Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001546.1 Hibiscus syriacus cultivar Beakdansim tig00003036_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: 47451
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:540 original size:21 final size:21
Alignment explanation
Indices: 507--584 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
497 TTAAAAATAT
507 TAAAGGAAGTATCGATATTCAC
1 TAAAGG-AGTATCGATATTCAC
529 TAAAGGAGTATCGATATT--C
1 TAAAGGAGTATCGATATTCAC
*
548 TAAAGGAGTATTGATATTCAC
1 TAAAGGAGTATCGATATTCAC
*
569 TAAAGGAGTATTGATA
1 TAAAGGAGTATCGATA
585 CTCCCTACTG
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
19 18 0.34
21 29 0.55
22 6 0.11
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.31
Consensus pattern (21 bp):
TAAAGGAGTATCGATATTCAC
Found at i:564 original size:40 final size:41
Alignment explanation
Indices: 507--584 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 41
497 TTAAAAATAT
507 TAAAGGAAGTATCGATATTCACTAAAGGAGTATCGATATTC
1 TAAAGGAAGTATCGATATTCACTAAAGGAGTATCGATATTC
* *
548 TAAAGG-AGTATTGATATTCACTAAAGGAGTATTGATA
1 TAAAGGAAGTATCGATATTCACTAAAGGAGTATCGATA
585 CTCCCTACTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 29 0.83
41 6 0.17
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.31
Consensus pattern (41 bp):
TAAAGGAAGTATCGATATTCACTAAAGGAGTATCGATATTC
Found at i:2329 original size:19 final size:20
Alignment explanation
Indices: 2307--2345 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2297 TGAATAGTAT
2307 AATATTAAATTAT-GTTTTA
1 AATATTAAATTATGGTTTTA
*
2326 AATATTACATTATGGTTTTA
1 AATATTAAATTATGGTTTTA
2346 TGTGATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (20 bp):
AATATTAAATTATGGTTTTA
Found at i:3734 original size:22 final size:22
Alignment explanation
Indices: 3706--3749 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3696 ATGAGAGATT
3706 CAGAATGTATCCAATAGTGTTA
1 CAGAATGTATCCAATAGTGTTA
3728 CAGAATGTATCCAATAGTGTTA
1 CAGAATGTATCCAATAGTGTTA
3750 AAGCATGCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (22 bp):
CAGAATGTATCCAATAGTGTTA
Found at i:9068 original size:32 final size:33
Alignment explanation
Indices: 8974--9068 Score: 122
Period size: 32 Copynumber: 2.9 Consensus size: 33
8964 TACGCAAGGG
*
8974 AGTACCTTAGGGCCTAAGAGCCTACCCAA-GAA
1 AGTACCTTGGGGCCTAAGAGCCTACCCAAGGAA
* * *
9006 AGTACCTTGGGACCTTATAGCCTACCCAAGGAA
1 AGTACCTTGGGGCCTAAGAGCCTACCCAAGGAA
* *
9039 A-TGCCTTGGGGCCTCAGAGCCTACCCAAGG
1 AGTACCTTGGGGCCTAAGAGCCTACCCAAGG
9069 TCACCTTAGG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
32 50 0.93
33 4 0.07
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.18
Consensus pattern (33 bp):
AGTACCTTGGGGCCTAAGAGCCTACCCAAGGAA
Found at i:10151 original size:27 final size:27
Alignment explanation
Indices: 10096--10170 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
10086 TCCAAAGCTT
* *
10096 GGGGATATTTTAATTCATTTTACACTTTA
1 GGGG-TATTTTAGTT-ATTTCACACTTTA
*
10125 GGGGTATTTTAGTTATTTCACAGTTTA
1 GGGGTATTTTAGTTATTTCACACTTTA
* *
10152 AGGGTATTTCAGTTATTTC
1 GGGGTATTTTAGTTATTTC
10171 CTTCTATCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
27 28 0.68
28 9 0.22
29 4 0.10
ACGTcount: A:0.24, C:0.09, G:0.19, T:0.48
Consensus pattern (27 bp):
GGGGTATTTTAGTTATTTCACACTTTA
Found at i:14321 original size:2 final size:2
Alignment explanation
Indices: 14314--14340 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14304 TTTTATTATT
14314 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 T
14341 TATCTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17375 original size:31 final size:28
