Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001962.1 Hibiscus syriacus cultivar Beakdansim tig00003966_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: 62768
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4528 original size:12 final size:12
Alignment explanation
Indices: 4511--4537 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4501 AGATCTCCTT
4511 CGACGCATCAAG
1 CGACGCATCAAG
4523 CGACGCATCAAG
1 CGACGCATCAAG
4535 CGA
1 CGA
4538 ACAGAGGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.26, T:0.07
Consensus pattern (12 bp):
CGACGCATCAAG
Found at i:7389 original size:3 final size:3
Alignment explanation
Indices: 7341--7375 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
7331 CTACAAAAAC
7341 ATT A-T ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
7376 ATCAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:13209 original size:86 final size:85
Alignment explanation
Indices: 13016--13465 Score: 514
Period size: 85 Copynumber: 5.3 Consensus size: 85
13006 ATATAGTTTT
* * * * * * *
13016 TTCTCGACTTAAGCTATGATGTAAATTTGG-CATGCCCTTGAGCAGAATAG-AATCGAACTCGAA
1 TTCTCGCCTTGAGTTATGCTGTAAA-TTGGATATGCCTTTGAGCTGAAT-GTAATCGAACTCGAA
* *
13079 GGTATTTGTTGATAGATAACCC
64 GGTCTTTGTTGACAGATAACCC
* * * * *
13101 TTATCACCTTGAGTTATACTGTAAATAGGATATGCCTTTAAGCTGAATGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
13166 TCTTTTGTTGACAGATAACCC
66 TC-TTTGTTGACAGATAACCC
* *
13187 TTCTCGCCTTGAGCTATGCTGTAAATT-CA-ATGCACCTTTGAGCT-AAGTGTAATCGAACTCGA
1 TTCTCGCCTTGAGTTATGCTGTAAATTGGATATG--CCTTTGAGCTGAA-TGTAATCGAACTCGA
* *
13249 AGGTCTTGGTTGACAAATAACCC
63 AGGTCTTTGTTGACAGATAACCC
* * * * *
13272 TTCTCGCATTGAGTTATGTTGTAAATTGGATATGCCTTTGAGTTGAATGCAATCGAACTCGAAAG
1 TTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
*
13337 TCTTTTGTTGACAGATATCCC
66 TC-TTTGTTGACAGATAACCC
* * * * *
13358 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGTCTTTGAGCTGATTGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
*
13423 TCTTGGTTGACAGATAACCC
66 TCTTTGTTGACAGATAACCC
* *
13443 TTTTCGCCTTGAGTTATGTTGTA
1 TTCTCGCCTTGAGTTATGCTGTA
13466 CTTGGTTGGG
Statistics
Matches: 307, Mismatches: 48, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
84 7 0.02
85 154 0.50
86 143 0.47
87 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (85 bp):
TTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGG
TCTTTGTTGACAGATAACCC
Found at i:13460 original size:171 final size:171
Alignment explanation
Indices: 13066--13465 Score: 593
Period size: 171 Copynumber: 2.3 Consensus size: 171
13056 AGCAGAATAG
* * * * **
13066 AATCGAACTCGAAGGTATTTGTTGATAGATAACCCTTATCACCTTGAGTTATACTGTAAATAGGA
1 AATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTATCGCCTTGAGTTATGTTGTAAATAGGA
* *
13131 TATGCCTTTAAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCT
66 TATGCCTTTAAGCTGAATGCAATCGAACTCGAAAGTCTTTTGTTGACAGATAACCCTTCTCGCCT
13196 TGAGCTATGCTGTAAATTCAATGCACCTTTGAGCTAAGTGT
131 TGAGCTATGCTGTAAATTCAATGCACCTTTGAGCTAAGTGT
* * * *
13237 AATCGAACTCGAAGGTCTTGGTTGACAAATAACCCTTCTCGCATTGAGTTATGTTGTAAATTGGA
1 AATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTATCGCCTTGAGTTATGTTGTAAATAGGA
* * *
13302 TATGCCTTTGAGTTGAATGCAATCGAACTCGAAAGTCTTTTGTTGACAGATATCCCTTCTCGCCT
66 TATGCCTTTAAGCTGAATGCAATCGAACTCGAAAGTCTTTTGTTGACAGATAACCCTTCTCGCCT
** *** * *
13367 TGAGCTATGCTGTAAATTTGATGTGTCTTTGAGCTGATTGT
