Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000072.1 Hibiscus syriacus cultivar Beakdansim tig00000126_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: 49656
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1296 original size:2 final size:2
Alignment explanation
Indices: 1281--1350 Score: 101
Period size: 2 Copynumber: 36.5 Consensus size: 2
1271 TAGTTTAATA
*
1281 AT AT A- AT A- AT AT AT AT AT AT AT AT AG A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1320 AT AT AT AG 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 AT AT AT A
1351 ACCAGGGCAC
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
1 3 0.05
2 59 0.95
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5041 original size:33 final size:33
Alignment explanation
Indices: 4988--5091 Score: 97
Period size: 32 Copynumber: 3.2 Consensus size: 33
4978 ACTCAAATCG
* * * **
4988 AAAGTAACCCAGATTTAATTTTAAACC-GATTCA
1 AAAGCAACCCAAATTGAATTTT-AACCTGACCCA
5021 AAAGCAACCCAAATTGAA-TTTAACCTGACCCA
1 AAAGCAACCCAAATTGAATTTTAACCTGACCCA
* * * *
5053 AAAGCAACTCAAACTGAA-TTTAACCCGACCCG
1 AAAGCAACCCAAATTGAATTTTAACCTGACCCA
5085 AAAGCAA
1 AAAGCAA
5092 TCCTAACAGA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 4 0.07
32 42 0.69
33 15 0.25
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.20
Consensus pattern (33 bp):
AAAGCAACCCAAATTGAATTTTAACCTGACCCA
Found at i:5055 original size:32 final size:32
Alignment explanation
Indices: 5019--5091 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
5009 TAAACCGATT
* *
5019 CAAAAGCAACCCAAATTGAATTTAACCTGACC
1 CAAAAGCAACCCAAACTGAATTTAACCCGACC
*
5051 CAAAAGCAACTCAAACTGAATTTAACCCGACC
1 CAAAAGCAACCCAAACTGAATTTAACCCGACC
*
5083 CGAAAGCAA
1 CAAAAGCAA
5092 TCCTAACAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.45, C:0.29, G:0.11, T:0.15
Consensus pattern (32 bp):
CAAAAGCAACCCAAACTGAATTTAACCCGACC
Found at i:10504 original size:16 final size:17
Alignment explanation
Indices: 10483--10514 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
10473 AGTTTAGTCT
10483 TTCTTCTTTT-TTCTTC
1 TTCTTCTTTTCTTCTTC
10499 TTCTTCTTTTCTTCTT
1 TTCTTCTTTTCTTCTT
10515 TTTTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTCTTCTTTTCTTCTTC
Found at i:17400 original size:19 final size:20
Alignment explanation
Indices: 17363--17400 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17353 TTTTTTTATA
*
17363 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
17383 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
17401 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:17451 original size:21 final size:21
Alignment explanation
Indices: 17427--17469 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17417 TTCATATTCG
* *
17427 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
17448 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
17469 T
1 T
17470 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:19587 original size:21 final size:21
Alignment explanation
Indices: 19557--19610 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
19547 GCGTTGCATT
19557 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
* *
19578 TCGTGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
19599 TCGCGTTGCGAT
1 TCGCGTTGCGAT
19611 TTTCCATTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:19624 original size:20 final size:20
Alignment explanation
Indices: 19599--19678 Score: 90
Period size: 20 Copynumber: 3.9 Consensus size: 20
19589 TAGTTGAAAA
*
19599 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
19619 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
19639 TCGCGTTGCAATATTCTACAGT
1 TCGCGTTGCGAT-TT-TCCAGT
