Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007345.1 Hibiscus syriacus cultivar Beakdansim tig00019682_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: 141317
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2716 original size:21 final size:21
Alignment explanation
Indices: 2692--2752 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
2682 AATCCCACTG
*
2692 ATTTACATGTTGAGCCCGTAA
1 ATTTACATGTCGAGCCCGTAA
* * *
2713 ATTTGCATGTCGAGCCTGTTA
1 ATTTACATGTCGAGCCCGTAA
**
2734 GGTTACATGTCGAGCCCGT
1 ATTTACATGTCGAGCCCGT
2753 CGAGGCATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (21 bp):
ATTTACATGTCGAGCCCGTAA
Found at i:5619 original size:30 final size:30
Alignment explanation
Indices: 5558--5620 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
5548 ATGGGATGAG
5558 ATCCCACATTCCCATTTTAGTTGACCGGGA
1 ATCCCACATTCCCATTTTAGTTGACCGGGA
* * *
5588 ATCCTACATTTCCATGTTTAGTTGATC-GGA
1 ATCCCACATTCCCAT-TTTAGTTGACCGGGA
5618 ATC
1 ATC
5621 TCATTCCTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (30 bp):
ATCCCACATTCCCATTTTAGTTGACCGGGA
Found at i:9839 original size:2 final size:2
Alignment explanation
Indices: 9832--9863 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9822 TTTGTTTTCA
9832 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
9864 GAGCCCTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12112 original size:11 final size:11
Alignment explanation
Indices: 12072--12119 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
12062 ATCTTTTTTA
12072 AAAAAATAA-T
1 AAAAAATAATT
12082 AAAAGAATAATT
1 AAAA-AATAATT
***
12094 ACGTAATAATT
1 AAAAAATAATT
12105 AAAAAATAATT
1 AAAAAATAATT
12116 AAAA
1 AAAA
12120 TATATCACGT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
10 4 0.13
11 24 0.80
12 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (11 bp):
AAAAAATAATT
Found at i:12635 original size:15 final size:15
Alignment explanation
Indices: 12615--12659 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
12605 TAAGATAATA
12615 TTTATTTAATAATTT
1 TTTATTTAATAATTT
*
12630 TTTATTT-TTAATATT
1 TTTATTTAATAAT-TT
*
12645 TTTATTTAATTATTT
1 TTTATTTAATAATTT
12660 GAGTATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 18 0.72
16 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTTAATAATTT
Found at i:12646 original size:14 final size:15
Alignment explanation
Indices: 12609--12654 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
12599 TGATTATAAG
12609 ATAATA-TTTATTTA
1 ATAATATTTTATTTA
*
12623 ATAATTTTTTATTT-
1 ATAATATTTTATTTA
*
12637 TTAATATTTTTATTTA
1 ATAATA-TTTTATTTA
12653 AT
1 AT
12655 TATTTGAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 9 0.36
15 15 0.60
16 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATAATATTTTATTTA
Found at i:13270 original size:60 final size:60
Alignment explanation
Indices: 13167--13281 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
13157 GAGGTGGCGG
* *
13167 AAGGCGCATCCCGGGGACGCGCTTTCCATGAATTTATGTTGACTCAGGTGACACGTGTGA
1 AAGGCGCATCCCGGGGACGCGCCTTCCATGAATTTATGCTGACTCAGGTGACACGTGTGA
**
13227 AAGGCGCATACCCGGGGACGCGCCTT-CATGGGGTTT-TGCTGACTCAGGTGACACG
1 AAGGCGCAT-CCCGGGGACGCGCCTTCCAT-GAATTTATGCTGACTCAGGTGACACG
13282 GTGGTATGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 30 0.61
61 19 0.39
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (60 bp):
AAGGCGCATCCCGGGGACGCGCCTTCCATGAATTTATGCTGACTCAGGTGACACGTGTGA
Found at i:13848 original size:16 final size:16
Alignment explanation
Indices: 13822--13876 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
13812 AATAATTAAT
13822 TAATAAATTTAAATAAA
1 TAAT-AATTTAAATAAA
*
13839 TAATAATTTATATAAA
