Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008058.1 Hibiscus syriacus cultivar Beakdansim tig00110553_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: 74730
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:849 original size:3 final size:3
Alignment explanation
Indices: 841--883 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
831 CCATTTTAAA
* *
841 ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
884 AATAAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:864 original size:12 final size:12
Alignment explanation
Indices: 849--887 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
839 AAATTATTAT
849 TATTATTATAAA
1 TATTATTATAAA
* *
861 TATTATTATTAT
1 TATTATTATAAA
873 TATTATTATTAAA
1 TATTATTA-TAAA
886 TA
1 TA
888 AAAAATATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTATTATAAA
Found at i:3965 original size:24 final size:24
Alignment explanation
Indices: 3931--3978 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3921 TCTATTTGTA
3931 GATACACTTTATTTTGCTTTAACT
1 GATACACTTTATTTTGCTTTAACT
*
3955 GATACATTTTATTTTGCTTTAACT
1 GATACACTTTATTTTGCTTTAACT
3979 TATTTATATT
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:0.25, C:0.15, G:0.08, T:0.52
Consensus pattern (24 bp):
GATACACTTTATTTTGCTTTAACT
Found at i:8143 original size:17 final size:18
Alignment explanation
Indices: 8107--8146 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
8097 CTCATTAATC
*
8107 AAAAAAAGGAAAAAAGGA
1 AAAAAAAAGAAAAAAGGA
*
8125 AAAAAAAAGAAAGAA-GA
1 AAAAAAAAGAAAAAAGGA
8142 AAAAA
1 AAAAA
8147 TAAATTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAGGA
Found at i:9112 original size:12 final size:12
Alignment explanation
Indices: 9095--9119 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9085 CTTCACATTA
9095 TTTGAAGGCAAG
1 TTTGAAGGCAAG
9107 TTTGAAGGCAAG
1 TTTGAAGGCAAG
9119 T
1 T
9120 GGTCCGAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.28
Consensus pattern (12 bp):
TTTGAAGGCAAG
Found at i:9681 original size:118 final size:118
Alignment explanation
Indices: 9469--9717 Score: 365
Period size: 118 Copynumber: 2.1 Consensus size: 118
9459 CCAGAAATAG
* * * *
9469 AATATTGAGGCATCTCGAAAGCCCATTTTAGACAGAAATGATCCATGTGGGGCATTTTGAAAGCC
1 AATATTGAGGCATCTCGAAAGCCCATTTCAGACAGAAATGATCCATGTAGGGAATTATGAAAGCC
*
9534 CATGTCAGTATGAATATTTGGAAAATTTTGAAAGCTCATATTAGCAAGAAGAA
66 CATGTCAGTATGAATATTTGGAAAATTTTGAAAGCTCATATCAGCAAGAAGAA
*
9587 AATATTGGGGCATCTCGAAAGCCCATTTCAGACAGAAATGATCCATGTAGGGAATTATG-AAGAC
1 AATATTGAGGCATCTCGAAAGCCCATTTCAGACAGAAATGATCCATGTAGGGAATTATGAAAG-C
** * * *
9651 CCATGTCAGTATGAATATTTGGGCATTTTTGAAAGCTCATATCATCAGGAAGAA
65 CCATGTCAGTATGAATATTTGGAAAATTTTGAAAGCTCATATCAGCAAGAAGAA
* *
9705 AATGTTGAAGCAT
1 AATATTGAGGCAT
9718 TTTGAAGGCT
Statistics
Matches: 116, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
117 3 0.03
118 113 0.97
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28
Consensus pattern (118 bp):
AATATTGAGGCATCTCGAAAGCCCATTTCAGACAGAAATGATCCATGTAGGGAATTATGAAAGCC
CATGTCAGTATGAATATTTGGAAAATTTTGAAAGCTCATATCAGCAAGAAGAA
Found at i:10541 original size:22 final size:22
Alignment explanation
Indices: 10495--10571 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
10485 ACATCTACAT
10495 TCTTCAAAGATGATAGA-T-TC
1 TCTTCAAAGATGATAGATTCTC
10515 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
10537 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
10559 TTTTCAAAGATGA
1 TCTTCAAAGATGA
10572 AAGCTTTATT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
20 17 0.31
21 1 0.02
22 36 0.67
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:11345 original size:44 final size:44
Alignment explanation
Indices: 11219--11738 Score: 592
Period size: 44 Copynumber: 12.0 Consensus size: 44
11209 ATTTCTCAAA
* *
11219 TTTATAAATCC-TCTGGGTCATCCATAAGACCTACAGTGCATGATG
1 TTTA-AAATCCTTC-GGGTCATCCATAAGACCTCCAGTGCAGGATG
* * *** *
11264 TTTAAAATTCTTTTGGGTCATTTGTAAGACCTCCAGTGTAGGATG
1 TTTAAAA-TCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATG
* * *
11309 TTTAAAATCCTCCGGGTCATCCATAAGACCTACAGTGCATGATG
1 TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATG
*** *
11353 TTTAAAATCCTTCGGGTCATTTGTAAGACCTCCAGTGTAGGATG
1 TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATG
*
11397 TTTAAAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAGGATG
1 TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATG
** * *
11441 TTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTACAAGATG
1 TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATG
* *** * **
11485 -TT-AAATCGTTCGGGTCATATGTAAGACCTCCAATGCAATATG