131 TGAGCTATGCTGTAAATTCAATGCACCTTTGAGCTAAGTGT
*
13408 AATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTTTCGCCTTGAGTTATGTTGTA
1 AATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTATCGCCTTGAGTTATGTTGTA
13466 CTTGGTTGGG
Statistics
Matches: 204, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
171 204 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (171 bp):
AATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTATCGCCTTGAGTTATGTTGTAAATAGGA
TATGCCTTTAAGCTGAATGCAATCGAACTCGAAAGTCTTTTGTTGACAGATAACCCTTCTCGCCT
TGAGCTATGCTGTAAATTCAATGCACCTTTGAGCTAAGTGT
Found at i:13839 original size:123 final size:124
Alignment explanation
Indices: 13536--13881 Score: 523
Period size: 124 Copynumber: 2.8 Consensus size: 124
13526 ATCTATCGGA
*
13536 CACGATATCCTTCATCGTGAAGTTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
* *
13601 ATTGGATATCCTTCGTTGTAAAGTTGAAATCCAATCTAGAGATGAATGCTTCTTGTGGG
66 ATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGAATGCTGCTTGTGGG
* * * * *
13660 CACGATATCCTTCGTCTTGAAGTTGAAATCGTGGATGGTTCTTTCGTTGTAAAGTTGAGCTTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
* * * *
13725 ATTGGATATCCTTCATTGTGAAGTTGAAATTCAATCTAGAGATG-GTGCTGCTTTTGGG
66 ATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGAATGCTGCTTGTGGG
* * *
13783 CACGATATCCTTCGTCGTAAAGTTGAAATTATGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
* * *
13848 ATTGGAAATCCTTTGTTGTGAAGTTAAAATCCAA
66 ATTGGATATCCTTCGTTGTGAAGTTGAAATCCAA
13882 CGGTTGTTTC
Statistics
Matches: 198, Mismatches: 24, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
123 98 0.49
124 100 0.51
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (124 bp):
CACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
ATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGAATGCTGCTTGTGGG
Found at i:14044 original size:64 final size:64
Alignment explanation
Indices: 13950--14134 Score: 255
Period size: 64 Copynumber: 2.8 Consensus size: 64
13940 AATCTTGTGT
* *
13950 AAGTTGTATTGTTTCGAGTCCAATATCCTTCGCTGTGATGTTGAAATTGACTCTAAATGAAACTG
1 AAGTTG-ATTG-TT-GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATAAAACTG
14015 GA
63 GA
* * *
14017 AAGTTGATTGTTGAGTCCAATACCCTTCGCTGTGAAATTGAAATTGACTCTGAATAAAACTGGA
1 AAGTTGATTGTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATAAAACTGGA
* * *
14081 AAGTT-ATTTGTTGAGTCCAATATCCTTCACTGTGAAGTTAAAATTGACTATAAA
1 AAGTTGA-TTGTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAA
14135 AGCTGCAAAA
Statistics
Matches: 106, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
63 1 0.01
64 93 0.88
65 2 0.02
66 4 0.04
67 6 0.06
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Consensus pattern (64 bp):
AAGTTGATTGTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATAAAACTGGA
Found at i:15205 original size:95 final size:95
Alignment explanation
Indices: 14994--15254 Score: 326
Period size: 95 Copynumber: 2.7 Consensus size: 95
14984 GGCTAGCTGG
* * * * *
14994 ATCCATAAAGCCGGGGCGTTTAACCAATTGTTCTAGAGGGATAGCTCAATATCATTGTA-TGGAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTC-A-AGC-TT-TATTGTAT
** * *
15058 ATTATAATCGTCTTTATTAGGCTAGCTGAATATT
62 ATTATAATCACCTTTATCAGGCTAGCTCAATATT
*
15092 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
*
15157 TAATCACCTTTATCAGGCTAGCTCAATCTT
66 TAATCACCTTTATCAGGCTAGCTCAATATT
* * * * *