1 TAATAATTTAAATAAA
* *
13855 -AATTATTTTAATAAA
1 TAATAATTTAAATAAA
*
13870 AAATAAT
1 TAATAAT
13877 ATTTATATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 12 0.38
16 16 0.50
17 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATAATTTAAATAAA
Found at i:13875 original size:31 final size:31
Alignment explanation
Indices: 13808--13904 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 31
13798 ATTAGCACAA
* *
13808 AAAAAATAATTAAT-TAATAA--ATTTAAAT
1 AAAAAATAATTTATATAATAATTATTTTAAT
* *
13836 AAATAATAATTTATATAAAAATTATTTTAAT
1 AAAAAATAATTTATATAATAATTATTTTAAT
*
13867 AAAAAATAATATT-TAT-ATAATTATATTAAT
1 AAAAAATAAT-TTATATAATAATTATTTTAAT
*
13897 ATAAAATA
1 AAAAAATA
13905 TAATAACTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
28 12 0.21
29 5 0.09
30 19 0.33
31 19 0.33
32 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAAAATAATTTATATAATAATTATTTTAAT
Found at i:27421 original size:3 final size:3
Alignment explanation
Indices: 27413--27459 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
27403 AAATAAAAAG
27413 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27460 ATCCTTTCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29758 original size:52 final size:53
Alignment explanation
Indices: 29657--29772 Score: 119
Period size: 52 Copynumber: 2.2 Consensus size: 53
29647 AACAAAAAAC
* *
29657 AAAATATTAAAAAATAAAATTATATAAATATTATGCTAAAAATCAAT-ACATAT
1 AAAAT-TTAGAAAAGAAAATTATATAAATATTATGCTAAAAATCAATAACATAT
* * * **
29710 AAAATTTAGAAAAGAAAATTATTTACAA-ATTATGGTAAAATTTGATACACATAT
1 AAAATTTAGAAAAGAAAATTATATA-AATATTATGCTAAAAATCAATA-ACATAT
*
29764 AAAGTTTAG
1 AAAATTTAG
29773 TTTACAAAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
52 31 0.60
53 7 0.13
54 14 0.27
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (53 bp):
AAAATTTAGAAAAGAAAATTATATAAATATTATGCTAAAAATCAATAACATAT
Found at i:33740 original size:22 final size:23
Alignment explanation
Indices: 33696--33742 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
33686 TTTTGGACCG
* *
33696 TTTTAATATTTAAATTTTCAATT
1 TTTTAATATTTAAACTTTAAATT
33719 TTTTAATATTT-AACTTTAAATT
1 TTTTAATATTTAAACTTTAAATT
33741 TT
1 TT
33743 AAATGAGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTAATATTTAAACTTTAAATT
Found at i:44027 original size:22 final size:23
Alignment explanation
Indices: 43983--44029 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
43973 TTTTGGACCG
* *
43983 TTTTAATATTTAAATTTTCAATT
1 TTTTAATATTTAAACTTTAAATT
44006 TTTTAATATTT-AACTTTAAATT
1 TTTTAATATTTAAACTTTAAATT
44028 TT
1 TT
44030 AAATGAGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTAATATTTAAACTTTAAATT
Found at i:48588 original size:3 final size:3
Alignment explanation
Indices: 48582--48646 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
48572 AAATAAAAAG
48582 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
48630 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
48647 ATCCTTTCAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54917 original size:23 final size:24
Alignment explanation
Indices: 54879--54926 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
54869 TTTTGGTCCG
*
54879 TTTTAATATCTAAACTTTCAATTT
1 TTTTAATATCTAAACTTTAAATTT
*
54903 TTTTAATAT-TTAACTTTAAATTT
1 TTTTAATATCTAAACTTTAAATTT
54926 T
1 T
54927 AAATGAGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTAATATCTAAACTTTAAATTT
Found at i:55387 original size:103 final size:103
Alignment explanation
Indices: 55267--55473 Score: 414
Period size: 103 Copynumber: 2.0 Consensus size: 103
55257 AAGATAACTT
55267 AATTTAAGGTCGAGGAACGATATGTAATAAATTTAACTGAAAATATTAAAGAAAGTATAATATTT