*
19661 T-GTCGATGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
19679 AATTCGTTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
20 33 0.65
21 5 0.10
22 13 0.25
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:19795 original size:6 final size:6
Alignment explanation
Indices: 19784--19832 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
19774 GACACGTATT
19784 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
19830 ACC
1 ACC
19833 CGAGACGGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.23
6 33 0.77
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:20326 original size:5 final size:5
Alignment explanation
Indices: 20316--20350 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
20306 GCCGTCCGTC
20316 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
20351 TTGTCGTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:20345 original size:6 final size:6
Alignment explanation
Indices: 20319--20408 Score: 132
Period size: 6 Copynumber: 15.5 Consensus size: 6
20309 GTCCGTCTCG
*
20319 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT TGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
* *
20364 GGTCGT TGTCGT TGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
20409 AATACGTGTC
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
5 15 0.19
6 65 0.81
ACGTcount: A:0.00, C:0.17, G:0.49, T:0.34
Consensus pattern (6 bp):
GGTCGT
Found at i:20569 original size:21 final size:22
Alignment explanation
Indices: 20509--20581 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
20499 AATTTGGAAA
*
20509 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAATTGTAGACT
* *
20531 TTCGCAACAACAATTGTAGACT
1 ATCGCAACGACAATTGTAGACT
20553 ATCGCAACGAC-ATTGTAGACT
1 ATCGCAACGACAATTGTAGACT
20574 ATCGCAAC
1 ATCGCAAC
20582 TTGAAATGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 18 0.39
22 28 0.61
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCGCAACGACAATTGTAGACT
Found at i:20965 original size:32 final size:32
Alignment explanation
Indices: 20919--21012 Score: 104
Period size: 32 Copynumber: 2.9 Consensus size: 32
20909 ACCTACACTG
*
20919 AAAATCAACCGATCCGATATTGACCCGACCC-
1 AAAATCAACTGATCCGATATTGACCCGACCCA
* *
20950 AAAATCTAACTGATCC-AGTATTAATCCGACCCA
1 AAAATC-AACTGATCCGA-TATTGACCCGACCCA
*
20983 AAAATCAA-TCGATCCGGTATTGACCCGACC
1 AAAATCAACT-GATCCGATATTGACCCGACC
21013 TGATATTGAC
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
31 8 0.15
32 38 0.73
33 6 0.12
ACGTcount: A:0.36, C:0.31, G:0.13, T:0.20
Consensus pattern (32 bp):
AAAATCAACTGATCCGATATTGACCCGACCCA
Found at i:24920 original size:8 final size:8
Alignment explanation
Indices: 24907--24945 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
24897 CATTTTCAGG
24907 GAATTTGA
1 GAATTTGA
24915 GAATTT-A
1 GAATTTGA
* *
24922 GAGTTTGG
1 GAATTTGA
24930 GAATTTGA
1 GAATTTGA
24938 GAATTTGA
1 GAATTTGA
24946 AAGATTGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.38
Consensus pattern (8 bp):
GAATTTGA
Found at i:25240 original size:128 final size:128
Alignment explanation
Indices: 25013--25386 Score: 714
Period size: 128 Copynumber: 2.9 Consensus size: 128
25003 CTATAATCGG
25013 TTCACTATTCATATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
25077 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
25140 TTCACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
25205 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
* *
25268 TTCACTATTCATATGAAGGCGCGTTCCTGTGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
25333 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGT
66 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGT
