Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008700.1 Hibiscus syriacus cultivar Beakdansim tig00111733_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: 112164
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:8045 original size:46 final size:46
Alignment explanation
Indices: 7991--8079 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 46
7981 AGTAGAGCGC
*
7991 TACCTAAAATGTTATTTTTTCTATCGA-AAATATTAATATCGGATAT
1 TACCTAAAATATTATTTTTTCTA-CGATAAATATTAATATCGGATAT
* *
8037 TACCTAAAATATTATTTTTTCTACTATAAATGTTAATATCGGA
1 TACCTAAAATATTATTTTTTCTACGATAAATATTAATATCGGA
8080 AAGATTCCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 2 0.05
46 37 0.95
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (46 bp):
TACCTAAAATATTATTTTTTCTACGATAAATATTAATATCGGATAT
Found at i:12783 original size:23 final size:23
Alignment explanation
Indices: 12755--12800 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
12745 TAAATTTTAA
12755 AAAAAATAAA-AATATATTTTTTAGT
1 AAAAAATAAATAA-A-A-TTTTTAGT
12780 AAAAAATAAATAAAATTTTTA
1 AAAAAATAAATAAAATTTTTA
12801 AAATTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 1 0.05
25 11 0.55
26 2 0.10
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
AAAAAATAAATAAAATTTTTAGT
Found at i:22425 original size:18 final size:18
Alignment explanation
Indices: 22402--22437 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
22392 AACATATAAC
22402 TTCAATGGAAGGGTGTAA
1 TTCAATGGAAGGGTGTAA
22420 TTCAATGGAAGGGTGTAA
1 TTCAATGGAAGGGTGTAA
22438 CATACAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.28
Consensus pattern (18 bp):
TTCAATGGAAGGGTGTAA
Found at i:23979 original size:29 final size:29
Alignment explanation
Indices: 23925--23980 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
23915 TGTTTTCGCC
* * *
23925 TCCCCTAAAATTTTATAAGTTTAAGTTTG
1 TCCCCTAAAATTTTAAAAATTCAAGTTTG
23954 TCCCCTAAAATTTTAAAAATTCAAGTT
1 TCCCCTAAAATTTTAAAAATTCAAGTT
23981 CATCCCAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (29 bp):
TCCCCTAAAATTTTAAAAATTCAAGTTTG
Found at i:29022 original size:15 final size:15
Alignment explanation
Indices: 29004--29033 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28994 AAAACCATGT
29004 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
29019 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
29034 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:29040 original size:15 final size:15
Alignment explanation
Indices: 29007--29041 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28997 ACCATGTTAG
* *
29007 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
29022 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
29037 ATAAA
1 ATAAA
29042 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:29468 original size:34 final size:34
Alignment explanation
Indices: 29427--29492 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
29417 GAATCCTAGC
29427 AAAATTCTATCATATCTTTAGGAGTTTGAATCTT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCTT
* *
29461 AAAATTCTATCCTATTTTTAGGAGTTTGAATC
1 AAAATTCTATCATATCTTTAGGAGTTTGAATC
29493 CTAGTAGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCTT
Found at i:30259 original size:105 final size:103
Alignment explanation
Indices: 30130--30320 Score: 312
Period size: 105 Copynumber: 1.8 Consensus size: 103
30120 CCTGAAACTG
30130 GGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCATAG-GTA
1 GGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC-TAGAGTA
* *
30194 GCATGATATCCTCCGTCGTGGAAAATCAGCTTTGAAATT
65 GCACGATATCCTCCATCGTGGAAAATCAGCTTTGAAATT
*
30233 GGAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