15187 ATCTATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGTTTTATTATATATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-T
15252 ATA
65 ATA
15255 TAATATTATA
Statistics
Matches: 144, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
94 2 0.01
95 92 0.64
96 6 0.04
97 1 0.01
98 43 0.30
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTCAATATT
Found at i:19598 original size:15 final size:15
Alignment explanation
Indices: 19586--19751 Score: 62
Period size: 15 Copynumber: 10.9 Consensus size: 15
19576 GGTAAAAACA
19586 AAAATAATAAAAAAT
1 AAAATAATAAAAAAT
*
19601 AAAATAAAGTAAAATAT
1 AAAAT-AA-TAAAAAAT
* *
19618 ATATATATTAACGTATAAAT
1 A-AAATAATAA---A-AAAT
* * *
19638 AAAACATTAGAAAA-
1 AAAATAATAAAAAAT
* *
19652 AATATAATAAATAAT
1 AAAATAATAAAAAAT
* *
19667 AAATTAA-AATAAAT
1 AAAATAATAAAAAAT
*
19681 -AAATAAT-AATAAT
1 AAAATAATAAAAAAT
19694 -AAATCAA-AAATAAA-
1 AAAAT-AATAAA-AAAT
*
19708 AAAATAGTAAAATAAT
1 AAAATAATAAAA-AAT
19724 AAAATAAT-AAAAAT
1 AAAATAATAAAAAAT
19738 AAAA-ACATAAAAAA
1 AAAATA-ATAAAAAA
19752 ATATATGTAT
Statistics
Matches: 111, Mismatches: 22, Indels: 36
0.66 0.13 0.21
Matches are distributed among these distances:
13 14 0.13
14 29 0.26
15 32 0.29
16 13 0.12
17 9 0.08
18 3 0.03
19 7 0.06
20 4 0.04
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAATAATAAAAAAT
Found at i:19662 original size:26 final size:25
Alignment explanation
Indices: 19632--19713 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 25
19622 ATATTAACGT
19632 ATAAATAA-AACATTAGAAA-AAATATA
1 ATAAATAATAA-ATTA-AAATAAATA-A
19658 ATAAATAATAAATTAAAATAAATAA
1 ATAAATAATAAATTAAAATAAATAA
* *
19683 ATAATAATAATAAATCAAAAATAAAAAA
1 AT-A-AATAATAAAT-TAAAATAAATAA
19711 ATA
1 ATA
19714 GTAAAATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.12
26 18 0.37
27 13 0.27
28 12 0.24
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.24
Consensus pattern (25 bp):
ATAAATAATAAATTAAAATAAATAA
Found at i:19669 original size:33 final size:33
Alignment explanation
Indices: 19632--19774 Score: 104
Period size: 33 Copynumber: 4.3 Consensus size: 33
19622 ATATTAACGT
19632 ATAAATAAAACATTAGAAAA-AATATAATAAATA
1 ATAAATAAAACA-TAGAAAATAATATAATAAATA
* *
19665 ATAAATTAAA-ATAAATAAATAATAATAATAAATCA
1 ATAAATAAAACATAGA-AAATAAT-ATAATAAAT-A
* *
19700 A-AAATAAAAAAATAGTAAAATAATAAAAT-AATA
1 ATAAAT-AAAACATAG-AAAATAATATAATAAATA
*
19733 A-AAATAAAAACATA-AAAA-AATATATGTATAATA
1 ATAAAT-AAAACATAGAAAATAATATA-ATA-AATA
19766 AT-AATAAAA
1 ATAAATAAAA
19775 GGGCTAATTT
Statistics
Matches: 91, Mismatches: 8, Indels: 23
0.75 0.07 0.19
Matches are distributed among these distances:
30 5 0.05
31 8 0.09
32 8 0.09
33 34 0.37
34 16 0.18
35 9 0.10
36 10 0.11
37 1 0.01
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (33 bp):
ATAAATAAAACATAGAAAATAATATAATAAATA
Found at i:19703 original size:28 final size:27
Alignment explanation
Indices: 19648--19739 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 27
19638 AAAACATTAG
*
19648 AAAAAATATAATAAATAATAAATTAAAAT
1 AAAAAA-ATAAT-AATAATAAATAAAAAT
*
19677 AAATAAATAATAATAATAAATCAAAAAT
1 AAAAAAATAATAATAATAAAT-AAAAAT
*
19705 AAAAAAATAGTAA-AAT-AAT-AAAAT
1 AAAAAAATAATAATAATAAATAAAAAT
19729 AATAAAAATAA
1 AA-AAAAATAA
19740 AAACATAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
24 7 0.12
25 7 0.12
26 3 0.05
27 13 0.23
28 21 0.38
29 5 0.09
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.24
Consensus pattern (27 bp):
