Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005951.1 Hibiscus syriacus cultivar Beakdansim tig00013972_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: 35192
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:121 original size:17 final size:17
Alignment explanation
Indices: 99--140 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
89 AAGAATTTCT
99 ATTATAATGTTTCCAAA
1 ATTATAATGTTTCCAAA
116 ATTATAATGTTTCCAAA
1 ATTATAATGTTTCCAAA
133 ATTATAAT
1 ATTATAAT
141 TAATTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (17 bp):
ATTATAATGTTTCCAAA
Found at i:1203 original size:21 final size:19
Alignment explanation
Indices: 1150--1203 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
1140 GATGCACCTA
*
1150 TCATCATCAAGAGGCGCCT
1 TCATCATCAAGAGGCCCCT
*
1169 TCTATCGTTCAAGAGGCCCCT
1 TC-ATC-ATCAAGAGGCCCCT
1190 CTCATCATCGAAGA
1 -TCATCATC-AAGA
1204 AGCCTTCCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 2 0.07
20 5 0.18
21 19 0.68
22 2 0.07
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (19 bp):
TCATCATCAAGAGGCCCCT
Found at i:2642 original size:14 final size:14
Alignment explanation
Indices: 2623--2662 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2613 TTTTGATTAA
2623 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
2637 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
2651 TTGATTTGTAAA
1 TTGATTTGTAAA
2663 TATTTTTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:3050 original size:39 final size:39
Alignment explanation
Indices: 2999--3082 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
2989 AAGTTGTAGA
2999 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGAT
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGAT
*
3038 TTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGGAT
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGAT
3077 TTTGAT
1 TTTGAT
3083 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.48
Consensus pattern (39 bp):
TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGAT
Found at i:3390 original size:6 final size:6
Alignment explanation
Indices: 3379--3417 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3369 ATTTATATTG
* * *
3379 AAATTC AAATTC AAACTC AAATTG AAATTT AAATTC AAA
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAA
3418 CTCCAATTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.31
Consensus pattern (6 bp):
AAATTC
Found at i:3398 original size:12 final size:12
Alignment explanation
Indices: 3383--3425 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3373 ATATTGAAAT
3383 TCAAATTCAAAC
1 TCAAATTCAAAC
* *
3395 TCAAATTGAAAT
1 TCAAATTCAAAC
*
3407 TTAAATTCAAAC
1 TCAAATTCAAAC
*
3419 TCCAATT
1 TCAAATT
3426 ACATATGAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33
Consensus pattern (12 bp):
TCAAATTCAAAC
Found at i:3407 original size:24 final size:24
Alignment explanation
Indices: 3375--3425 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
3365 CGGAATTTAT
3375 ATTGAAATTCAAATTCAAACTCAA
1 ATTGAAATTCAAATTCAAACTCAA
* *
3399 ATTGAAATTTAAATTCAAACTCCA
1 ATTGAAATTCAAATTCAAACTCAA
3423 ATT
1 ATT
3426 ACATATGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (24 bp):
ATTGAAATTCAAATTCAAACTCAA
Found at i:3842 original size:25 final size:24
Alignment explanation
Indices: 3800--3847 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
3790 TTATTTTTCC
*
3800 AAATAATAACCCATAACAATGTTG
1 AAATAATAACCCACAACAATGTTG
*
3824 AAATAATGTACCCACAACAATGTT
1 AAATAAT-AACCCACAACAATGTT
3848 TAATTGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (24 bp):
AAATAATAACCCACAACAATGTTG
Found at i:3972 original size:19 final size:20
Alignment explanation
Indices: 3938--3978 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
3928 AATAAGCGTT
3938 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
3958 GCGATAGTC-AATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
3977 GC
1 GC
3979 TTATTTCGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.20
