Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001770.1 Hibiscus syriacus cultivar Beakdansim tig00003569_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: 60662
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Found at i:5548 original size:54 final size:54
Alignment explanation
Indices: 5503--5786 Score: 236
Period size: 54 Copynumber: 5.3 Consensus size: 54
5493 TTTGAGATGA
* * * * *
5503 ACACGTAGTACCGATACAGTCGTTCATAAACATATTATGAATTCTTTGGGTTGC
1 ACACCTAGTGCCGATACGGTCGTCCATAAACACATTATGAATTCTTTGGGTTGC
* *
5557 ACACCTAGTGCTGATACGGTCGTCCATAAACACATTATAAATT-TTGTGGGTTGC
1 ACACCTAGTGCCGATACGGTCGTCCATAAACACATTATGAATTCTT-TGGGTTGC
* * *
5611 ACACTTAGTGCCGATACGGTTGTCCATAAACACATTATGAATT-TCGTGGGTTGC
1 ACACCTAGTGCCGATACGGTCGTCCATAAACACATTATGAATTCT-TTGGGTTGC
* * * * * * ** * *
5665 ACACTTAGTGCCTATACGATCCTTCATCAACATGTGATGAATTATGTT-GGTTGC
1 ACACCTAGTGCCGATACGGTCGTCCATAAACACATTATGAATTCT-TTGGGTTGC
* * * * * * * *
5719 ACACTTAGTGCCTATAAGGTCGTTCATCAACATATGATGAATTC-GTGGGTT-C
1 ACACCTAGTGCCGATACGGTCGTCCATAAACACATTATGAATTCTTTGGGTTGC
* *
5771 ACACTTAGAGCCGATA
1 ACACCTAGTGCCGATA
5787 GTACACATAG
Statistics
Matches: 195, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
52 16 0.08
53 6 0.03
54 171 0.88
55 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (54 bp):
ACACCTAGTGCCGATACGGTCGTCCATAAACACATTATGAATTCTTTGGGTTGC
Found at i:5674 original size:108 final size:107
Alignment explanation
Indices: 5503--5778 Score: 313
Period size: 108 Copynumber: 2.6 Consensus size: 107
5493 TTTGAGATGA
* * * * *
5503 ACACGTAGTACCGATACAGTCGTTCATAAACATATTATGAATTCTTTGGGTTGCACACCTAGTG-
1 ACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTC-GTGGGTTGCACACTTAGTGC
* * * *
5567 CTGATACGGTCGTCCATAAACACATTATAAATTTTGTGGGTTGC
65 CT-ATACGATCCTCCATAAACACATGATAAATTATGTGGGTTGC
* * *
5611 ACACTTAGTGCCGATACGGTTGTCCATAAACACATTATGAATTTCGTGGGTTGCACACTTAGTGC
1 ACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAA-TTCGTGGGTTGCACACTTAGTGC
* * ** * *
5676 CTATACGATCCTTCATCAACATGTGATGAATTATGTTGGTTGC
65 CTATACGATCCTCCATAAACACATGATAAATTATGTGGGTTGC
* * * *
5719 ACACTTAGTGCCTATAAGGTCGTTCATCAACATATGATGAATTCGTGGGTT-CACACTTAG
1 ACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCGTGGGTTGCACACTTAG
5779 AGCCGATAGT
Statistics
Matches: 141, Mismatches: 25, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
106 9 0.06
107 10 0.07
108 117 0.83
109 5 0.04
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (107 bp):
ACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCGTGGGTTGCACACTTAGTGCC
TATACGATCCTCCATAAACACATGATAAATTATGTGGGTTGC
Found at i:6174 original size:19 final size:19
Alignment explanation
Indices: 6150--6193 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
6140 ACTATGGTAC
6150 CGATACTCCCTTGCAATAT
1 CGATACTCCCTTGCAATAT
*
6169 CGATACTCCCTTGCAGTAT
1 CGATACTCCCTTGCAATAT
6188 CGATAC
1 CGATAC
6194 CATTTATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.30
Consensus pattern (19 bp):
CGATACTCCCTTGCAATAT
Found at i:8017 original size:25 final size:25
Alignment explanation