AAAAAAATAATAATAATAAATAAAAAT
Found at i:19719 original size:8 final size:8
Alignment explanation
Indices: 19655--19754 Score: 73
Period size: 8 Copynumber: 12.4 Consensus size: 8
19645 TAGAAAAAAT
19655 ATAAT-AA
1 ATAATAAA
19662 ATAATAAA
1 ATAATAAA
* *
19670 TTAAAATAA
1 ATAATA-AA
19679 ATAAATAATA
1 AT-AATAA-A
19689 ATAAT-AA
1 ATAATAAA
*
19696 ATCA-AAA
1 ATAATAAA
*
19703 ATAAAAAA
1 ATAATAAA
*
19711 ATAGTAAA
1 ATAATAAA
19719 ATAATAAA
1 ATAATAAA
19727 ATAATAAAA
1 ATAAT-AAA
19736 ATAA-AAA
1 ATAATAAA
*
19743 CATAAAAAA
1 -ATAATAAA
19752 ATA
1 ATA
19755 TATGTATAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
7 17 0.23
8 35 0.47
9 17 0.23
10 6 0.08
ACGTcount: A:0.74, C:0.02, G:0.01, T:0.23
Consensus pattern (8 bp):
ATAATAAA
Found at i:19736 original size:17 final size:17
Alignment explanation
Indices: 19655--19754 Score: 82
Period size: 16 Copynumber: 5.7 Consensus size: 17
19645 TAGAAAAAAT
19655 ATAATAAATAATAAATTAAA
1 ATAATAAA-AAT-AA-TAAA
*
19675 ATAA-ATAAATAATAATA
1 ATAATAAAAATAATAA-A
*
19692 ATAAATCAAAAATAAAAAA
1 AT-AAT-AAAAATAATAAA
*
19711 ATAGT-AAAATAATAAA
1 ATAATAAAAATAATAAA
19727 ATAATAAAAATAA-AAA
1 ATAATAAAAATAATAAA
19743 CATAA-AAAAATA
1 -ATAATAAAAATA
19755 TATGTATAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
16 27 0.40
17 16 0.24
18 7 0.10
19 5 0.07
20 13 0.19
ACGTcount: A:0.74, C:0.02, G:0.01, T:0.23
Consensus pattern (17 bp):
ATAATAAAAATAATAAA
Found at i:19741 original size:14 final size:14
Alignment explanation
Indices: 19655--19750 Score: 58
Period size: 14 Copynumber: 6.7 Consensus size: 14
19645 TAGAAAAAAT
19655 ATAATAAATAATAAA
1 ATAATAAA-AATAAA
*
19670 TTAA-AATAAATAAATA
1 ATAATAA-AAAT-AA-A
*
19686 ATAATAATAAATCAA
1 ATAATAA-AAATAAA
19701 A-AATAAAAA-AATA
1 ATAATAAAAATAA-A
* *
19714 GTAA-AATAATAAA
1 ATAATAAAAATAAA
19727 ATAATAAAAATAAA
1 ATAATAAAAATAAA
19741 A-ACATAAAAA
1 ATA-ATAAAAA
19751 AATATATGTA
Statistics
Matches: 64, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
12 1 0.02
13 13 0.20
14 30 0.47
15 8 0.12
16 5 0.08
17 7 0.11
ACGTcount: A:0.74, C:0.02, G:0.01, T:0.23
Consensus pattern (14 bp):
ATAATAAAAATAAA
Found at i:19754 original size:16 final size:15
Alignment explanation
Indices: 19648--19751 Score: 73
Period size: 17 Copynumber: 6.4 Consensus size: 15
19638 AAAACATTAG
*
19648 AAAAAATATAATAAAT
1 AAAAAATA-AAAAAAT
*
19664 AATAAATTAAAATAAAT
1 AA-AAAATAAAA-AAAT
*
19681 AAATAATAATAATAAAT
1 AAAAAATAA-AA-AAAT
*
19698 CAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
* *
19713 AGTAAAATAATAAAAT
1 A-AAAAATAAAAAAAT
*
19729 AATAAAAATAAAAACAT
1 -A-AAAAATAAAAAAAT
19746 AAAAAA
1 AAAAAA
19752 ATATATGTAT
Statistics
Matches: 70, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
15 9 0.13
16 24 0.34
17 37 0.53
ACGTcount: A:0.75, C:0.02, G:0.01, T:0.22
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:19764 original size:41 final size:42
Alignment explanation
Indices: 19692--19772 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 42
19682 AATAATAATA
*
19692 ATAAATCAAAAATAAAAAAATAGTAAAATAATAA-AATAATA
1 ATAAATAAAAAATAAAAAAATAGTAAAATAATAATAATAATA
**
19733 A-AAATAAAAACATAAAAAAATA-TATGTATAATAATAATAA
1 ATAAATAAAAA-ATAAAAAAATAGTA-AAATAATAATAATAA
19773 AAGGGCTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
40 10 0.29
41 19 0.56
42 5 0.15
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (42 bp):
ATAAATAAAAAATAAAAAAATAGTAAAATAATAATAATAATA
