size:20 final size:20
Alignment explanation
Indices: 56475--56539 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
56465 GGAGTTAAAA
*
56475 TTTAAAATAAATTTATTATT
1 TTTAAATTAAATTTATTATT
* *
56495 TTTAAATTAAATTCAATATT
1 TTTAAATTAAATTTATTATT
*
56515 TTTCATATTAAATTTATTATT
1 TTT-AAATTAAATTTATTATT
56536 TTTA
1 TTTA
56540 TATTTCTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAAATTAAATTTATTATT
Found at i:56542 original size:20 final size:20
Alignment explanation
Indices: 56482--56543 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
56472 AAATTTAAAA
*
56482 TAAATTTATTATTTTTAAAT
1 TAAATTTATTATTTTTATAT
* *
56502 TAAATTCAATATTTTTCATAT
1 TAAATTTATTATTTTT-ATAT
56523 TAAATTTATTATTTTTATAT
1 TAAATTTATTATTTTTATAT
56543 T
1 T
56544 TCTAAATTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TAAATTTATTATTTTTATAT
Found at i:61085 original size:59 final size:59
Alignment explanation
Indices: 61035--61160 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 59
61025 AATAGTCATC
* * * * *
61035 TAACTATATGGTGTTGTTTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATGTCTCT
1 TAACTATAGGGTATTGTTTTGTTGAGTCACCCAACTATTAAAAGTTACAAAATGTCTCT
* * *
61094 TGATTATAGGGTATTGTTTTGTTGAGTCACCCAACTATTAAAAGTTACAAAATTGTCACT
1 TAACTATAGGGTATTGTTTTGTTGAGTCACCCAACTATTAAAAGTTACAAAA-TGTCTCT
*
61154 TGACTAT
1 TAACTAT
61161 TCATATGTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
59 45 0.79
60 12 0.21
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (59 bp):
TAACTATAGGGTATTGTTTTGTTGAGTCACCCAACTATTAAAAGTTACAAAATGTCTCT
Found at i:61790 original size:316 final size:318
Alignment explanation
Indices: 61216--61832 Score: 812
Period size: 316 Copynumber: 1.9 Consensus size: 318
61206 ATCTGAGCTA
* * * * *
61216 AACGTTAACATGCTGATTGGGATATGGTAAAATCATATTTTAACAATGTATGTTGGCATCACCGT
1 AACGTTAACATGCTAATTGGGATATGATAAAATCATATTTTAACAATGTATATTGGCACCACCAT
* * * * * *
61281 TACTTTCAAGCATTTGACTTGACAATATTATGTTTCAAGCAGTGACTCGACGACATAATGTGAAC
66 TACTTTCAAGCAGTTGACTCGACAACATTATGATTCAAACAGTGACTCGACGACATAATGTAAAC
*
61346 GAAGAGTTGATACATAAAATACAACTCAAACGATTCTGAGATAAGATTTTACTATATCTCAATCA
131 GAAGAGTTGATACAAAAAATACAACTCAAACGATTCTGAGATAAGATTTTACTATATCTCAATCA
** *
61411 ACTAGTTAACATCCATTTCAAACAACTGCAAATTAATTAACGAAAAATGACGAGTTTAGAATATA
196 ACTAGTTAACATCCAGCTCAAACAACCGCAAATTAATTAACGAAAAATGACGAGTTTAGAATATA
* ** *
61476 TGAATAGTCTTGTGACTA-TTTTGTAACTTTTAATAGTCGACAAGTCCATCTAAGTTG
261 TGAATAATCGGGCGACTATTTTTGTAACTTTTAATAGTCGACAAGTCCATCTAAGTTG
* *
61533 AACGTTAACATGCTAATTGTGATATGATAAAATCATATTTTAACAATGTCTATTGGCACCACCAT
1 AACGTTAACATGCTAATTGGGATATGATAAAATCATATTTTAACAATGTATATTGGCACCACCAT
** * * *
61598 TGTTTTCTAGC-GTTGACTCGACAACATTATGATTCAAACATTGACTCGACGATATAATGTAAAC
66 TACTTTCAAGCAGTTGACTCGACAACATTATGATTCAAACAGTGACTCGACGACATAATGTAAAC
* * * * * * * **
61662 GAATAGTCT-ATGCAAAAAATACAACTTAAACTATTCTGAGATCATATTTTAGTATATCTCTGTC
131 GAAGAGT-TGATACAAAAAATACAACTCAAACGATTCTGAGATAAGATTTTACTATATCTCAATC
* * ** *
61726 AA-TAAGTTAACGTCCAGCTCAAACAACCGCCAATTTTTTAAC-AGAAAATGATGAGTTTAGAAT
195 AACT-AGTTAACATCCAGCTCAAACAACCGCAAATTAATTAACGA-AAAATGACGAGTTTAGAAT
61789 ATATGAATAATCGGGCGACTATTTTTGTAACTTTTAATAGTCGA
258 ATATGAATAATCGGGCGACTATTTTTGTAACTTTTAATAGTCGA
61833 ATGACTCAAT
Statistics
Matches: 256, Mismatches: 40, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
315 2 0.01
316 165 0.64
317 89 0.35
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (318 bp):
AACGTTAACATGCTAATTGGGATATGATAAAATCATATTTTAACAATGTATATTGGCACCACCAT