Indices: 7989--8062 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
7979 ATCCTATAAG
7989 CTTATAAGCTTATTTTACCAATATA
1 CTTATAAGCTTATTTTACCAATATA
* *
8014 CTTATCA--TT-TGTT-CC-ATA-A
1 CTTATAAGCTTATTTTACCAATATA
8033 GC-TAGTAAGCTTATTTTACCAATATA
1 -CTTA-TAAGCTTATTTTACCAATATA
8059 CTTA
1 CTTA
8063 CCATTTGTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 17
0.63 0.07 0.30
Matches are distributed among these distances:
19 3 0.08
20 6 0.17
21 2 0.06
22 5 0.14
23 5 0.14
24 2 0.06
25 10 0.28
26 3 0.08
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (25 bp):
CTTATAAGCTTATTTTACCAATATA
Found at i:8035 original size:45 final size:45
Alignment explanation
Indices: 7984--8099 Score: 182
Period size: 45 Copynumber: 2.6 Consensus size: 45
7974 TATTTATCCT
*
7984 ATAAGCTTATAAGCTTATTTTACCAATATACTTATCATTTGTTCC
1 ATAAGCTTATAAGCTTATTTTACCAATATACTTACCATTTGTTCC
8029 ATAAGC-TAGTAAGCTTATTTTACCAATATACTTACCATTTGTTCC
1 ATAAGCTTA-TAAGCTTATTTTACCAATATACTTACCATTTGTTCC
**
8074 ATAAGCTCGTAAGCTTATTTT-CCAAT
1 ATAAGCTTATAAGCTTATTTTACCAAT
8100 TTATCATTTA
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
44 7 0.11
45 59 0.89
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (45 bp):
ATAAGCTTATAAGCTTATTTTACCAATATACTTACCATTTGTTCC
Found at i:32176 original size:7 final size:7
Alignment explanation
Indices: 32164--32192 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
32154 AAAACTCGTA
32164 CTAAATC
1 CTAAATC
32171 CTAAATC
1 CTAAATC
32178 CTAAATC
1 CTAAATC
32185 CTAAATC
1 CTAAATC
32192 C
1 C
32193 ACAAAGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (7 bp):
CTAAATC
Found at i:33893 original size:27 final size:25
Alignment explanation
Indices: 33850--33911 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
33840 CAAGTAATAA
*
33850 TTTAAAAAGT-TAGAAAACTTAATTTTT
1 TTTAAAAA-TATAGAAAA-ATAA-TTTT
*
33877 TTTAAAAATATATAAAAATAATTTT
1 TTTAAAAATATAGAAAAATAATTTT
*
33902 TTAAAAAATA
1 TTTAAAAATA
33912 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 13 0.42
26 4 0.13
27 14 0.45
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (25 bp):
TTTAAAAATATAGAAAAATAATTTT
Found at i:34324 original size:15 final size:15
Alignment explanation
Indices: 34304--34333 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34294 ATATAAATTA
34304 ATATTTAATTTATTT
1 ATATTTAATTTATTT
*
34319 ATATTTATTTTATTT
1 ATATTTAATTTATTT
34334 TCAATTCAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATATTTAATTTATTT
Found at i:35837 original size:52 final size:49
Alignment explanation
Indices: 35745--35883 Score: 149
Period size: 52 Copynumber: 2.8 Consensus size: 49
35735 TAAGATGATG
* ** *
35745 AATTTTAATAAAAATA--TTTTATT-GAAACTTTTTATCTCGATGTGATA
1 AATTTAAATAAAAATATTTTTTATTAG-AACTAGTTATCTCGATGTGACA
* * *
35792 AATTTTAATAAAAATATTATATTTCATTAGAACTCGTTATCTCGATGTGACG
1 AATTTAAATAAAAATATT-T-TTT-ATTAGAACTAGTTATCTCGATGTGACA
*
35844 AGTTTAAATAAAAATATTTTTTATTAGAACTAGTTATCTC
1 AATTTAAATAAAAATATTTTTTATTAGAACTAGTTATCTC
35884 TACGTAACCA
Statistics
Matches: 79, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
47 16 0.20
49 17 0.22
50 4 0.05
51 4 0.05
52 37 0.47
