Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001384.1 Hibiscus syriacus cultivar Beakdansim tig00002700_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: 58684
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:6472 original size:21 final size:22
Alignment explanation
Indices: 6423--6484 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
6413 ATACTTTACA
*
6423 ATATAAGCGCTACCTATTAATT
1 ATATAAGCGCTACCTATTAAAT
6445 ATATAAGCGCTACCTATTAAAT
1 ATATAAGCGCTACCTATTAAAT
6467 -TATAAGCGCTACCTATTA
1 ATATAAGCGCTACCTATTA
6485 CATCATATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
21 18 0.46
22 21 0.54
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (22 bp):
ATATAAGCGCTACCTATTAAAT
Found at i:9954 original size:184 final size:184
Alignment explanation
Indices: 9637--9981 Score: 620
Period size: 184 Copynumber: 1.9 Consensus size: 184
9627 GCGTTACTTA
*
9637 AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
1 AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTATCATAAAACCGG
* *
9702 TATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
66 TATATCTATACCAGTTATATTACAAAATTACCTATTACATTATAACTATGGGTTCCGATGTTTTT
*
9767 TCAATTGACACTTTTTGAAAAGGTATCGACATTTTTTTCATCCATTCTGGACAT
131 TCAATCGACACTTTTTGAAAAGGTATCGACATTTTTTTCATCCATTCTGGACAT
9821 AAAGTA-GCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTATCATAAAACCG
1 AAAGTATG-GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTATCATAAAACCG
*
9885 GTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAACTATGGGTTCCGATGTTTT
65 GTATATCTATACCAGTTATATTACAAAATTACCTATTACATTATAACTATGGGTTCCGATGTTTT
*
9950 TTCAATCGATACTTTTTGAAAAGGTATCGACA
130 TTCAATCGACACTTTTTGAAAAGGTATCGACA
9982 CTTTATGCTG
Statistics
Matches: 154, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
183 1 0.01
184 153 0.99
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (184 bp):
AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTATCATAAAACCGG
TATATCTATACCAGTTATATTACAAAATTACCTATTACATTATAACTATGGGTTCCGATGTTTTT
TCAATCGACACTTTTTGAAAAGGTATCGACATTTTTTTCATCCATTCTGGACAT
Found at i:11048 original size:33 final size:33
Alignment explanation
Indices: 11010--11075 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
11000 CTTCTTAAGA
*
11010 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
**
11043 TCACCCCTCAACACCTTTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
11076 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.32
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:11134 original size:21 final size:21
Alignment explanation
Indices: 11112--11194 Score: 139
Period size: 21 Copynumber: 4.0 Consensus size: 21
11102 CTTATGCCTC
* * *
11112 TCAAGTGTATCTTCGACTCTC
1 TCAAGTTTCTCTTCGACTCTA
11133 TCAAGTTTCTCTTCGACTCTA
1 TCAAGTTTCTCTTCGACTCTA
11154 TCAAGTTTCTCTTCGACTCTA
1 TCAAGTTTCTCTTCGACTCTA
11175 TCAAGTTTCTCTTCGACTCT
1 TCAAGTTTCTCTTCGACTCT
11195 TGATTGTCTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (21 bp):
TCAAGTTTCTCTTCGACTCTA
Found at i:13484 original size:20 final size:19
Alignment explanation
Indices: 13429--13484 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
13419 TCCGGTAGCA
13429 TTTTACCTGTTTTATCATT
1 TTTTACCTGTTTTATCATT
* *
13448 TTGATACCGGTTTTATCATAT