25387 TTGAATAACT
Statistics
Matches: 243, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
127 28 0.12
128 215 0.88
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (128 bp):
TTCACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:25839 original size:33 final size:34
Alignment explanation
Indices: 25780--25877 Score: 126
Period size: 33 Copynumber: 2.9 Consensus size: 34
25770 ATTTAATGTT
*
25780 AAATTTCGAATACTATAATTTATATTTTAAATTG
1 AAATTTCGAATAATATAATTTATATTTTAAATTG
* * * * *
25814 AAATTT-GAATAATATTATTTTTATTTTTATTTT
1 AAATTTCGAATAATATAATTTATATTTTAAATTG
*
25847 AAATTTCGAATAATATAATTTGTATTTTAAA
1 AAATTTCGAATAATATAATTTATATTTTAAA
25878 AACATTTATC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 27 0.51
34 26 0.49
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (34 bp):
AAATTTCGAATAATATAATTTATATTTTAAATTG
Found at i:26445 original size:20 final size:21
Alignment explanation
Indices: 26395--26465 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
26385 TATGGTATAA
*
26395 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
26416 AA-CCTG-GCGGCTAGGAATGT
1 AACCCTGCG-GGCTAGGAATGT
*
26436 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
26457 AACCCTGCG
1 AACCCTGCG
26466 AGATGGCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.38
21 26 0.58
22 1 0.02
ACGTcount: A:0.21, C:0.28, G:0.32, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:26495 original size:21 final size:21
Alignment explanation
Indices: 26469--26516 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
26459 CCCTGCGAGA
*
26469 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
26490 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
26511 GGGCAT
1 TGGCAT
26517 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:28277 original size:34 final size:32
Alignment explanation
Indices: 28237--28307 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 32
28227 AATTCTAAAT
* *
28237 AATAATAATTATATAAATATTATTTTAATAAAAA
1 AATAATAATTACATAAATA-TATTAT-ATAAAAA
* *
28271 AATAATATTTACATAAATATATTATATAAAAT
1 AATAATAATTACATAAATATATTATATAAAAA
28303 AATAA
1 AATAA
28308 CTATTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 11 0.33
33 5 0.15
34 17 0.52
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
AATAATAATTACATAAATATATTATATAAAAA
Found at i:28297 original size:19 final size:18
Alignment explanation
Indices: 28251--28297 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
28241 ATAATTATAT
28251 AAATATTAT-TTTAATAA
1 AAATATTATATTTAATAA
* *
28268 AAAAATAATATTTACATAA
1 AAATATTATATTTA-ATAA
*
28287 ATATATTATAT
1 AAATATTATAT
28298 AAAATAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 7 0.30
18 4 0.17
19 12 0.52
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATTATATTTAATAA
Found at i:34923 original size:38 final size:40
Alignment explanation
Indices: 34881--34992 Score: 115
Period size: 38 Copynumber: 2.8 Consensus size: 40
34871 GTCCAAAATA
* *
34881 TTTTTGAAAA-ATACAATATATAGTTTTT-AGAAAAT-AG
1 TTTTTGAAAACATATAATATATAGTTTTTAAAAAAATCAG
*
34918 CTTTTT-AAAACATATAATATATACTTTTTAAAAAAATCAG
1 -TTTTTGAAAACATATAATATATAGTTTTTAAAAAAATCAG
* * *
34958 TTTTCGAAAATATATATATTATATAGTTTTGAAAA
1 TTTTTGAAAACATATA-A-TATATAGTTTTTAAAA
34993 CGGTTTTCGA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
37 4 0.07
38 21 0.34
39 10 0.16
40 11 0.18
41 1 0.02
42 14 0.23
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (40 bp):
TTTTTGAAAACATATAATATATAGTTTTTAAAAAAATCAG
Found at i:35078 original size:28 final size:28
Alignment explanation
Indices: 35029--35082 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
