Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007304.1 Hibiscus syriacus cultivar Beakdansim tig00019450_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: 79031
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1303 original size:23 final size:23
Alignment explanation
Indices: 1269--1322 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1259 CCAACCAAAT
* * *
1269 ATGGGAACGTAAATTCTATTCCC
1 ATGGGAATGTAAATTCCATTCAC
1292 ATGGGAATGTAAATTCCATTCAC
1 ATGGGAATGTAAATTCCATTCAC
1315 ATGGGAAT
1 ATGGGAAT
1323 CCCACATTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (23 bp):
ATGGGAATGTAAATTCCATTCAC
Found at i:3267 original size:11 final size:11
Alignment explanation
Indices: 3251--3279 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3241 GTTGAAGAAA
3251 TGAAGTAGATG
1 TGAAGTAGATG
3262 TGAAGTAGATG
1 TGAAGTAGATG
3273 TGAAGTA
1 TGAAGTA
3280 AATGGCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (11 bp):
TGAAGTAGATG
Found at i:7419 original size:3 final size:3
Alignment explanation
Indices: 7411--7445 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
7401 TTAGTGAGGC
7411 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7446 GTATCTCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:7732 original size:32 final size:32
Alignment explanation
Indices: 7653--8058 Score: 472
Period size: 32 Copynumber: 12.9 Consensus size: 32
7643 GAATGACCTA
* *
7653 TCCATATGTTCC-TAAGAACATAGGTAA-T-TG
1 TCCATATGTCCCGAAAG-ACATAGGTAATTATG
* *
7683 TCCAAATGTCCCTAAAGACATAGGTAATTATG
1 TCCATATGTCCCGAAAGACATAGGTAATTATG
* *
7715 TCTATATGTCCCGAAAGAC--AGGTAATTCTG
1 TCCATATGTCCCGAAAGACATAGGTAATTATG
* * * * *
7745 TTCATGTGTCCCAAAAGACATAGTTAATTCTG
1 TCCATATGTCCCGAAAGACATAGGTAATTATG
* *
7777 TCCATATATCCCGAAAGACATAGGTAATTCTG
1 TCCATATGTCCCGAAAGACATAGGTAATTATG
*
7809 TCCATATGTCCCAAAAGACAT--GTAA-TACTG
1 TCCATATGTCCCGAAAGACATAGGTAATTA-TG
* * *
7839 TCCATATGTCCTGAAAGACATAGGTAATTCTA
1 TCCATATGTCCCGAAAGACATAGGTAATTATG
*
7871 TCTATATGTCCCGAAAGACATAGGTAA-TACTG
1 TCCATATGTCCCGAAAGACATAGGTAATTA-TG
* *
7903 TCCATATGTCCCAAAAGACATAGGTAATTATA
1 TCCATATGTCCCGAAAGACATAGGTAATTATG
* *
7935 TCCATATGTCCAGAAAGACGTAGGTAATTATG
1 TCCATATGTCCCGAAAGACATAGGTAATTATG
* * * *
7967 TCTAAATGCCCCGAAAGACATAGGTAA-TACTA
1 TCCATATGTCCCGAAAGACATAGGTAATTA-TG
7999 TCCATATGTCCCGAAAGACATAGGTAATTATG
1 TCCATATGTCCCGAAAGACATAGGTAATTATG
8031 TCCATATGTCCCGAAAGACATAGGTAAT
1 TCCATATGTCCCGAAAGACATAGGTAAT
8059 ACCCGACTCT
Statistics
Matches: 318, Mismatches: 45, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.00
30 70 0.22
31 7 0.02
32 235 0.74
33 5 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (32 bp):
TCCATATGTCCCGAAAGACATAGGTAATTATG
Found at i:7801 original size:94 final size:95
Alignment explanation
Indices: 7653--8058 Score: 468
Period size: 94 Copynumber: 4.3 Consensus size: 95
7643 GAATGACCTA
* * *
7653 TCCATATGTTCC-TAAGAACATAGGTAA-T-TGTCCAAATGTCCCTAAAGACATAGGTAATTA-T
1 TCCATATGTCCCAAAAG-ACATAGGTAATTCTGTCCAAATGTCCCGAAAGACATAGGTAA-TACT
* * *
7714 GTCTATATGTCCCGAAAGAC-AGGTAATTCTG
64 GTCCATATGTCCCAAAAGACAAGGTAATTATG
* * * * * *
7745 TTCATGTGTCCCAAAAGACATAGTTAATTCTGTCCATATATCCCGAAAGACATAGGTAATTCTGT
1 TCCATATGTCCCAAAAGACATAGGTAATTCTGTCCAAATGTCCCGAAAGACATAGGTAATACTGT
*
7810 CCATATGTCCCAAAAGAC-ATGTAA-TACTG
66 CCATATGTCCCAAAAGACAAGGTAATTA-TG
** * * *
7839 TCCATATGTCCTGAAAGACATAGGTAATTCTATCTATATGTCCCGAAAGACATAGGTAATACTGT
1 TCCATATGTCCCAAAAGACATAGGTAATTCTGTCCAAATGTCCCGAAAGACATAGGTAATACTGT
*