1 GGAAA-TTGTT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAGAGT
*
30298 GGCACGATATCCTCCATCGTGGA
64 AGCACGATATCCTCCATCGTGGA
30321 GTTGAAATCG
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
103 5 0.06
104 7 0.09
105 69 0.85
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (103 bp):
GGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAGAGTAG
CACGATATCCTCCATCGTGGAAAATCAGCTTTGAAATT
Found at i:31075 original size:67 final size:67
Alignment explanation
Indices: 30892--31197 Score: 271
Period size: 67 Copynumber: 4.5 Consensus size: 67
30882 GTCTTAAAAA
* * * * * * * *
30892 AGACAAAATTCGTTTCAAGGGAAACGATCTTAAAGATATATGTTGTTTTATGAGAAACGGCCTCA
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCA
30957 AGGG
64 AGGG
* * * *
30961 AGACAAAATTTTGTTTTAAAGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAA
1 AGACAAAA-TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAA
31026 GGG
65 GGG
* *
31029 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAACAT-TTTCAA
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAC-TGTCTCAA
31093 ---
65 GGG
***** * * *
31093 AG-GTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTGTGTTTCAAGAGAAACTGT
1 AGACAAAATT-TGTTTCAAGGGAAACAATCTCAAA-G----ATTTTGTGTTTCAAGAGAAACTGT
31157 CTCAAGGG
60 CTCAAGGG
**
31165 AGACAAAATTTGTTTCAAGGGAAATTATCTCAA
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAA
31198 GAGAGACGAA
Statistics
Matches: 188, Mismatches: 36, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
63 2 0.01
64 24 0.13
65 1 0.01
67 48 0.26
68 32 0.17
69 36 0.19
70 22 0.12
72 21 0.11
73 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (67 bp):
AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAG
GG
Found at i:31144 original size:36 final size:33
Alignment explanation
Indices: 31039--31153 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
31029 AGACAAAATT
* *
31039 TGTTTCAAGGGAAACAATCTCAAAGG--TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
*
31070 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
31103 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG--T-TTTTTG
31139 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
31154 TGTCTCAAGG
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 23 0.31
33 30 0.40
35 1 0.01
36 21 0.28
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
Found at i:31312 original size:102 final size:102
Alignment explanation
Indices: 31139--31617 Score: 766
Period size: 102 Copynumber: 4.7 Consensus size: 102
31129 TTTCTTTTTG
*
31139 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
31203 ACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
31240 TGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
31305 ACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * *
31342 TGTTTCAAGAGAAATTGTCTCAATGGAGACAAAATTTTGTTTCAAAGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
31407 AC--AATTTATTTCAAGGGAAATGCTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * *
31442 TGTTTCAAGAGAAACTGTCTCAAGTGAGATAAAATTTTGTTTCAAGGGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
31507 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * * *
31544 TGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTTCTGTTTCGAGGGAAACTATCTCAAGCG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT-TGTTTCAAGGGAAACTATCTCAAGAG
*
31609 AGATAAAAT
64 AGACAAAAT
31618 CTTGTTTTTA
Statistics
Matches: 348, Mismatches: 25, Indels: 7
0.92 0.07 0.02
Matches are distributed among these distances:
100 91 0.26
101 33 0.09
102 190 0.55
103 3 0.01
104 31 0.09
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:31486 original size:202 final size:202