53 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (49 bp):
AATTTAAATAAAAATATTTTTTATTAGAACTAGTTATCTCGATGTGACA
Found at i:36655 original size:60 final size:56
Alignment explanation
Indices: 36543--36655 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 56
36533 TTTGTACTAC
**
36543 ATTTAAAAGTTTATTTATTTTTAGTATAAAAATAATTATTTTACTTTTTATATCAT
1 ATTTAAAAGTTTATTTATTTTTAGTATAAAAATAATTATTTTACTTAATATATCAT
* *
36599 ATTTAAAATTTTTATTTAATCTTTATATTATAAAAATAA-TATTTTACTTCAATATAT
1 ATTTAAAA-GTTTATTT-AT-TTT-TAGTATAAAAATAATTATTTTACTT-AATATAT
36656 TTGAAAAGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
56 8 0.17
57 7 0.15
58 2 0.04
59 13 0.27
60 18 0.38
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (56 bp):
ATTTAAAAGTTTATTTATTTTTAGTATAAAAATAATTATTTTACTTAATATATCAT
Found at i:37284 original size:40 final size:40
Alignment explanation
Indices: 37234--37318 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 40
37224 CTTACAATAT
* *
37234 CGATACTATATAAACAGTATCGATATTGTTCATGTGGTAC
1 CGATAATATATAAACAGTACCGATATTGTTCATGTGGTAC
* *
37274 TGATAATATATGAACAGTACCGATATTGTTCATGTGGTAC
1 CGATAATATATAAACAGTACCGATATTGTTCATGTGGTAC
37314 CGATA
1 CGATA
37319 CCAAAGGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (40 bp):
CGATAATATATAAACAGTACCGATATTGTTCATGTGGTAC
Found at i:37621 original size:20 final size:20
Alignment explanation
Indices: 37574--37623 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
37564 AGAAAACATC
*
37574 CCCAACGACTCCAAATCACT
1 CCCAACGGCTCCAAATCACT
*
37594 TCCAACGGCTCCAAATCACT
1 CCCAACGGCTCCAAATCACT
37614 CCCAACGGCT
1 CCCAACGGCT
37624 AAAAACGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.44, G:0.10, T:0.16
Consensus pattern (20 bp):
CCCAACGGCTCCAAATCACT
Found at i:42057 original size:29 final size:29
Alignment explanation
Indices: 41973--42229 Score: 172
Period size: 30 Copynumber: 8.8 Consensus size: 29
41963 TTAATTTTAC
*
41973 ATCTTAACATTAAAAATAAATTTTATT-TT
1 ATCTTAAC-TTAAAAATATATTTTATTCTT
* *
42002 CATATTAACTTATTAAATATATTTTATTCTT
1 -ATCTTAACTTA-AAAATATATTTTATTCTT
*
42033 ATCTTAACCTAAAAATATATTTTATTCTT
1 ATCTTAACTTAAAAATATATTTTATTCTT
* * *
42062 ATTTTAACATAAAAATATATTTTAGTCTTT
1 ATCTTAACTTAAAAATATATTTTATTC-TT
* *
42092 ATCCTT-A-TTACAAA-A-ATTATATTCTT
1 AT-CTTAACTTAAAAATATATTTTATTCTT
* * * *
42118 AACTTAAATTATTAAATATATTCTATTCTT
1 ATCTTAACTTA-AAAATATATTTTATTCTT
* * *
42148 ACCTTAAATTATTAAATATGATTAATTATT-TT
1 ATCTTAACTTA-AAAATAT-ATT--TTATTCTT
* *
42180 -T-TT-ACTTAAAACGTATCTTTTATTCTT
1 ATCTTAACTTAAAA-ATATATTTTATTCTT
* *
42207 ATCTTAATTTTAAAATATATTTT
1 ATCTTAACTTAAAAATATATTTT
42230 TATTTTAAAA
Statistics
Matches: 182, Mismatches: 28, Indels: 35
0.74 0.11 0.14
Matches are distributed among these distances:
25 3 0.02
26 9 0.05
27 12 0.07
28 9 0.05
29 66 0.36
30 70 0.38
31 7 0.04
32 2 0.01
33 4 0.02
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (29 bp):
ATCTTAACTTAAAAATATATTTTATTCTT
Found at i:42094 original size:59 final size:60
Alignment explanation
Indices: 41973--42090 Score: 152
Period size: 59 Copynumber: 2.0 Consensus size: 60
41963 TTAATTTTAC
* * * *
