Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007500.1 Hibiscus syriacus cultivar Beakdansim tig00020793_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: 81517
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1019 original size:16 final size:16
Alignment explanation
Indices: 986--1034 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
976 TAAGGTAAAG
986 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
1004 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
1020 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
1035 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:8632 original size:6 final size:6
Alignment explanation
Indices: 8618--8652 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
8608 TGTAGGAGTC
*
8618 TTTTCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
8653 GTTGCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:8647 original size:13 final size:12
Alignment explanation
Indices: 8618--8652 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
8608 TGTAGGAGTC
*
8618 TTTTCTTTTTGT
1 TTTTCTTTTTCT
8630 TTTTCTTCTTTCT
1 TTTTCTT-TTTCT
8643 TTTTCTTTTT
1 TTTTCTTTTT
8653 GTTGCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:9444 original size:22 final size:21
Alignment explanation
Indices: 9410--9453 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
9400 GGCTACGGAA
* *
9410 TTGATGGTCTTGATAGATGAAG
1 TTGATGATCTTGAT-GATAAAG
*
9432 TTGATGATGTTGATGATAAAG
1 TTGATGATCTTGATGATAAAG
9453 T
1 T
9454 GGAGATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.30, C:0.02, G:0.30, T:0.39
Consensus pattern (21 bp):
TTGATGATCTTGATGATAAAG
Found at i:9841 original size:18 final size:19
Alignment explanation
Indices: 9804--9850 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
9794 ACCCCTTTGA
*
9804 AAATACATGATTTTTGATG
1 AAATACATGATTTTTAATG
9823 AAATACATGA-TTTTAATG
1 AAATACATGATTTTTAATG
9841 AAGATACATG
1 AA-ATACATG
9851 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (19 bp):
AAATACATGATTTTTAATG
Found at i:14365 original size:15 final size:15
Alignment explanation
Indices: 14354--14382 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
14344 ACTCAAAAAG
14354 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
14369 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
14383 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:17130 original size:11 final size:13
Alignment explanation
Indices: 17098--17123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17088 TGGCCAAAGA
17098 TGAAAAGGTATGT
1 TGAAAAGGTATGT
17111 TGAAAAGGTATGT
1 TGAAAAGGTATGT
17124 AAAAGGTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:18749 original size:11 final size:11
Alignment explanation
Indices: 18733--18757 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18723 GTTGAACTAT
18733 TTGGAGCTGAG
1 TTGGAGCTGAG
18744 TTGGAGCTGAG
1 TTGGAGCTGAG
18755 TTG
1 TTG
18758 TCAAAAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.44, T:0.32
Consensus pattern (11 bp):
TTGGAGCTGAG
Found at i:20441 original size:23 final size:25
Alignment explanation
Indices: 20388--20441 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
20378 CTTTTTGAAC
* *
20388 TTCTTTTTCTTTTCTTTTTTTCTGA
1 TTCTTTTTCTCTTCTTTTTGTCTGA
*
20413 AT-TTTTTC-CTTCTTTTTGTCT-A
1 TTCTTTTTCTCTTCTTTTTGTCTGA
20435 TTCTTTT
1 TTCTTTT
20442 CTTTTTGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 2 0.08
23 15 0.62
24 6 0.25
25 1 0.04
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.74
Consensus pattern (25 bp):