1 TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATG
*
11527 -TT-AAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAGGATG
1 TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATG
** *
11569 TTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATG
1 TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATG
11613 -TT-AAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATG
1 TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATG
* *** * *
11655 TTTAAAATCATTCGGGTCATTTGTAAGACCTCCAGTGCAAGACG
1 TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATG
* *
11699 -TT-AAATCCTTCGGGCCATCCATAAGACCTTCA-TGCAGGAT
1 TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGAT
11739 ATTTTCAAAT
Statistics
Matches: 401, Mismatches: 68, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
41 6 0.01
42 130 0.32
43 10 0.02
44 216 0.54
45 38 0.09
46 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATG
Found at i:11568 original size:128 final size:130
Alignment explanation
Indices: 11243--11727 Score: 609
Period size: 128 Copynumber: 3.7 Consensus size: 130
11233 GGGTCATCCA
* * * ** *** *
11243 TAAGACCTACAGTGCATGATGTTTAAAATTCTTTTGGGTCATTTGTAAGACCTCCAGTGTAGGAT
1 TAAGACCTCCAGTGCAGGATGTTTAAAA-TCCTCCGGGTCATCCATAAGACCTCCAGTGCAGGAT
* * *
11308 GTTTAAAATCCTCCGGGTCATCCATAAGACCTACAGTGCATGATGTTTAAAATCCTTCGGGTCAT
65 GTTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAAGATG-TT-AAATCCTTCGGGTCAT
*
11373 TTG
128 ATG
*
11376 TAAGACCTCCAGTGTAGGATGTTTAAAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAGGATG
1 TAAGACCTCCAGTGCAGGATGTTTAAAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAGGATG
** * *
11441 TTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTACAAGATGTTAAATCGTTCGGGTCATATG
66 TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATATG
* **
11506 TAAGACCTCCAATGCAATATG-TT-AAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAGGATG
1 TAAGACCTCCAGTGCAGGATGTTTAAAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAGGATG
** ***
11569 TTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCA
66 TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATATG
* * *** * *
11634 TAAGACCTCCAGTGCAGGATGTTTAAAATCATTCGGGTCATTTGTAAGACCTCCAGTGCAAGACG
1 TAAGACCTCCAGTGCAGGATGTTTAAAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAGGATG
*
11699 -TT-AAATCCTTCGGGCCATCCATAAGACCT
66 TTTAAAATCCTTCGGGTCATCCATAAGACCT
11728 TCATGCAGGA
Statistics
Matches: 310, Mismatches: 40, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
128 142 0.46
129 6 0.02
130 67 0.22
131 2 0.01
132 68 0.22
133 25 0.08
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (130 bp):
TAAGACCTCCAGTGCAGGATGTTTAAAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAGGATG
TTTAAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATATG
Found at i:11583 original size:86 final size:86
Alignment explanation
Indices: 11219--11738 Score: 598
Period size: 86 Copynumber: 6.0 Consensus size: 86
11209 ATTTCTCAAA
** * * * *
11219 TTTATAAATCC-TCTGGGTCATCCATAAGACCTACAGTGCATGATGTTTAAAATTCTTTTGGGTC
1 TTTA-AAATCCTTC-GGGTCATCTGTAAGACCTCCAGTGCAAGATG-TT-AAA-TCCTTCGGGTC
*** *
11283 ATTTGTAAGACCTCCAGTGTAGGATG
61 ATCCATAAGACCTCCAGTGCAGGATG
* ** * * *
11309 TTTAAAATCCTCCGGGTCATCCATAAGACCTACAGTGCATGATGTTTAAAATCCTTCGGGTCATT
1 TTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATG-TT-AAATCCTTCGGGTCATC
** *
11374 TGTAAGACCTCCAGTGTAGGATG
64 CATAAGACCTCCAGTGCAGGATG
* ** *
11397 TTTAAAATCCTCCGGGTCATCCATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATC
1 TTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATG-TT-AAATCCTTCGGGTCATC
** * *
11462 TGTAAGACCTCCAGTACAAGATG
64 CATAAGACCTCCAGTGCAGGATG
* * * * *
11485 -TT-AAATCGTTCGGGTCATATGTAAGACCTCCAATGCAATATGTTAAATCCTCCGGGTCATCCA
1 TTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCA
11548 TAAGACCTCCAGTGCAGGATG
66 TAAGACCTCCAGTGCAGGATG
11569 TTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCA
1 TTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCA
11634 TAAGACCTCCAGTGCAGGATG
66 TAAGACCTCCAGTGCAGGATG
* * * *
11655 TTTAAAATCATTCGGGTCATTTGTAAGACCTCCAGTGCAAGACGTTAAATCCTTCGGGCCATCCA
1 TTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCA
*
11720 TAAGACCTTCA-TGCAGGAT
66 TAAGACCTCCAGTGCAGGAT
11739 ATTTTCAAAT
Statistics
Matches: 395, Mismatches: 32, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
84 35 0.09
85 12 0.03
86 180 0.46
87 2 0.01
88 117 0.30
89 44 0.11
90 5 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (86 bp):
TTTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCA
TAAGACCTCCAGTGCAGGATG
Found at i:12055 original size:3 final size:3