Alignment explanation
Indices: 31139--31611 Score: 761
Period size: 202 Copynumber: 2.3 Consensus size: 202
31129 TTTCTTTTTG
*
31139 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
31203 ACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAGGAGAAACTGTCTCAAGGGAG
65 AC-AAATTCATTTCAAGGGAAATGCTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAG
31268 ACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTC
129 ACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTC
31333 CAATGTTTA
194 CAATGTTTA
* *
31342 TGTTTCAAGAGAAATTGTCTCAATGGAGACAAAATTTTGTTTCAAAGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
31407 AC-AATTTATTTCAAGGGAAATGCTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGTGAGA
65 ACAAATTCATTTCAAGGGAAATGCTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
* * *
31471 TAAAATTTTGTTTCAAGGGAAATTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
130 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCC
31536 AATGTTTA
195 AATGTTTA
* * *
31544 TGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTTCTGTTTCGAGGGAAACTATCTCAAGCG
1 TGTTTCAAGAGAAACTGTCTCAAG-GAGACAAAA-TTT-TGTTTCAAGGGAAACTATCTCAAGAG
31609 AGA
63 AGA
31612 TAAAATCTTG
Statistics
Matches: 250, Mismatches: 16, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
201 1 0.00
202 158 0.63
203 35 0.14
204 56 0.22
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (202 bp):
TGTTTCAAGAGAAACTGTCTCAAGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
CAAATTCATTTCAAGGGAAATGCTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
AAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCA
ATGTTTA
Found at i:31529 original size:36 final size:37
Alignment explanation
Indices: 31444--31529 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 37
31434 AATGTTTATG
* * * * * **
31444 TTTCAAGAGAAACTGTCTCAAGTGAGATAAAATTTTG
1 TTTCAAGGGAAATTATCTCAAGAGAGACAAAATTTCA
31481 TTTCAAGGGAAATTATCTCAAGAGAGACAAAA-TTCA
1 TTTCAAGGGAAATTATCTCAAGAGAGACAAAATTTCA
31517 TTTCAAGGGAAAT
1 TTTCAAGGGAAAT
31530 GTTTTCAATG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 15 0.36
37 27 0.64
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.29
Consensus pattern (37 bp):
TTTCAAGGGAAATTATCTCAAGAGAGACAAAATTTCA
Found at i:33124 original size:183 final size:183
Alignment explanation
Indices: 32816--33165 Score: 637
Period size: 183 Copynumber: 1.9 Consensus size: 183
32806 GGTTTAACTA
32816 AAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
* **
32881 AGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
32946 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
* *
32999 AAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
* *
33064 AGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGTCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
33129 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
33166 CGGATTTAAT
Statistics
Matches: 160, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 160 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (183 bp):
AAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
Found at i:37069 original size:15 final size:15
Alignment explanation
Indices: 37051--37080 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
37041 AAAACCATGT
37051 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
37066 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
37081 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:37087 original size:15 final size:15
Alignment explanation
Indices: 37054--37088 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
37044 ACCATGTTAG
* *