1 AATTTAAGGTCGAGGAACGATATGTAATAAATTTAACTGAAAATATTAAAGAAAGTATAATATTT
55332 TTGATTGACGTAACCTAAAATATATATATATTTTTCTA
66 TTGATTGACGTAACCTAAAATATATATATATTTTTCTA
55370 AATTTAAGGTCGAGGAACGATATGTAATAAATTTAACTGAAAATATTAAAGAAAGTATAATATTT
1 AATTTAAGGTCGAGGAACGATATGTAATAAATTTAACTGAAAATATTAAAGAAAGTATAATATTT
55435 TTGATTGACGTAACCTAAAATATATATATATTTTTCTA
66 TTGATTGACGTAACCTAAAATATATATATATTTTTCTA
55473 A
1 A
55474 TATCTACGGT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.37
Consensus pattern (103 bp):
AATTTAAGGTCGAGGAACGATATGTAATAAATTTAACTGAAAATATTAAAGAAAGTATAATATTT
TTGATTGACGTAACCTAAAATATATATATATTTTTCTA
Found at i:58510 original size:30 final size:31
Alignment explanation
Indices: 58476--58534 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
58466 AAAACGAATT
* *
58476 TGAACTTTTAAAATTTTAAGGGG-ACGAACA
1 TGAACTTGTAAAATTCTAAGGGGTACGAACA
*
58506 TGAACTTGTAAAATTCTAGGGGGTACGAA
1 TGAACTTGTAAAATTCTAAGGGGTACGAA
58535 AACATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (31 bp):
TGAACTTGTAAAATTCTAAGGGGTACGAACA
Found at i:59647 original size:23 final size:23
Alignment explanation
Indices: 59616--59679 Score: 101
Period size: 23 Copynumber: 2.7 Consensus size: 23
59606 CATCTAGTCA
59616 GCGACTGATGTGGTAGCTAATGTG
1 GCGA-TGATGTGGTAGCTAATGTG
*
59640 GCGATGATGTGTTAGCTAATGTG
1 GCGATGATGTGGTAGCTAATGTG
*
59663 GCGATGACGTGGTAGCT
1 GCGATGATGTGGTAGCT
59680 GACGTGGCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 33 0.89
24 4 0.11
ACGTcount: A:0.20, C:0.12, G:0.38, T:0.30
Consensus pattern (23 bp):
GCGATGATGTGGTAGCTAATGTG
Found at i:59686 original size:23 final size:23
Alignment explanation
Indices: 59616--59699 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
59606 CATCTAGTCA
*
59616 GCGACTGATGTGGTAGCTAATGTG
1 GCGA-TGACGTGGTAGCTAATGTG
* *
59640 GCGATGATGTGTTAGCTAATGTG
1 GCGATGACGTGGTAGCTAATGTG
* *
59663 GCGATGACGTGGTAGCTGACGTG
1 GCGATGACGTGGTAGCTAATGTG
*
59686 GCAGGTGACGTGGT
1 GC-GATGACGTGGT
59700 GCTCAGTCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 39 0.74
24 14 0.26
ACGTcount: A:0.19, C:0.13, G:0.40, T:0.27
Consensus pattern (23 bp):
GCGATGACGTGGTAGCTAATGTG
Found at i:61390 original size:10 final size:12
Alignment explanation
Indices: 61365--61411 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 12
61355 AAATTTAAAA
61365 TTATTATATATT
1 TTATTATATATT
61377 TTATTA-AT-TT
1 TTATTATATATT
61387 TTATT-T-TATT
1 TTATTATATATT
*
61397 TTATTA-AAATT
1 TTATTATATATT
61408 TTAT
1 TTAT
61412 AAGTTCGTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
9 1 0.03
10 14 0.47
11 9 0.30
12 6 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTATATATT
Found at i:61975 original size:5 final size:5
Alignment explanation
Indices: 61965--61990 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
61955 AGTCATATAT
61965 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
61991 GAAACCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:63338 original size:60 final size:60
Alignment explanation
Indices: 63225--63338 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
63215 CTATGCATTA
* * ** *
63225 TTGCTTTATTAAATCTCTCGATTATGAAAAGTTAAAAAATGATCTTCCTACTATAGAGTG
1 TTGCTTTATTAAATCCCTCGACTATGAAAAGTTAAAAAATGATCACCCGACTATAGAGTG
** * * *
63285 TTGCTTTATTGGATCCCTCGACTATTAAAAGTTACAAAATGGTCACCCGACTAT
1 TTGCTTTATTAAATCCCTCGACTATGAAAAGTTAAAAAATGATCACCCGACTAT
63339 TCATTATAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (60 bp):
TTGCTTTATTAAATCCCTCGACTATGAAAAGTTAAAAAATGATCACCCGACTATAGAGTG
Found at i:77470 original size:26 final size:26
Alignment explanation
Indices: 77434--77486 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
77424 TAGAGCCCAT