Alignment explanation
Indices: 17329--17423 Score: 81
Period size: 31 Copynumber: 3.4 Consensus size: 28
17319 AATTTATTTT
*
17329 TTAATAATTTATAATTTATCATTTTATACC
1 TTAAT-ATTTTTAATTTATCATTTTATA-C
17359 TTCAAATATTTTTAATTTAT-ATTTT-TAC
1 TT--AATATTTTTAATTTATCATTTTATAC
* **
17387 TTAATTTTTTTAA--TATCATTTTAATTT
1 TTAATATTTTTAATTTATCATTTT-ATAC
17414 TTAATATTTT
1 TTAATATTTT
17424 AATAATTTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
24 3 0.05
25 5 0.09
26 10 0.18
27 10 0.18
28 3 0.05
29 2 0.04
30 7 0.13
31 12 0.22
32 3 0.05
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (28 bp):
TTAATATTTTTAATTTATCATTTTATAC
Found at i:17450 original size:18 final size:16
Alignment explanation
Indices: 17393--17450 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 16
17383 TTACTTAATT
17393 TTTTTAATATCATTTTAA
1 TTTTTAATAT-A-TTTAA
17411 TTTTTAATAT-TTTAA
1 TTTTTAATATATTTAA
17426 TAATTTTAATGATATCTTAA
1 T--TTTTAAT-ATAT-TTAA
17446 TTTTT
1 TTTTT
17451 CTAAAATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
15 6 0.17
17 7 0.20
18 16 0.46
19 1 0.03
20 5 0.14
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTTTAATATATTTAA
Found at i:21229 original size:20 final size:21
Alignment explanation
Indices: 21195--21235 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
21185 GGTATCGATA
21195 CTTGAGGTGAGTATTGATACC
1 CTTGAGGTGAGTATTGATACC
*
21216 CTTGAGGT-AGTATTTATACC
1 CTTGAGGTGAGTATTGATACC
21236 AATTAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (21 bp):
CTTGAGGTGAGTATTGATACC
Found at i:26537 original size:14 final size:14
Alignment explanation
Indices: 26518--26600 Score: 65
Period size: 14 Copynumber: 6.5 Consensus size: 14
26508 TGTTCGGTAC
26518 TATGTTCGTTCATT
1 TATGTTCGTTCATT
26532 TA---T-GTTCATT
1 TATGTTCGTTCATT
*
26542 TACGTTCGTTCATT
1 TATGTTCGTTCATT
26556 TA---T-GTTCATT
1 TATGTTCGTTCATT
**
26566 TATGTTCGTTTGTT
1 TATGTTCGTTCATT
**
26580 TATGTTCGTTTGTT
1 TATGTTCGTTCATT
26594 TATGTTC
1 TATGTTC
26601 ATTTATGTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
10 18 0.31
11 2 0.03
13 2 0.03
14 37 0.63
ACGTcount: A:0.13, C:0.12, G:0.16, T:0.59
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:26550 original size:24 final size:24
Alignment explanation
Indices: 26521--26586 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
26511 TCGGTACTAT
26521 GTTCGTTCATTTATGTTCATTTAC
1 GTTCGTTCATTTATGTTCATTTAC
*
26545 GTTCGTTCATTTATGTTCATTTAT
1 GTTCGTTCATTTATGTTCATTTAC
**
26569 GTTCGTTTGTTTATGTTC
1 GTTCGTTCATTTATGTTC
26587 GTTTGTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.14, C:0.14, G:0.15, T:0.58
Consensus pattern (24 bp):
GTTCGTTCATTTATGTTCATTTAC
Found at i:26587 original size:38 final size:38
Alignment explanation
Indices: 26540--26614 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
26530 TTTATGTTCA
*
26540 TTTACGTTCGTTCATTTATGTTCATTTATGTTCGTTTG
1 TTTACGTTCGTTCATTTATGTTCATTTATGTTAGTTTG
* **
26578 TTTATGTTCGTTTGTTTATGTTCATTTATGTTAGTTT
1 TTTACGTTCGTTCATTTATGTTCATTTATGTTAGTTT
26615 ATATGCGTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.13, C:0.09, G:0.16, T:0.61
Consensus pattern (38 bp):
TTTACGTTCGTTCATTTATGTTCATTTATGTTAGTTTG
Found at i:26590 original size:10 final size:10
Alignment explanation
Indices: 26525--26572 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 10
26515 TACTATGTTC
26525 GTTCATTTAT
1 GTTCATTTAT
26535 GTTCATTTACGTT
1 GTTCATTTA---T
26548 CGTTCATTTAT
1 -GTTCATTTAT
26559 GTTCATTTAT
1 GTTCATTTAT
26569 GTTC
1 GTTC
26573 GTTTGTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 23 0.68