35019 TTTGAAAATA
*
35029 TTTTGAAAACATATATATAATATATACT
1 TTTTGAAAACATATATAAAATATATACT
*
35057 TTTTGAAAACAT-TTTAAAAATATATA
1 TTTTGAAAACATATAT-AAAATATATA
35083 ATATATAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (28 bp):
TTTTGAAAACATATATAAAATATATACT
Found at i:35088 original size:73 final size:71
Alignment explanation
Indices: 34964--35334 Score: 263
Period size: 73 Copynumber: 5.2 Consensus size: 71
34954 TCAGTTTTCG
* * ** * * *
34964 AAAATATATATATTATATAGTTTTGAAAACGGTTTTCGAGAT-TATATTATATAGTTTTGAAAAT
1 AAAATATATATATTATATATTTTTGAAAAC-ATTTTAAAAATATATAATATATAGTTTTGAAAAC
35028 ATTTTGA
65 ATTTTGA
*
35035 AAACATATATATAATATATACTTTTTGAAAACATTTTAAAAATATATAATATATAGTTTTGAAAA
1 AAA-ATATATATATTATATA-TTTTTGAAAACATTTTAAAAATATATAATATATAGTTTTGAAAA
35100 CATTTTTG-
64 CA-TTTTGA
* *
35108 AAAATATATATATTATATAATTTTT-AAAACATTTTGAAAACATATACAATATACAGTTTTTGAA
1 AAAATATATATATTATAT-ATTTTTGAAAACATTTT-AAAA-ATATATAATATATAG-TTTTGAA
35172 AACA-TTT--
62 AACATTTTGA
* * *
35179 --AA-A-A-ATA-TATA-GTTTTTGAAAATATTTTGAAAATATATATAATATATA-TTTT-TAAA
1 AAAATATATATATTATATATTTTTGAAAACATTTT-AAAA-ATATATAATATATAGTTTTGAAAA
*
35235 CGTTTTG-
64 CATTTTGA
* * * * * *
35242 AAAATATATATAATATATAGTTTAGAAAATATTTTTTCGAAAATATATATAATGTGTAGTTTTGA
1 AAAATATATATATTATATATTTTTGAAAACA--TTTT--AAAA-ATATATAATATATAGTTTTGA
**
35307 AAGTATTTTTTG-
61 AA--ACATTTTGA
35319 AAAATATATAATATTA
1 AAAATATAT-ATATTA
35335 GTTTTTTATA
Statistics
Matches: 247, Mismatches: 27, Indels: 45
0.77 0.08 0.14
Matches are distributed among these distances:
61 4 0.02
62 7 0.03
63 5 0.02
64 26 0.11
65 6 0.02
66 4 0.02
67 2 0.01
68 4 0.02
69 6 0.02
70 10 0.04
71 13 0.05
72 52 0.21
73 66 0.27
74 20 0.08
75 2 0.01
77 15 0.06
78 5 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (71 bp):
AAAATATATATATTATATATTTTTGAAAACATTTTAAAAATATATAATATATAGTTTTGAAAACA
TTTTGA
Found at i:35089 original size:37 final size:34
Alignment explanation
Indices: 34919--35276 Score: 216
Period size: 34 Copynumber: 10.1 Consensus size: 34
34909 AGAAAATAGC
* * *
34919 TTTTTAAAACATATAATATATACTTTTTAAAAAAATCA
1 TTTTAAAAATATATAATATATA-TTTTT--GAAAA-CA
* * *
34957 GTTTTCGAAAATATATATATTATATAGTTTTGAAAACGG
1 -TTTT--AAAA-ATATATAATATATATTTTTGAAAAC-A
** * * * *
34996 TTTTCGAGAT-TATATTATATAGTTTTGAAAATA
1 TTTTAAAAATATATAATATATATTTTTGAAAACA
35029 TTTTGAAAACATATATATAATATATACTTTTTGAAAACA
1 TTTT--AAA-A-ATATATAATATATA-TTTTTGAAAACA
*
35068 TTTTAAAAATATATAATATATAGTTTTGAAAACA
1 TTTTAAAAATATATAATATATATTTTTGAAAACA
*
35102 TTTTTGAAAATATATATATTATATAATTTTT-AAAACA
1 -TTTT-AAAA-ATATATAATATAT-ATTTTTGAAAACA
* *
35139 TTTTGAAAACATATACAATATACAGTTTTTGAAAACA
1 TTTT-AAAA-ATATATAATATATA-TTTTTGAAAACA
* *
35176 -TTT--AAA-A-AT-ATATA-GTTTTTGAAAATA
1 TTTTAAAAATATATAATATATATTTTTGAAAACA
*
35203 TTTTGAAAATATATATAATATATATTTTT--AAACG
1 TTTT-AAAA-ATATATAATATATATTTTTGAAAACA
* * *
35237 TTTTGAAAATATATATAATATATAGTTTAGAAAATA
1 TTTT-AAAA-ATATATAATATATATTTTTGAAAACA
35273 TTTT
1 TTTT
35277 TTCGAAAATA
Statistics
Matches: 258, Mismatches: 34, Indels: 57
0.74 0.10 0.16
Matches are distributed among these distances:
27 11 0.04
28 3 0.01
29 5 0.02
30 1 0.00
31 3 0.01
32 2 0.01
33 7 0.03
34 64 0.25
35 27 0.10
36 45 0.17
37 29 0.11
38 20 0.08
39 22 0.09
41 7 0.03
42 12 0.05
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (34 bp):
TTTTAAAAATATATAATATATATTTTTGAAAACA
Found at i:35184 original size:72 final size:71
Alignment explanation
Indices: 35011--35189 Score: 227
Period size: 72 Copynumber: 2.5 Consensus size: 71
35001 GAGATTATAT
* * *
35011 TATATAGTTTTGAAAATATTTTGAAAACATATATATAATATATACTTTTTGAAAACATTTTAAAA
1 TATACAGTTTTGAAAACATTTT-AAAA-ATATATATAATATATAATTTTTGAAAACATTTTAAAA
*
