Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005079.1 Hibiscus syriacus cultivar Beakdansim tig00011408_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: 63544
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:225 original size:19 final size:19
Alignment explanation
Indices: 181--219 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
171 GTTGTTAGTT
181 TAGAGGAAAGATAAAACAA
1 TAGAGGAAAGATAAAACAA
* *
200 TAGAGGAAAGTTATAACAA
1 TAGAGGAAAGATAAAACAA
219 T
1 T
220 GAAGGATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (19 bp):
TAGAGGAAAGATAAAACAA
Found at i:1542 original size:23 final size:22
Alignment explanation
Indices: 1507--1557 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
1497 TAATCAAAAC
**
1507 AAAGAGAAAAGAAGCAAAGAAA
1 AAAGAGAAAAGAAAAAAAGAAA
1529 AAAGAGCAAAAGAAAAAAAGAAA
1 AAAGAG-AAAAGAAAAAAAGAAA
1552 AAAGAG
1 AAAGAG
1558 GATACGTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.75, C:0.04, G:0.22, T:0.00
Consensus pattern (22 bp):
AAAGAGAAAAGAAAAAAAGAAA
Found at i:1545 original size:15 final size:15
Alignment explanation
Indices: 1506--1546 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1496 CTAATCAAAA
*
1506 CAAAGAGAAAAGAAG
1 CAAAGAAAAAAGAAG
1521 CAAAGAAAAAAG-AG
1 CAAAGAAAAAAGAAG
1535 CAAAAGAAAAAA
1 C-AAAGAAAAAA
1547 AGAAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (15 bp):
CAAAGAAAAAAGAAG
Found at i:2820 original size:36 final size:36
Alignment explanation
Indices: 2733--2822 Score: 92
Period size: 37 Copynumber: 2.5 Consensus size: 36
2723 CTTTGAGATT
* *
2733 GTTTCTCTCGAAACAAATGTTGTCTCGCTAGAGACA
1 GTTTCTCTTGAAACAAATGTTGTCTCGCTAGAAACA
* * * * *
2769 GTTT-TCTTTAAAAACAAGTTTTGTCTCTCTTGAAACA
1 GTTTCTC-TT-GAAACAAATGTTGTCTCGCTAGAAACA
2806 GTTTCTCTTGAAACAAA
1 GTTTCTCTTGAAACAAA
2823 AGTCCTTGAG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
35 2 0.05
36 11 0.26
37 27 0.64
38 2 0.05
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATGTTGTCTCGCTAGAAACA
Found at i:2988 original size:65 final size:65
Alignment explanation
Indices: 2780--3081 Score: 294
Period size: 66 Copynumber: 4.6 Consensus size: 65
2770 TTTTCTTTAA
* * * *
2780 AAACAAGTTTTGTCTCTCTTGAAACAGTTTCTCTTGAAACAAAAGTC-CTTGAGTC-TGTTGCTC
1 AAACAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAAATCTC-TGAGTCAT-TT-CCC
2843 TTG
63 TTG
* * * *
2846 AAACAAAATTTTGTCTCTCTTGAGATAGTTTTTCTTG---GAAAAATCTTTGAGT-ATGTTTCCC
1 AAAC-AAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAAATCTCTGAGTCA--TTTCCC
2907 TTG
63 TTG
* *
2910 AAACAAGTTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACAAAAATCTCTGAGTCATTTCCCTTG
1 AAACAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAAATCTCTGAGTCATTTCCCTTG
* * *** * *
2975 AAACGAA-TTTTGTCTCTCTTGTGATAGTTTCTATTGAAACACCCATCTTTGAGATCGTTTCCCT
1 AAAC-AAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAAATCTCTGAG-TCATTTCCCT
3039 TG
64 TG
* * * *
3041 AAACAATTTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 AAACAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA
3082 TCATCTTTAA
Statistics
Matches: 196, Mismatches: 28, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
63 28 0.14
64 20 0.10
65 55 0.28
66 64 0.33
67 29 0.15
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (65 bp):
AAACAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAAATCTCTGAGTCATTTCCCTTG
Found at i:3101 original size:131 final size:129
Alignment explanation
Indices: 2780--3112 Score: 404
Period size: 131 Copynumber: 2.6 Consensus size: 129
2770 TTTTCTTTAA
* * * *
2780 AAACAAGTTTTGTCTCTCTTGAAACAGTTTCTCTTGAAACAAAAGTCCTTGAGTCTGTTGCTCTT
1 AAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAA-TCTTTGAGTCTGTTTCCCTT
* *
2845 GAAACAAAATTTTGTCTCTCTTGAGATAGTTTTTCTTGGAAAAATCTTTGAGTATGTTTCCCTTG
65 GAAACAAAATTTTGTCTCTCTTGAGATAGTTTCTATTGGAAAAATCTTTGAGTATGTTTCCCTTG
* * * * *
2910 AAACAAGTTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACAAAAATCTCTGAGTC-ATTTCCCTT
1 AAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAAATCTTTGAGTCTGTTTCCCTT
* *
2974 GAAAC-GAATTTTGTCTCTCTTGTGATAGTTTCTATT-GAAACACCCATCTTTGAG-ATCGTTTC
65 GAAACAAAATTTTGTCTCTCTTGAGATAGTTTCTATTGGAAA-A---ATCTTTGAGTAT-GTTTC
3036 CCTTG
125 CCTTG
* * * ** *
3041 AAACAATTTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACATCATCTTTAAGTCTGTTTCCCTTG
1 AAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAGTCTGTTTCCCTTG
3106 AAACAAA
66 AAACAAA
3113 TCCCTAAAGA
Statistics
Matches: 170, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
127 4 0.02
128 28 0.16
129 11 0.06
130 56 0.33
131 70 0.41
132 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (129 bp):
AAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAGTCTGTTTCCCTTG
AAACAAAATTTTGTCTCTCTTGAGATAGTTTCTATTGGAAAAATCTTTGAGTATGTTTCCCTTG
Found at i:3104 original size:65 final size:65
Alignment explanation
Indices: 2780--3111 Score: 359
Period size: 65 Copynumber: 5.1 Consensus size: 65
2770 TTTTCTTTAA
* * * * *
2780 AAACAAGTTTTGTCTCTCTTGAAACAGTTTCTCTTGAAACAAAAGTCCTTGAGTCTGTTGCTCTT
1 AAACAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAA-TCTTTGAGTCTGTTTCCCTT
2845 G
65 G
* * * *
2846 AAACAAAATTTTGTCTCTCTTGAGATAGTTTTTCTTG-GA-AAAATCTTTGAGTATGTTTCCCTT
1 AAAC-AAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAGTCTGTTTCCCTT
2909 G
65 G
* * * *
2910 AAACAAGTTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACAAAAATCTCTGAGTC-ATTTCCCTT
1 AAACAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAAC-AAAATCTTTGAGTCTGTTTCCCTT
2974 G
65 G
* * **
2975 AAACGAA-TTTTGTCTCTCTTGTGATAGTTTCTATTGAAACACCCATCTTTGAGATC-GTTTCCC
1 AAAC-AAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTGAG-TCTGTTTCCC
3038 TTG
63 TTG
* * * * ** *
3041 AAACAATTTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACATCATCTTTAAGTCTGTTTCCCTTG
1 AAACAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAGTCTGTTTCCCTTG
3106 AAACAA
1 AAACAA
3112 ATCCCTAAAG
Statistics
Matches: 225, Mismatches: 32, Indels: 19
0.82 0.12 0.07
Matches are distributed among these distances:
63 28 0.12
64 25 0.11
65 81 0.36
66 63 0.28
67 28 0.12
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (65 bp):
AAACAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAGTCTGTTTCCCTTG
Found at i:6513 original size:23 final size:23
Alignment explanation
Indices: 6483--6600 Score: 111
Period size: 23 Copynumber: 5.2 Consensus size: 23
6473 GATTCCCATG
*
6483 GGGGGAATCAGTTCCTCTTCAAA
1 GGGGGAATCAGTTCCCCTTCAAA
*
6506 GGGGGAATCAGTTCCCCTTTAAA