Alignment explanation
Indices: 12047--12086 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
12037 CCATTTTAAA
* * *
12047 ATT ATT ATT ATT ATT TTT ATA AAT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
12087 AATAAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:12065 original size:21 final size:20
Alignment explanation
Indices: 12040--12088 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
12030 AATTTTTCCA
12040 TTTTAAAATTATTATTATTAT
1 TTTTAAAA-TATTATTATTAT
12061 TTTTATAAATATTATTATTAT
1 TTTTA-AAATATTATTATTAT
*
12082 TATTAAA
1 TTTTAAA
12089 TAAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.81
22 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAAAATATTATTATTAT
Found at i:12075 original size:18 final size:19
Alignment explanation
Indices: 12052--12090 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
12042 TTAAAATTAT
*
12052 TATTATTATTTTTA-TAAA
1 TATTATTATTATTATTAAA
12070 TATTATTATTATTATTAAA
1 TATTATTATTATTATTAAA
12089 TA
1 TA
12091 AAAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTATTATTATTATTAAA
Found at i:13064 original size:17 final size:17
Alignment explanation
Indices: 13042--13081 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
13032 TTCGGTCGTG
13042 TAATTTTATATACTTTA
1 TAATTTTATATACTTTA
*
13059 TAATTTTATTTACTTTA
1 TAATTTTATATACTTTA
13076 TAATTT
1 TAATTT
13082 AGTCACTGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATTTTATATACTTTA
Found at i:16391 original size:21 final size:23
Alignment explanation
Indices: 16366--16407 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
16356 TTATATTCAT
*
16366 TTATGA-TTATTTTT-TTGTTTA
1 TTATGACTCATTTTTATTGTTTA
16387 TTATGACTCATTTTTATTGTT
1 TTATGACTCATTTTTATTGTT
16408 GTGATTGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.19, C:0.05, G:0.10, T:0.67
Consensus pattern (23 bp):
TTATGACTCATTTTTATTGTTTA
Found at i:21852 original size:13 final size:14
Alignment explanation
Indices: 21821--21855 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
21811 ATTTAATTTA
21821 AAATAATATTAAAT
1 AAATAATATTAAAT
*
21835 AAATAATA-TAATT
1 AAATAATATTAAAT
21848 AAATAATA
1 AAATAATA
21856 CTCTATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATAATATTAAAT
Found at i:22587 original size:21 final size:23
Alignment explanation
Indices: 22554--22596 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
22544 TGATTTGGTC
22554 TTATCTCAATTAAAT-GAATATT
1 TTATCTCAATTAAATGGAATATT
* *
22576 TTAT-TCATTTAAGTGGAATAT
1 TTATCTCAATTAAATGGAATAT
22597 AATGTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (23 bp):
TTATCTCAATTAAATGGAATATT
Found at i:24012 original size:40 final size:40
Alignment explanation
Indices: 23957--24078 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
23947 TGCAGGTTTA
23957 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
23997 TAATACATTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
24037 TAATACACTTCGGTGTATATGGTGGGCACGATCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
24077 TA
1 TA
24079 GCACTACGGT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:24268 original size:46 final size:46
Alignment explanation
Indices: 24176--24437 Score: 449
Period size: 46 Copynumber: 5.8 Consensus size: 46
24166 GTAAGCATGC
*
24176 AAATAAGCTTACGAGCTTAT-GGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGAATAAATGGTAAGTATATTGGTA
24220 AAATAAGCTTACGAGCTTATGGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGAATAAATGGTAAGTATATTGGTA
* *
24266 AAATAAGCTTACGCGTTTATGGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGAATAAATGGTAAGTATATTGGTA
24312 AAATAAGCTTACGAGCTTATGGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGAATAAATGGTAAGTATATTGGTA
* * *
24358 AAATAAGCTTACGAGCTTATAGGAATAAATGGTAAGTATGTTAGTA
1 AAATAAGCTTACGAGCTTATGGGAATAAATGGTAAGTATATTGGTA
24404 AAATAAGCTTACGAGCTTATGGG-ATAAATGGTAA
1 AAATAAGCTTACGAGCTTATGGGAATAAATGGTAA
24438 ATATTTTGAA
Statistics
Matches: 207, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
44 20 0.10
45 16 0.08
46 171 0.83
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGGAATAAATGGTAAGTATATTGGTA
Found at i:33406 original size:29 final size:29
Alignment explanation
Indices: 33357--33412 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
33347 AATCTACATA
* *
33357 ATAAATATATATATATCTAAAATAAAATC
1 ATAAATATATATAAATCTAAAAAAAAATC
*
33386 ATAAATATTTATTAAAT-TAAAAAAAAA
1 ATAAATATATA-TAAATCTAAAAAAAAA
33413 GTATCTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (29 bp):
ATAAATATATATAAATCTAAAAAAAAATC
Found at i:35103 original size:13 final size:13
Alignment explanation