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:6608 original size:24 final size:24
Alignment explanation
Indices: 6557--6608 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
6547 ATCTGAGTAT
** *
6557 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
6581 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
6605 TGAC
1 TGAC
6609 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:6741 original size:12 final size:12
Alignment explanation
Indices: 6720--6753 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6710 GGTTGTAGGT
*
6720 TTTGAGATTGTG
1 TTTGATATTGTG
6732 TTTGATATTGTG
1 TTTGATATTGTG
*
6744 TTTGGTATTG
1 TTTGATATTG
6754 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:7522 original size:19 final size:19
Alignment explanation
Indices: 7498--7561 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
7488 ACTAAAACCT
* *
7498 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTC-A
7517 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
7536 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
7555 ATTGCGA
1 GTTGCGA
7562 TTTACAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 35 0.85
20 6 0.15
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:7570 original size:19 final size:19
Alignment explanation
Indices: 7518--7572 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
7508 TAAATTCGCG
* *
7518 TTGCGAATTTGAAATTCAG
1 TTGCGAATTTCAAATTCAA
*
7537 TTGCGAATTTGAAATTCAA
1 TTGCGAATTTCAAATTCAA
7556 TTGCG-ATTTACAAATTC
1 TTGCGAATTT-CAAATTC
7573 GCGTTACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.12
19 29 0.88
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (19 bp):
TTGCGAATTTCAAATTCAA
Found at i:8420 original size:20 final size:20
Alignment explanation
Indices: 8397--8440 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
8387 TGTGTGTGCA
8397 TGTGCGCGTGTACGTGCGTG
1 TGTGCGCGTGTACGTGCGTG
8417 TGTGCGCGTGTACGTGCGTG
1 TGTGCGCGTGTACGTGCGTG
8437 TGTG
1 TGTG
8441 TGCATGTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.05, C:0.18, G:0.45, T:0.32
Consensus pattern (20 bp):
TGTGCGCGTGTACGTGCGTG
Found at i:11694 original size:22 final size:21
Alignment explanation
Indices: 11646--11713 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
11636 GAATAGCATC
* *
11646 TCTTGATATTAATATTAGATT
1 TCTTTATATTAATATTATATT
11667 TCTTTATATTAACTATTATATCT
1 TCTTTATATTAA-TATTATAT-T
* * *
11690 T-TTTATGTTAAAATTATATA
1 TCTTTATATTAATATTATATT
11710 TCTT
1 TCTT
11714 CATGTTAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 20 0.51
22 16 0.41
23 2 0.05
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.56
Consensus pattern (21 bp):
TCTTTATATTAATATTATATT
Found at i:11791 original size:26 final size:25
Alignment explanation
Indices: 11758--11813 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
11748 AATTTAAATA
11758 ATTAATAT-TATTAAAT-ATAATTAAT
1 ATTAATATGTA-TAAATAAT-ATTAAT
*
11783 ATTATATATGTATATATAATATTAAT
1 ATTA-ATATGTATAAATAATATTAAT
11809 ATTAA
1 ATTAA
11814 GCTTAAGAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
25 5 0.19
26 18 0.67
27 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTAATATGTATAAATAATATTAAT
Found at i:12570 original size:18 final size:19
Alignment explanation
Indices: 12524--12570 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
12514 TTGGAATGAG
12524 TGAGTATCGATACTGATCCTA
1 TGAGTATCGATAC--ATCCTA
*
12545 TG-GTATCGATAC-TCCTT
1 TGAGTATCGATACATCCTA
12562 TGAGTATCG
1 TGAGTATCG
12571 GTATTGCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 6 0.25
18 6 0.25
20 10 0.42
21 2 0.08
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (19 bp):
TGAGTATCGATACATCCTA
Found at i:12818 original size:19 final size:18
Alignment explanation
Indices: 12787--12838 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
12777 ATTTACTATT
12787 GTTTAAAGTTTTAAGTTAG
1 GTTT-AAGTTTTAAGTTAG
**
12806 GATTTGGGTTTTAAGTTAG
1 G-TTTAAGTTTTAAGTTAG
12825 GTTTAAGTTTTAAG
1 GTTTAAGTTTTAAG