7904 CCATATGTCCCAAAAGACATAGGTAATTATA
66 CCATATGTCCCAAAAGACA-AGGTAATTATG
* * * * *
7935 TCCATATGT-CCAGAAAGACGTAGGTAATTATGTCTAAATGCCCCGAAAGACATAGGTAATACTA
1 TCCATATGTCCCA-AAAGACATAGGTAATTCTGTCCAAATGTCCCGAAAGACATAGGTAATACTG
*
7999 TCCATATGTCCCGAAAGACATAGGTAATTATG
65 TCCATATGTCCCAAAAGACA-AGGTAATTATG
*
8031 TCCATATGTCCCGAAAGACATAGGTAAT
1 TCCATATGTCCCAAAAGACATAGGTAAT
8059 ACCCGACTCT
Statistics
Matches: 268, Mismatches: 36, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
92 18 0.07
93 6 0.02
94 126 0.47
95 1 0.00
96 113 0.42
97 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (95 bp):
TCCATATGTCCCAAAAGACATAGGTAATTCTGTCCAAATGTCCCGAAAGACATAGGTAATACTGT
CCATATGTCCCAAAAGACAAGGTAATTATG
Found at i:12064 original size:21 final size:22
Alignment explanation
Indices: 12024--12076 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
12014 AATTCCAGAA
* *
12024 TGCTACAGGGGTATCGATACCC-
1 TGCTACA-GTGTACCGATACCCT
12046 TGCTACAGTGTACCGATACCCT
1 TGCTACAGTGTACCGATACCCT
12068 TGCTACAGT
1 TGCTACAGT
12077 AATTTCGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (22 bp):
TGCTACAGTGTACCGATACCCT
Found at i:12410 original size:3 final size:3
Alignment explanation
Indices: 12402--12439 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
12392 GGTATAAAAT
12402 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12440 GCATTTCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12705 original size:32 final size:32
Alignment explanation
Indices: 12665--12982 Score: 433
Period size: 32 Copynumber: 9.9 Consensus size: 32
12655 CATATGTAAA
12665 TGTCCATATGTCCCGAAAGACATAGGTAATTC
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
* *
12697 TGTCCATATGTCCCGAAAAACATAGGTAATTA
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
*
12729 TGTCCATATGTCCCAAAAGACATAGGTAATTC
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
* *
12761 TGTTCATATGTCCCGAAAGACATAGGTAATAC
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
* * *
12793 CGTCAATATGTCCCAAAAGACATAGGTAATTC
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
* * *
12825 TGTCCATATGTCTCAAAAGACATAGGTAATAC
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
* * *
12857 TATCCATATGTCCCGAAAGACGTATGTAATT-
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
* *
12888 TCATCCATATGTCCCAAAAGACATAGGTAATAT-
1 T-GTCCATATGTCCCGAAAGACATAGGTAAT-TC
12921 TGTCCATATGTCCCGAAAGACATAGGTAATTC
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
* * *
12953 TGTCTATATGTCCTGAAAGACTTAGGTAAT
1 TGTCCATATGTCCCGAAAGACATAGGTAAT
12983 ACTTGACTCT
Statistics
Matches: 252, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
31 2 0.01
32 248 0.98
33 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAAGACATAGGTAATTC
Found at i:23653 original size:39 final size:38
Alignment explanation
Indices: 23599--23712 Score: 155
Period size: 34 Copynumber: 3.1 Consensus size: 38
23589 AAAGTCAAGT
* *
23599 CTTCACCAAAGAGTAGTAAAGCAAATCCATTTTGTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCA-TCTGTAAGC
23638 CTTCACCAAAGAGTAGTGAAGC--A-CCATCT-TAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATCTGTAAGC
**
23672 CTTCACGGAAGAGTAGTGAAGCAAATCCATCTGTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATCTGTAAGC
23710 CTT
1 CTT
23713 TAGAGCAAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
34 25 0.37
35 2 0.03
36 4 0.06
37 7 0.10
38 8 0.12
39 21 0.31
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (38 bp):
CTTCACCAAAGAGTAGTGAAGCAAATCCATCTGTAAGC