1 TT-TTACCTGTTTTATCAT-T
*
13469 TTTTACCTGTTATATC
1 TTTTACCTGTTTTATC
13485 GTTGTGGATC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.07
20 25 0.83
21 3 0.10
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCTGTTTTATCATT
Found at i:13700 original size:181 final size:182
Alignment explanation
Indices: 13396--13868 Score: 768
Period size: 181 Copynumber: 2.6 Consensus size: 182
13386 CGTACTTACG
* *
13396 AAAGTATCGACACTTTCAATATATCCGGTAGCATTTTACCTGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
13461 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
*
13526 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTAT-AT
131 AGGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATGAT
* *
13577 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTCATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
13642 TATCATATTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
* *
13707 AGGCGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATGTT
131 AGGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATGAT
* * * * * * **
13759 AAAGTACCAACACTTTGAATATATCTGGTACCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
13824 TGTCATAGTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
13869 AATTTGGATC
Statistics
Matches: 269, Mismatches: 22, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
181 171 0.64
182 98 0.36
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
AGGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATGAT
Found at i:14269 original size:38 final size:38
Alignment explanation
Indices: 14220--14358 Score: 165
Period size: 38 Copynumber: 3.7 Consensus size: 38
14210 TCAATTAAAA
***
14220 TTATGAATTTATATTCGATTGAAATAGGCATATATTAT
1 TTATGAATTTATATTCGATTGAAATACAAATATATTAT
* *
14258 TTATAAATTTATATTTGATT-AAATACAAATATATTATT
1 TTATGAATTTATATTCGATTGAAATACAAATATATTA-T
* * *
14296 TTATGAATTTATATTCAATTAAAATATAAATATATTA-
1 TTATGAATTTATATTCGATTGAAATACAAATATATTAT
* *
14333 TTATGAATTTATATTTGATTGGAATA
1 TTATGAATTTATATTCGATTGAAATA
14359 TAATACTGTA
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
37 35 0.41
38 36 0.42
39 15 0.17
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (38 bp):
TTATGAATTTATATTCGATTGAAATACAAATATATTAT
Found at i:14359 original size:37 final size:38
Alignment explanation
Indices: 14220--14361 Score: 171
Period size: 37 Copynumber: 3.8 Consensus size: 38
14210 TCAATTAAAA
***
14220 TTATGAATTTATATTCGATTGAAATAGGCATATATTAT
1 TTATGAATTTATATTCGATTGAAATATAAATATATTAT
* * *
14258 TTATAAATTTATATTTGATT-AAATACAAATATATTATT
1 TTATGAATTTATATTCGATTGAAATATAAATATATTA-T
* *
14296 TTATGAATTTATATTCAATTAAAATATAAATATATTA-
1 TTATGAATTTATATTCGATTGAAATATAAATATATTAT
* *
14333 TTATGAATTTATATTTGATTGGAATATAA
1 TTATGAATTTATATTCGATTGAAATATAA
14362 TACTGTAATT
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
37 38 0.43
38 36 0.40
39 15 0.17
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (38 bp):
TTATGAATTTATATTCGATTGAAATATAAATATATTAT
Found at i:21427 original size:509 final size:509
Alignment explanation
Indices: 20470--21491 Score: 1999
Period size: 509 Copynumber: 2.0 Consensus size: 509
20460 GGCATGGGCA
*
20470 ACCTTAACTCGGGGACATAGGTTCAAATCTCACGACCACCAACTCATTATTTTTTTCACTTCTGA