Indices: 35085--35109 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35075 TAGAACTAGC
35085 AAGAGTTCCTCTA
1 AAGAGTTCCTCTA
35098 AAGAGTTCCTCT
1 AAGAGTTCCTCT
35110 CCTATGAGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (13 bp):
AAGAGTTCCTCTA
Found at i:35770 original size:32 final size:31
Alignment explanation
Indices: 35734--35810 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
35724 CGGGGCCGTG
*
35734 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
35766 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
35797 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
35811 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:35793 original size:63 final size:63
Alignment explanation
Indices: 35687--35810 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
35677 CCCTAAGGGA
* * ** *
35687 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
35750 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
35811 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:36344 original size:21 final size:21
Alignment explanation
Indices: 36320--36368 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
36310 ACAATAATAA
36320 TTAATCAG-CCCCAAATCTTAC
1 TTAAT-AGTCCCCAAATCTTAC
*
36341 TTAATTGTTCCCCCAAATCTTAC
1 TTAATAG-T-CCCCAAATCTTAC
36364 TTAAT
1 TTAAT
36369 TGTTCAAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.04
21 5 0.21
23 18 0.75
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.37
Consensus pattern (21 bp):
TTAATAGTCCCCAAATCTTAC
Found at i:36355 original size:23 final size:23
Alignment explanation
Indices: 36328--36373 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
36318 AATTAATCAG
36328 CCCCAAATCTTACTTAATTGTTC
1 CCCCAAATCTTACTTAATTGTTC
36351 CCCCAAATCTTACTTAATTGTTC
1 CCCCAAATCTTACTTAATTGTTC
36374 AAAGCTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (23 bp):
CCCCAAATCTTACTTAATTGTTC
Found at i:36726 original size:5 final size:5
Alignment explanation
Indices: 36716--36790 Score: 69
Period size: 5 Copynumber: 13.8 Consensus size: 5
36706 AACGGTCAAC
* *
36716 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
36765 GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTC--G GGTCG GGTCG GGTC
36791 AGACCGGTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
5 46 0.79
7 12 0.21
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:36741 original size:17 final size:17
Alignment explanation
Indices: 36721--36791 Score: 97
Period size: 17 Copynumber: 3.9 Consensus size: 17
36711 TCAACGGTCG
36721 GGTCGGGTCGGGTCAACGGTC
1 GGTCGGGTCGGGTCAA----C
36742 GGGTCGGGTCGGGTCAAC
1 G-GTCGGGTCGGGTCAAC
36760 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
36777 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
36792 GACCGGTCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 31 0.63
18 2 0.04
21 1 0.02
22 15 0.31
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:36786 original size:22 final size:22
Alignment explanation
Indices: 36709--36773 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
36699 GAAAGTCAAC
36709 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
36731 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
36753 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
36774 AACGGTCGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:36805 original size:9 final size:9
Alignment explanation
Indices: 36787--36863 Score: 73
Period size: 9 Copynumber: 8.1 Consensus size: 9
36777 GGTCGGGTCG
*
36787 GGTCAGACC
1 GGTCAAACC
36796 GGTCAAACC
1 GGTCAAACC
* *
36805 GATTCAGACC
1 G-GTCAAACC
36815 GGTCAAACC
1 GGTCAAACC
*
36824 GGTTCGAACC
1 GG-TCAAACC
*
36834 GGTTGAAACC
1 GG-TCAAACC
36844 GGTCAAACC
1 GGTCAAACC
36853 GGTCAGAACC
1 GGTCA-AACC
36863 G
1 G
36864 ATTGAAAATC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
9 28 0.50
10 28 0.50
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:36811 original size:19 final size:19
Alignment explanation
Indices: 36789--36866 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
36779 TCGGGTCGGG
36789 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGAT
*
36808 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGAT
* *
36827 TC-GAACCGGTTGAAACCG-G
1 TCAG-ACCGG-TCAAACCGAT
*
36846 TCAAACCGGTCAGAACCGAT
1 TCAGACCGGTCA-AACCGAT
36866 T
1 T
36867 GAAAATCGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.06
19 37 0.77
20 8 0.17
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGAT
Found at i:43162 original size:32 final size:31
Alignment explanation
Indices: 43126--43202 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
43116 CGGGGCCGTG
*
