Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000957.1 Hibiscus syriacus cultivar Beakdansim tig00001913_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: 73636
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6182 original size:2 final size:2
Alignment explanation
Indices: 6175--6217 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
6165 TCAATCTACA
6175 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
6217 A
1 A
6218 ACAAATTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6385 original size:85 final size:85
Alignment explanation
Indices: 6238--6401 Score: 195
Period size: 85 Copynumber: 1.9 Consensus size: 85
6228 GAAATACAAT
* * * * * * ** *
6238 CACACGAATGTGTGTCATCTTTTTTAATGATGTGTGCTTCAATGACACGCAATGTATGTCATACA
1 CACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGAACATCATAAA
**
6303 TGCGTGTCATAAATTTATGA
66 TGCGCATCATAAATTTATGA
* *
6323 CACACAAATGTGTGTTATCTTAATTT-ATGACGGGGGCTTCAATGACACTCAATGAACATCATAA
1 CACACAAATGTGTGTCATCTT-ATTTAATGACGGGGGCTTCAATGACACGCAATGAACATCATAA
6387 ATGCGCATCATAAAT
65 ATGCGCATCATAAAT
6402 GTGTGTCATA
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
85 62 0.95
86 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (85 bp):
CACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGAACATCATAAA
TGCGCATCATAAATTTATGA
Found at i:6420 original size:13 final size:13
Alignment explanation
Indices: 6381--6424 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
6371 TCAATGAACA
**
6381 TCATAAATGCGCA
1 TCATAAATGCGTG
*
6394 TCATAAATGTGTG
1 TCATAAATGCGTG
6407 TCATAAATGCGTG
1 TCATAAATGCGTG
6420 TCATA
1 TCATA
6425 GATTTATGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TCATAAATGCGTG
Found at i:6834 original size:25 final size:24
Alignment explanation
Indices: 6799--6847 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
6789 GATATAAGCA
* *
6799 TGCATTTCATTTATTTCATTTACAT
1 TGCATTCCATTTATTT-AGTTACAT
6824 TGCATTCCATTTATTTAGTTACAT
1 TGCATTCCATTTATTTAGTTACAT
6848 ATTATATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.24, C:0.16, G:0.06, T:0.53
Consensus pattern (24 bp):
TGCATTCCATTTATTTAGTTACAT
Found at i:7272 original size:48 final size:46
Alignment explanation
Indices: 7219--7368 Score: 160
Period size: 47 Copynumber: 3.2 Consensus size: 46
7209 ATTAAAGGAC
*
7219 ATGACTTTTCATACAACATGAAGGGATATAACTCAAAGCTATAAATAG
1 ATGACTTTTCATACAACATGAAGGGACATAACTCAAAGCT-TAAA-AG
* * *
7267 ATGACTTTTAATACAACATGAAGAGACATAACTC-TAGCCTTAAAAG
1 ATGACTTTTCATACAACATGAAGGGACATAACTCAAAG-CTTAAAAG
* * * *
7313 AGAGACTTTTCATA-ACACATGAAGGGACACAACTCAAACCTTAAAGAC
1 A-TGACTTTTCATACA-ACATGAAGGGACATAACTCAAAGCTTAAA-AG
7361 ATGACTTT
1 ATGACTTT
7369 CAAGAAGGAA
Statistics
Matches: 85, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
46 4 0.05
47 45 0.53
48 36 0.42
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (46 bp):
ATGACTTTTCATACAACATGAAGGGACATAACTCAAAGCTTAAAAG
Found at i:7367 original size:47 final size:47
Alignment explanation
Indices: 7210--7368 Score: 178
Period size: 48 Copynumber: 3.3 Consensus size: 47
7200 TATGGTCACA
* *
7210 TTAAAGGACATGACTTTTCATACAACATGAAGGGATATAACTCAAAGC
1 TTAAA-GACATGACTTTTCATACAACATGAAGGGACATAACTCAAACC
* * * * * *
7258 TATAAATAGATGACTTTTAATACAACATGAAGAGACATAACTCTAGCC
1 T-TAAAGACATGACTTTTCATACAACATGAAGGGACATAACTCAAACC
* *
7306 TTAAAAGAGA-GACTTTTCATA-ACACATGAAGGGACACAACTCAAACC
1 TT-AAAGACATGACTTTTCATACA-ACATGAAGGGACATAACTCAAACC
7353 TTAAAGACATGACTTT
1 TTAAAGACATGACTTT
7369 CAAGAAGGAA
Statistics
Matches: 92, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
46 7 0.08
47 39 0.42
48 42 0.46
49 4 0.04
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (47 bp):
TTAAAGACATGACTTTTCATACAACATGAAGGGACATAACTCAAACC
Found at i:10290 original size:25 final size:25
Alignment explanation
Indices: 10225--10291 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 25
10215 TTTGATTTAC
*
10225 TAAAATATTAATAAATTTGAATAGT
1 TAAAATATTAATATATTTGAATAGT
* **
10250 TAAAATTATTTTATATATTT-AATCTT
1 TAAAA-TA-TTAATATATTTGAATAGT
10276 TAAAATATTAA-ATATT
1 TAAAATATTAATATATT