11 1 0.03
13 1 0.03
14 9 0.26
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:26605 original size:24 final size:24
Alignment explanation
Indices: 26578--26632 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
26568 TGTTCGTTTG
* * * *
26578 TTTATGTTCGTTTGTTTATGTTCA
1 TTTATGTTAGTTTATATACGTTCA
*
26602 TTTATGTTAGTTTATATGCGTTCA
1 TTTATGTTAGTTTATATACGTTCA
26626 TTTATGT
1 TTTATGT
26633 GTAGACCAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.07, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTATGTTAGTTTATATACGTTCA
Found at i:26894 original size:176 final size:177
Alignment explanation
Indices: 26598--26971 Score: 669
Period size: 176 Copynumber: 2.1 Consensus size: 177
26588 TTTGTTTATG
* *
26598 TTCATTTATGTTAGTTTATATGCGTTCATTTATGTGTAGACCAATCTCTCTAGACCCATTTAAAA
1 TTCATTTATGTTCGTTTATGTGCGTTCATTTATGTGTAGACCAATCTCTCTAGACCCATTTAAAA
* * *
26663 TATTAAAGCCCAATAAATTTTAATATGATACCCATAAATATTTTACAATTCAATTAATTTTAAAT
66 TATTAAAGCCCAATAAAATTTAATATGATACCCATAAATATTTTAAAACTCAATTAATTTTAAAT
*
26728 TCAAAT-AAAAAAGATCAAAACAATTAAATAAAATATAATCCTAAAA
131 ACAAATAAAAAAAGATCAAAACAATTAAATAAAATATAATCCTAAAA
*
26774 TTCATTTATGTTCGTTTATGTGCGTTCATTTATGTTTAGACCAATCTCTCTAGACCCATTTAAAA
1 TTCATTTATGTTCGTTTATGTGCGTTCATTTATGTGTAGACCAATCTCTCTAGACCCATTTAAAA
*
26839 TATTAAAGCCCAATAAAATTTAATCTGATACCCATAAATATTTTAAAACTCAATTAATTTTAAAT
66 TATTAAAGCCCAATAAAATTTAATATGATACCCATAAATATTTTAAAACTCAATTAATTTTAAAT
26904 ACAAATAAAAAAAGATCAAAACAATTAAATAAAATATAATCCTAAAA
131 ACAAATAAAAAAAGATCAAAACAATTAAATAAAATATAATCCTAAAA
26951 TTCATTTATGTTCGTTTATGT
1 TTCATTTATGTTCGTTTATGT
26972 TCATTTATTG
Statistics
Matches: 189, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
176 128 0.68
177 61 0.32
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (177 bp):
TTCATTTATGTTCGTTTATGTGCGTTCATTTATGTGTAGACCAATCTCTCTAGACCCATTTAAAA
TATTAAAGCCCAATAAAATTTAATATGATACCCATAAATATTTTAAAACTCAATTAATTTTAAAT
ACAAATAAAAAAAGATCAAAACAATTAAATAAAATATAATCCTAAAA
Found at i:28038 original size:17 final size:18
Alignment explanation
Indices: 28018--28054 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
28008 TGATATTCGA
28018 ATAA-TTGAATCGAATAT
1 ATAATTTGAATCGAATAT
28035 ATAATTTTGAATCGAATAT
1 ATAA-TTTGAATCGAATAT
28054 A
1 A
28055 AAATCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
ATAATTTGAATCGAATAT
Found at i:28074 original size:13 final size:13
Alignment explanation
Indices: 28056--28080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28046 TCGAATATAA
28056 AATCTTAAAATTT
1 AATCTTAAAATTT
28069 AATCTTAAAATT
1 AATCTTAAAATT
28081 CATTAAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
AATCTTAAAATTT
Found at i:28194 original size:14 final size:13
Alignment explanation
Indices: 28173--28199 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28163 ATTTTTGTCT
28173 TTTGAAAAATTAC
1 TTTGAAAAATTAC
28186 TTTGAAAAATTAC
1 TTTGAAAAATTAC
28199 T
1 T
28200 CCCCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTGAAAAATTAC
Found at i:36275 original size:18 final size:18
Alignment explanation
Indices: 36252--36317 Score: 123
Period size: 18 Copynumber: 3.7 Consensus size: 18
36242 TATGTAAATA
36252 GGTATCGATACCTGTCAT
1 GGTATCGATACCTGTCAT
36270 GGTATCGATACCTGTCAT
1 GGTATCGATACCTGTCAT
36288 GGTATCGATACCTGTCAT
1 GGTATCGATACCTGTCAT
*
36306 GGTATCGGTACC
1 GGTATCGATACC
36318 CATTTTGCTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (18 bp):
GGTATCGATACCTGTCAT
Found at i:38026 original size:23 final size:24
Alignment explanation