12839 GTTTAGGCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 11 0.39
19 14 0.50
20 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (18 bp):
GTTTAAGTTTTAAGTTAG
Found at i:15426 original size:13 final size:13
Alignment explanation
Indices: 15410--15464 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
15400 AATTAAAATA
15410 ATTAAATAAAAAC
1 ATTAAATAAAAAC
*
15423 ATTAAATACAAAC
1 ATTAAATAAAAAC
**
15436 ATTACAATTCAAAC
1 ATTA-AATAAAAAC
*
15450 AATTAAATAATAAC
1 -ATTAAATAAAAAC
15464 A
1 A
15465 ACATTAAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 17 0.49
14 14 0.40
15 4 0.11
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.25
Consensus pattern (13 bp):
ATTAAATAAAAAC
Found at i:15450 original size:14 final size:13
Alignment explanation
Indices: 15410--15458 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
15400 AATTAAAATA
*
15410 ATTAAATAAAAAC
1 ATTAAATACAAAC
15423 ATTAAATACAAAC
1 ATTAAATACAAAC
*
15436 ATTACAATTCAAAC
1 ATTA-AATACAAAC
15450 AATTAAATA
1 -ATTAAATA
15459 ATAACAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 16 0.52
14 11 0.35
15 4 0.13
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (13 bp):
ATTAAATACAAAC
Found at i:16026 original size:21 final size:21
Alignment explanation
Indices: 15983--16026 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
15973 CTGAACCGAC
*
15983 TGCAGTGACATCTGAAATAGT
1 TGCAGTGACATCTGAAACAGT
* *
16004 TGCAGTGCCATCTGAAACGGT
1 TGCAGTGACATCTGAAACAGT
16025 TG
1 TG
16027 TGATGTACCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TGCAGTGACATCTGAAACAGT
Found at i:18506 original size:42 final size:42
Alignment explanation
Indices: 18442--18603 Score: 297
Period size: 42 Copynumber: 3.9 Consensus size: 42
18432 TTTCCACGAA
18442 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATTTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATTTT
*
18484 TTCCTGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATTTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATTTT
**
18526 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATTTT
18568 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
18604 TGTAATTCAT
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 116 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATTTT
Found at i:18823 original size:21 final size:21
Alignment explanation
Indices: 18785--18845 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
18775 AAAATATTAA
*
18785 TTATTAAAATATTA-AATATAT
1 TTATTAATAT-TTATAATATAT
18806 TTATTAATATTTATAATA-AT
1 TTATTAATATTTATAATATAT
* * *
18826 ATAATATATATTTTTAATAT
1 TTATTA-ATATTTATAATAT
18846 TATATAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 9 0.27
21 24 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTAATATTTATAATATAT
Found at i:18835 original size:31 final size:30
Alignment explanation
Indices: 18784--18856 Score: 98
Period size: 30 Copynumber: 2.4 Consensus size: 30
18774 CAAAATATTA
18784 ATTAT-TAAAATATTAAATATATTTATTAAT
1 ATTATATAAAATATTAAATATATTT-TTAAT
18814 ATT-TATAATAATA-TAATATATATTTTTAAT
1 ATTATATAA-AATATTAA-ATATATTTTTAAT
18844 ATTATATAAAATA
1 ATTATATAAAATA
18857 ATCAATTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
29 1 0.03
30 21 0.54
31 17 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTATATAAAATATTAAATATATTTTTAAT
Found at i:18867 original size:31 final size:30
Alignment explanation
Indices: 18784--18875 Score: 95
Period size: 30 Copynumber: 3.1 Consensus size: 30
18774 CAAAATATTA
*
18784 ATTAT-TAAAATATTAAATATATTTATTAAT
1 ATTATATAAAATA-TAATTATATTTATTAAT
18814 ATT-TATAATAATATAATATATATTT-TTAAT
1 ATTATATAA-AATATAAT-TATATTTATTAAT
18844 ATTATATAAAATAATCAATTATA-TTA-TAAT
1 ATTATATAAAAT-AT-AATTATATTTATTAAT
18874 AT
1 AT
18876 AAGATATTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 14
0.78 0.01 0.20
Matches are distributed among these distances:
29 1 0.02
30 28 0.52
31 22 0.41
32 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTATATAAAATATAATTATATTTATTAAT