37054 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
37069 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
37084 ATAAA
1 ATAAA
37089 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:37211 original size:8 final size:9
Alignment explanation
Indices: 37187--37212 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
37177 ATAAAAAATA
37187 AAGAAAAAG
1 AAGAAAAAG
37196 AAGAAAAAG
1 AAGAAAAAG
37205 AAGAAAAA
1 AAGAAAAA
37213 AAATATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:37523 original size:34 final size:34
Alignment explanation
Indices: 37482--37547 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
37472 GAATCCTAGC
37482 AAAATTCTATCATATCTTTAGGAGTTTGAATCTT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCTT
* *
37516 AAAATTCTATCTTATTTTTAGGAGTTTGAATC
1 AAAATTCTATCATATCTTTAGGAGTTTGAATC
37548 CTAGTAGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCTT
Found at i:42178 original size:22 final size:23
Alignment explanation
Indices: 42136--42178 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
42126 TAAATTATAA
*
42136 AAAATAAAATATTATTTTAAAAT
1 AAAATAAAATATTATTATAAAAT
*
42159 AAAATGAAA-ATTATTATAAA
1 AAAATAAAATATTATTATAAA
42179 GCTTTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAATAAAATATTATTATAAAAT
Found at i:55849 original size:28 final size:28
Alignment explanation
Indices: 55809--55865 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
55799 GTTTTGCAGC
55809 AATCATTTCTGCAGGGCATAGAGAATGA
1 AATCATTTCTGCAGGGCATAGAGAATGA
55837 AATCATTTCTGCAGGGCATAGAGAATGA
1 AATCATTTCTGCAGGGCATAGAGAATGA
55865 A
1 A
55866 GGTATTAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (28 bp):
AATCATTTCTGCAGGGCATAGAGAATGA
Found at i:59524 original size:32 final size:31
Alignment explanation
Indices: 59482--59554 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 31
59472 AAAAGTGTTT
* *
59482 TTGCCTTATTTTAACCCCAAAAAAAATAGAG
1 TTGCCCTATTTTAACCCAAAAAAAAATAGAG
59513 TGTGCCCTATTTTAACCCAAAAAAAAATAGAG
1 T-TGCCCTATTTTAACCCAAAAAAAAATAGAG
*
59545 TTACCCTATT
1 TTGCCCTATT
59555 GTGCCAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 9 0.24
32 29 0.76
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.30
Consensus pattern (31 bp):
TTGCCCTATTTTAACCCAAAAAAAAATAGAG
Found at i:63345 original size:15 final size:15
Alignment explanation
Indices: 63325--63355 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
63315 ATTTTATTTA
63325 AATTTAAACTAATAG
1 AATTTAAACTAATAG
*
63340 AATTTAAATTAATAG
1 AATTTAAACTAATAG
63355 A
1 A
63356 CTAAAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (15 bp):
AATTTAAACTAATAG
Found at i:68379 original size:25 final size:25
Alignment explanation
Indices: 68351--68401 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
68341 ATACTATTTT
*
68351 TATTATCATATAAAATATAAAAATA
1 TATTAACATATAAAATATAAAAATA
* * *
68376 TATTAAGATATTAAATATAATAATA
1 TATTAACATATAAAATATAAAAATA
68401 T
1 T
68402 CAATTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (25 bp):
TATTAACATATAAAATATAAAAATA
Found at i:74515 original size:183 final size:183
Alignment explanation
Indices: 74197--74566 Score: 507
Period size: 183 Copynumber: 2.0 Consensus size: 183
74187 CTTCATTTGT
* *
74197 GAACCAAACGATTCACTTGATCCATTGTCATATCCTTCATAGGTGACATTACTATGAACTTCCTC
1 GAACCAAACGATTCACTTGATCCATTGTCAAATCCTTCATAGGTGACATTACGATGAACTTCCTC
* * *
74262 TCTCATTCTCCCTGATCTTGAACACGGAGGAACCAGGGAACCTAAAACATCACTCTCATCAAATT
66 TCTCATTCTACATGATCTTGAACACGGAGGAACCAGGGAACCTAAAACATCACTCTCATCAAACT
* *
74327 TCTCCAAATTTTCAGAACCTAAATCACCAAATGCC-CTACCTCTACTCTTATTA
131 TCTCCAAATTTTCAGAACCCAAATCACCAAAT-CCTCTACCTCCACTCTTATTA
*