1 GGGGGAATCAGTTCCCCTTCAAA
*
6529 GGGGGGATC-GATTCCCCTTC-AA
1 GGGGGAATCAG-TTCCCCTTCAAA
* *
6551 TGGGGTATC-GATTCCCCTTC-AA
1 GGGGGAATCAG-TTCCCCTTCAAA
* *
6573 GGGGGTATC-GATTCCCCTTCAAG
1 GGGGGAATCAG-TTCCCCTTCAAA
6596 GGGGG
1 GGGGG
6601 TATCGATTCC
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
22 42 0.49
23 43 0.51
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (23 bp):
GGGGGAATCAGTTCCCCTTCAAA
Found at i:6533 original size:24 final size:24
Alignment explanation
Indices: 6482--6600 Score: 96
Period size: 22 Copynumber: 5.2 Consensus size: 24
6472 CGATTCCCAT
*
6482 GGGGGGAATCAGTTCCTCTTCAAA
1 GGGGGGAATCAGTTCCCCTTCAAA
*
6506 -GGGGGAATCAGTTCCCCTTTAAA
1 GGGGGGAATCAGTTCCCCTTCAAA
6529 GGGGGG-ATC-GATTCCCCTTC-AA
1 GGGGGGAATCAG-TTCCCCTTCAAA
* *
6551 -TGGGGTATC-GATTCCCCTTC-AA
1 GGGGGGAATCAG-TTCCCCTTCAAA
*
6573 -GGGGGTATC-GATTCCCCTTC-AA
1 GGGGGGAATCAG-TTCCCCTTCAAA
6595 GGGGGG
1 GGGGGG
6601 TATCGATTCC
Statistics
Matches: 86, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.05
22 40 0.47
23 37 0.43
24 5 0.06
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (24 bp):
GGGGGGAATCAGTTCCCCTTCAAA
Found at i:6583 original size:44 final size:46
Alignment explanation
Indices: 6494--6611 Score: 152
Period size: 45 Copynumber: 2.6 Consensus size: 46
6484 GGGGAATCAG
* * *
6494 TTCCTCTTCAAAGGGGGAATC-AGTTCCCCTTTAAAGGGGGGATCGA
1 TTCCCCTTCAAGGGGGGTATCGA-TTCCCCTTTAAAGGGGGGATCGA
* * *
6540 TTCCCCTTCAA-TGGGGTATCGATTCCCC-TTCAAGGGGGTATCGA
1 TTCCCCTTCAAGGGGGGTATCGATTCCCCTTTAAAGGGGGGATCGA
6584 TTCCCCTTCAAGGGGGGTATCGATTCCC
1 TTCCCCTTCAAGGGGGGTATCGATTCCC
6612 TTTGTCTTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
44 25 0.39
45 28 0.44
46 11 0.17
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (46 bp):
TTCCCCTTCAAGGGGGGTATCGATTCCCCTTTAAAGGGGGGATCGA
Found at i:6603 original size:23 final size:22
Alignment explanation
Indices: 6494--6611 Score: 148
Period size: 22 Copynumber: 5.2 Consensus size: 22
6484 GGGGAATCAG
* *
6494 TTCCTCTTCAAAGGGGGAATC-A
1 TTCCCCTTC-AAGGGGGTATCGA
* *
6516 GTTCCCCTTTAAAGGGGGGATCGA
1 -TTCCCC-TTCAAGGGGGTATCGA
*
6540 TTCCCCTTCAATGGGGTATCGA
1 TTCCCCTTCAAGGGGGTATCGA
6562 TTCCCCTTCAAGGGGGTATCGA
1 TTCCCCTTCAAGGGGGTATCGA
6584 TTCCCCTTCAAGGGGGGTATCGA
1 TTCCCCTTCAA-GGGGGTATCGA
6607 TTCCC
1 TTCCC
6612 TTTGTCTTAT
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
22 45 0.53
23 37 0.44
24 3 0.04
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (22 bp):
TTCCCCTTCAAGGGGGTATCGA
Found at i:6613 original size:44 final size:44
Alignment explanation
Indices: 6463--6611 Score: 148
Period size: 45 Copynumber: 3.4 Consensus size: 44
6453 CAGAACCCTC
* *
6463 AGGGGGTATCGATT--CC--CATGGGGGGAATC-AGTTCCTCTTCAA
1 AGGGGGTATCGATTCCCCTTCAAGGGGGG-ATCGA-TTCCCCTTC-A
* *
6505 AGGGGGAATC-AGTTCCCCTTTAAAGGGGGGATCGATTCCCCTTCA
1 AGGGGGTATCGA-TTCCCC-TTCAAGGGGGGATCGATTCCCCTTCA
* *
6550 ATGGGGTATCGATTCCCCTTCAAGGGGGTATCGATTCCCCTTCA
1 AGGGGGTATCGATTCCCCTTCAAGGGGGGATCGATTCCCCTTCA
6594 AGGGGGGTATCGATTCCC
1 A-GGGGGTATCGATTCCC
6612 TTTGTCTTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
41 1 0.01
42 11 0.12
44 27 0.30
45 30 0.34
46 12 0.13
47 8 0.09
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (44 bp):
AGGGGGTATCGATTCCCCTTCAAGGGGGGATCGATTCCCCTTCA