Found at i:18867 original size:33 final size:31
Alignment explanation
Indices: 18792--18856 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
18782 TAATTATTAA
18792 AATATTAA-ATATATTTATTAATATTTATAAT
1 AATA-TAATATATATTTATTAATATTTATAAT
18823 AATATAATATATATTT-TTAATATTATATAA-
1 AATATAATATATATTTATTAATATT-TATAAT
18853 AATA
1 AATA
18857 ATCAATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
AATATAATATATATTTATTAATATTTATAAT
Found at i:19209 original size:20 final size:20
Alignment explanation
Indices: 19131--19200 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
19121 TTTCCAGATG
19131 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
19151 TTTTTCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
19171 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
19191 TTTTCCAGAA
1 TTTTCCAGAA
19201 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:19209 original size:40 final size:40
Alignment explanation
Indices: 19131--19209 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
19121 TTTCCAGATG
* * **
19131 TTTTCCAGAAATGTAATTCATTTTTCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
19171 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
19210 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:19219 original size:15 final size:15
Alignment explanation
Indices: 19183--19249 Score: 91
Period size: 15 Copynumber: 4.5 Consensus size: 15
19173 TTACAGAAAT
**
19183 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
19198 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
19212 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
19227 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
19242 GTAATTCA
1 GTAATTCA
19250 TTTTCTGGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.27
15 33 0.73
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:19225 original size:29 final size:30
Alignment explanation
Indices: 19183--19254 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
19173 TTACAGAAAT
19183 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
19212 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
19242 GTAATTCATTTTC
1 GTAATTCATTTTC
19255 TGGAAAACCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:20578 original size:2 final size:2
Alignment explanation
Indices: 20571--20596 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20561 AATGGAAGTT
20571 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
20597 GGCCAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21275 original size:2 final size:2
Alignment explanation
Indices: 21268--21297 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21258 ATCCTAACCC
21268 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
21298 TAGAAAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25180 original size:2 final size:2
Alignment explanation
Indices: 25173--25207 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25163 AAACTTTATT
25173 TA 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 TA T
25208 TATTAACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27543 original size:92 final size:92
Alignment explanation
Indices: 27336--27540 Score: 378
Period size: 92 Copynumber: 2.2 Consensus size: 92
27326 TGCACACGAG
27336 ATAA-ATAAAATAAATTAATAAACATATAATAATAAATAAATATCATAAATTTAAGTGAATTTTG
1 ATAATATAAAATAAATTAATAAACATATAATAATAAATAAATATCATAAATTTAAGTGAATTTTG
27400 ATAATTAAAGTTTTGAAAATAAATGAT
66 ATAATTAAAGTTTTGAAAATAAATGAT
*
27427 ATAATATAAAATAAATTAATAAACATATAATAATAAATAAATATCGTAAATTTAAGTGAATTTTG
1 ATAATATAAAATAAATTAATAAACATATAATAATAAATAAATATCATAAATTTAAGTGAATTTTG
27492 ATAATTAAAGTTTTGAAAATAAATGAT
66 ATAATTAAAGTTTTGAAAATAAATGAT
*
27519 ATAATATAAAATATATT-ATAAA
1 ATAATATAAAATAAATTAATAAA
27541 ACAGGTTTTA
Statistics
Matches: 111, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
91 9 0.08
92 102 0.92
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (92 bp):
ATAATATAAAATAAATTAATAAACATATAATAATAAATAAATATCATAAATTTAAGTGAATTTTG
ATAATTAAAGTTTTGAAAATAAATGAT
Done.