1 ACCTTAACTCGGGGACATAGGTTCAAACCTCACGACCACCAACTCATTATTTTTTTCACTTCTGA
*
20535 TAAAAATGGGGAAATTAATGATTAAGTACCTGAACTTCCTACAAATGCTAAAACAGGCTGCAAGT
66 TAAAAATGGGGAAATTAATGATTAAGTACCTAAACTTCCTACAAATGCTAAAACAGGCTGCAAGT
20600 TCTAAAAAATTATAATTTAGTCCCTAATTATTTTAAATTGAATAAATTTTAGTTTTTTATATGAA
131 TCTAAAAAATTATAATTTAGTCCCTAATTATTTTAAATTGAATAAATTTTAGTTTTTTATATGAA
*
20665 ATTAGGGTTGTGACAATTCTCTCCCTTAAAAGAAATTTAATCCTCGAAATTTACCCAAGTTATAA
196 ATTAGGGTTGTGACAATTCTCCCCCTTAAAAGAAATTTAATCCTCGAAATTTACCCAAGTTATAA
*
20730 AATTGTGGGAACTGAGCTTTAATCAATTCTTCAATCTCTTAGGTATCTTTTAAAGGGTTACGATT
261 AAATGTGGGAACTGAGCTTTAATCAATTCTTCAATCTCTTAGGTATCTTTTAAAGGGTTACGATT
20795 CCTCTACTAAACCTTAACCAGCTGATTATGCACAAATATCTTTTTTGTCAAAATTTCAGAATCTA
326 CCTCTACTAAACCTTAACCAGCTGATTATGCACAAATATCTTTTTTGTCAAAATTTCAGAATCTA
20860 AACATAATTATACTCGTATAACCAAACATACCTTAATTACCAATCCTTAATTAGAATAATACTTG
391 AACATAATTATACTCGTATAACCAAACATACCTTAATTACCAATCCTTAATTAGAATAATACTTG
20925 CTTAACTTCAATGCAACATATAGACATAACTGATTTTTTTATACGAGCAGCGTC
456 CTTAACTTCAATGCAACATATAGACATAACTGATTTTTTTATACGAGCAGCGTC
20979 ACCTTAACTCGGGGACATAGGTTCAAACCTCACGACCACCAACTCATTATTTTTTTCACTTCTGA
1 ACCTTAACTCGGGGACATAGGTTCAAACCTCACGACCACCAACTCATTATTTTTTTCACTTCTGA
21044 TAAAAATGGGGAAATTAATGATTAAGTACCTAAACTTCCTACAAATGCTAAAACAGGCTGCAAGT
66 TAAAAATGGGGAAATTAATGATTAAGTACCTAAACTTCCTACAAATGCTAAAACAGGCTGCAAGT
21109 TCTAAAAAATTATAATTTAGTCCCTAATTATTTTAAATTGAATAAATTTTAGTTTTTTATATGAA
131 TCTAAAAAATTATAATTTAGTCCCTAATTATTTTAAATTGAATAAATTTTAGTTTTTTATATGAA
21174 ATTAGGGTTGTGACAATTCTCCCCCTTAAAAGAAATTTAATCCTCGAAATTTACCCAAGTTATAA
196 ATTAGGGTTGTGACAATTCTCCCCCTTAAAAGAAATTTAATCCTCGAAATTTACCCAAGTTATAA
21239 AAATGTGGGAACTGAGCTTTAATCAATTCTTCAATCTCTTAGGTATCTTTTAAAGGGTTACGATT
261 AAATGTGGGAACTGAGCTTTAATCAATTCTTCAATCTCTTAGGTATCTTTTAAAGGGTTACGATT
21304 CCTCTACTAAACCTTAACCAGCTGATTATGCACAAATATCTTTTTTGTCAAAATTTCAGAATCTA
326 CCTCTACTAAACCTTAACCAGCTGATTATGCACAAATATCTTTTTTGTCAAAATTTCAGAATCTA
21369 AACATAATTATACTCGTATAACCAAACATACCTTAATTACCAATCCTTAATTAGAATAATACTTG
391 AACATAATTATACTCGTATAACCAAACATACCTTAATTACCAATCCTTAATTAGAATAATACTTG
*
21434 CTTAACTTCAATGCAACATATAGACATAACTGATTTTTTTATACGAGTAGCGTC
456 CTTAACTTCAATGCAACATATAGACATAACTGATTTTTTTATACGAGCAGCGTC
21488 ACCT
1 ACCT
21492 CGAGATTTAT
Statistics
Matches: 508, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
509 508 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (509 bp):
ACCTTAACTCGGGGACATAGGTTCAAACCTCACGACCACCAACTCATTATTTTTTTCACTTCTGA
TAAAAATGGGGAAATTAATGATTAAGTACCTAAACTTCCTACAAATGCTAAAACAGGCTGCAAGT
TCTAAAAAATTATAATTTAGTCCCTAATTATTTTAAATTGAATAAATTTTAGTTTTTTATATGAA
ATTAGGGTTGTGACAATTCTCCCCCTTAAAAGAAATTTAATCCTCGAAATTTACCCAAGTTATAA
AAATGTGGGAACTGAGCTTTAATCAATTCTTCAATCTCTTAGGTATCTTTTAAAGGGTTACGATT
CCTCTACTAAACCTTAACCAGCTGATTATGCACAAATATCTTTTTTGTCAAAATTTCAGAATCTA
AACATAATTATACTCGTATAACCAAACATACCTTAATTACCAATCCTTAATTAGAATAATACTTG
CTTAACTTCAATGCAACATATAGACATAACTGATTTTTTTATACGAGCAGCGTC
Found at i:26019 original size:16 final size:16
Alignment explanation
Indices: 25994--26025 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25984 ATTTAACTTT
*
25994 TTGGTTAAAGTCAACG
1 TTGGTCAAAGTCAACG
26010 TTGGTCAAAGTCAACG
1 TTGGTCAAAGTCAACG
26026 GTCAGTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (16 bp):