Indices: 38000--38046 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
37990 AAAAATCACA
* *
38000 TAAAACATTTATAATTTA-AATTT
1 TAAAAAATTTATAATATATAATTT
38023 TAAAAAATTTATAATATATAATTT
1 TAAAAAATTTATAATATATAATTT
38047 ATATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAAAAATTTATAATATATAATTT
Found at i:39796 original size:7 final size:7
Alignment explanation
Indices: 39784--39808 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39774 AGAAGTTTTC
39784 TTTTGAG
1 TTTTGAG
39791 TTTTGAG
1 TTTTGAG
39798 TTTTGAG
1 TTTTGAG
39805 TTTT
1 TTTT
39809 TTTTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.64
Consensus pattern (7 bp):
TTTTGAG
Found at i:40925 original size:29 final size:31
Alignment explanation
Indices: 40868--40927 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
40858 CAATTTAAGG
*
40868 CAAAATGGTGTTTGGACTTGAATTGAATTTA
1 CAAAATGGTGTTTGGAATTGAATTGAATTTA
* *
40899 CAAAAT-GTTTTTGGAATT-AATTTAATTTA
1 CAAAATGGTGTTTGGAATTGAATTGAATTTA
40928 TTCAAAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 10 0.38
30 10 0.38
31 6 0.23
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (31 bp):
CAAAATGGTGTTTGGAATTGAATTGAATTTA
Found at i:41054 original size:20 final size:21
Alignment explanation
Indices: 41007--41063 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
40997 AGGGTGTCAA
41007 AGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCACCTG-ACT
*
41029 AGTGCATCGATGCACCATG-C-
1 AGTGCATCCATGCACC-TGACT
41049 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
41064 TCAAACACCG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.44
21 1 0.03
22 15 0.47
23 2 0.06
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCTGACT
Found at i:41109 original size:20 final size:19
Alignment explanation
Indices: 41084--41157 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
41074 AATGCAATTA
*
41084 GTGCATCAATGCATCCTTAT
1 GTGCATCGATGCATCCTT-T
* **
41104 GTGCATTGATGCATCAAGGTT
1 GTGCATCGATGCATC--CTTT
41125 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCT-TT
*
41145 GTGCATCTATGCA
1 GTGCATCGATGCA
41158 CAAAGGTTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 27 0.63
21 15 0.35
22 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.34
Consensus pattern (19 bp):
GTGCATCGATGCATCCTTT
Found at i:41131 original size:41 final size:41
Alignment explanation
Indices: 41084--41166 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 41
41074 AATGCAATTA
41084 GTGCATCAATGCATCCT-TATGTGCAT-TGATGCATC-AAGGTT
1 GTGCATCAATGCATCCTGT-TGTGCATCT-ATGCA-CAAAGGTT
*
41125 GTGCATCGATGCATCCTGTTGTGCATCTATGCACAAAGGTT
1 GTGCATCAATGCATCCTGTTGTGCATCTATGCACAAAGGTT
41166 G
1 G
41167 CAACGACTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
40 1 0.03
41 35 0.92
42 2 0.05
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (41 bp):
GTGCATCAATGCATCCTGTTGTGCATCTATGCACAAAGGTT
Found at i:41554 original size:34 final size:32
Alignment explanation
Indices: 41515--41584 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
41505 TTTTGTAAAG
* *
41515 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
41549 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
41581 GGGA
1 GGGA
41585 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:41783 original size:23 final size:23
Alignment explanation
Indices: 41756--41811 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
41746 CTAAACTCAT
41756 AAACCGTTCCGACCCCTATTTAC
1 AAACCGTTCCGACCCCTATTTAC
41779 AAACCGTTCCGACCCCTATTTAC
1 AAACCGTTCCGACCCCTATTTAC
41802 AAACCGTTCC
1 AAACCGTTCC
41812 CGGTTATCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.39, G:0.09, T:0.25