TTCTTTTTCTCTTCTTTTTGTCTGA
Found at i:20787 original size:22 final size:21
Alignment explanation
Indices: 20761--20804 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
20751 GGTTACGGAA
*
20761 TTGATGGTCTTGATGGATGAAG
1 TTGATGATCTTGAT-GATGAAG
*
20783 TTGATGATGTTGATGATGAAG
1 TTGATGATCTTGATGATGAAG
20804 T
1 T
20805 GGAGATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.25, C:0.02, G:0.34, T:0.39
Consensus pattern (21 bp):
TTGATGATCTTGATGATGAAG
Found at i:21198 original size:19 final size:20
Alignment explanation
Indices: 21157--21207 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
21147 GAAACCCCTT
*
21157 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
21177 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
21196 TGAAGATACATG
1 TGAAAATACATG
21208 CTCTTGGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:22144 original size:30 final size:31
Alignment explanation
Indices: 22105--22164 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
22095 ACATGCTGCC
* **
22105 ATGATATCTATATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
22136 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
22165 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:25933 original size:5 final size:5
Alignment explanation
Indices: 25919--25955 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
25909 AGCACTCAAA
*
25919 AAAAG AAAAG CAAAG AAAAG -AAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
25956 GAAGTTGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:25944 original size:19 final size:18
Alignment explanation
Indices: 25916--25955 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
25906 TCCAGCACTC
*
25916 AAAAAAAGAAAAGCAAAG
1 AAAAAAAGAAAAGAAAAG
25934 AAAAGAAAGAAAAGAAAAG
1 AAAA-AAAGAAAAGAAAAG
25953 AAA
1 AAA
25956 GAAGTTGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAGAAAAG
Found at i:25957 original size:14 final size:14
Alignment explanation
Indices: 25919--25958 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
25909 AGCACTCAAA
*
25919 AAAAGAAAAGCAAAG
1 AAAAG-AAAGAAAAG
25934 AAAAGAAAGAAAAG
1 AAAAGAAAGAAAAG
25948 AAAAGAAAGAA
1 AAAAGAAAGAA
25959 GTTGAAGCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.78, C:0.03, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAAAAG
Found at i:36411 original size:23 final size:24
Alignment explanation
Indices: 36383--36436 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
36373 AAATTCAGCA
*
36383 AAGAAAATCAAAGCACTCAAAA-G
1 AAGAAAATCAAAGCACCCAAAAGG
* *
36406 AAGAAATTTAAAGCACCCAAAATGG
1 AAGAAAATCAAAGCACCCAAAA-GG
36431 AAGAAA
1 AAGAAA
36437 GAGAAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 19 0.73
25 7 0.27
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.11
Consensus pattern (24 bp):
AAGAAAATCAAAGCACCCAAAAGG
Found at i:41345 original size:20 final size:20
Alignment explanation
Indices: 41322--41386 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
41312 AAATTTTGGC
*
41322 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGGCTTTTTTTTTGT
* **
41342 TTTTTTGCCTTTTTTTTTCC
1 TTTTTTGGCTTTTTTTTTGT
41362 TTTTTT-G-TTTTTTTTTGT
1 TTTTTTGGCTTTTTTTTTGT
41380 TTTTTTG
1 TTTTTTG
41387 AAAAAAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 15 0.41
20 22 0.59
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (20 bp):
TTTTTTGGCTTTTTTTTTGT
Found at i:41347 original size:29 final size:28
Alignment explanation
Indices: 41315--41375 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
41305 TTTTTTGAAA