77434 TGATTAAGCACTACTTAGGTTATTAA
1 TGATTAAGCACTACTTAGGTTATTAA
77460 TGATTAAGCACTACTTAGGTTATTAA
1 TGATTAAGCACTACTTAGGTTATTAA
77486 T
1 T
77487 AGGGTAAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (26 bp):
TGATTAAGCACTACTTAGGTTATTAA
Found at i:83535 original size:2 final size:2
Alignment explanation
Indices: 83528--83579 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
83518 TTCAGGCAGG
* *
83528 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA CA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
83569 TA TG TA TA TA T
1 TA TA TA TA TA T
83580 GGCTTTTGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:91553 original size:28 final size:27
Alignment explanation
Indices: 91514--91595 Score: 103
Period size: 28 Copynumber: 3.0 Consensus size: 27
91504 TTGTAATACA
91514 ATGGATCTGTGAAATGACCAAAATATCC
1 ATGG-TCTGTGAAATGACCAAAATATCC
*
91542 ATGGTTCTGTGAAATGACCAAAATACCC
1 ATGG-TCTGTGAAATGACCAAAATATCC
* *
91570 CTGGTATG-GAAATGACCAAGAATATC
1 ATGGTCTGTGAAATGACCAA-AATATC
91596 ATCAAACTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 11 0.23
27 8 0.17
28 29 0.60
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (27 bp):
ATGGTCTGTGAAATGACCAAAATATCC
Found at i:92667 original size:24 final size:24
Alignment explanation
Indices: 92640--92754 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
92630 TTCGATTTGA
92640 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
92664 ATTCTGATATGATA-TATGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* * *
92688 ATTTTGATGTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
92712 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
92736 ATTTTGATGTGATACTTGA
1 ATTCTGATCTGATACTTGA
92755 TATGAATTAT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 78 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:92704 original size:48 final size:48
Alignment explanation
Indices: 92644--92754 Score: 179
Period size: 48 Copynumber: 2.3 Consensus size: 48
92634 ATTTGAATTC
*
92644 TGATCTGATACTTGACATGGATTCTGATATGATA-TATGACATGGATTT
1 TGATGTGATACTTGACATGGATTCTGATATGATACT-TGACATGGATTT
* *
92692 TGATGTGATACTTGACTTGGATTCTGATCTGATACTTGACATGGATTT
1 TGATGTGATACTTGACATGGATTCTGATATGATACTTGACATGGATTT
92740 TGATGTGATACTTGA
1 TGATGTGATACTTGA
92755 TATGAATTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 58 0.98
49 1 0.02
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.41
Consensus pattern (48 bp):
TGATGTGATACTTGACATGGATTCTGATATGATACTTGACATGGATTT
Found at i:100052 original size:148 final size:148
Alignment explanation
Indices: 99869--100170 Score: 597
Period size: 148 Copynumber: 2.0 Consensus size: 148
99859 TTGAATTATT
99869 TAAA-TAATTAGATAATTCGATTGATAAAATAAAAAAAATCAATGATAAAAATAAATAATAATTA
1 TAAACTAATTAGATAATTCGATTGATAAAATAAAAAAAATCAATGATAAAAATAAATAATAATTA
99933 AATGATCATACAAATAGTTTACCTTAAAGAAAATGTTTAATATAAAAATAAGTGTATAAAGTATA
66 AATGATCATACAAATAGTTTACCTTAAAGAAAATGTTTAATATAAAAATAAGTGTATAAAGTATA
99998 CCTTTTTTTCTAGATTTC
131 CCTTTTTTTCTAGATTTC
100016 TAAACTAATTAGATAATTCGATTGATAAAATAAAAAAAATCAATGATAAAAATAAATAATAATTA
1 TAAACTAATTAGATAATTCGATTGATAAAATAAAAAAAATCAATGATAAAAATAAATAATAATTA
100081 AATGATCATACAAATAGTTTACCTTAAAGAAAATGTTTAATATAAAAATAAGTGTATAAAGTATA
66 AATGATCATACAAATAGTTTACCTTAAAGAAAATGTTTAATATAAAAATAAGTGTATAAAGTATA
100146 CCTTTTTTTCTAGATTTC
131 CCTTTTTTTCTAGATTTC
100164 TAAACTA
1 TAAACTA
100171 TTTTTTAACT
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
147 4 0.03
148 150 0.97
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.34
Consensus pattern (148 bp):
TAAACTAATTAGATAATTCGATTGATAAAATAAAAAAAATCAATGATAAAAATAAATAATAATTA