Found at i:22525 original size:21 final size:21
Alignment explanation
Indices: 22492--22531 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22482 CCGTTAAATA
22492 ACAAAAATAAAATAATTTATT
1 ACAAAAATAAAATAATTTATT
* *
22513 ACAAGAATTAAATAATTTA
1 ACAAAAATAAAATAATTTA
22532 GAAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
ACAAAAATAAAATAATTTATT
Found at i:30584 original size:45 final size:48
Alignment explanation
Indices: 30502--30594 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
30492 AAAATATATG
* * ** *
30502 TATATATATAATATATTATTTAATAAACAAATAAAATAATATAAAATA
1 TATACATATAAAATATTAGGTAATAAACAAATAAAATAATAAAAAATA
30550 TATACATATAAAATATTAGGTAA-AAAC-AA-AAAATAATAAAAAATA
1 TATACATATAAAATATTAGGTAATAAACAAATAAAATAATAAAAAATA
30595 AAATAAAGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
45 15 0.38
46 2 0.05
47 4 0.10
48 19 0.47
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.31
Consensus pattern (48 bp):
TATACATATAAAATATTAGGTAATAAACAAATAAAATAATAAAAAATA
Found at i:30594 original size:7 final size:8
Alignment explanation
Indices: 30579--30740 Score: 79
Period size: 8 Copynumber: 20.1 Consensus size: 8
30569 GTAAAAACAA
30579 AAAATAAT
1 AAAATAAT
30587 AAAA-AAT
1 AAAATAAT
30594 AAAATAAAGT
1 AAAAT-AA-T
30604 AAAATATAT
1 AAAATA-AT
* *
30613 ATATTAACGT
1 AAAATAA--T
30623 ATAAATAA-
1 A-AAATAAT
* * *
30631 AACATTAG
1 AAAATAAT
30639 AAAA-AAT
1 AAAATAAT
*
30646 ATAATAAAT
1 AAAAT-AAT
30655 AATAA-AAT
1 AA-AATAAT
30663 AAAATAA-
1 AAAATAAT
*
30670 ATAATAAT
1 AAAATAAT
30678 AATAATAAT
1 AA-AATAAT
*
30687 -AAATCA-
1 AAAATAAT
*
30693 AAAATAAA
1 AAAATAAT
*
30701 AAAATAGT
1 AAAATAAT
30709 AAAATAAT
1 AAAATAAT
*
30717 AAAATAAA
1 AAAATAAT
30725 AAAATAA-
1 AAAATAAT
*
30732 AAAAAAAT
1 AAAATAAT
30740 A
1 A
30741 TGTATAATAA
Statistics
Matches: 117, Mismatches: 20, Indels: 34
0.68 0.12 0.20
Matches are distributed among these distances:
7 38 0.32
8 46 0.39
9 18 0.15
10 11 0.09
11 4 0.03
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Found at i:30658 original size:3 final size:3
Alignment explanation
Indices: 30646--30756 Score: 60
Period size: 3 Copynumber: 38.3 Consensus size: 3
30636 TAGAAAAAAT
30646 ATA ATAA ATA ATA A-A ATA A-A ATAA ATA ATA ATA ATA ATA ATAA ATCA
1 ATA AT-A ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT-A AT-A
* * * *
30693 AAA ATA A-A AAA ATA GTA A-A ATA ATA A-A ATA A-A AAA ATA A-A A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
30735 AAA AT- ATGT ATA ATA ATA ATA A
1 ATA ATA AT-A ATA ATA ATA ATA A
30757 AAGGGCTAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 24
0.73 0.08 0.20
Matches are distributed among these distances:
2 18 0.21
3 56 0.64
4 13 0.15
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (3 bp):
ATA
Found at i:30666 original size:23 final size:23
Alignment explanation
Indices: 30640--30741 Score: 79
Period size: 23 Copynumber: 4.3 Consensus size: 23
30630 AAACATTAGA
30640 AAAAATATAATAAATAATAAAAT
1 AAAAATATAATAAATAATAAAAT
*
30663 AAAATAAATAATAATAATAATAATAAAT
1 AAAA-ATATAAT-A-AATAAT-A-AAAT
* *
30691 CAAAAATA-AAAAAATAGTAAAAT
1 -AAAAATATAATAAATAATAAAAT
30714 AATAAA-ATAA-AAA-AATAAAA-
1 AA-AAATATAATAAATAATAAAAT
30734 AAAAATAT
1 AAAAATAT
30742 GTATAATAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 21
0.71 0.05 0.23
Matches are distributed among these distances:
19 3 0.05
20 4 0.06
21 6 0.09