* *
41315 TTTTGGCTTTTTTGGCTCTTTTTTTGTTT
1 TTTTGCCTTTTTT-GCTCCTTTTTTGTTT
**
41344 TTTTGCCTTTTTTTTTCCTTTTTTGTTT
1 TTTTGCCTTTTTTGCTCCTTTTTTGTTT
41372 TTTT
1 TTTT
41376 TTGTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.77
Consensus pattern (28 bp):
TTTTGCCTTTTTTGCTCCTTTTTTGTTT
Found at i:44571 original size:6 final size:6
Alignment explanation
Indices: 44557--44591 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
44547 TGTAGGAGTC
*
44557 TTTTCT TTTTAT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
44592 GTTGCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:44586 original size:13 final size:12
Alignment explanation
Indices: 44557--44591 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
44547 TGTAGGAGTC
44557 TTTTCTTTTTAT
1 TTTTCTTTTTAT
*
44569 TTTTCTTCTTTCT
1 TTTTCTT-TTTAT
44582 TTTTCTTTTT
1 TTTTCTTTTT
44592 GTTGCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTTAT
Found at i:49263 original size:16 final size:16
Alignment explanation
Indices: 49224--49264 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
49214 TAAGAAATTA
49224 AAAGTGAATGAAATTGG
1 AAAG-GAATGAAATTGG
49241 AAA-GAATAGAAA-TGG
1 AAAGGAAT-GAAATTGG
49256 AAAGGAATG
1 AAAGGAATG
49265 TTATCAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 11 0.50
16 8 0.36
17 3 0.14
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (16 bp):
AAAGGAATGAAATTGG
Found at i:55748 original size:192 final size:192
Alignment explanation
Indices: 55408--55797 Score: 665
Period size: 192 Copynumber: 2.0 Consensus size: 192
55398 ATTATATTAC
55408 AAATAAACAATATAAATATTAAAAATTCGTAATATTTACAAAATCACGTATTAATCCCGTATAGG
1 AAATAAACAATATAAATATTAAAAATTCGTAATATTTACAAAATCACGTATTAATCCCGTATAGG
* *
55473 ATTTTCTGCATGCACCGTCTTCAGTAAAATGGTCATATATTGAGTTCCTAATATCAGATTGATGT
66 ATTTTCTGCATGCACCATCTTCAGTAAAATGGTCATATATTGAGTTCCTAATATCAGATTGATGC
55538 AATTAAATAACCGTTAAAAACATAAGAGACAGACGGTTGTATCTCTAGAAGACATGTTGACA
131 AATTAAATAACCGTTAAAAACATAAGAGACAGACGGTTGTATCTCTAGAAGACATGTTGACA
* * *
55600 AAATAATCAATATAAATATTGAAAATTCGTAATATTTACAAAATCACGTATTAATCTCGTATAGG
1 AAATAAACAATATAAATATTAAAAATTCGTAATATTTACAAAATCACGTATTAATCCCGTATAGG
* **
55665 ATTTTTTGCATGCACCATCTTCAGTAAAATGGTCATATATTGAGTTACC-AATATTGGATTGATG
66 ATTTTCTGCATGCACCATCTTCAGTAAAATGGTCATATATTGAGTT-CCTAATATCAGATTGATG
* * *
55729 CAATTAAATAACTGTTAAAAACATAAGAGACAGACGGTTGTATCTTTAGAAGACATGTTGACC
130 CAATTAAATAACCGTTAAAAACATAAGAGACAGACGGTTGTATCTCTAGAAGACATGTTGACA
55792 AAATAA
1 AAATAA
55798 GATCAGAATC
Statistics
Matches: 186, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
192 184 0.99
193 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (192 bp):
AAATAAACAATATAAATATTAAAAATTCGTAATATTTACAAAATCACGTATTAATCCCGTATAGG
ATTTTCTGCATGCACCATCTTCAGTAAAATGGTCATATATTGAGTTCCTAATATCAGATTGATGC
AATTAAATAACCGTTAAAAACATAAGAGACAGACGGTTGTATCTCTAGAAGACATGTTGACA
Found at i:56625 original size:16 final size:15
Alignment explanation
Indices: 56606--56644 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
56596 TTTGATAAAT
56606 AAGAAATGAAAATGGA
1 AAGAAATG-AAATGGA
*
56622 AAGAATTGAAATGGA
1 AAGAAATGAAATGGA
*
56637 TAGAAATG
1 AAGAAATG
56645 TTATCAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (15 bp):
AAGAAATGAAATGGA
Found at i:56745 original size:35 final size:36
Alignment explanation
Indices: 56702--56785 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 36
56692 TGGTTAAGGA
56702 ATGGTGATGATATAAGCAT-TA-AATGGTGATAGAAG
1 ATGGTGATGATATAAG-ATGTACAATGGTGATAGAAG
* *
56737 ATGGTGATGATAT-AGGTGTACAATGGTGATGGAAG