41973 ATCTTAACATTAAAAATAAATTTTATTTTCATATTAACTTATTAAATATATTTTATTCTT
1 ATCTTAACACTAAAAATAAATTTTATTTTCATATTAACATATAAAATATATTTTAGTCTT
* *
42033 ATCTTAAC-CTAAAAATATATTTTATTCTT-ATTTTAACATA-AAAATATATTTTAGTCTT
1 ATCTTAACACTAAAAATAAATTTTATT-TTCATATTAACATATAAAATATATTTTAGTCTT
42091 TATCCTTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
58 16 0.31
59 25 0.49
60 10 0.20
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (60 bp):
ATCTTAACACTAAAAATAAATTTTATTTTCATATTAACATATAAAATATATTTTAGTCTT
Found at i:42233 original size:30 final size:29
Alignment explanation
Indices: 41985--42229 Score: 113
Period size: 29 Copynumber: 8.4 Consensus size: 29
41975 CTTAACATTA
* *
41985 AAAATAAATTTTATT-TTCATATTAACTTATT
1 AAAATATATTTTATTCTT-ATCTTAA-TT-TT
** *
42016 -AAATATATTTTATTCTTATCTTAACCTA
1 AAAATATATTTTATTCTTATCTTAATTTT
* ** *
42044 AAAATATATTTTATTCTTATTTTAACATA
1 AAAATATATTTTATTCTTATCTTAATTTT
*
42073 AAAATATATTTTAGTCTTTATCCTT-A--TT
1 AAAATATATTTTATTC-TTAT-CTTAATTTT
* *
42101 ACAAA-A-ATTATATTCTTAACTTAAATTATT
1 A-AAATATATTTTATTCTTATCTT-AATT-TT
* *
42131 -AAATATATTCTATTCTTACCTTAAATTATT
1 AAAATATATTTTATTCTTATCTT-AATT-TT
*
42161 -AAATATGATTAATTATT-TT-T-TT-A-CTT
1 AAAATAT-ATT--TTATTCTTATCTTAATTTT
*
42187 AAAACGTATCTTTTATTCTTATCTTAATTTT
1 AAAA--TATATTTTATTCTTATCTTAATTTT
42218 AAAATATATTTT
1 AAAATATATTTT
42230 TATTTTAAAA
Statistics
Matches: 170, Mismatches: 21, Indels: 48
0.71 0.09 0.20
Matches are distributed among these distances:
25 3 0.02
26 10 0.06
27 13 0.08
28 11 0.06
29 57 0.34
30 57 0.34
31 13 0.08
32 2 0.01
33 4 0.02
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (29 bp):
AAAATATATTTTATTCTTATCTTAATTTT
Found at i:42366 original size:33 final size:29
Alignment explanation
Indices: 42329--42464 Score: 112
Period size: 29 Copynumber: 4.5 Consensus size: 29
42319 AATATAAATA
42329 TTTAAATTAAGATAAGCA-TAAATTATATATTTT
1 TTTAAATTAAGATAAG-ATTAAA--ATATA--TT
*
42362 TTTAATTTAAGATAAGATTAAAATATATT
1 TTTAAATTAAGATAAGATTAAAATATATT
* * * *
42391 TTTAAATTAAAATAAGAATGAAATATACT
1 TTTAAATTAAGATAAGATTAAAATATATT
* * * *
42420 TTCAAATTACGAAAAGAATAAAATATATT
1 TTTAAATTAAGATAAGATTAAAATATATT
* *
42449 TAATAAGTTAAGATAA
1 T-TTAAATTAAGATAA
42465 AAAAATTTAA
Statistics
Matches: 84, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
29 50 0.60
30 9 0.11
31 5 0.06
32 1 0.01
33 19 0.23
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.38
Consensus pattern (29 bp):
TTTAAATTAAGATAAGATTAAAATATATT
Found at i:42387 original size:29 final size:29
Alignment explanation
Indices: 42312--42449 Score: 116
Period size: 29 Copynumber: 4.6 Consensus size: 29
42302 AAATATTATC
* *
42312 AGAATAAAATATAAATATTTAAATTAAGATA
1 AGAATAAAATAT--ATTTTTAAATTAAAATA
* * *
42343 AGCATAAATTATATATTTTTTTAATTTAAGATA
1 AGAATAAA--ATATA--TTTTTAAATTAAAATA
*
42376 AGATTAAAATATATTTTTAAATTAAAATA
1 AGAATAAAATATATTTTTAAATTAAAATA
* * * *
42405 AGAATGAAATATACTTTCAAATTACGAA-A
1 AGAATAAAATATATTTTTAAATTA-AAATA
42434 AGAATAAAATATATTT
1 AGAATAAAATATATTT
42450 AATAAGTTAA
Statistics
Matches: 88, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
29 49 0.56
30 2 0.02