10292 AATAATTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 5 0.14
24 3 0.09
25 7 0.20
26 11 0.31
27 9 0.26
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (25 bp):
TAAAATATTAATATATTTGAATAGT
Found at i:12488 original size:17 final size:17
Alignment explanation
Indices: 12466--12498 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12456 CGAGACTATA
12466 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
12483 ATATTATATTTTATAT
1 ATATTATATTTTATAT
12499 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:15451 original size:3 final size:3
Alignment explanation
Indices: 15443--15525 Score: 91
Period size: 3 Copynumber: 28.3 Consensus size: 3
15433 TTTTACTTAA
** * *
15443 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
15491 A-T ATT ATAT ATT A-T ATT ATT ATT AAT A-T ATT ATT A
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A
15526 CAAGCCCAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
2 6 0.09
3 58 0.87
4 3 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:15463 original size:12 final size:12
Alignment explanation
Indices: 15445--15525 Score: 105
Period size: 12 Copynumber: 6.9 Consensus size: 12
15435 TTACTTAAAT
15445 TATTATTATTAA
1 TATTATTATTAA
* *
15457 AATTATTATTAT
1 TATTATTATTAA
*
15469 TATTATTATAAA
1 TATTATTATTAA
15481 TATTATTATT-A
1 TATTATTATTAA
15492 TATTATATATT-A
1 TATTAT-TATTAA
15504 TATTATTATTAA
1 TATTATTATTAA
15516 TA-TATTATTA
1 TATTATTATTA
15526 CAAGCCCAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
11 19 0.31
12 42 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:15980 original size:19 final size:20
Alignment explanation
Indices: 15934--15984 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 20
15924 AGAGAAAAAC
15934 AAAAGAAAAAAAACAGAAAG
1 AAAAGAAAAAAAACAGAAAG
15954 AGAGAAGAAAAAAAAC-GAAAG
1 A-A-AAGAAAAAAAACAGAAAG
15975 AAAAGAAAAA
1 AAAAGAAAAA
15985 CTACCAACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.28
20 2 0.07
21 7 0.24
22 12 0.41
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAACAGAAAG
Found at i:16890 original size:23 final size:22
Alignment explanation
Indices: 16856--16908 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
16846 GTTTTAATTT
16856 TATTTTAA--TTATA-GTTTAAA
1 TATTTTAATTTTATATGTTT-AA
16876 TATATTTAATTTTATATGTTTAA
1 TAT-TTTAATTTTATATGTTTAA
16899 TATTTTAATT
1 TATTTTAATT
16909 AGTATTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.10
21 5 0.17
22 7 0.24
23 10 0.34
24 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TATTTTAATTTTATATGTTTAA
Found at i:20209 original size:8 final size:7
Alignment explanation
Indices: 20185--20225 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
20175 TTTTCATATA
20185 TGCATTT
1 TGCATTT
20192 T-CATTT
1 TGCATTT
20198 TGCATCTT
1 TGCAT-TT
20206 TGCATTT
1 TGCATTT
20213 T-CATTTT
1 TGCA-TTT
20220 TGCATT
1 TGCATT
20226 CATACTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 8 0.27
7 13 0.43
8 9 0.30
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:22472 original size:2 final size:2
Alignment explanation
Indices: 22465--22518 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
22455 TTATCCTTTA
22465 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
22507 AT AT AT AT AT AT
1 AT AT AT AT AT AT
22519 CATTTGTTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25316 original size:114 final size:114
Alignment explanation
Indices: 25116--25338 Score: 356
Period size: 114 Copynumber: 2.0 Consensus size: 114
25106 TGCCATGTGA
* * *
25116 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
* * * *
25181 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGC
*
25230 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
* *
25295 TTCGGTAGGAATCCCATAACCAATCATTGAAATTGAAAGATGAA
66 TTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAA
25339 CTGCATGATC
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
TTCGGTAGGAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGC
Found at i:27395 original size:54 final size:54
Alignment explanation
Indices: 27330--27484 Score: 247
Period size: 54 Copynumber: 2.9 Consensus size: 54
27320 GAAATCTTGG