1 ATGGTGATGATATAAGATGTACAATGGTGATAGAAG
* *
56772 ATAGTGATGTTATA
1 ATGGTGATGATATA
56786 GGCGTGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 1 0.02
34 4 0.10
35 37 0.88
ACGTcount: A:0.36, C:0.02, G:0.31, T:0.31
Consensus pattern (36 bp):
ATGGTGATGATATAAGATGTACAATGGTGATAGAAG
Found at i:56786 original size:35 final size:36
Alignment explanation
Indices: 56722--56817 Score: 122
Period size: 35 Copynumber: 2.7 Consensus size: 36
56712 TATAAGCATT
* * * *
56722 AAATGGTGATAGAAGATGGTGATGATATAGGTGT-A
1 AAATGGTGATGGAAGATAGTGATGTTATAGGCGTGA
*
56757 CAATGGTGATGGAAGATAGTGATGTTATAGGCGTGA
1 AAATGGTGATGGAAGATAGTGATGTTATAGGCGTGA
* *
56793 AAATAGTGATGGAATATAGTGATGT
1 AAATGGTGATGGAAGATAGTGATGT
56818 GATCCTACCG
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 29 0.56
36 23 0.44
ACGTcount: A:0.35, C:0.02, G:0.33, T:0.29
Consensus pattern (36 bp):
AAATGGTGATGGAAGATAGTGATGTTATAGGCGTGA
Found at i:57107 original size:16 final size:16
Alignment explanation
Indices: 57086--57117 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
57076 TAGTTAGCTC
57086 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
57102 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
57118 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:60438 original size:35 final size:35
Alignment explanation
Indices: 60390--60503 Score: 158
Period size: 35 Copynumber: 3.2 Consensus size: 35
60380 TGGTTAAGGA
* * *
60390 ATGGTAATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATTATATAGGCGTGAAATGGTGATGGAAG
*
60425 ATGGTGATTATATAGGCGTGCAATGGTGATGGAAG
1 ATGGTGATTATATAGGCGTGAAATGGTGATGGAAG
*
60460 ATGGTGATGT-TTTAGGCGTGAAAATGGTGATGGAAG
1 ATGGTGAT-TATATAGGCGTG-AAATGGTGATGGAAG
60496 ATGGTGAT
1 ATGGTGAT
60504 GAACATATAG
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
35 48 0.68
36 23 0.32
ACGTcount: A:0.31, C:0.04, G:0.37, T:0.29
Consensus pattern (35 bp):
ATGGTGATTATATAGGCGTGAAATGGTGATGGAAG
Found at i:66571 original size:20 final size:20
Alignment explanation
Indices: 66535--66578 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
66525 ATGGTCTTAA
*
66535 GAAATGAATATATAATAAAG
1 GAAATGAATATAAAATAAAG
*
66555 GAAATGAA-ATAGAAATAAAT
1 GAAATGAATATA-AAATAAAG
66575 GAAA
1 GAAA
66579 GAGAGATGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (20 bp):
GAAATGAATATAAAATAAAG
Found at i:69006 original size:15 final size:15
Alignment explanation
Indices: 68975--69016 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
68965 GGATAATTAA
68975 GAAAGGAAATAGAAATG
1 GAAA-GAAAT-GAAATG
68992 GAAAGAAATGAAATG
1 GAAAGAAATGAAATG
69007 GAAAGAAATG
1 GAAAGAAATG
69017 TTATCAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 16 0.64
16 5 0.20
17 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.12
Consensus pattern (15 bp):
GAAAGAAATGAAATG
Found at i:69229 original size:13 final size:13
Alignment explanation
Indices: 69211--69268 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
69201 TAGGCATGCA
69211 ATGGTGATGGAAG
1 ATGGTGATGGAAG
** *
69224 ATGGTGATGTTAT
1 ATGGTGATGGAAG
* *
69237 A-GGCG-T-GAAA
1 ATGGTGATGGAAG
69247 ATGGTGATGGAAG
1 ATGGTGATGGAAG
69260 ATGGTGATG
1 ATGGTGATG
69269 AACAGATAGT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 23 0.70
ACGTcount: A:0.29, C:0.02, G:0.41, T:0.28
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:69257 original size:36 final size:35
Alignment explanation
Indices: 69163--69269 Score: 160
Period size: 35 Copynumber: 3.0 Consensus size: 35
69153 ATTGGTGGTT
* *