TACTTTCAAGCAGTTGACTCGACAACATTATGATTCAAACAGTGACTCGACGACATAATGTAAAC
GAAGAGTTGATACAAAAAATACAACTCAAACGATTCTGAGATAAGATTTTACTATATCTCAATCA
ACTAGTTAACATCCAGCTCAAACAACCGCAAATTAATTAACGAAAAATGACGAGTTTAGAATATA
TGAATAATCGGGCGACTATTTTTGTAACTTTTAATAGTCGACAAGTCCATCTAAGTTG
Found at i:67576 original size:45 final size:46
Alignment explanation
Indices: 67505--67600 Score: 158
Period size: 45 Copynumber: 2.1 Consensus size: 46
67495 ATGAGAAAAA
*
67505 TATAAATGTAAATTATAACAATTATCCTTAAATATATAAATATAAAT
1 TATAAATGT-AATTATAACAAATATCCTTAAATATATAAATATAAAT
*
67552 TATAAATGT-ATTATAACAAATATCCTTAAATATATAAATGTAAAT
1 TATAAATGTAATTATAACAAATATCCTTAAATATATAAATATAAAT
67597 TATA
1 TATA
67601 TTATTATTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 38 0.81
47 9 0.19
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (46 bp):
TATAAATGTAATTATAACAAATATCCTTAAATATATAAATATAAAT
Found at i:67587 original size:21 final size:21
Alignment explanation
Indices: 67513--67588 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 21
67503 AATATAAATG
*
67513 TAAAT-TATAACAATTATCCT
1 TAAATATATAACAAATATCCT
* ***
67533 TAAATATATAA-ATATAAATT
1 TAAATATATAACAAATATCCT
67553 ATAAATGTATTATAACAAATATCCT
1 -TAAA--TA-TATAACAAATATCCT
67578 TAAATATATAA
1 TAAATATATAA
67589 ATGTAAATTA
Statistics
Matches: 41, Mismatches: 9, Indels: 11
0.67 0.15 0.18
Matches are distributed among these distances:
20 9 0.22
21 14 0.34
22 2 0.05
23 2 0.05
24 9 0.22
25 5 0.12
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (21 bp):
TAAATATATAACAAATATCCT
Found at i:67905 original size:15 final size:15
Alignment explanation
Indices: 67868--67898 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
67858 ATAAACTTAG
67868 CCACACATTTAATAT
1 CCACACATTTAATAT
67883 CCACACATTTAATAT
1 CCACACATTTAATAT
67898 C
1 C
67899 TTAACATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (15 bp):
CCACACATTTAATAT
Found at i:74319 original size:45 final size:44
Alignment explanation
Indices: 74244--74328 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
74234 TTATTTTTTA
*
74244 AAAAATAAGTGTATAAATTATGTATAAAAAACGTTTTAGTATAT
1 AAAAATAAGTGTATAAACTATGTATAAAAAACGTTTTAGTATAT
*
74288 AAAAATAAGTGT-TCAAACTATG-ACTCAAAAAATGTTTTAGT
1 AAAAATAAGTGTAT-AAACTATGTA-T-AAAAAACGTTTTAGT
74329 GCCTATAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
43 2 0.06
44 20 0.56
45 14 0.39
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (44 bp):
AAAAATAAGTGTATAAACTATGTATAAAAAACGTTTTAGTATAT
Found at i:74493 original size:18 final size:18
Alignment explanation
Indices: 74470--74506 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
74460 TATTTAAAAA
*
74470 ATTAAAAAAATATTTTTT
1 ATTAAAAAAATATTATTT
*
74488 ATTAAAAATATATTATTT
1 ATTAAAAAAATATTATTT
74506 A
1 A
74507 AAAAAGAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAAAAAAATATTATTT
Found at i:77441 original size:13 final size:14
Alignment explanation
Indices: 77425--77455 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
77415 GAAAAATAAG
77425 AAAAT-AAAAAAAT
1 AAAATAAAAAAAAT
77438 AAAATAAAAAAAAT
1 AAAATAAAAAAAAT
77452 AAAA
1 AAAA
77456 GGGGTTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAATAAAAAAAAT
Found at i:79404 original size:2 final size:2
Alignment explanation
Indices: 79397--79429 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
79387 CGTTTGTGTT
79397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
79430 GTTATTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.