*
27330 CAGAAGCCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* * *
27384 CAGAAACCACAGGAAAGGATGAATGTGTTTTCAAATGTTTTACGAACATCTGAG
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
***
27438 CAGAAGCCACAGGAAAGGATGAATGCACTGTCAAATGTTTTACGAAC
1 CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
27485 CTGCTATTCT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (54 bp):
CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
Found at i:28649 original size:76 final size:76
Alignment explanation
Indices: 28550--28959 Score: 748
Period size: 76 Copynumber: 5.4 Consensus size: 76
28540 CTATTTCCCA
* *
28550 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
28615 AACCTTCGGGT
66 AACCTTCGGGT
*
28626 CATCTGTAAGCCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
28691 AACCTTCGGGT
66 AACCTTCGGGT
*
28702 CATCTGTAAGCCCTTCAGTGCATAATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
28767 AACCTTCGGGT
66 AACCTTCGGGT
28778 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
28843 AACCTTCGGGT
66 AACCTTCGGGT
28854 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
28919 AGCCTTCAGGT
66 AACCTTCGGGT
* *
28930 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTT
28960 TTAAGACCTC
Statistics
Matches: 324, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 324 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTCGGGT
Found at i:29166 original size:15 final size:14
Alignment explanation
Indices: 29113--29201 Score: 84
Period size: 12 Copynumber: 6.7 Consensus size: 14
29103 TTTTACTTAA
*
29113 ATTATTATTATTAAA
1 ATTATTATTA-TAAT
29128 ATTATTATTAT--T
1 ATTATTATTATAAT
29140 ATTATTATTATAA-
1 ATTATTATTATAAT
*
29153 A-TATTATTATTAT
1 ATTATTATTATAAT
*
29166 ATTA-TATATATTAT
1 ATTATTAT-TATAAT
29180 ATTATTATTA-AAT
1 ATTATTATTATAAT
29193 A-TATTATTA
1 ATTATTATTA
29202 CAAGCCCAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
12 29 0.45
13 8 0.12
14 15 0.23
15 13 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTATTATTATAAT
Found at i:29175 original size:9 final size:9
Alignment explanation
Indices: 29136--29199 Score: 58
Period size: 9 Copynumber: 6.7 Consensus size: 9
29126 AAATTATTAT
29136 TATTAT-TA
1 TATTATATA
*
29144 TTATTATAAA
1 -TATTATATA
29154 TATTATTATTA
1 TATTA-TA-TA
29165 TATTATATA
1 TATTATATA
29174 TATTATATTA
1 TATTATA-TA
*
29184 TTATTAAATA
1 -TATTATATA
29194 TATTAT
1 TATTAT
29200 TACAAGCCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
9 25 0.54
10 9 0.20
11 12 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTATATA
Found at i:29201 original size:3 final size:3
Alignment explanation
Indices: 29113--29189 Score: 88
Period size: 3 Copynumber: 26.3 Consensus size: 3
29103 TTTTACTTAA
** * *
29113 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29161 ATT A-T ATT A-T ATAT ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT A
29190 AATATATTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
2 6 0.10
3 53 0.85
4 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:29625 original size:11 final size:10
Alignment explanation
Indices: 29609--29668 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 10
29599 AACAGAGAGC
29609 AGAAAAACAAA
1 AGAAAAA-AAA
29620 AGAAAAAAGAA
1 AGAAAAAA-AA
29631 AGAAAAAAAA
1 AGAAAAAAAA
* *
29641 CAGAAAGAGAGA
1 -AGAAA-AAAAA
29653 AGAAAAAAAA
1 AGAAAAAAAA
29663 ACGAAA
1 A-GAAA
29669 GAAAGAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 7 0.17
11 31 0.76
12 3 0.07
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:29635 original size:22 final size:21
Alignment explanation
Indices: 29609--29676 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 21
29599 AACAGAGAGC
29609 AGAAAAACAAAAGAAAAAAGAA
1 AGAAAAA-AAAAGAAAAAAGAA
*
29631 AGAAAAAAAACAG-AAAGAGAGA
1 AGAAAAAAAA-AGAAAAAAGA-A
29653 AGAAAAAAAAACGAAAGAAAGAA
1 AGAAAAAAAAA-GAAA-AAAGAA
29676 A
1 A
29677 AACTACCAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
21 10 0.26
22 21 0.54
23 4 0.10
24 4 0.10
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAAAGAAAAAAGAA
Found at i:30538 original size:11 final size:11
Alignment explanation