35076 ATATATAA
64 ATATACAA
* * *
35084 TATATAGTTTTGAAAACATTTTTGAAAATATATATATTATATAATTTTT-AAAACATTTTGAAAA
1 TATACAGTTTTGAAAACA-TTTTAAAAATATATATAATATATAATTTTTGAAAACATTTT-AAAA
35148 CATATACAA
64 -ATATACAA
35157 TATACAGTTTTTGAAAACA-TTTAAAAATATATA
1 TATACAG-TTTTGAAAACATTTTAAAAATATATA
35190 GTTTTTGAAA
Statistics
Matches: 95, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
71 10 0.11
72 37 0.39
73 33 0.35
74 15 0.16
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (71 bp):
TATACAGTTTTGAAAACATTTTAAAAATATATATAATATATAATTTTTGAAAACATTTTAAAAAT
ATACAA
Found at i:35212 original size:28 final size:27
Alignment explanation
Indices: 35139--35217 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
35129 TTTTAAAACA
* * *
35139 TTTTGAAAACATAT-ACAATATACAGT
1 TTTTGAAAACATTTAAAAATATATAGT
35165 TTTTGAAAACATTTAAAAATATATAGT
1 TTTTGAAAACATTTAAAAATATATAGT
* *
35192 TTTTGAAAATATTTTGAAAATATATA
1 TTTTGAAAACA-TTTAAAAATATATA
35218 TAATATATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 13 0.28
27 20 0.43
28 13 0.28
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.41
Consensus pattern (27 bp):
TTTTGAAAACATTTAAAAATATATAGT
Found at i:35214 original size:100 final size:98
Alignment explanation
Indices: 35082--35264 Score: 278
Period size: 100 Copynumber: 1.8 Consensus size: 98
35072 AAAAATATAT
*
35082 AATATATAGTTTTGAAAACATTTTTGAAAATATATATATTATATAATTTTTAAAACATTTTGAAA
1 AATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATAT-ATTTTT-AAACATTTTGAAA
35147 ACATATACAATATACAGTTTTTGAAAACATTTAAA
64 ACATATACAATATACAGTTTTTGAAAACATTTAAA
* *
35182 AATATATAGTTTTTGAAAATA-TTTTGAAAATATATATAATATATATTTTTAAACGTTTTGAAAA
1 AATATATAG-TTTTGAAAACATTTTTGAAAATATATATAATATATATTTTTAAACATTTTGAAAA
* * *
35246 TATATATAATATATAGTTT
65 CATATACAATATACAGTTT
35265 AGAAAATATT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
98 29 0.38
99 6 0.08
100 31 0.41
101 10 0.13
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (98 bp):
AATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATATTTTTAAACATTTTGAAAAC
ATATACAATATACAGTTTTTGAAAACATTTAAA
Found at i:35253 original size:64 final size:62
Alignment explanation
Indices: 35121--35251 Score: 158
Period size: 64 Copynumber: 2.1 Consensus size: 62
35111 ATATATATAT
35121 TATATAATTTTTAAAACATTTTGAAAACATATACAATATACAGTTTTTGAAAACATTTAAAAA
1 TATATAATTTTTAAAACATTTTGAAAACATATACAATATACAGTTTTT-AAAACATTTAAAAA
* * * * * * *
35184 TATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATA-TTTTT-AAACGTTTTGAAAA
1 TATATAATTTTT-AAAACATTTTGAAAACATATACAATATACAGTTTTTAAAAC-ATTTAAAAA
35246 TATATA
1 TATATA
35252 TAATATATAG
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
61 4 0.07
62 13 0.22
63 16 0.27
64 26 0.44
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.43
Consensus pattern (62 bp):
TATATAATTTTTAAAACATTTTGAAAACATATACAATATACAGTTTTTAAAACATTTAAAAA
Found at i:35284 original size:39 final size:38
Alignment explanation
Indices: 35164--35339 Score: 172
Period size: 39 Copynumber: 4.8 Consensus size: 38
35154 CAATATACAG
* * *
35164 TTTTTGAAAACATTTAAAAATATATAGTTTTTGAAAATA-
1 TTTTTGAAAATATAT-ATAATATATAG-TTTTGAAAATAT
* *
35203 -TTTTGAAAATATATATAATATATA-TTTT--TAA-AC
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAATAT
* *
35236 GTTTTGAAAATATATATAATATATAGTTTAGAAAATAT
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAATAT
* * *
35274 TTTTTCGAAAATATATATAATGTGTAGTTTTGAAAGTAT
1 TTTTT-GAAAATATATATAATATATAGTTTTGAAAATAT
35313 TTTTTG-AAA-ATATATAATAT-TAGTTTT
1 TTTTTGAAAATATATATAATATATAGTTTT
35340 TTATATTATA
Statistics
Matches: 117, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
32 1 0.01
33 2 0.02
34 24 0.21
35 14 0.12