22 6 0.09
23 13 0.20
24 7 0.11
25 6 0.09
26 7 0.11
27 3 0.05
28 6 0.09
29 4 0.06
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.23
Consensus pattern (23 bp):
AAAAATATAATAAATAATAAAAT
Found at i:30682 original size:30 final size:29
Alignment explanation
Indices: 30646--30740 Score: 103
Period size: 30 Copynumber: 3.3 Consensus size: 29
30636 TAGAAAAAAT
30646 ATAATAAATAATAAAATAAAATAAATAATA
1 ATAATAAATAATAAAATAAAATAAATAA-A
30676 ATAAT-AATAAT-AAATCAAAAATAAA-AAA
1 ATAATAAATAATAAAAT--AAAATAAATAAA
*
30704 ATAGTAAAATAATAAAATAAAA-AAATAAA
1 ATAAT-AAATAATAAAATAAAATAAATAAA
30733 A-AA-AAATA
1 ATAATAAATA
30741 TGTATAATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
26 5 0.09
28 13 0.23
29 16 0.28
30 19 0.33
31 4 0.07
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.22
Consensus pattern (29 bp):
ATAATAAATAATAAAATAAAATAAATAAA
Found at i:30753 original size:30 final size:31
Alignment explanation
Indices: 30645--30758 Score: 81
Period size: 32 Copynumber: 3.5 Consensus size: 31
30635 TTAGAAAAAA
* *
30645 TATAATAAATAATAAAATAAAATAAATAATAATAA
1 TATAATAAATAAAAAAATAAAA-AAA-AAT-AT-G
* * *
30680 TAATAATAAAT-CAAAAATAAAAAAATAGTA-A
1 T-ATAATAAATAAAAAAATAAAAAAA-AATATG
*
30711 AATAATAAAATAAAAAAATAAAAAAAAATATG
1 TATAAT-AAATAAAAAAATAAAAAAAAATATG
*
30743 TATAAT-AATAATAAAA
1 TATAATAAATAAAAAAA
30759 GGGCTAATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
30 14 0.21
31 8 0.12
32 18 0.27
33 1 0.02
34 6 0.09
35 10 0.15
36 9 0.14
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.25
Consensus pattern (31 bp):
TATAATAAATAAAAAAATAAAAAAAAATATG
Found at i:40876 original size:31 final size:31
Alignment explanation
Indices: 40841--40942 Score: 186
Period size: 31 Copynumber: 3.3 Consensus size: 31
40831 CTGAATAACC
*
40841 TAGGTAATCAGTCCATATGTCCCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
40872 TAGGTAAACAGTCCATATGTCCCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
*
40903 TAAGTAAACAGTCCATATGTCCCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
40934 TAGGTAAAC
1 TAGGTAAAC
40943 CCTCGACCCT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
TAGGTAAACAGTCCATATGTCCCGAAGAACA
Found at i:45197 original size:3 final size:3
Alignment explanation
Indices: 45189--45267 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
45179 GCAGTTGTGC
45189 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
45237 AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
45268 TGGGGAGTTA
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:46327 original size:198 final size:197
Alignment explanation
Indices: 45957--46507 Score: 526
Period size: 198 Copynumber: 2.8 Consensus size: 197
45947 GCAAGAATTT
* * ** *
45957 ATAGACATGTTCGA-GGGGTATTTTCGAGA-AGTTAATATGAAAATTTTCATAATTTATAAGATT
1 ATAGACATATTCGAGGGGGTATTTTTG-GATAGTTAATA--AATTTTTTTATAATTTATAAGATT
* * * *
46020 AGAGGCGTAATATTGGAACTTATCTTTCT-ATTGATGCCAATAACGAGACATACGGTTTATTGTA
63 AGAGGCGTAGTATTGGAACTTATCTTT-TAATTGAGGCCAATAACGACACATACGGTATATTGTA
* * * * *
46084 AGCGGTGTAAGAATTACGTTGAAAATGGTTCCAAATCATGTTTTGTGCATGAAG-AAGCTAAAAT
127 AGCGGTGTAAAAATTACATTGAAAATGATTCCAAAGCATGTTTTGTGCATGAAGAAAACTAAAAT
*
46148 GGCTTG
192 GACTTG
* * * *
46154 ATATACATGTTCGAGGGGGTATTTTTAGG-TAGTTATTCTAAATTTTTTTGTAATTTATAAGATT
1 ATAGACATATTCGAGGGGGTATTTTT-GGATAGTTA--ATAAATTTTTTTATAATTTATAAGATT
* * * *
46218 AGAGACATAGTATTGGAACTTATCTTTTAATTGAGGCCAATATCGACACATATGAG-ATATTGTA