Indices: 30519--30568 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
30509 ACTTTTTATA
30519 TTTAGTTTTAAT
1 TTTA-TTTTAAT
30531 TTTATTTTAAT
1 TTTATTTTAAT
* * *
30542 TATAGTTTAAA
1 TTTATTTTAAT
*
30553 TATATTTTAAT
1 TTTATTTTAAT
30564 TTTAT
1 TTTAT
30569 ATGTTTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 28 0.88
12 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (11 bp):
TTTATTTTAAT
Found at i:30610 original size:23 final size:24
Alignment explanation
Indices: 30577--30623 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
30567 ATATGTTTAA
*
30577 TATTTTAATTAGTAT-TATTATTT
1 TATTTTAATTAATATATATTATTT
*
30600 TATTTTTATTAATATATATTATTT
1 TATTTTAATTAATATATATTATTT
30624 GATTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTTTAATTAATATATATTATTT
Found at i:35987 original size:37 final size:41
Alignment explanation
Indices: 35946--36039 Score: 117
Period size: 44 Copynumber: 2.3 Consensus size: 41
35936 ATATATTAGG
35946 CAAAAATA-AT-C-ACTT-GTCTTTCGAAAGTTGAAGATAA
1 CAAAAATATATACAACTTAGTCTTTCGAAAGTTGAAGATAA
*
35983 CAAAAATATATACATAACTTCATTCTTTCGAAAGTTGAAGATAA
1 CAAAAATATATAC--AACTT-AGTCTTTCGAAAGTTGAAGATAA
36027 C-AAAATATATACA
1 CAAAAATATATACA
36040 TAACTTCATT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
37 8 0.16
38 2 0.04
39 1 0.02
41 1 0.02
42 4 0.08
43 11 0.22
44 22 0.45
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (41 bp):
CAAAAATATATACAACTTAGTCTTTCGAAAGTTGAAGATAA
Found at i:36046 original size:43 final size:44
Alignment explanation
Indices: 35962--36050 Score: 171
Period size: 43 Copynumber: 2.0 Consensus size: 44
35952 TAATCACTTG
35962 TCTTTCGAAAGTTGAAGATAACAAAAATATATACATAACTTCAT
1 TCTTTCGAAAGTTGAAGATAACAAAAATATATACATAACTTCAT
36006 TCTTTCGAAAGTTGAAGATAAC-AAAATATATACATAACTTCAT
1 TCTTTCGAAAGTTGAAGATAACAAAAATATATACATAACTTCAT
36049 TC
1 TC
36051 CAATGTCTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 23 0.51
44 22 0.49
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.33
Consensus pattern (44 bp):
TCTTTCGAAAGTTGAAGATAACAAAAATATATACATAACTTCAT
Found at i:42209 original size:16 final size:15
Alignment explanation
Indices: 42167--42223 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
42157 TAGTTACTTA
* *
42167 AATTTGAATTAATTA
1 AATTTAAATTAATTT
**
42182 AATTATTTATTAATGTT
1 AATT-TAAATTAAT-TT
*
42199 ATTTTAAATTAATTT
1 AATTTAAATTAATTT
42214 AATTTAAATT
1 AATTTAAATT
42224 TAAATTGAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 15 0.45
16 14 0.42
17 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (15 bp):
AATTTAAATTAATTT
Found at i:42226 original size:16 final size:16
Alignment explanation
Indices: 42190--42223 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
42180 TAAATTATTT
*
42190 ATTAATGTTATTTTAA
1 ATTAATGTTAATTTAA
42206 ATTAAT-TTAATTTAA
1 ATTAATGTTAATTTAA
42221 ATT
1 ATT
42224 TAAATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
ATTAATGTTAATTTAA
Found at i:45285 original size:3 final size:3
Alignment explanation
Indices: 45279--45336 Score: 66
Period size: 3 Copynumber: 19.0 Consensus size: 3
45269 GTTTGGTTTT
*
45279 TTA TTA TTTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TTTA TTAA TT-
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA
45326 TTA TTA -TA TTA
1 TTA TTA TTA TTA
45337 CAGACCCAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 4 0.08
3 35 0.73
4 9 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:47504 original size:16 final size:16
Alignment explanation
Indices: 47483--47515 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47473 TTGCTTTTAA
47483 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
47499 ATTTATTTATAATATT
1 ATTTATTTATAATATT
47515 A
1 A
47516 ATTTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:47543 original size:17 final size:17
Alignment explanation
Indices: 47521--47554 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
47511 TATTAATTTG
47521 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
47538 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
47555 GTCACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:47694 original size:31 final size:33