31 13 0.15
33 24 0.27
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (29 bp):
AGAATAAAATATATTTTTAAATTAAAATA
Found at i:42481 original size:21 final size:23
Alignment explanation
Indices: 42437--42499 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
42427 TACGAAAAGA
*
42437 ATAAAATATATTTAATAAGTTAAG
1 ATAAAATAAATTTAAT-AGTTAAG
42461 ATAAAA-AAATTTAAT-GTTAAG
1 ATAAAATAAATTTAATAGTTAAG
* *
42482 ATGTAAATTAATTTAATA
1 AT-AAAATAAATTTAATA
42500 TGTGAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 8 0.24
22 3 0.09
23 16 0.48
24 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (23 bp):
ATAAAATAAATTTAATAGTTAAG
Found at i:42488 original size:23 final size:22
Alignment explanation
Indices: 42437--42483 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
42427 TACGAAAAGA
*
42437 ATAAAATATATTTAATAAGTTAAG
1 ATAAAA-AAATTTAAT-AGTTAAG
42461 ATAAAAAAATTTAAT-GTTAAG
1 ATAAAAAAATTTAATAGTTAAG
42482 AT
1 AT
42484 GTAAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (22 bp):
ATAAAAAAATTTAATAGTTAAG
Found at i:42510 original size:18 final size:17
Alignment explanation
Indices: 42468--42515 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
42458 AAGATAAAAA
42468 AATTTAATGTTAAGATGT
1 AATTTAAT-TTAAGATGT
* *
42486 AAATTAATTTAATATGT
1 AATTTAATTTAAGATGT
*
42503 GAATTTAAGTTAA
1 -AATTTAATTTAA
42516 AATATATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (17 bp):
AATTTAATTTAAGATGT
Found at i:43015 original size:21 final size:22
Alignment explanation
Indices: 42991--43043 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
42981 GGTCACTTGT
42991 ATAATTTATCCTTT-A-TTTTAA
1 ATAATTTAT-CTTTAATTTTTAA
*
43012 ATAATCTATCTTTAAATTTTTAA
1 ATAATTTATCTTT-AATTTTTAA
*
43035 CTAATTTAT
1 ATAATTTAT
43044 AATTATGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 4 0.15
21 8 0.31
22 1 0.04
23 13 0.50
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (22 bp):
ATAATTTATCTTTAATTTTTAA
Found at i:44501 original size:16 final size:17
Alignment explanation
Indices: 44476--44509 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
44466 ATATAATTCA
44476 TTTTACGAAAAATATTT
1 TTTTACGAAAAATATTT
*
44493 TTTTA-GAAAAATGTTT
1 TTTTACGAAAAATATTT
44509 T
1 T
44510 CAGTAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (17 bp):
TTTTACGAAAAATATTT
Found at i:46104 original size:136 final size:138
Alignment explanation
Indices: 45854--46209 Score: 368
Period size: 136 Copynumber: 2.6 Consensus size: 138
45844 TTTTATAAAT
* *
45854 TTTATTGAATCGAATAATCAATTTGGAACCCCAAGCAATGGCAAGGACCATTTTGAATATTCACC
1 TTTATTGAATCAAATAATCAATTTGGAACCCCAAGCAATAGCAAGGACCATTTTGAATATTCACC
* * * * * *
45919 TAAATTAAAGGATTGAATTGAAATTAAAACTAAGATGAAGGCTCGAATATTAAAACCTAATCAAT
66 TAAATTAAAGGACTAAAATGAAATTAAAACTAAGATGAACGATCGAATATTAAAACCTAACCAAT
45984 TGCAACAA
131 TGCAACAA
* **
45992 TTTATTAAATCAAATAATC-A-TTGGAACCCTGAGCAATAGC-AGAGACCATTTTGAATATTCAC
1 TTTATTGAATCAAATAATCAATTTGGAACCCCAAGCAATAGCAAG-GACCATTTTGAATATTCAC
* * * * *
46054 TTAAATT-AAGGAACTAAAGATGAAATT-AATCTAA-AGTGAACTATCTAATATTAGAACCTAAC
65 CTAAATTAAAGG-ACTAAA-ATGAAATTAAAACTAAGA-TGAACGATCGAATATTAAAACCTAAC