Found at i:12882 original size:131 final size:132
Alignment explanation
Indices: 12661--12992 Score: 450
Period size: 131 Copynumber: 2.5 Consensus size: 132
12651 ATCGTCTTTT
* * * * *
12661 TCACGTATGAACCATGCCATCCCCCGACCAGACCTCCTCACCACGTAGGAGTCGTGTCACCCCTA
1 TCACGTAGGAACCATGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGACGTGTCACCCCTA
*
12726 GATAAACAGTCGTCCTCATCACGTAGGAACAATGTTATCA-TCCCTAAAGATGGCATGTCATCCT
66 GATAAACAGTCATCCTCATCACGTAGGAACAATGTTATCACTCCCTAAAGATGGCATGTCATCCT
12790 CA
131 CA
** * * * *
12792 TCACGTAGGAACTGTGTCATCCCCTGACCAGACCTTCTCATCACTTAGGAGCCGTTTCACCCCTA
1 TCACGTAGGAACCATGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGACGTGTCACCCCTA
* * * **
12857 GATAATCAGTCATCCTTATCGCGTAGGAACCGTGTTATCACCCTCCCTAAAGATGGCATGTCATC
66 GATAAACAGTCATCCTCATCACGTAGGAACAATGTTATCA--CTCCCTAAAGATGGCATGTCATC
12922 CTCA
129 CTCA
* * * *
12926 TCGCGTAGGAACCATGTCATCCCCTGACCAGATCTCCTCATCGCGTAGGAGACGTGTCACCCTTA
1 TCACGTAGGAACCATGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGACGTGTCACCCCTA
12991 GA
66 GA
12993 CGACCAAAAC
Statistics
Matches: 172, Mismatches: 26, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
131 89 0.52
134 83 0.48
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (132 bp):
TCACGTAGGAACCATGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGACGTGTCACCCCTA
GATAAACAGTCATCCTCATCACGTAGGAACAATGTTATCACTCCCTAAAGATGGCATGTCATCCT
CA
Found at i:13668 original size:2 final size:2
Alignment explanation
Indices: 13663--13699 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
13653 AATATCAAAC
* *
13663 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13700 TTATGCATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15082 original size:43 final size:43
Alignment explanation
Indices: 15022--15107 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
15012 ATCCTACCTC
15022 CCCCTTACCCAATTACATATGGGAATAAGGTCAACCAATTTTT
1 CCCCTTACCCAATTACATATGGGAATAAGGTCAACCAATTTTT
* * * *
15065 CCCCTTACCCCATTACATATGGGAATATGGTCAGCTAATTTTT
1 CCCCTTACCCAATTACATATGGGAATAAGGTCAACCAATTTTT
15108 TTTTATATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (43 bp):
CCCCTTACCCAATTACATATGGGAATAAGGTCAACCAATTTTT
Found at i:16915 original size:12 final size:12
Alignment explanation
Indices: 16898--16922 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16888 GAAGTATATC
16898 ATAATTGATTAA
1 ATAATTGATTAA
16910 ATAATTGATTAA
1 ATAATTGATTAA
16922 A
1 A
16923 CTTTCGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
ATAATTGATTAA
Found at i:30805 original size:21 final size:23
Alignment explanation
Indices: 30781--30829 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
30771 ATATATAAAA
30781 GTTA-ATA-ATTTGTTTCGAGTT
1 GTTAGATATATTTGTTTCGAGTT
*
30802 GTTATGTTATATTTGTTTCGAGTT
1 GTTA-GATATATTTGTTTCGAGTT
30826 -TTAG
1 GTTAG
30830 TGTTACTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.17
22 1 0.04
23 5 0.21
24 14 0.58
ACGTcount: A:0.20, C:0.04, G:0.20, T:0.55
Consensus pattern (23 bp):
GTTAGATATATTTGTTTCGAGTT
Found at i:30819 original size:24 final size:24
Alignment explanation
Indices: 30788--30834 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
30778 AAAGTTAATA
30788 ATTTGTTTCGAGTTGTTA-TGTTAT