Found at i:23913 original size:42 final size:41
Alignment explanation
Indices: 23858--23959 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 41
23848 TTCACAATTT
* * *
23858 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCA-AGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTT-AGAGCAAGATG
* * * *
23899 CTTAAATCTTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
*
23941 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
23960 CATAAAACCT
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 16 0.33
42 32 0.67
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:24272 original size:174 final size:171
Alignment explanation
Indices: 23908--24300 Score: 588
Period size: 174 Copynumber: 2.3 Consensus size: 171
23898 GCTTAAATCT
* * *
23908 TTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCG
1 TTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCG
* ** *
23973 GGTAAGATGTTTTTACATGAATTTGAAAATGAAAATTATGTTTTAAGAAGATGAAATTTTTGAAA
66 GGTAAGATGTTTTCACATGAATTTGAAAATGAAAACGATGTTTTAAGAAGATGAAACTTTTGAAA
* *
24038 ACGAAGAATGCGATTTTCAAAATTTCATAATTTATAAGTCC
131 ACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCC
* * **
24079 GTCGGGCTATCAGTAAGTCTTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCTGTAAAACCTTC
1 TTCGGGCCATCAGTAAGTC-TTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTC
* *
24144 GGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAACGATGTTTTGAGAAGATGAAACTTTTG
65 GGGTAAGATGTTTTCACATGAATTTGAAAATG--AAAACGATGTTTTAAGAAGATGAAACTTTTG
24209 AAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCC
128 AAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCC
* * *
24253 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 TTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGA-TAAGTCCTTCGGG
24301 TAACTGGTAA
Statistics
Matches: 198, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
171 14 0.07
172 73 0.37
173 13 0.07
174 98 0.49
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (171 bp):
TTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCG
GGTAAGATGTTTTCACATGAATTTGAAAATGAAAACGATGTTTTAAGAAGATGAAACTTTTGAAA
ACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCC
Found at i:24393 original size:80 final size:80
Alignment explanation
Indices: 24259--24541 Score: 467
Period size: 80 Copynumber: 3.5 Consensus size: 80
24249 GTCCTTCGGG
* * **
24259 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG
24324 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAT
* *
24339 TCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG
*
24404 AGTAGTGAAGCAAAC
66 AGTAGTGAAGCAAAT
24419 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG
*
24484 AGCAGTGAAGCAAAT
66 AGTAGTGAAGCAAAT
* * *
24499 CCGTCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGT
1 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGT
24542 CATCAGTAAG
Statistics
Matches: 189, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 189 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAG
AGTAGTGAAGCAAAT
Found at i:24538 original size:22 final size:21
Alignment explanation
Indices: 24510--24580 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
24500 CGTCAGTAAG
24510 TCTTTCGAGCATGATGATGAAA
1 TCTTTCGAGCATGATGAT-AAA
* * * *
24532 TCCTTCGGGTCATCA-G-TAAG
1 TCTTTCGAG-CATGATGATAAA
24552 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATGA-TAAA
24574 TCTTTCG
1 TCTTTCG
24581 GGTCATTTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 4 0.11