AATGATCATACAAATAGTTTACCTTAAAGAAAATGTTTAATATAAAAATAAGTGTATAAAGTATA
CCTTTTTTTCTAGATTTC
Found at i:100950 original size:29 final size:30
Alignment explanation
Indices: 100880--100952 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
100870 ATCGGGTGAC
** *
100880 ATTTTGGGAA-TTAATTCGAAATGGGTGTT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
*
100909 ATTTTTGGAATTTAATTC-AAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
100938 ATTTTGGGAATTTAA
1 ATTTTGGGAATTTAA
100953 CTTTGGCCGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 31 0.82
30 7 0.18
ACGTcount: A:0.32, C:0.04, G:0.22, T:0.42
Consensus pattern (30 bp):
ATTTTGGGAATTTAATTCGAAAAAGGTGCT
Found at i:107973 original size:17 final size:18
Alignment explanation
Indices: 107951--107987 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
107941 TTTGACCGGT
107951 CCCGACCCGTTGA-CCGA
1 CCCGACCCGTTGACCCGA
107968 CCCGACCCGTTGACCCGA
1 CCCGACCCGTTGACCCGA
107986 CC
1 CC
107988 GGTTGACCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.16, C:0.51, G:0.22, T:0.11
Consensus pattern (18 bp):
CCCGACCCGTTGACCCGA
Found at i:107984 original size:13 final size:13
Alignment explanation
Indices: 107966--107995 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
107956 CCCGTTGACC
107966 GACCCGACCCGTT
1 GACCCGACCCGTT
*
107979 GACCCGACCGGTT
1 GACCCGACCCGTT
107992 GACC
1 GACC
107996 GTTTGATCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.27, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:108037 original size:29 final size:30
Alignment explanation
Indices: 108011--108159 Score: 175
Period size: 29 Copynumber: 5.2 Consensus size: 30
108001 ATCGGGTGAC
* *
108011 ATTTTGAGAA-TTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGGTGCT
*
108040 ATTTTGGGAATTTAATTC-AAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGGTGCT
*
108069 ATTTTGGGAATTTAATTTGAAAA--GTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGGTGCT
*
108097 ATTTTTGGAA-TTAATTCGAAAAGGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGGTGCT
* * **
108126 ATTTTGGTAA-TTATTTTAAAAAGGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGGTGCT
108155 ATTTT
1 ATTTT
108160 TGTAAAATGA
Statistics
Matches: 105, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
27 11 0.10
28 14 0.13
29 69 0.66
30 11 0.10
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (30 bp):
ATTTTGGGAATTTAATTCGAAAAGGGTGCT
Found at i:108124 original size:57 final size:57
Alignment explanation
Indices: 108011--108161 Score: 171
Period size: 57 Copynumber: 2.6 Consensus size: 57
108001 ATCGGGTGAC
* * ** *
108011 ATTTTGAGAATTAATTCGAAATGGGTGCTATTTTGGGAATTTAATTCAAAAAGGTGCT
1 ATTTTGGGAATTAATT-TAAAAAGGTGCTATTTTTGGAATTTAATTCAAAAAGGTGCT
* *
108069 ATTTTGGGAATTTAATTTGAAAA-GTGCTATTTTTGGAA-TTAATTCGAAAAGGGTGCT
1 ATTTTGGGAA-TTAATTTAAAAAGGTGCTATTTTTGGAATTTAATTC-AAAAAGGTGCT
* *
108126 ATTTTGGTAATTATTTTAAAAAGGGTGCTATTTTTG
1 ATTTTGGGAATTAATTTAAAAA-GGTGCTATTTTTG
108162 TAAAATGATT
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
56 17 0.22
57 33 0.42
58 23 0.29
59 6 0.08
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.42
Consensus pattern (57 bp):
ATTTTGGGAATTAATTTAAAAAGGTGCTATTTTTGGAATTTAATTCAAAAAGGTGCT
Found at i:113166 original size:24 final size:24
Alignment explanation
Indices: 113139--113188 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
113129 TCAAATTTTT
*
113139 AACGATGAG-TATTAAAATGAAACA
1 AACGATGAGATACTAAAAT-AAACA
*
113163 AACGATGGGATACTAAAATAAACA
1 AACGATGAGATACTAAAATAAACA
113187 AA
1 AA
113189 AACTAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.56, C:0.10, G:0.16, T:0.18
Consensus pattern (24 bp):
AACGATGAGATACTAAAATAAACA
Done.