74380 GAACCAGAA-GATTCACTTGATCCATTGTCAAATCCTTCATATGTGACATTACGATGAAC-TCTC
1 GAACCA-AACGATTCACTTGATCCATTGTCAAATCCTTCATAGGTGACATTACGATGAACTTC-C
* * * * * ** *
74443 TCTTTCATTCTTACAT-ATCTTGAGCGCTGAGGGA-TTGAGGAACCTAAAACATCACTCTCATTA
64 TCTCTCATTC-TACATGATCTTGAACACGGAGGAACCAG-GGAACCTAAAACATCACTCTCATCA
*
74506 AACTTCTCCAAATTTTCAGAACCCAAATTACCAAATCCTCTACCTCCACTCTTATTA
127 AACTTCTCCAAATTTTCAGAACCCAAATCACCAAATCCTCTACCTCCACTCTTATTA
74563 GAAC
1 GAAC
74567 TATCCGACGA
Statistics
Matches: 165, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
182 5 0.03
183 155 0.94
184 5 0.03
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (183 bp):
GAACCAAACGATTCACTTGATCCATTGTCAAATCCTTCATAGGTGACATTACGATGAACTTCCTC
TCTCATTCTACATGATCTTGAACACGGAGGAACCAGGGAACCTAAAACATCACTCTCATCAAACT
TCTCCAAATTTTCAGAACCCAAATCACCAAATCCTCTACCTCCACTCTTATTA
Found at i:74878 original size:210 final size:209
Alignment explanation
Indices: 74379--74883 Score: 615
Period size: 210 Copynumber: 2.4 Consensus size: 209
74369 TACTCTTATT
*
74379 AGAACCAGAAGATTCACTTGATCCATTGTCAAATCCTTCATATGTGACATTACGATGAACTCTCT
1 AGAACCAGAAGATTCACTTGATCCATTGT-AAATCCTTCATATGTGACATTACTATGAACTCTCT
* * * ** * *
74444 CTTTCATTCTTACATATCTTGAGCGCTGAGGGATTGAGGAACCTAAAACATCACTCTCATTAAAC
65 CTCTCATTCTTCCAGATCTCAAACGCTGAGGAATTGAGGAACCTAAAACATCACTCTCATTAAAC
* *
74509 TTCTCCAAATTTTCAGAACCCAAATTACCAAATCCTCTACCTCCACTCTTATTAGAACTATCCGA
130 TTCTCCAAATTTTCAGAACCCAAATCACCAAATCCTCTACCTCCACTCTTATTAGAACTAGCCGA
*
74574 CGAATCCTTCATTTG
195 CGAATCATTCATTTG
* * * * * *
74589 TGAACCTGAAGATTCACTTGATCCATGGCTATATCCTTCATATGTGACATTACTGTGAACTCTCA
1 AGAACCAGAAGATTCACTTGATCCATTG-TAAATCCTTCATATGTGACATTACTATGAACTCTCT
* *
74654 CTCTCGTTCTTCCAGATCTCAAACGCTGA-GAATTTGAGGAACCTAAAACATCAGC-CTCATTAG
65 CTCTCATTCTTCCAGATCTCAAACGCTGAGGAA-TTGAGGAACCTAAAACATCA-CTCTCATTAA
* * * *
74717 A-TATCTCCAAATTTTCCGAGCCCAAATCA-CATAATCC-CTTACCTCTACTCTTATTGGAACTA
128 ACT-TCTCCAAATTTTCAGAACCCAAATCACCA-AATCCTC-TACCTCCACTCTTATTAGAACTA
*
74779 GCTGACGAATCATTCATTTG
190 GCCGACGAATCATTCATTTG
* * * *
74799 AGAACCAGAAGATTCACTTGAGCCATTGTAGGATCCTTGATAAGTGACATTACTATGAACTCTCT
1 AGAACCAGAAGATTCACTTGATCCATTGTA-AATCCTTCATATGTGACATTACTATGAACTCTCT
* * * *
74864 CACCCCTCCTTCCAGATCTC
65 CTCTCATTCTTCCAGATCTC
74884 GGCGTCCGAG
Statistics
Matches: 251, Mismatches: 37, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
209 8 0.03
210 241 0.96
211 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.31
Consensus pattern (209 bp):
AGAACCAGAAGATTCACTTGATCCATTGTAAATCCTTCATATGTGACATTACTATGAACTCTCTC
TCTCATTCTTCCAGATCTCAAACGCTGAGGAATTGAGGAACCTAAAACATCACTCTCATTAAACT
TCTCCAAATTTTCAGAACCCAAATCACCAAATCCTCTACCTCCACTCTTATTAGAACTAGCCGAC
GAATCATTCATTTG
Found at i:74913 original size:210 final size:210
Alignment explanation
Indices: 74379--74949 Score: 514
Period size: 210 Copynumber: 2.7 Consensus size: 210
74369 TACTCTTATT
* * * * *
74379 AGAACCAGAAGATTCACTTGATCCATTG-TCAAATCCTTCATATGTGACATTACGATGAACTCTC
1 AGAACCAGAAGATTCACTTGAGCCATGGCT-AGATCCTTCATAAGTGACATTACTATGAACTCTC
* *** * * * * ** * * * *
74443 TCTTTCATTCTTACATATCTTGAGCGCTGAGGGATT-GAGGAACCTAAAACATCACTCTCATTAA
65 ACACCCCTCCTTCCAGATCTCAAACGCCGA-GAATTCGAGGAACCTAAAACATCACACTCATTAA
* *
74507 ACTTCTCCAAATTTTCAGAACCCAAATTACCAAATCCTCTACCTCCACTCTTATTAGAACTATCC
129 ACTTCTCCAAATTTTCAGAACCCAAATCACCAAATCCTCTACCTCCACTCTTATTAGAACTAGCC
*
74572 GACGAATCCTTCATTTG
194 GACGAATCATTCATTTG
* * * * * *
74589 TGAACCTGAAGATTCACTTGATCCATGGCTATATCCTTCATATGTGACATTACTGTGAACTCTCA
1 AGAACCAGAAGATTCACTTGAGCCATGGCTAGATCCTTCATAAGTGACATTACTATGAACTCTCA
* * * * * * *
74654 CTCTCGTTCTTCCAGATCTCAAACGCTGAGAATTTGAGGAACCTAAAACATCAGC-CTCATTAGA
66 CACCCCTCCTTCCAGATCTCAAACGCCGAGAATTCGAGGAACCTAAAACATCA-CACTCATTAAA