1 ATTTGTTTCGAGTT-TTAGTGTTAT
30812 ATTTGTTTCGAGTTTTAGTGTTA
1 ATTTGTTTCGAGTTTTAGTGTTA
30835 CTAATCTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.17, C:0.04, G:0.21, T:0.57
Consensus pattern (24 bp):
ATTTGTTTCGAGTTTTAGTGTTAT
Found at i:31361 original size:43 final size:43
Alignment explanation
Indices: 31247--31364 Score: 191
Period size: 43 Copynumber: 2.7 Consensus size: 43
31237 TCTATTTTGT
* *
31247 TAAAGCAAATAAATTGTTAAATTTATTTCCTTGGAAATCTTGAA
1 TAAAG-AAATAAATTGTTGAATTTATTTTCTTGGAAATCTTGAA
* *
31291 TAAATAAATAAATTGTTGAATTTATTTTCTTGGGAATCTTGAA
1 TAAAGAAATAAATTGTTGAATTTATTTTCTTGGAAATCTTGAA
31334 TAAAGAAATAAATTGTTGAATTTATTTTCTT
1 TAAAGAAATAAATTGTTGAATTTATTTTCTT
31365 ATATGATTCT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
43 65 0.94
44 4 0.06
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (43 bp):
TAAAGAAATAAATTGTTGAATTTATTTTCTTGGAAATCTTGAA
Found at i:31436 original size:39 final size:39
Alignment explanation
Indices: 31387--31489 Score: 143
Period size: 39 Copynumber: 2.6 Consensus size: 39
31377 TTTAAAATGA
* *
31387 AAATAGATCGTTGAATTTATTTTCATGTTTTGTAAAAAT
1 AAATAAATCGTTGAATTTATTTTCATGTTTTGTAAAAAG
* *
31426 AAATAAATCGTTAAATTTATTTTCATGTTTTGTAAAAGG
1 AAATAAATCGTTGAATTTATTTTCATGTTTTGTAAAAAG
**
31465 AAATAAATTATTGAATTTTATTTTC
1 AAATAAATCGTTGAA-TTTATTTTC
31490 CTTAGAATCT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
39 47 0.84
40 9 0.16
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.47
Consensus pattern (39 bp):
AAATAAATCGTTGAATTTATTTTCATGTTTTGTAAAAAG
Found at i:31567 original size:39 final size:38
Alignment explanation
Indices: 31513--31586 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
31503 ATGATTATAA
* *
31513 TTTGTAAAAGGAAATAAAT-CGTAGAATTTAGTTTTCTAT
1 TTTGAAAAAGAAAATAAATACGTA-AATTTA-TTTTCTAT
*
31552 TTTGAAAAAGAAAATAAATATGTAAATTTATTTTC
1 TTTGAAAAAGAAAATAAATACGTAAATTTATTTTC
31587 CTAAGAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 5 0.16
39 23 0.74
40 3 0.10
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (38 bp):
TTTGAAAAAGAAAATAAATACGTAAATTTATTTTCTAT
Found at i:31676 original size:97 final size:95
Alignment explanation
Indices: 31417--31683 Score: 291
Period size: 97 Copynumber: 2.7 Consensus size: 95
31407 TTTCATGTTT
** * * * * *
31417 TGTAAAAATAAATAAATCGTTAAATTTATTTTCATGTTTTGTAAAAGGAAATAAATTATTGAATT
1 TGTAAAAGGAAATAAATCGTTGAATTTATTTTC-TATTTTGAAAAAGGAAATAAA-TA-TAAAAT
* *
31482 TTATTTTCCTTAGAATCTCACATGATTATAATT
63 TTATTTTCCTAAGAATCTCACATGATTATAATA
* * *
31515 TGTAAAAGGAAATAAATCGTAGAATTTAGTTTTCTATTTTGAAAAAGAAAATAAATATGTAAATT
1 TGTAAAAGGAAATAAATCGTTGAATTTA-TTTTCTATTTTGAAAAAGGAAATAAATAT-AAAATT
*** * *
31580 TATTTTCCTAAGAATCTTGTATGATTCTGATA
64 TATTTTCCTAAGAATCTCACATGATTATAATA
* *
31612 TGTAAAAGGAATTAAATCATTGAATTTATTTTTCTATTTTGAAAAAGGAAATAAATCATAAAATT
1 TGTAAAAGGAAATAAATCGTTGAATTTA-TTTTCTATTTTGAAAAAGGAAATAAAT-ATAAAATT
*
31677 TAGTTTC
64 TATTTTC
31684 ATGGTTTGTA
Statistics
Matches: 143, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
96 1 0.01
97 93 0.65
98 44 0.31
99 5 0.03
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.41
Consensus pattern (95 bp):
TGTAAAAGGAAATAAATCGTTGAATTTATTTTCTATTTTGAAAAAGGAAATAAATATAAAATTTA
TTTTCCTAAGAATCTCACATGATTATAATA