Alignment explanation
Indices: 47659--47721 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
47649 ATAATTAAAC
47659 ATTATAAAAATTAT-A-ATTTAGTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
* * *
47690 ATTATTAAAATTTTAATATTTATTTTTATTTA
1 ATTATAAAAATTATAATATTTAGTTTTATTTA
47722 TTAATATCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 12 0.44
32 1 0.04
33 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
ATTATAAAAATTATAATATTTAGTTTTATTTAA
Found at i:50099 original size:6 final size:6
Alignment explanation
Indices: 50090--50135 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
50080 ACATTCACAT
* * * *
50090 ATTTAC ATTTGC ATTTAC ATTTAC ATTTGC ATTTAC CTTTGC ATTT
1 ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTT
50136 TTTACGTTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (6 bp):
ATTTAC
Found at i:50113 original size:18 final size:18
Alignment explanation
Indices: 50090--50135 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
50080 ACATTCACAT
50090 ATTTACATTTGCATTTAC
1 ATTTACATTTGCATTTAC
50108 ATTTACATTTGCATTTAC
1 ATTTACATTTGCATTTAC
* *
50126 CTTTGCATTT
1 ATTTACATTT
50136 TTTACGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (18 bp):
ATTTACATTTGCATTTAC
Found at i:52235 original size:2 final size:2
Alignment explanation
Indices: 52228--52256 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52218 CATTTATCCT
52228 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 T
52257 CCTTTGTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55079 original size:114 final size:114
Alignment explanation
Indices: 54875--55211 Score: 577
Period size: 114 Copynumber: 3.0 Consensus size: 114
54865 GTGTCACGTT
* *
54875 CTCGTAGCAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCGTAGTAGAAATAAGGAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTG
54940 ATTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTG
66 ATTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTG
54989 CTCGTAGTAGAAATAAGGAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCGTAGTAGAAATAAGGAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTG
*
55054 ATTTGGTATGAACCCCAAAATCAATCATTGGATTTAAAAGATGAATTTG
66 ATTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTG
* *
55103 CTCGTAGTAGAAATAAGGAGACCCAATAGTATCTTTTGGAAGTGTTCTTTGAGTTATTTGATCTG
1 CTCGTAGTAGAAATAAGGAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * * *
55168 GTTCGGTA-GAACCACAGAACCAATCATTGGAATTAAAAGATGAA
66 ATTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAA
55212 CTGCATGATC
Statistics
Matches: 212, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
113 32 0.15
114 180 0.85
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
CTCGTAGTAGAAATAAGGAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTG
ATTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTG
Found at i:57356 original size:3 final size:3
Alignment explanation
Indices: 57350--57407 Score: 75
Period size: 3 Copynumber: 19.0 Consensus size: 3
57340 ATTTGGTTTT
57350 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTAA TT-
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA
57397 TTA TTA -TA TTA
1 TTA TTA TTA TTA
57408 CAAGCCCAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.08
3 37 0.74
4 9 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:58643 original size:16 final size:16
Alignment explanation
Indices: 58622--58654 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
58612 TTGCTTTTAA
58622 ATTTATTTTTAATATT
1 ATTTATTTTTAATATT
58638 ATTTATTTTTAATATT
1 ATTTATTTTTAATATT
58654 A
1 A
58655 ATTTGTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTATTTTTAATATT
Found at i:58682 original size:17 final size:17
Alignment explanation
Indices: 58660--58693 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
58650 TATTAATTTG
58660 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
58677 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
58694 GTCACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:58858 original size:31 final size:33