69163 ATATAGGCGTGAAATGGTGATAGAAGTTGGTGATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
* *
69198 ATATAGGCATGCAATGGTGATGGAAGATGGTGATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
*
69233 TTATAGGCGTGAAAATGGTGATGGAAGATGGTGATG
1 ATATAGGCGTG-AAATGGTGATGGAAGATGGTGATG
69269 A
1 A
69270 ACAGATAGTA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 40 0.63
36 23 0.37
ACGTcount: A:0.32, C:0.04, G:0.37, T:0.27
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
Found at i:71098 original size:36 final size:35
Alignment explanation
Indices: 71025--71129 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 35
71015 ATTTATAAGT
* *
71025 TGGTGATAATATAGGCGTGATATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGACTA
71060 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
*
71096 TGGCGATGATATAGGCGTGATGATGGTGATGGAC
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGAC
71130 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.28, C:0.06, G:0.37, T:0.30
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGACTA
Found at i:73184 original size:23 final size:23
Alignment explanation
Indices: 73141--73191 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
73131 ATGAACACAA
* **
73141 CTCTTGGCACTTCAAGTGACGTT
1 CTCTTGGAACTTCAAACGACGTT
73164 CTCTTGGAACTTCAAACGACGTT
1 CTCTTGGAACTTCAAACGACGTT
*
73187 ATCTT
1 CTCTT
73192 TGAAACATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (23 bp):
CTCTTGGAACTTCAAACGACGTT
Found at i:74960 original size:36 final size:35
Alignment explanation
Indices: 74897--74994 Score: 142
Period size: 36 Copynumber: 2.7 Consensus size: 35
74887 TATAAGTTGA
* *
74897 TGATAATATAGGCGTTATATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATATGGTGATGGAATATGG
*
74932 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGAT-ATGGTGATGGAATATGG
*
74968 CGATGATATAGGCGTGATGATGGTGAT
1 TGATGATATAGGCGTGAT-ATGGTGAT
74995 TGACAGATTG
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 16 0.28
36 41 0.72
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.32
Consensus pattern (35 bp):
TGATGATATAGGCGTGATATGGTGATGGAATATGG
Found at i:80052 original size:10 final size:10
Alignment explanation
Indices: 80037--80084 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 10
80027 GATGTAGGAG
80037 TCTTTTCTTT
1 TCTTTTCTTT
80047 TCTTTTCTTTT
1 TCTTTTC-TTT
80058 TCTTTTTCTTCT
1 TC-TTTTCTT-T
*
80070 TCTTTT-TTC
1 TCTTTTCTTT
80079 TCTTTT
1 TCTTTT
80085 GTTGCTTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 6 0.18
10 9 0.26
11 11 0.32
12 8 0.24
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TCTTTTCTTT
Found at i:80060 original size:6 final size:6
Alignment explanation
Indices: 80039--80076 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
80029 TGTAGGAGTC
*
80039 TTTTC- TTTTC- TTTTCT TTTTCT TTTTCT TCTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
80077 TCTCTTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:80525 original size:34 final size:35
Alignment explanation
Indices: 80461--80554 Score: 154
Period size: 34 Copynumber: 2.7 Consensus size: 35
80451 TGGTAAGGGA
* * *
80461 TTGGTGGTTATATAGGCGTGAAATGGTGATAGAAG
1 TTGGTGATGATATAGGCGTGCAATGGTGATAGAAG
80496 TTGGTGATGATATAGG-GTGCAATGGTGATAGAAG
1 TTGGTGATGATATAGGCGTGCAATGGTGATAGAAG
80530 TTGGTGATGATATAGGCGTGCAATG
1 TTGGTGATGATATAGGCGTGCAATG
80555 ATGGAAGATG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
34 33 0.60
35 22 0.40
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.31
Consensus pattern (35 bp):
TTGGTGATGATATAGGCGTGCAATGGTGATAGAAG
Done.