63 AGAGGCGTAGTATTGGAACTTATCTTTTAATTGAGGCCAATAACGACACATACG-GTATATTGTA
*
46282 AGCGG-GTAAAAATCT-CATTGAAAATGATTCCAAAGCTTGGTTTTGTGCATGAAGAAAAAACTA
127 AGCGGTGTAAAAAT-TACATTGAAAATGATTCCAAAGCAT-GTTTTGTGCATGAAG--AAAACTA
46345 AAATGACTTG
188 AAATGACTTG
* * ** * * *
46355 ATAGGCATATTCGATGGGGTATTTTTGGATAGTTAATATTTTTTTTTATAATTTATATGATCAGT
1 ATAGACATATTCGAGGGGGTATTTTTGGATAGTTAATAAATTTTTTTATAATTTATAAGATTAGA
* * * * * * * * * * *
46420 GGCGTAGTATTAGAACTTATCTTTCAATAGAGGCTAATACCGGCATAAACCAG-ATGTTATAAGC
66 GGCGTAGTATTGGAACTTATCTTTTAATTGAGGCCAATAACGACACATA-CGGTATATTGTAAGC
* *
46484 GGTGTAAAATTTGCATTGAAAATG
130 GGTGTAAAAATTACATTGAAAATG
46508 GTTTGAAACC
Statistics
Matches: 290, Mismatches: 48, Indels: 29
0.79 0.13 0.08
Matches are distributed among these distances:
197 40 0.14
198 109 0.38
199 77 0.27
200 22 0.08
201 42 0.14
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.36
Consensus pattern (197 bp):
ATAGACATATTCGAGGGGGTATTTTTGGATAGTTAATAAATTTTTTTATAATTTATAAGATTAGA
GGCGTAGTATTGGAACTTATCTTTTAATTGAGGCCAATAACGACACATACGGTATATTGTAAGCG
GTGTAAAAATTACATTGAAAATGATTCCAAAGCATGTTTTGTGCATGAAGAAAACTAAAATGACT
TG
Found at i:48195 original size:80 final size:80
Alignment explanation
Indices: 48055--48289 Score: 312
Period size: 80 Copynumber: 2.9 Consensus size: 80
48045 GCTATGATGA
* * * *
48055 TCGATACTTTAACTTTTGAAAACGTCAATGAATAAAAGATC-ACTAGTTAAGTTTAAATATCGAT
1 TCGATACTTTAAATTTTGAAAACGTCAATGAATATAAGATCGA-TAGTTAATTTTAAATATCAAT
*
48119 ACTTAATTTATAAGAT
65 ACTTAATCTATAAGAT
* * ** *
48135 TTGATATTTTAAATTTTGAAAAATTCAATGAAGATAAGATCGATAGTTAATTTTAAATATCAATA
1 TCGATACTTTAAATTTTGAAAACGTCAATGAATATAAGATCGATAGTTAATTTTAAATATCAATA
*
48200 CTTAATCTATAAGGT
66 CTTAATCTATAAGAT
* * *
48215 TCAATACTTTAGAA-TTTGAAAACGTCAATGAATATAAGATTGATAGTTTATTTTAAATATCAAT
1 TCGATACTTTA-AATTTTGAAAACGTCAATGAATATAAGATCGATAGTTAATTTTAAATATCAAT
48279 ACTTAATCTAT
65 ACTTAATCTAT
48290 GAGGTTCAAT
Statistics
Matches: 134, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
80 131 0.98
81 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.39
Consensus pattern (80 bp):
TCGATACTTTAAATTTTGAAAACGTCAATGAATATAAGATCGATAGTTAATTTTAAATATCAATA
CTTAATCTATAAGAT
Found at i:48586 original size:35 final size:36
Alignment explanation
Indices: 48503--48588 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 36
48493 ACCATGTATA
* *
48503 ATGGAATAAGAAG-GTTCTCGAGAAGGCCAGATTTG
1 ATGGAAGAAGAAGTTTTCTCGAGAAGGCCAGATTTG
* * *
48538 ATGGAACG-AGAAGTTTTCT-GAGAATGCTAGGTTTG
1 ATGGAA-GAAGAAGTTTTCTCGAGAAGGCCAGATTTG
48573 ATGGAAGAAGAAGTTT
1 ATGGAAGAAGAAGTTT
48589 CACGATACCA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
34 1 0.02
35 38 0.88
36 4 0.09
ACGTcount: A:0.34, C:0.08, G:0.31, T:0.27
Consensus pattern (36 bp):
ATGGAAGAAGAAGTTTTCTCGAGAAGGCCAGATTTG
Found at i:53423 original size:35 final size:35
Alignment explanation
Indices: 53370--53444 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
53360 TTCATGTTCA
*
53370 AAATTCCAAAACACTTTAATTACATTCTAAATCCC-
1 AAATTCCAAAACAATTTAATTACATTCTAAA-CCCT
* * *
53405 AAATTCTAAAATAATTTAATTACATTTTAAACCCT
1 AAATTCCAAAACAATTTAATTACATTCTAAACCCT
53440 AAATT
1 AAATT
53445 AAAGTATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 3 0.09
35 32 0.91
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (35 bp):
AAATTCCAAAACAATTTAATTACATTCTAAACCCT
Found at i:57960 original size:18 final size:18