** *
46116 CAATTTTAACTA
127 CAATTGCAACAA
* * * * * *
46128 TTTATGGAATCAAATAATTAATTTGGAACCTCAAG-AAAAGGAGAGGACCAAATTTTTAA-ATTC
1 TTTATTGAATCAAATAATCAATTTGGAACCCCAAGCAATAGCA-AGGACC--ATTTTGAATATTC
46191 ACCTAAATTAAAGGACTAA
63 ACCTAAATTAAAGGACTAA
46210 GGCGAATGCT
Statistics
Matches: 178, Mismatches: 29, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
135 7 0.04
136 97 0.54
137 13 0.07
138 31 0.17
139 19 0.11
140 11 0.06
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (138 bp):
TTTATTGAATCAAATAATCAATTTGGAACCCCAAGCAATAGCAAGGACCATTTTGAATATTCACC
TAAATTAAAGGACTAAAATGAAATTAAAACTAAGATGAACGATCGAATATTAAAACCTAACCAAT
TGCAACAA
Found at i:49909 original size:2 final size:2
Alignment explanation
Indices: 49902--49934 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49892 CTGAAAAATC
49902 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 T
49935 TGAATGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52330 original size:18 final size:17
Alignment explanation
Indices: 52303--52336 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
52293 TAATTTTATT
52303 AAGGATACTAAACTTAA
1 AAGGATACTAAACTTAA
52320 AAGGTATACTAAACTTA
1 AAGG-ATACTAAACTTA
52337 TTTAATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (17 bp):
AAGGATACTAAACTTAA
Found at i:52422 original size:35 final size:33
Alignment explanation
Indices: 52354--52423 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
52344 TCTAATTAAG
* * *
52354 GAACCTAAACTAAGGCTTTAATTAATAACTAAA
1 GAACCTAAACTAAGGCATTAATTAAAAAATAAA
52387 GAACCTAAAATCTAAGG-ATTAATTAAAAATATAAA
1 GAACCT-AAA-CTAAGGCATTAATTAAAAA-ATAAA
52422 GA
1 GA
52424 CTAATTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
33 6 0.19
34 13 0.42
35 12 0.39
ACGTcount: A:0.53, C:0.11, G:0.10, T:0.26
Consensus pattern (33 bp):
GAACCTAAACTAAGGCATTAATTAAAAAATAAA
Found at i:53034 original size:46 final size:46
Alignment explanation
Indices: 52981--53258 Score: 411
Period size: 46 Copynumber: 6.1 Consensus size: 46
52971 TATACACTTA
* * *
52981 AATTATGGCATCCTTTCATGCATTAATGCATCATTTCTTGCATTTT
1 AATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
53027 AATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
1 AATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
* *
53073 AGTTATGGCATCCTTTCATGCCTTAAGGCATCCTTTCATGCATTTT
1 AATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
* *
53119 AGTTTTGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
1 AATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
* *
53165 AATTATGG----CTTTCATGCCTTAATGAATCTTTTCATGCATTTT
1 AATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
* * *
53207 AATTATGACATCCTTTTATGCCTTAATGCATCATTTCATGCATTTT
1 AATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
*
53253 AGTTAT
1 AATTAT
53259 CATAATCAAC
Statistics
Matches: 212, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
42 39 0.18
46 173 0.82
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (46 bp):
AATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
Found at i:53176 original size:22 final size:21
Alignment explanation