20 10 0.27
21 1 0.03
22 18 0.49
23 4 0.11
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (21 bp):
TCTTTCGAGCATGATGATAAA
Found at i:24561 original size:42 final size:41
Alignment explanation
Indices: 24502--24628 Score: 166
Period size: 42 Copynumber: 3.0 Consensus size: 41
24492 AGCAAATCCG
24502 TCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCA
1 TCAGTAAGTCTTTCGAGCATGATGAT-AAATCCTTCGGGTCA
*
24544 TCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCA
1 TCAGTAAGTCTTTCGAGCATGATGA-TAAATCCTTCGGGTCA
** * * *
24586 TTTGTGAGT-TTCTCGAACAAGATGATAAATCCTTCGGGTCA
1 TCAGTAAGTCTT-TCGAGCATGATGATAAATCCTTCGGGTCA
24627 TC
1 TC
24629 CATAAGACCT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 18 0.24
42 56 0.75
43 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (41 bp):
TCAGTAAGTCTTTCGAGCATGATGATAAATCCTTCGGGTCA
Found at i:25008 original size:53 final size:53
Alignment explanation
Indices: 24928--25181 Score: 384
Period size: 53 Copynumber: 4.8 Consensus size: 53
24918 GAATCACACT
*
24928 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
24981 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
* *
25034 AGAAGATTGTTCTAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAAC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
* * ****
25087 AGAAGAGTGTTCGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCGTTTTT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
* *
25140 AGAAGATTGTTCAAGTTTCTTAATCCCTGAA-CAAGAGGGAGC
1 AGAAGATTGTTCGAG-TTC-TACTCCCTGAAGCAAGAGGGAGC
25182 AGACCTATCA
Statistics
Matches: 185, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
53 162 0.88
54 13 0.07
55 10 0.05
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (53 bp):
AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
Found at i:37628 original size:13 final size:14
Alignment explanation
Indices: 37605--37633 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
37595 ATAATAATAC
37605 TAATATTTAAATTA
1 TAATATTTAAATTA
37619 TAAT-TTTAAATTA
1 TAATATTTAAATTA
37632 TA
1 TA
37634 TTAATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATATTTAAATTA
Found at i:37679 original size:26 final size:25
Alignment explanation
Indices: 37615--37679 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
37605 TAATATTTAA
*
37615 ATTATAATTTTAAATTATATTAATAT
1 ATTATAA-TTTAAATTATATAAATAT
*
37641 ATTCTTAATTTAAATTATTATAAAT-T
1 ATT-ATAATTTAAATTA-TATAAATAT
37667 ATTATAATATTAA
1 ATTATAAT-TTAA
37680 TTGAAATCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 4 0.12
26 20 0.61
27 9 0.27
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTATAATTTAAATTATATAAATAT
Found at i:39881 original size:13 final size:13
Alignment explanation
Indices: 39863--39887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39853 TAATATTAAT
39863 ATTTAAATTATAA
1 ATTTAAATTATAA
39876 ATTTAAATTATA
1 ATTTAAATTATA
39888 GTAATATATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTAAATTATAA
Found at i:44029 original size:22 final size:21
Alignment explanation
Indices: 44004--44071 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
43994 TTTATTCTTA
44004 AATTAATTTAAATTAT-ATATAT
1 AATT-ATTTAAATTATAATAT-T
* *
44026 AATTTATTAAAATCATAATATT
1 AA-TTATTTAAATTATAATATT
44048 AA-TATTTAAATTATAA-ATT
1 AATTATTTAAATTATAATATT
44067 -ATTAT
1 AATTAT
44072 ATATTTGGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
18 1 0.03
19 6 0.15
20 12 0.31
22 14 0.36
23 6 0.15
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTATTTAAATTATAATATT
Found at i:69370 original size:9 final size:9
Alignment explanation
Indices: 69356--69388 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
69346 CGATTCATAC
69356 ATTCACGTT
1 ATTCACGTT
69365 ATTCACGTT
1 ATTCACGTT
69374 ATTCACGTT
1 ATTCACGTT
*
69383 ACTCAC
1 ATTCAC
69389 ATAGGTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.39
Consensus pattern (9 bp):
ATTCACGTT
Found at i:69428 original size:32 final size:32
Alignment explanation
Indices: 69387--69621 Score: 303
Period size: 32 Copynumber: 7.3 Consensus size: 32
69377 CACGTTACTC
*
69387 ACATAGGTAATTCTGTTCATATGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
* * * *
69419 ACATAGGTAATACCGTCAATATGTCCCAAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
* * *
69451 ACATAGGTAATTTTGTCCATATGTCTCAAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
* *
69483 ACATAGGTAATACTATCCATATGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
* * *
69515 ACGTATGTAATT-TCATCCATATGTCCCGAAAG
1 ACATAGGTAATTCT-GTCCATATGTCCCGAAAG
69547 ACATAGGTAATAT-TGTCCATATGTCCCGAAAG
1 ACATAGGTAAT-TCTGTCCATATGTCCCGAAAG
* *
69579 ACATAGGTAATTCTGTCTATATGTCCTGAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
69611 ACATAGGTAAT
1 ACATAGGTAAT
69622 ACTTGACTCT
Statistics
Matches: 177, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
31 2 0.01
32 173 0.98
33 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (32 bp):
ACATAGGTAATTCTGTCCATATGTCCCGAAAG
Found at i:69488 original size:64 final size:64
Alignment explanation
Indices: 69387--69624 Score: 334
Period size: 64 Copynumber: 3.7 Consensus size: 64
69377 CACGTTACTC
* * * *
69387 ACATAGGTAATTCTGTTCATATGTCCCGAAAGACATAGGTAATACCGTCAATATGTCCCAAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAG
* * * *
69451 ACATAGGTAATTTTGTCCATATGTCTCAAAAGACATAGGTAATACTATCCATATGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAG
* * * *
69515 ACGTATGTAATT-TCATCCATATGTCCCGAAAGACATAGGTAATATTGTCCATATGTCCCGAAAG
1 ACATAGGTAATTCT-GTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAG
* *
69579 ACATAGGTAATTCTGTCTATATGTCCTGAAAGACATAGGTAATACT
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACT
69625 TGACTCTTGG
Statistics
Matches: 151, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
63 1 0.01
64 149 0.99
65 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (64 bp):
ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAG
Found at i:69551 original size:96 final size:96
Alignment explanation
Indices: 69387--69623 Score: 339
Period size: 96 Copynumber: 2.5 Consensus size: 96
69377 CACGTTACTC
* *
69387 ACATAGGTAATTCTGTTCATATGTCCCGAAAGACATAGGTAATACCGTCAATATGTCCCAAAAGA
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACCATCAATATGTCCCAAAAGA
* *
69452 CATAGGTAATTTTGTCCATATGTCTCAAAAG
66 CATAGGTAATATTGTCCATATGTCCCAAAAG
* * * * ** * *
69483 ACATAGGTAATACTATCCATATGTCCCGAAAGACGTATGTAATTTCATCCATATGTCCCGAAAGA
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACCATCAATATGTCCCAAAAGA
*
69548 CATAGGTAATATTGTCCATATGTCCCGAAAG
66 CATAGGTAATATTGTCCATATGTCCCAAAAG
* *
69579 ACATAGGTAATTCTGTCTATATGTCCTGAAAGACATAGGTAATAC
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATAC
69624 TTGACTCTTG
Statistics
Matches: 120, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 120 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (96 bp):
ACATAGGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATACCATCAATATGTCCCAAAAGA
CATAGGTAATATTGTCCATATGTCCCAAAAG
Done.