Consensus pattern (23 bp):
AAACCGTTCCGACCCCTATTTAC
Found at i:42489 original size:19 final size:20
Alignment explanation
Indices: 42465--42512 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
42455 AACGATTTTC
*
42465 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
42484 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
42504 TTTTGAAAA
1 TTTTGAAAA
42513 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:43793 original size:29 final size:31
Alignment explanation
Indices: 43738--43797 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
43728 CAATTTAAGG
*
43738 CAAAATGGTATTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGAATTGAATTGAATTTA
*
43769 CAAAAT-GTTTTTGGAATT-AATTGAATTTA
1 CAAAATGGTATTTGGAATTGAATTGAATTTA
43798 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGAATTGAATTGAATTTA
Found at i:43903 original size:21 final size:21
Alignment explanation
Indices: 43877--43975 Score: 123
Period size: 21 Copynumber: 4.7 Consensus size: 21
43867 AGGGTGTCAA
43877 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
43898 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
43919 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCACCCCTG--C
* *
43940 TAGTGCATCGATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTGC
*
43961 AATGCATCCATGCAC
1 AGTGCATCCATGCAC
43976 TCAAACACCA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
19 4 0.06
20 12 0.17
21 37 0.54
22 13 0.19
23 3 0.04
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:44022 original size:20 final size:18
Alignment explanation
Indices: 43997--44069 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 18
43987 ATACAATTAG
43997 TGCATCGATGCATCCTTCT
1 TGCATCGATGCATCCTT-T
*
44016 ATGCATCGATGCATCAAGGTTT
1 -TGCATCGATGCATC---CTTT
44038 TGCATCGATGCATCCTGTT
1 TGCATCGATGCATCCT-TT
44057 GTGCATCGATGCA
1 -TGCATCGATGCA
44070 CGAAGGCTGC
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 26 0.57
21 14 0.30
22 1 0.02
23 2 0.04
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.33
Consensus pattern (18 bp):
TGCATCGATGCATCCTTT
Found at i:46484 original size:13 final size:15
Alignment explanation
Indices: 46454--46485 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
46444 ATTTACCAAT
46454 TTCCATTACAATATA
1 TTCCATTACAATATA
46469 TTCCATTA-AA-ATA
1 TTCCATTACAATATA
46482 TTCC
1 TTCC
46486 TAAGTCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (15 bp):
TTCCATTACAATATA
Found at i:47164 original size:3 final size:3
Alignment explanation
Indices: 47156--47451 Score: 498
Period size: 3 Copynumber: 99.3 Consensus size: 3
47146 GATTTTGGTC
47156 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
47204 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCTT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T
47253 TCT TCT TCT TCT TC- TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
47299 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC- TCT TCT TCTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT
47344 TCT TCT TCT TCT TCT TCT TC- TCT TCT TC- TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
47390 TCTT TCT TC- TCT TCT TCT TCT TCT TCT TCT TCT TC- TCTT TCTT TCT
1 TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TC-T TCT
47436 TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT T
Statistics
Matches: 282, Mismatches: 0, Indels: 22
0.93 0.00 0.07
Matches are distributed among these distances:
2 14 0.05
3 253 0.90
4 15 0.05
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Done.