Found at i:31753 original size:40 final size:40
Alignment explanation
Indices: 31615--31787 Score: 176
Period size: 39 Copynumber: 4.4 Consensus size: 40
31605 TCTGATATGT
* *
31615 AAAAGGAATTAAATCATTGAATTTATTTTTCTATTTTG-A
1 AAAAGGAAATAAATCGTTGAATTTATTTTTCTATTTTGTA
* ** *
31654 AAAAGGAAATAAATCATAAAATTTA-GTTTC-ATGGTTTGTA
1 AAAAGGAAATAAATCGTTGAATTTATTTTTCTAT--TTTGTA
* *
31694 AAAA-TAAATAAATCGTTGGATTTATTTTTCTATTTTGTA
1 AAAAGGAAATAAATCGTTGAATTTATTTTTCTATTTTGTA
* * * *
31733 AAAAGGAAATAAATCGTTGGATATAGTTTCCTATTTTGT-
1 AAAAGGAAATAAATCGTTGAATTTATTTTTCTATTTTGTA
*
31772 AAAATGAAATAAATCG
1 AAAAGGAAATAAATCG
31788 AAACAAATCG
Statistics
Matches: 113, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 66 0.58
40 39 0.35
41 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (40 bp):
AAAAGGAAATAAATCGTTGAATTTATTTTTCTATTTTGTA
Found at i:31774 original size:79 final size:78
Alignment explanation
Indices: 31612--31787 Score: 219
Period size: 79 Copynumber: 2.2 Consensus size: 78
31602 GATTCTGATA
* * * *
31612 TGTAAAAGGAATTAAATCATTGAATTTATTTTTCTATTTTGAAAAAGGAAATAAATCATAAAATT
1 TGTAAAATGAAATAAATCGTTGAATTTATTTTTCTATTTTGAAAAAGGAAATAAATCATAAAATA
*
31677 TAGTTTCATGGTT
66 TAGTTTCATAGTT
* * ***
31690 TGTAAAAAT-AAATAAATCGTTGGATTTATTTTTCTATTTTGTAAAAAGGAAATAAATCGTTGGA
1 TGT-AAAATGAAATAAATCGTTGAATTTATTTTTCTATTTTG-AAAAAGGAAATAAATCATAAAA
* *
31754 TATAGTTTCCTATTT
64 TATAGTTTCATAGTT
31769 TGTAAAATGAAATAAATCG
1 TGTAAAATGAAATAAATCG
31788 AAACAAATCG
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
78 37 0.45
79 46 0.55
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (78 bp):
TGTAAAATGAAATAAATCGTTGAATTTATTTTTCTATTTTGAAAAAGGAAATAAATCATAAAATA
TAGTTTCATAGTT
Found at i:31799 original size:49 final size:49
Alignment explanation
Indices: 31738--31835 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
31728 TTGTAAAAAG
*
31738 GAAATAAATCGTTGGATATAGTTTCCTATTTTGTAAAA-TGAAATAAATC
1 GAAACAAATCGTTGGATATAGTTTCCTATTTTGTAAAAGT-AAATAAATC
* * * *
31787 GAAACAAATCGTTTGATTTATTTTTCTATTTTGTAAAAGTAAATAAATC
1 GAAACAAATCGTTGGATATAGTTTCCTATTTTGTAAAAGTAAATAAATC
31836 TTTGAATTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 42 0.98
50 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (49 bp):
GAAACAAATCGTTGGATATAGTTTCCTATTTTGTAAAAGTAAATAAATC
Found at i:38382 original size:18 final size:17
Alignment explanation
Indices: 38336--38387 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
38326 GCGTGTCAAT
38336 TAATT-TTGTTTTATTA
1 TAATTATTGTTTTATTA
* *
38352 -AATAATATATTTTGATTA
1 TAATTAT-TGTTTT-ATTA
38370 TAATTATTGTTTTATTA
1 TAATTATTGTTTTATTA
38387 T
1 T
38388 CTCGGATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
15 3 0.11
16 1 0.04
17 10 0.36
18 9 0.32
19 5 0.18
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TAATTATTGTTTTATTA
Found at i:39720 original size:83 final size:83
Alignment explanation
Indices: 39470--39986 Score: 401
Period size: 83 Copynumber: 6.3 Consensus size: 83
39460 AGGGGATGTA
* * * * * **
39470 TTTTCCCATTATTATTCAGAGAATATCTG-GAT-TATAATAGTGATCCATCCCATCCAAAATGAA
1 TTTT-CCATTATTATTCAGAGAATCTCTGCCATGT-CAA-AGTGTTACATCCCATCTGAAATGAA
* * *
39533 AAGCACGTTCCAGGGAAAGCG
63 AGGCACGTTTCGGGGAAAGCG
* * * * * *