Indices: 53151--53213 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
53141 TTAATGCATC
53151 CTTTCATGCATTTTAATTATGG
1 CTTTCATGCATTTTAATTAT-G
* *
53173 CTTTCATGC--CTTAATGAAT-
1 CTTTCATGCATTTTAAT-TATG
53192 CTTTTCATGCATTTTAATTATG
1 C-TTTCATGCATTTTAATTATG
53214 ACATCCTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
21 4 0.12
22 14 0.44
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (21 bp):
CTTTCATGCATTTTAATTATG
Found at i:53230 original size:134 final size:135
Alignment explanation
Indices: 52986--53256 Score: 418
Period size: 134 Copynumber: 2.0 Consensus size: 135
52976 ACTTAAATTA
*
52986 TGGCATCCTTTCATGCATTAATGCATCATTTCTTGCATTTTAATTATGGCATCCTTTCATGCCTT
1 TGGCATCCTTTCATGCATTAATGCATCATTTCATGCATTTTAATTATGG---CCTTTCATGCCTT
* * * *
53051 AATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAGGCATCCTTTCATGCAT
63 AATGAATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAAGGCATCATTTCATGCAT
53116 TTTAGTTT
128 TTTAGTTT
* *
53124 TGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGG-CTTTCATGCCTTAAT
1 TGGCATCCTTTCATGCATTAATGCATCATTTCATGCATTTTAATTATGGCCTTTCATGCCTTAAT
* * *
53188 GAATCTTTTCATGCATTTTAATTATGACATCCTTTTATGCCTTAATGCATCATTTCATGCATTTT
66 GAATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAAGGCATCATTTCATGCATTTT
53253 AGTT
131 AGTT
53257 ATCATAATCA
Statistics
Matches: 123, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
134 77 0.63
138 46 0.37
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (135 bp):
TGGCATCCTTTCATGCATTAATGCATCATTTCATGCATTTTAATTATGGCCTTTCATGCCTTAAT
GAATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAAGGCATCATTTCATGCATTTT
AGTTT
Found at i:53786 original size:96 final size:90
Alignment explanation
Indices: 53600--53793 Score: 244
Period size: 92 Copynumber: 2.1 Consensus size: 90
53590 TACCCTAGTA
** * * *
53600 TCGATACTTTTATACTATGGTCCGATACCCCTTTCCAGTATCGATATCAAATTAACTGATGTTTC
1 TCGATACTAATATACTATGATCCGATACCCCTTTACAGTATCGATACCAAATTAACTGATGTTTC
*
53665 CTAGTATCGATACCCTTACCATGGTT
66 CTAGTATCGATACCCTTACAATGG-T
* *
53691 TCGATACTAATATACTATGATACCGATACCCCTTTACGGTATCGATACCGAAATTAGATTCGATG
1 TCGATACTAATATACTATGAT-CCGATACCCCTTTACAGTATCGATACC-AAATTA-ACT-GATG
* *
53756 TTTGCTTGGTATCGATACCCTTACAATGGT
62 TTT-CCTAGTATCGATACCCTTACAATGGT
53786 TCGATACT
1 TCGATACT
53794 GCCTCAACGG
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
91 18 0.20
92 24 0.27
93 6 0.07
94 2 0.02
95 16 0.18
96 22 0.25
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (90 bp):
TCGATACTAATATACTATGATCCGATACCCCTTTACAGTATCGATACCAAATTAACTGATGTTTC
CTAGTATCGATACCCTTACAATGGT
Found at i:59932 original size:46 final size:46
Alignment explanation
Indices: 59851--60081 Score: 376
Period size: 46 Copynumber: 5.1 Consensus size: 46
59841 CCATTTACAT
*
59851 TTTTAATTATGGCATCCTTTCATG-CTTAATGCATCCTTTTATGCA
1 TTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
* *
59896 TTTTAATTATGGCATCCTTTCATGTCTTAATCCATCCTTTCATGCA
1 TTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
*
59942 TTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