* * * *
74718 -TATCTCCAAATTTTCCGAGCCCAAATCA-CATAATCC-CTTACCTCTACTCTTATTGGAACTAG
130 CT-TCTCCAAATTTTCAGAACCCAAATCACCA-AATCCTC-TACCTCCACTCTTATTAGAACTAG
*
74780 CTGACGAATCATTCATTTG
192 CCGACGAATCATTCATTTG
* *
74799 AGAACCAGAAGATTCACTTGAGCCATTG-TAGGATCCTTGATAAGTGACATTACTATGAACTCTC
1 AGAACCAGAAGATTCACTTGAGCCATGGCTA-GATCCTTCATAAGTGACATTACTATGAACTCTC
* ** **
74863 TCACCCCTCCTTCCAGATCTC-GGCGTCCGAGTAA-TCG-GGAAATGTAAAACATCACACTCATT
65 ACACCCCTCCTTCCAGATCTCAAACG-CCGAG-AATTCGAGG-AACCTAAAACATCACACTCATT
* *
74925 TAACTTCCCATTCAAATTTTCAGAA
127 AAACTT--C-TCCAAATTTTCAGAA
74950 GCAACACCAC
Statistics
Matches: 298, Mismatches: 48, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
209 15 0.05
210 265 0.89
211 5 0.02
212 1 0.00
213 12 0.04
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (210 bp):
AGAACCAGAAGATTCACTTGAGCCATGGCTAGATCCTTCATAAGTGACATTACTATGAACTCTCA
CACCCCTCCTTCCAGATCTCAAACGCCGAGAATTCGAGGAACCTAAAACATCACACTCATTAAAC
TTCTCCAAATTTTCAGAACCCAAATCACCAAATCCTCTACCTCCACTCTTATTAGAACTAGCCGA
CGAATCATTCATTTG
Found at i:84309 original size:14 final size:14
Alignment explanation
Indices: 84290--84316 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
84280 CTCAATTAAT
84290 TTTATGTTCGTTTG
1 TTTATGTTCGTTTG
84304 TTTATGTTCGTTT
1 TTTATGTTCGTTT
84317 ACGTTCGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.19, T:0.67
Consensus pattern (14 bp):
TTTATGTTCGTTTG
Found at i:92471 original size:14 final size:13
Alignment explanation
Indices: 92452--92487 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
92442 CTCTTTTTTG
92452 TTTTTTTTTGCCT
1 TTTTTTTTTGCCT
92465 TTTTTTTTTGCCT
1 TTTTTTTTTGCCT
92478 TTTTTGTTTT
1 TTTTT-TTTT
92488 TTGTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTGCCT
Found at i:92472 original size:15 final size:15
Alignment explanation
Indices: 92452--92506 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
92442 CTCTTTTTTG
92452 TTTTTTTTTGCC--T
1 TTTTTTTTTGCCTTT
92465 TTTTTTTTTGCCTTT
1 TTTTTTTTTGCCTTT
**
92480 TTTGTTTTTTGTTTTT
1 TTT-TTTTTTGCCTTT
92496 TTGTTTTTTTG
1 TT-TTTTTTTG
92507 AAAAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
13 12 0.33
15 4 0.11
16 19 0.53
17 1 0.03
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTGCCTTT
Found at i:100737 original size:16 final size:18
Alignment explanation
Indices: 100693--100737 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
100683 TGTTTATAAG
*
100693 GGAATTGAAATATGTGAA
1 GGAATTGGAATATGTGAA
*
100711 GGAATTAGAATATGT-AA
1 GGAATTGGAATATGTGAA
100728 -GAATTGGAAT
1 GGAATTGGAAT
100738 TTGAATCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 9 0.38
17 2 0.08
18 13 0.54
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATATGTGAA
Found at i:101369 original size:28 final size:28
Alignment explanation
Indices: 101318--101422 Score: 120
Period size: 28 Copynumber: 3.8 Consensus size: 28
101308 TTTTCATCCT
* * * *
101318 AAACTCGACCCGAATATTACACTTAAAA
1 AAACCCGACACGAATATCAAACTTAAAA
* *
101346 AAGCCCGACACGATTATCAAACTTAAAA
1 AAACCCGACACGAATATCAAACTTAAAA
* *
101374 AAACCCGACCCGAATATTAAACTTAAAA
1 AAACCCGACACGAATATCAAACTTAAAA
* *
101402 AAACCCGACCCGAATACCAAA
1 AAACCCGACACGAATATCAAA
101423 AAATTGATGA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.48, C:0.28, G:0.09, T:0.16
Consensus pattern (28 bp):
AAACCCGACACGAATATCAAACTTAAAA
Found at i:106167 original size:2 final size:2
Alignment explanation
Indices: 106160--106197 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
106150 CCCTTACCCC
106160 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
106198 GAGAAAAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.