39554 TTTTTCC---ATTATT-AGCGAATCTCTTG-AATAT-AATAGTGATCCAT-CCATCCGAAATGAA
1 -TTTTCCATTATTATTCAGAGAATCTC-TGCCATGTCAA-AGTGTTACATCCCATCTGAAATGAA
* * * *
39612 AGACGCATTTC-GGGAGAAGCA
63 AGGCACGTTTCGGGGA-AAGCG
* * *
39633 TTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAGAGTGTTACATCCTATCTGAAATGAAAGG
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCAAAGTGTTACATCCCATCTGAAATGAAAGG
* **
39698 TACGTTTCGGGGAAAGTA
66 CACGTTTCGGGGAAAGCG
* * ** *
39716 TTTTCCATTATTATTTAGAGAATCTCTGCCATGTCAAAGTGTTCCATCATATCTAAAATGAAAGG
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCAAAGTGTTACATCCCATCTGAAATGAAAGG
*
39781 CACGGTTT-AGGGAAAGCG
66 CAC-GTTTCGGGGAAAGCG
* * * *
39799 TTTTCCATTATTATTCAGAGAATCTTTGCCATATCAGAGTGTTACATCCCATCTGAAATGAAATG
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCAAAGTGTTACATCCCATCTGAAATGAAAGG
** *
39864 CACAATCCGGGGAAAGCG
66 CACGTTTCGGGGAAAGCG
* * * * * * ** * * * *
39882 TTTT-TATTATTATTTATATAATATATATCATGTCAAACTATTCCATCCCATCCGAAATGAAAGG
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCAAAGTGTTACATCCCATCTGAAATGAAAGG
* *
39946 CACGTTTCGAGGAAAGTG
66 CACGTTTCGGGGAAAGCG
39964 TTTTCCATTATTATTCAGAGAAT
1 TTTTCCATTATTATTCAGAGAAT
39987 TTTTGTCACT
Statistics
Matches: 348, Mismatches: 70, Indels: 30
0.78 0.16 0.07
Matches are distributed among these distances:
78 10 0.03
79 23 0.07
80 21 0.06
81 18 0.05
82 84 0.24
83 178 0.51
84 10 0.03
85 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (83 bp):
TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCAAAGTGTTACATCCCATCTGAAATGAAAGG
CACGTTTCGGGGAAAGCG
Found at i:39984 original size:165 final size:165
Alignment explanation
Indices: 39593--39991 Score: 478
Period size: 166 Copynumber: 2.4 Consensus size: 165
39583 ATAATAGTGA
* * * *
39593 TCCAT-CCATCCGAAATGAAAGACGCATTTCGGGAGAAGCATTTTCCATTATTATTCAGAGAATC
1 TCCATCCCATCCGAAATGAAAGGCACGTTTCGGGA-AAGCGTTTTCCATTATTATTCAGAGAATC
* * * * * ** * *
39657 TCTGTCATGTCAGAGTGTTACATCCTATCTGAAATGAAAGGTACGTTTCGGGGAAAGTATTTTCC
65 TTTGCCATATCAGAGTGTTACATCCCATCTGAAATGAAAGGCACAATCCGGGGAAAGCATTTTCC
* * * * *
39722 ATTATTATTTAGAGAATCTCTGCCATGTCAAAGTGT
130 ATTATTATTTAGAGAATATATACCATGTCAAACTAT
** ** *
39758 TCCATCATATCTAAAATGAAAGGCACGGTTTAGGGAAAGCGTTTTCCATTATTATTCAGAGAATC
1 TCCATCCCATCCGAAATGAAAGGCAC-GTTTCGGGAAAGCGTTTTCCATTATTATTCAGAGAATC
* * *
39823 TTTGCCATATCAGAGTGTTACATCCCATCTGAAATGAAATGCACAATCCGGGGAAAGCGTTTT-T
65 TTTGCCATATCAGAGTGTTACATCCCATCTGAAATGAAAGGCACAATCCGGGGAAAGCATTTTCC
* * *
39887 ATTATTATTTATATAATATATATCATGTCAAACTAT
130 ATTATTATTTAGAGAATATATACCATGTCAAACTAT
* *
39923 TCCATCCCATCCGAAATGAAAGGCACGTTTCGAGGAAAGTGTTTTCCATTATTATTCAGAGAATT
1 TCCATCCCATCCGAAATGAAAGGCACGTTTCG-GGAAAGCGTTTTCCATTATTATTCAGAGAATC
39988 TTTG
65 TTTG
39992 TCACTTCACA
Statistics
Matches: 195, Mismatches: 36, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
164 5 0.03
165 89 0.46
166 94 0.48
167 7 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (165 bp):
TCCATCCCATCCGAAATGAAAGGCACGTTTCGGGAAAGCGTTTTCCATTATTATTCAGAGAATCT
TTGCCATATCAGAGTGTTACATCCCATCTGAAATGAAAGGCACAATCCGGGGAAAGCATTTTCCA
TTATTATTTAGAGAATATATACCATGTCAAACTAT
Found at i:47586 original size:2 final size:2
Alignment explanation
Indices: 47581--47605 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47571 AAAAAAATTA