43126 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
43158 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
43189 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
43203 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:43185 original size:63 final size:63
Alignment explanation
Indices: 43079--43202 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
43069 CCCTAAGGGA
* * ** *
43079 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
43142 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
43203 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:43736 original size:21 final size:22
Alignment explanation
Indices: 43712--43760 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
43702 ACAATAATAA
43712 TTAAT-CAACCCCAAATCTTAC
1 TTAATGCAACCCCAAATCTTAC
***
43733 TTAATTGTTCCCCCAAATCTTAC
1 TTAA-TGCAACCCCAAATCTTAC
43756 TTAAT
1 TTAAT
43761 TGTTCAAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 2 0.09
23 17 0.74
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.37
Consensus pattern (22 bp):
TTAATGCAACCCCAAATCTTAC
Found at i:43747 original size:23 final size:23
Alignment explanation
Indices: 43720--43765 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
43710 AATTAATCAA
43720 CCCCAAATCTTACTTAATTGTTC
1 CCCCAAATCTTACTTAATTGTTC
43743 CCCCAAATCTTACTTAATTGTTC
1 CCCCAAATCTTACTTAATTGTTC
43766 AAAGCTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (23 bp):
CCCCAAATCTTACTTAATTGTTC
Found at i:44125 original size:5 final size:5
Alignment explanation
Indices: 44115--44172 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
44105 AACGGTCAAC
* * *
44115 GGTCG GGTCG GGTCG GGTCAAC GATCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
44164 GGTCG GGTC
1 GGTCG GGTC
44173 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 36 0.84
7 7 0.16
ACGTcount: A:0.09, C:0.22, G:0.50, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:44136 original size:22 final size:22
Alignment explanation
Indices: 44108--44172 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
44098 AACGGTCAAC
44108 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
44130 GGTCAACGATCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
44152 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
44173 AGACCGGTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:44187 original size:9 final size:9
Alignment explanation
Indices: 44169--44235 Score: 71
Period size: 9 Copynumber: 7.1 Consensus size: 9
44159 GGTCGGGTCG
*
44169 GGTCAGACC
1 GGTCAAACC
44178 GGTCAAACC
1 GGTCAAACC
* *
44187 GATTCAGACC
1 G-GTCAAACC
44197 GGTCAAACC
1 GGTCAAACC
*
44206 GGTTGAAACC
1 GG-TCAAACC
44216 GGTCAAACC
1 GGTCAAACC
44225 GGTCAGAACC
1 GGTCA-AACC
44235 G
1 G
44236 ATTGAAAACC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
9 28 0.58
10 20 0.42
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.13
Consensus pattern (9 bp):
GGTCAAACC
Found at i:44193 original size:19 final size:19
Alignment explanation
Indices: 44171--44225 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
44161 TCGGGTCGGG
44171 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGAT
*
44190 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGAT
* *
44209 TGAAACCGGTCAAACCG
1 TCAGACCGGTCAAACCG
44226 GTCAGAACCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.15
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGAT
Found at i:44206 original size:28 final size:28
Alignment explanation
Indices: 44170--44257 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 28
44160 GTCGGGTCGG
* * *
44170 GTCAGACCGGTCAAACCGATTCAGACCG
1 GTCAAACCGGTCAAACCGGTTCAAACCG
*
44198 GTCAAACCGGTTGAAACCGG-TCAAACCG
1 GTCAAACCGG-TCAAACCGGTTCAAACCG
* *
44226 GTCAGAACCGATTGAAAACCGGTT-AAACCG
1 GTCA-AACCG-GT-CAAACCGGTTCAAACCG
44256 GT
1 GT
44258 TTCCAGCAGC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
28 20 0.41
29 13 0.27
30 15 0.31
31 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTCAAACCG
Found at i:44214 original size:10 final size:10
Alignment explanation
Indices: 44175--44258 Score: 70
Period size: 9 Copynumber: 8.7 Consensus size: 10
44165 GTCGGGTCAG
44175 ACCGG-TCAA
1 ACCGGTTCAA
* *
44184 ACCGATTCAG
1 ACCGGTTCAA
44194 ACCGG-TCAA
1 ACCGGTTCAA
*
44203 ACCGGTTGAA
1 ACCGGTTCAA
44213 ACCGG-TCAA
1 ACCGGTTCAA
44222 ACCGG-TCAGA
1 ACCGGTTCA-A
* *
44232 ACCGATTGAAA
1 ACCGGTT-CAA
44243 ACCGGTT-AA
1 ACCGGTTCAA
44252 ACCGGTT
1 ACCGGTT
44259 TCCAGCAGCC
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
9 32 0.52
10 20 0.33
11 8 0.13
12 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:44226 original size:19 final size:19