Alignment explanation
Indices: 57934--58002 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
57924 CACTAACTTA
*
57934 AAACTATAAATTATACCT
1 AAACCATAAATTATACCT
**
57952 AAACCATAACCCTATTACCTCT
1 AAACCATAA-ATTA-TA-C-CT
*
57974 AAATCATAAATTATACCT
1 AAACCATAAATTATACCT
*
57992 AAACCTTAAAT
1 AAACCATAAAT
58003 CCTAAATCCT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
18 19 0.49
19 3 0.08
20 4 0.10
21 3 0.08
22 10 0.26
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.30
Consensus pattern (18 bp):
AAACCATAAATTATACCT
Found at i:58279 original size:24 final size:26
Alignment explanation
Indices: 58228--58277 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
58218 GAGTTGATTC
*
58228 TAAAGGACAGATTTATAAAATTTAAA
1 TAAAGGACAAATTTATAAAATTTAAA
*
58254 TAAA-GACAAATTTATAAATTTTAA
1 TAAAGGACAAATTTATAAAATTTAA
58278 TAGAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (26 bp):
TAAAGGACAAATTTATAAAATTTAAA
Found at i:58290 original size:18 final size:19
Alignment explanation
Indices: 58269--58308 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
58259 ACAAATTTAT
58269 AAATTT-TAATAGAAATA-A
1 AAATTTCTAATA-AAATATA
58287 AAATTTCTAATAAAATATA
1 AAATTTCTAATAAAATATA
58306 AAA
1 AAA
58309 AAGTATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
AAATTTCTAATAAAATATA
Found at i:58564 original size:16 final size:16
Alignment explanation
Indices: 58543--58576 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
58533 TAATAAATAA
58543 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
58559 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
58575 AC
1 AC
58577 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.26, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:58665 original size:16 final size:16
Alignment explanation
Indices: 58640--58682 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
58630 CATTTAATAA
58640 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
58656 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
*
58672 ATAAACAAACA
1 ATAAACGAACA
58683 TAAACGTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.21, G:0.09, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:58678 original size:22 final size:20
Alignment explanation
Indices: 58636--58688 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
58626 CGTTCATTTA
*
58636 ATAAATAAACGAACACGAAC
1 ATAAATAAACGAACACAAAC
*
58656 ATAAATGAACACGAACATAAAC
1 ATAAAT-AA-ACGAACACAAAC
58678 A-AACATAAACG
1 ATAA-ATAAACG
58689 TTGGAGACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 9 0.32
21 6 0.21
22 13 0.46
ACGTcount: A:0.60, C:0.19, G:0.09, T:0.11
Consensus pattern (20 bp):
ATAAATAAACGAACACAAAC
Found at i:59429 original size:14 final size:14
Alignment explanation
Indices: 59410--59440 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
59400 GTTAAACATA
*
59410 AACGAACATAATCG
1 AACGAACATAAACG
59424 AACGAACATAAACG
1 AACGAACATAAACG
59438 AAC
1 AAC
59441 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:59436 original size:24 final size:24
Alignment explanation
Indices: 59404--59451 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
59394 GATTGTGTTA
*
59404 AACATAAACGAACATAATCGAACG
1 AACATAAACGAACATAACCGAACG
59428 AACATAAACGAACATAACCGAACG
1 AACATAAACGAACATAACCGAACG
59452 TTCACAACGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (24 bp):
AACATAAACGAACATAACCGAACG
Done.