47581 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
47606 ACCCCTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51537 original size:2 final size:2
Alignment explanation
Indices: 51532--51601 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
51522 AAAATAAAAT
51532 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
51574 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
51602 ACAAAATTTG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58417 original size:21 final size:20
Alignment explanation
Indices: 58393--58431 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58383 AAAAATCTTA
58393 TCAAATCGACTTAAATAAAGT
1 TCAAATCGA-TTAAATAAAGT
* *
58414 TCAACTCGATTCAATAAA
1 TCAAATCGATTAAATAAA
58432 TTTATAGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (20 bp):
TCAAATCGATTAAATAAAGT
Found at i:61072 original size:156 final size:156
Alignment explanation
Indices: 60788--61108 Score: 615
Period size: 156 Copynumber: 2.1 Consensus size: 156
60778 ATCAAGTGAA
60788 GGTCAAAATACAACCAAGCAAGAATCGGCAATGGATTATGGAAAGACGGATAAACCAAGTCCAGT
1 GGTCAAAATACAACCAAGCAAGAATCGGCAATGGATTATGGAAAGACGGATAAACCAAGTCCAGT
*
60853 TTACGAGGAAGCTGCCGGAGCGGGAACCACCGTCATGTCGAAGGTACACGGTCCTGGCTCTGGAA
66 TTACGAGGAAGCTGCCGGAGCGGGAACAACCGTCATGTCGAAGGTACACGGTCCTGGCTCTGGAA
60918 CTGCAACCGAAGTGGAAACAGAGCAG
131 CTGCAACCGAAGTGGAAACAGAGCAG
*
60944 GGTCAAAATACAACCAAGCAAGAATCGGCAATGGATTATGGAAAGGCGGATAAACCAAGTCCAGT
1 GGTCAAAATACAACCAAGCAAGAATCGGCAATGGATTATGGAAAGACGGATAAACCAAGTCCAGT
61009 TTACGAGGAAGCTGCCGGAGCGGGAACAACCGTCATGTCGAAGGTACACGGTCCTGGCTCTGGAA
66 TTACGAGGAAGCTGCCGGAGCGGGAACAACCGTCATGTCGAAGGTACACGGTCCTGGCTCTGGAA
61074 CTGCAACCGAAGTGGAAACAGAGCAG
131 CTGCAACCGAAGTGGAAACAGAGCAG
*
61100 GTTCAAAAT
1 GGTCAAAAT
61109 CAGGATAAAG
Statistics
Matches: 162, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
156 162 1.00
ACGTcount: A:0.34, C:0.22, G:0.29, T:0.15
Consensus pattern (156 bp):
GGTCAAAATACAACCAAGCAAGAATCGGCAATGGATTATGGAAAGACGGATAAACCAAGTCCAGT
TTACGAGGAAGCTGCCGGAGCGGGAACAACCGTCATGTCGAAGGTACACGGTCCTGGCTCTGGAA
CTGCAACCGAAGTGGAAACAGAGCAG
Found at i:62284 original size:14 final size:14
Alignment explanation
Indices: 62265--62296 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
62255 AAATTGAATT
62265 TTATATAAATTTTA
1 TTATATAAATTTTA
*
62279 TTATATAACTTTTA
1 TTATATAAATTTTA
62293 TTAT
1 TTAT
62297 TTATATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATATAAATTTTA
Found at i:62414 original size:10 final size:10
Alignment explanation
Indices: 62384--62415 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
62374 TACTTCATGC
62384 TATTAAAATT
1 TATTAAAATT
*
62394 CATTAAAATT
1 TATTAAAATT
62404 TATTAAAATT
1 TATTAAAATT
62414 TA
1 TA
62416 ATAGTTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (10 bp):
TATTAAAATT
Found at i:62912 original size:22 final size:23
Alignment explanation
Indices: 62876--62928 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
62866 AACTTATTAA
62876 AAAAATTAAAAATGTCATAAA-AT
1 AAAAA-TAAAAATGTCATAAAGAT
* * *
62899 ATAAATAAATATGTTATAAAGAT
1 AAAAATAAAAATGTCATAAAGAT
62922 AAAAATA
1 AAAAATA
62929 TTTGGATATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (23 bp):
AAAAATAAAAATGTCATAAAGAT
Done.