Alignment explanation
Indices: 58823--58885 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
58813 ATAATTAAAC
58823 ATTATAAAAATTAT-A-ATTTAGTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
* * *
58854 ATTATTAAAATTTTAATATTTATTTTTATTTA
1 ATTATAAAAATTATAATATTTAGTTTTATTTA
58886 TTAATCTCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 12 0.44
32 1 0.04
33 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
ATTATAAAAATTATAATATTTAGTTTTATTTAA
Found at i:61994 original size:13 final size:14
Alignment explanation
Indices: 61975--62008 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
61965 TAATTACAAG
61975 TTATAATAATATAA
1 TTATAATAATATAA
61989 TT-TAATAATATAA
1 TTATAATAATATAA
62002 TTATAAT
1 TTATAAT
62009 GAAACAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTATAATAATATAA
Found at i:62270 original size:35 final size:37
Alignment explanation
Indices: 62187--62278 Score: 127
Period size: 35 Copynumber: 2.6 Consensus size: 37
62177 TCTGATCTTG
* * * *
62187 CTTCACTACTCTATTGTAAAGGTTGGATTTGTATTGT
1 CTTCACTACTCTTTTGTGAAGGTTGGAGTTGCATTGT
62224 -TTCACTACTCTTTTGTGAAGGTTGG-GTTGCA-TGT
1 CTTCACTACTCTTTTGTGAAGGTTGGAGTTGCATTGT
62258 CTTCACTACTCTTTTGTGAAG
1 CTTCACTACTCTTTTGTGAAG
62279 AATGAAAATG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 3 0.06
35 24 0.48
36 23 0.46
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.45
Consensus pattern (37 bp):
CTTCACTACTCTTTTGTGAAGGTTGGAGTTGCATTGT
Found at i:62454 original size:43 final size:42
Alignment explanation
Indices: 62303--62456 Score: 141
Period size: 43 Copynumber: 3.5 Consensus size: 42
62293 GAGAAGAATC
* * *
62303 TGTTTCACTACTCTTTCGTGAAGATCAGATTCGAGGTTGATT
1 TGTTCCACTACTCTTCCGTGAAGATCAGATTCAAGGTTGATT
* ** * *
62345 TGCTTCCACTACTCTTCCGTGGAGATTGGATTGAA--TTAAAAAGAATC
1 TG-TTCCACTACTCTTCCGTGAAGATCAGATTCAAGGTT-----G-ATT
*
62392 TGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGGTTGATT
1 TGTTCCACTACTCTTCCGTGAAGATCAGATTCAAGGTTGATT
62434 TGATTCCACTACTCTTCCGTGAA
1 TG-TTCCACTACTCTTCCGTGAA
62457 TACTATGCTT
Statistics
Matches: 87, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
41 2 0.02
42 6 0.07
43 45 0.52
46 28 0.32
47 4 0.05
48 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (42 bp):
TGTTCCACTACTCTTCCGTGAAGATCAGATTCAAGGTTGATT
Found at i:65160 original size:31 final size:31
Alignment explanation
Indices: 65122--65184 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
65112 TTCTACTTGC
65122 AATAAATTCAGCTATTGCACTCCATTTTACT
1 AATAAATTCAGCTATTGCACTCCATTTTACT
65153 AATAAATTCAGCTATTGCACTCCATTTTACT
1 AATAAATTCAGCTATTGCACTCCATTTTACT
65184 A
1 A
65185 CTTTTTGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.38
Consensus pattern (31 bp):
AATAAATTCAGCTATTGCACTCCATTTTACT
Found at i:66806 original size:2 final size:2
Alignment explanation
Indices: 66799--66864 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
66789 TAATCAAGAG
66799 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66841 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
66865 ATCACGAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:73475 original size:74 final size:75
Alignment explanation
Indices: 73302--73496 Score: 204
Period size: 74 Copynumber: 2.7 Consensus size: 75
73292 CCGTTGAACA
* * * * * *
73302 GGGGGAATCGTACCCCCT-TGGGGGGGATCGTTTCCCTCCGAGCATACTGGAATTCTCGGAACAA
1 GGGGGAATCGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAACAA
** *
73366 AAATGTTTAG
66 AAACATTCAG
* *
73376 GGGGGAATCAGTTCCTCCTAT--GGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATC-GTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAACA
*
73439 AAACCATTCA-
65 AAAACATTCAG
* * *
73449 TGGGGAATCGTTCCTCCTATGGGGGGAAT--GTTCCCTCTGAGCAATCTG
1 GGGGGAATCGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTG
73497 TAATTTTTTT
Statistics
Matches: 102, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
72 28 0.27
73 8 0.08
74 58 0.57
75 7 0.07
76 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.25
Consensus pattern (75 bp):
GGGGGAATCGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAACAA
AAACATTCAG
Done.