36 10 0.09
37 14 0.12
38 18 0.15
39 34 0.29
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (38 bp):
TTTTTGAAAATATATATAATATATAGTTTTGAAAATAT
Found at i:35288 original size:135 final size:136
Alignment explanation
Indices: 35029--35276 Score: 351
Period size: 134 Copynumber: 1.8 Consensus size: 136
35019 TTTGAAAATA
*
35029 TTTTGAAAACATATATATAATATATACTTTTTGAAAACATTTTAAAAATATATAATATATAGTTT
1 TTTTGAAAACATATATAAAATATATACTTTTTGAAAACATTTTAAAAATATATAATATATAGTTT
* * **
35094 TGAAAACATTTTTGAAAATATATATATTATATAATTTTTAAAACATTTTGAAAACATATACAATA
66 TGAAAACAGTTTTGAAAATATATATAATATATAATTTAGAAAACATTTTGAAAACATATACAATA
35159 TACAGT
131 TACAGT
* * *
35165 TTTTGAAAACATTTA-AAAATATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATA-T
1 TTTTGAAAACATATATAAAATATATACTTTTTGAAAACATTTT-AAAA-ATATATAATATATAGT
* * *
35228 TTT-TAAAC-GTTTTGAAAATATATATAATATATAGTTTAGAAAATATTTT
64 TTTGAAAACAGTTTTGAAAATATATATAATATATAATTTAGAAAACATTTT
35277 TTCGAAAATA
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
134 35 0.35
135 28 0.28
136 22 0.22
137 14 0.14
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (136 bp):
TTTTGAAAACATATATAAAATATATACTTTTTGAAAACATTTTAAAAATATATAATATATAGTTT
TGAAAACAGTTTTGAAAATATATATAATATATAATTTAGAAAACATTTTGAAAACATATACAATA
TACAGT
Found at i:35359 original size:16 final size:18
Alignment explanation
Indices: 35323--35357 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35313 TTTTTGAAAA
35323 TATATAATATTAGTTTTT
1 TATATAATATTAGTTTTT
*
35341 TATATTATA-TAGTTTTT
1 TATATAATATTAGTTTTT
35358 ATTTACATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TATATAATATTAGTTTTT
Found at i:35362 original size:20 final size:19
Alignment explanation
Indices: 35339--35382 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
35329 ATATTAGTTT
35339 TTTATATTATATAGTT-TTTA
1 TTTATATTATAT--TTATTTA
*
35359 TTTACATTATATTTATTTA
1 TTTATATTATATTTATTTA
35378 TTTAT
1 TTTAT
35383 TTTGTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 2 0.10
19 8 0.38
20 11 0.52
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTATATTATATTTATTTA
Found at i:36743 original size:25 final size:24
Alignment explanation
Indices: 36692--36744 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
36682 TCCTTTATTA
* *
36692 TTTAATTATTTATTTTTTCTCTCT
1 TTTAAATATTTATTTTTTCTCTAT
36716 TTTAAATATTTAATTTTTTC-CTGAT
1 TTTAAATATTT-ATTTTTTCTCT-AT
36741 TTTA
1 TTTA
36745 TTTAATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTAAATATTTATTTTTTCTCTAT
Found at i:36764 original size:22 final size:21
Alignment explanation
Indices: 36722--36765 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
36712 CTCTTTTAAA
* **
36722 TATTTAATTTTTTCCTGATTT
1 TATTTAATTTTTTACACATTT
36743 TATTTAATGTTTTTACACATTT
1 TATTTAAT-TTTTTACACATTT
36765 T
1 T
36766 TTAAAAATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.23, C:0.09, G:0.05, T:0.64
Consensus pattern (21 bp):
TATTTAATTTTTTACACATTT
Found at i:44319 original size:17 final size:17
Alignment explanation
Indices: 44297--44329 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
44287 TTATGTTATA
44297 AAGTCATAACGTATTAG
1 AAGTCATAACGTATTAG
44314 AAGTCATAACGTATTA
1 AAGTCATAACGTATTA
44330 TAAATTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
AAGTCATAACGTATTAG
Found at i:44949 original size:17 final size:17
Alignment explanation
Indices: 44929--44972 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
44919 CTTAATCACC
44929 AAGAATTCTTATTCAAT
1 AAGAATTCTTATTCAAT
44946 AAGAATTCTTATTCAAT
1 AAGAATTCTTATTCAAT
44963 AAGAATTCTT
1 AAGAATTCTT
44973 GCCTAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (17 bp):
AAGAATTCTTATTCAAT
Done.