Alignment explanation
Indices: 44175--44257 Score: 80
Period size: 19 Copynumber: 4.3 Consensus size: 19
44165 GTCGGGTCAG
* *
44175 ACCGGTCAAACCGATTCAG
1 ACCGGTCAAACCGGTTCAA
*
44194 ACCGGTCAAACCGGTTGAA
1 ACCGGTCAAACCGGTTCAA
44213 ACCGGTCAAACCGG-TCAGA
1 ACCGGTCAAACCGGTTCA-A
* *
44232 ACCGATTGAAAACCGGTT-AA
1 ACCG-GT-CAAACCGGTTCAA
44252 ACCGGT
1 ACCGGT
44258 TTCCAGCAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
18 2 0.04
19 36 0.68
20 6 0.11
21 8 0.15
22 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:44247 original size:30 final size:28
Alignment explanation
Indices: 44194--44257 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
44184 ACCGATTCAG
* *
44194 ACCGGTCAAACCGGTTGAAACCGGTCAA
1 ACCGGTCAAACCGATTGAAAACGGTCAA
*
44222 ACCGGTCAGAACCGATTGAAAACCGGTTAA
1 ACCGGTCA-AACCGATTGAAAA-CGGTCAA
44252 ACCGGT
1 ACCGGT
44258 TTCCAGCAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 8 0.26
29 11 0.35
30 12 0.39
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.16
Consensus pattern (28 bp):
ACCGGTCAAACCGATTGAAAACGGTCAA
Found at i:45671 original size:9 final size:9
Alignment explanation
Indices: 45630--45703 Score: 53
Period size: 9 Copynumber: 8.1 Consensus size: 9
45620 TATTTTCTAG
45630 TATTTTATT
1 TATTTTATT
*
45639 TATTTCATT
1 TATTTTATT
* *
45648 TGTTTTTATG
1 T-ATTTTATT
*
45658 GATTTTATT
1 TATTTTATT
*
45667 TATTTATTTT
1 TATTT-TATT
*
45677 TATGTCT-TT
1 TAT-TTTATT
45686 TATTTTATT
1 TATTTTATT
45695 TA-TTTATT
1 TATTTTATT
45703 T
1 T
45704 TTCTTTTCGT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
8 9 0.18
9 28 0.56
10 12 0.24
11 1 0.02
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.73
Consensus pattern (9 bp):
TATTTTATT
Found at i:45708 original size:24 final size:23
Alignment explanation
Indices: 45637--45727 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 23
45627 TAGTATTTTA
* **
45637 TTTATTTCATTTGTTTTTATGGAT
1 TTTATTT-ATTTATTTTTATGTCT
45661 TTTATTTATTTATTTTTATGTCT
1 TTTATTTATTTATTTTTATGTCT
*
45684 TTTATTTTATTTATTTATT-TTTCT
1 TTTA-TTTATTTATTT-TTATGTCT
* *
45708 TTTCGTTTCTTTATTTTTAT
1 TTT-ATTTATTTATTTTTAT
45728 TTAATTTACT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
23 19 0.33
24 36 0.63
25 2 0.04
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (23 bp):
TTTATTTATTTATTTTTATGTCT
Found at i:45720 original size:28 final size:28
Alignment explanation
Indices: 45661--45723 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
45651 TTTTATGGAT
* *
45661 TTTATTTATTTATTTTTATGTCTTTTAT
1 TTTATTTATTTATTTTTATGTCGTTTAC
* *
45689 TTTATTTATTTATTTTTCTTTTCGTTT-C
1 TTTATTTATTTATTTTT-ATGTCGTTTAC
45717 TTTATTT
1 TTTATTT
45724 TTATTTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.76
Consensus pattern (28 bp):
TTTATTTATTTATTTTTATGTCGTTTAC
Found at i:51453 original size:73 final size:72
Alignment explanation
Indices: 51231--51455 Score: 283
Period size: 73 Copynumber: 3.1 Consensus size: 72
51221 CTCACTTGTG
* *
51231 ATTGTTTTTCTTAAAGCATACTTTGTCTCACTTGAGACTGTTTTACTCAAAAGAAGATTTATTTT
1 ATTGTTTTTCTTAAAGCAGACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTA-TTT
51296 CACTCAAGT
65 CACTCAA-T
* * * * *
51305 -TTGCTTTGCTTAAAGCAGACTTTGTGTCACCTGAGACTGTTTTACTCGAAAGAAGATTTATTCC
1 ATTGTTTTTCTTAAAGCAGACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTTC
*
51369 ACTCAAG
66 ACTCAAT
* * * *
51376 ATTGTTTTTCTTAAAACCAGA-TTTGTCTCTCTTGGGACCGTTTTCACTCGAAAGAAGATTTATT
1 ATTGTTTTTCTT-AAAGCAGACTTTGTCTCACTTGAGACTGTTTT-ACTCGAAAGAAGATTTATT
*
51440 TCAGTCAAT
64 TCACTCAAT
51449 ATTGTTT
1 ATTGTTT
51456 CTTTGAAACA
Statistics
Matches: 129, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
72 36 0.28
73 93 0.72
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (72 bp):
ATTGTTTTTCTTAAAGCAGACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTTC
ACTCAAT
Found at i:51488 original size:20 final size:20
Alignment explanation
Indices: 51465--51502 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
51455 TCTTTGAAAC
*
51465 AAATTTTGTCTCTCTTGAAT
1 AAATTTTGTCTCCCTTGAAT
51485 AAATTTTGTCTCCCTTGA
1 AAATTTTGTCTCCCTTGA
51503 GACATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (20 bp):
AAATTTTGTCTCCCTTGAAT
Found at i:51612 original size:65 final size:65
Alignment explanation
Indices: 51529--51679 Score: 178
Period size: 65 Copynumber: 2.3 Consensus size: 65
51519 ACTAAGTTTC
*
51529 GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAACATTTCCCTTGAAATGAATTT
1 GTCTCTCTTAAGACAGTTTCTCTTGAAACA-AAATCATTGAAAACATTTCCCTTGAAATGAATTT
51593 T
65 T
* * * ** ** *
51594 GTCTCTCTTAAGATAGTTTCTCTTGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAATTTC
1 GTCTCTCTTAAGACAGTTTCTCTTGAAACAAAATCATTGAAAACATTTCCCTTGAAATGAATTTT
* * *
51659 GTCTCCCTTGAGACATTTTCT
1 GTCTCTCTTAAGACAGTTTCT
51680 TTTGGAACTA
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
64 3 0.04
65 69 0.96
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (65 bp):
GTCTCTCTTAAGACAGTTTCTCTTGAAACAAAATCATTGAAAACATTTCCCTTGAAATGAATTTT
Found at i:51731 original size:167 final size:166
Alignment explanation
Indices: 51485--51798 Score: 502
Period size: 167 Copynumber: 1.9 Consensus size: 166
51475 TCTCTTGAAT
*
51485 AAATTTTGTCTCCCTTGAGACATTTTCTTTTACAACTAAGTTTCGTCTCTCTTGAGACAGTTTCT
1 AAATTTCGTCTCCCTTGAGACATTTTCTTTTACAACTAAGTTTCGTCTCTCTTGAGACAGTTTCT
* * * * *
51550 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTAAGATAGTTTCT
66 CTTGAAACATAAACATTAAAAACATTTCCCTTGAAACGAATTTTATCTCTCTTAAGATAGGTTCC
51615 CTTGAAACAAAATCTTTGAATATGTTTCCCTTGAAAC
131 CTTGAAACAAAAT-TTTGAATATGTTTCCCTTGAAAC
** * * *
51652 AAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTGTTTCTCTTGAGATAGTTTCT
1 AAATTTCGTCTCCCTTGAGACATTTTCTTTTACAACTAAGTTTCGTCTCTCTTGAGACAGTTTCT
**
51717 CTTGAAACATAAACATTAAAAACATTTCCCTTGAAACGAATTTTATCTCTCTTGGGATAGGTTCC
66 CTTGAAACATAAACATTAAAAACATTTCCCTTGAAACGAATTTTATCTCTCTTAAGATAGGTTCC
51782 CTTGAAACAAAATTTTG
131 CTTGAAACAAAATTTTG
51799 TCTCCCTTGA
Statistics
Matches: 134, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
166 4 0.03
167 130 0.97
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.40
Consensus pattern (166 bp):
AAATTTCGTCTCCCTTGAGACATTTTCTTTTACAACTAAGTTTCGTCTCTCTTGAGACAGTTTCT
CTTGAAACATAAACATTAAAAACATTTCCCTTGAAACGAATTTTATCTCTCTTAAGATAGGTTCC
CTTGAAACAAAATTTTGAATATGTTTCCCTTGAAAC
Found at i:51798 original size:102 final size:102
Alignment explanation
Indices: 51574--51957 Score: 432
Period size: 102 Copynumber: 3.8 Consensus size: 102
51564 ATTGAAAACA
* * * * * *
51574 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACA-AAATCTTTGAATA
1 TTTCCCTTGAAACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAA
** * * * * *
51637 TGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAT
65 CATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAG
** * * * * * *
51675 TTTCTTTTGGAACTAAGTTTTGTTTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTAAAAAC
1 TTTCCCTTGAAACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
51740 ATTTCCCTTGAAACGAATTTTATCTCTCTTGGGATAG
66 ATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAG
* * *
51777 GTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTCCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* * *
51842 ATTTCCCTTGAAATGAATTTTGTCACTCATGAGATAG
66 ATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAG
* * *
51879 TTTCCCTTGAAAC-AAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAGCATAAACTTTGAAAAC
1 TTTCCCTTGAAACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
*
51943 ATTTTCCTTTGAAAC
66 A-TTTCCCTTGAAAC
51958 AAAATCTTTG
Statistics
Matches: 238, Mismatches: 42, Indels: 5
0.84 0.15 0.02
Matches are distributed among these distances:
101 57 0.24
102 178 0.75
103 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.39
Consensus pattern (102 bp):
TTTCCCTTGAAACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAG
Found at i:51823 original size:37 final size:37
Alignment explanation
Indices: 51742--51827 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
51732 TTAAAAACAT
* * * *
51742 TTCCCTTGAAAC-GAATTTTATCTCTCTTGGGATAGG
1 TTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGG
*
51778 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA-G
1 TTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGG
51814 TTCCTCTTGAAACA
1 TTCC-CTTGAAACA
51828 TAAACATTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 17 0.40
37 26 0.60
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (37 bp):
TTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGG
Found at i:51897 original size:36 final size:36
Alignment explanation
Indices: 51843--51925 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
51833 ATTGAAAACA
** * *
51843 TTTCCCTTGAAATGAATTTTGTCACTCATGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCACCCATGAGACAG
* * *
51879 TTTCCCTTGAAACAAATTTTTTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCACCCATGAGACAG
*
51915 TTTCTCTTGAA
1 TTTCCCTTGAA
51926 GCATAAACTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCACCCATGAGACAG
Found at i:52053 original size:15 final size:15
Alignment explanation
Indices: 52033--52090 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
52023 GTTTTTGTCC
52033 CTCTTGAGACAGTTT