1 TTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
* *
59988 TTTTAATTATGGCATCCTTTCATGCCTTAATACATCATTTCATGCA
1 TTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
* *
60034 TTTTAATTAT-GTATCCTTTTATGCCTTAATGCATCCTTTCATGCA
1 TTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
60079 TTT
1 TTT
60082 AGTTATCATA
Statistics
Matches: 173, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 58 0.34
46 115 0.66
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.47
Consensus pattern (46 bp):
TTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
Found at i:59964 original size:26 final size:25
Alignment explanation
Indices: 59851--60012 Score: 140
Period size: 26 Copynumber: 7.0 Consensus size: 25
59841 CCATTTACAT
59851 TTTTAATTATGGCATCCTTTCATGC-
1 TTTT-ATTATGGCATCCTTTCATGCA
*
59876 --TTA--AT-GCATCCTTTTATGCA
1 TTTTATTATGGCATCCTTTCATGCA
59896 TTTTAATTATGGCATCCTTTCATG--
1 TTTT-ATTATGGCATCCTTTCATGCA
* *
59920 TCTTA--AT-CCATCCTTTCATGCA
1 TTTTATTATGGCATCCTTTCATGCA
59942 TTTTATTTATGGCATCCTTTCATGC-
1 TTTTA-TTATGGCATCCTTTCATGCA
*
59967 -CTTA--AT-GCATCCTTTCATGCA
1 TTTTATTATGGCATCCTTTCATGCA
59988 TTTTAATTATGGCATCCTTTCATGC
1 TTTT-ATTATGGCATCCTTTCATGC
60013 CTTAATACAT
Statistics
Matches: 110, Mismatches: 8, Indels: 37
0.71 0.05 0.24
Matches are distributed among these distances:
19 13 0.12
20 28 0.25
21 4 0.04
22 9 0.08
23 5 0.05
24 6 0.05
25 6 0.05
26 39 0.35
ACGTcount: A:0.21, C:0.22, G:0.10, T:0.46
Consensus pattern (25 bp):
TTTTATTATGGCATCCTTTCATGCA
Found at i:60077 original size:20 final size:20
Alignment explanation
Indices: 59862--60077 Score: 119
Period size: 20 Copynumber: 9.7 Consensus size: 20
59852 TTTAATTATG
59862 GCATCCTTTCATG-CTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
59881 GCATCCTTTTATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
*
59906 GGCATCCTTTCATGTCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
59927 CCATCCTTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
59952 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
59973 GCATCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
59998 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * *
60019 ACATCATTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
* *
60044 GTATCCTTTTATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
60064 GCATCCTTTCATGC
1 GCATCCTTTCATGC
60078 ATTTAGTTAT
Statistics
Matches: 151, Mismatches: 22, Indels: 47
0.69 0.10 0.21
Matches are distributed among these distances:
19 12 0.08
20 52 0.34
21 6 0.04
22 10 0.07
23 7 0.05
24 7 0.05
25 18 0.12
26 39 0.26
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.45
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:60527 original size:20 final size:21
Alignment explanation
Indices: 60502--60556 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
60492 CGATATTTCC
60502 TGGTATCGATACCCT-TACCA
1 TGGTATCGATACCCTATACCA
* ** *
60522 TGGTATTGATACAATATACTA
1 TGGTATCGATACCCTATACCA
*
60543 TGGTAGCGATACCC
1 TGGTATCGATACCC
60557 CCTTACGGTA
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (21 bp):
TGGTATCGATACCCTATACCA
Done.