1 CTCTTGAGACAGTTT
*
52048 CTCTTGAAACAAATTGTGTCT
1 CTCTTGAGAC--A--GT-T-T
52069 CTCTTGAGACAGTTT
1 CTCTTGAGACAGTTT
52084 CTCTTGA
1 CTCTTGA
52091 AACTTCAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
15 17 0.49
16 1 0.03
17 3 0.09
19 3 0.09
20 1 0.03
21 10 0.29
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (15 bp):
CTCTTGAGACAGTTT
Found at i:52153 original size:33 final size:34
Alignment explanation
Indices: 52111--52195 Score: 136
Period size: 36 Copynumber: 2.5 Consensus size: 34
52101 TTTGAATACA
*
52111 GTTTCTCTTGAAACAC-AAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
52144 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACAC--AAAAAAACCTTTGAAAAT
52180 GTTTCTCTTGAAACAC
1 GTTTCTCTTGAAACAC
52196 CAAACCCTCG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 16 0.33
36 32 0.67
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
Found at i:53388 original size:2 final size:2
Alignment explanation
Indices: 53381--53423 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
53371 TTTATTAATT
53381 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
53423 T
1 T
53424 TTACTATTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53603 original size:9 final size:9
Alignment explanation
Indices: 53585--53655 Score: 51
Period size: 9 Copynumber: 8.1 Consensus size: 9
53575 TATTTTCTAG
53585 TATTTTATT
1 TATTTTATT
*
53594 TATTTCATT
1 TATTTTATT
* *
53603 TGTTTTTATG
1 T-ATTTTATT
*
53613 GATTTTATT
1 TATTTTATT
53622 TA-TTT-TT
1 TATTTTATT
*
53629 TATGTCT-TT
1 TAT-TTTATT
53638 TATTTTATT
1 TATTTTATT
53647 TA-TTTATT
1 TATTTTATT
53655 T
1 T
53656 TTCTTTTTGT
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
7 4 0.08
8 12 0.25
9 27 0.56
10 5 0.10
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (9 bp):
TATTTTATT
Found at i:53630 original size:20 final size:21
Alignment explanation
Indices: 53605--53653 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
53595 ATTTCATTTG
53605 TTTTTATGGATTTTA-TTTAT
1 TTTTTATGGATTTTATTTTAT
**
53625 TTTTTATGTCTTTTATTTTAT
1 TTTTTATGGATTTTATTTTAT
53646 TTATTTAT
1 TT-TTTAT
53654 TTTTCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.52
21 7 0.28
22 5 0.20
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTTTATGGATTTTATTTTAT
Found at i:53672 original size:24 final size:25
Alignment explanation
Indices: 53614--53677 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
53604 GTTTTTATGG
53614 ATTTTATTTATTTTTTATGTCTTTT
1 ATTTTATTTATTTTTTATGTCTTTT
53639 ATTTTATTTATTTATTT-T-TCTTTT
1 ATTTTATTTATTT-TTTATGTCTTTT
*
53663 -TGTTTCTTTATTTTT
1 AT-TTTATTTATTTTT
53678 ATTTAATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 3 0.08
24 16 0.44
25 14 0.39
26 3 0.08
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (25 bp):
ATTTTATTTATTTTTTATGTCTTTT
Found at i:61368 original size:29 final size:31
Alignment explanation
Indices: 61332--61407 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 31
61322 TAAGAATGTG
61332 CTCATAATAACAAATATT-AAAAAAA-TGGA
1 CTCATAATAACAAATATTGAAAAAAATTGGA
61361 CCTC-TAATCAA-AAGA-ATTGAAAAAAATTGGA
1 -CTCATAAT-AACAA-ATATTGAAAAAAATTGGA
61392 CTCATAATAACAAATA
1 CTCATAATAACAAATA
61408 AATATAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
29 9 0.23
30 19 0.49
31 11 0.28
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.24
Consensus pattern (31 bp):
CTCATAATAACAAATATTGAAAAAAATTGGA
Found at i:61526 original size:30 final size:30
Alignment explanation
Indices: 61492--61556 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
61482 AAGTATTGAT
* * *
61492 AAAATTAAACCCTTGATAACTAATGTTAGA
1 AAAATTAAACCATTAATAACAAATGTTAGA
** *
61522 AAAATTGGACTATTAATAACAAATGTTAGA
1 AAAATTAAACCATTAATAACAAATGTTAGA
61552 AAAAT
1 AAAAT
61557 AAATAAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (30 bp):
AAAATTAAACCATTAATAACAAATGTTAGA
Found at i:62224 original size:16 final size:16
Alignment explanation
Indices: 62203--62236 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
62193 ATGAATTATG
62203 ATAAAATAAAGTAAAA
1 ATAAAATAAAGTAAAA
*
62219 ATAAAATAAATTAAAA
1 ATAAAATAAAGTAAAA
62235 AT
1 AT
62237 GATCAATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
ATAAAATAAAGTAAAA
Found at i:64827 original size:23 final size:23
Alignment explanation
Indices: 64801--64853 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
64791 ACCCATAAAT
*
64801 ATAACTAATAGTAATATATAA-TC
1 ATAACTAATAGTAATA-ATAATTA
64824 ATAACTAATAGTAATAATAATTA
1 ATAACTAATAGTAATAATAATTA
64847 ATAACTA
1 ATAACTA
64854 CCCCATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.34
Consensus pattern (23 bp):
ATAACTAATAGTAATAATAATTA
Done.