TTGGTCAAAGTCAACG
Found at i:26035 original size:17 final size:17
Alignment explanation
Indices: 26000--26042 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
25990 CTTTTTGGTT
**
26000 AAAGTCAAC-GTTGGTC
1 AAAGTCAACGGTCAGTC
26016 AAAGTCAACGGTCAGTC
1 AAAGTCAACGGTCAGTC
*
26033 AAAGTTAACG
1 AAAGTCAACG
26043 AGTTGACTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (17 bp):
AAAGTCAACGGTCAGTC
Found at i:26864 original size:38 final size:38
Alignment explanation
Indices: 26817--26954 Score: 129
Period size: 37 Copynumber: 3.7 Consensus size: 38
26807 AATTAAATAA
* *
26817 TTATCAATTTATATTCGATTGAAATAGGAATATATTAT
1 TTATAAATTTATATTCGATTGAAATACGAATATATTAT
** * *
26855 TTATAAATTTATATTTAATT-AAACACAAATATATTAT
1 TTATAAATTTATATTCGATTGAAATACGAATATATTAT
* * * * *
26892 TTATGAATTTGTATTCTATTAAAATACGAATATAGTA-
1 TTATAAATTTATATTCGATTGAAATACGAATATATTAT
* *
26929 TTA-AAATTTTATATTTGATTGGAATA
1 TTATAAA-TTTATATTCGATTGAAATA
26955 TAATATTGTA
Statistics
Matches: 79, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
36 2 0.03
37 47 0.59
38 30 0.38
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (38 bp):
TTATAAATTTATATTCGATTGAAATACGAATATATTAT
Found at i:30508 original size:3 final size:3
Alignment explanation
Indices: 30500--30536 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
30490 ACAATGATAT
*
30500 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30537 CATCATCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30692 original size:25 final size:25
Alignment explanation
Indices: 30640--30704 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
30630 TTTCGTTGTC
* * *
30640 TAAAATTTCATAAATTCACTCTTCT
1 TAAAATTTTATAAACTCACCCTTCT
30665 TAAAATTTTATAAACTCACCCGTT-T
1 TAAAATTTTATAAACTCACCC-TTCT
*
30690 TAAAGTTTTATAAAC
1 TAAAATTTTATAAAC
30705 CTGTCTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 33 0.94
26 2 0.06
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.42
Consensus pattern (25 bp):
TAAAATTTTATAAACTCACCCTTCT
Found at i:35961 original size:35 final size:34
Alignment explanation
Indices: 35915--36005 Score: 146
Period size: 35 Copynumber: 2.6 Consensus size: 34
35905 TTAAAAATAT
*
35915 ATATAATATATAGTTTTATAAATTGTTCTGAAAGC
1 ATATAATATATAGTTTT-TAAATAGTTCTGAAAGC
*
35950 ATATAATATATAGTTTTTAAAATAGTTTTGAAAGC
1 ATATAATATATAGTTTTT-AAATAGTTCTGAAAGC
35985 ATATAATATATAGTTTTTAAA
1 ATATAATATATAGTTTTTAAA
36006 GCGGTTTAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
34 4 0.08
35 49 0.92
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (34 bp):
ATATAATATATAGTTTTTAAATAGTTCTGAAAGC
Found at i:36044 original size:72 final size:69
Alignment explanation
Indices: 35915--36097 Score: 190
Period size: 72 Copynumber: 2.6 Consensus size: 69
35905 TTAAAAATAT
** * * *
35915 ATATAATATATAGTTTTATAAATTGTTCTGAAAGCATATAATATATAGTTTTTAAAATAGTTTTG
1 ATATAATATATAGTTTTATAAACGGTTCTGAAAACATATAATAAATAGTTTTTAAAATAATTTTG
*
35980 AAAGC
66 AAA-A
*
35985 ATATAATATATAGTTTT-TAAAGCGGTT-TAGAAAAACATATAGTAAATAGTTTTTTAAAATAAT
1 ATATAATATATAGTTTTATAAA-CGGTTCT-G-AAAACATATAATAAATAG-TTTTTAAAATAAT
36048 TTTGAAAA
62 TTTGAAAA
* * * *
36056 AGTATAATATATAGTTTAAAAAAACGGTTTTAAAAACATATA
1 A-TATAATATATAGTTT-TATAAACGGTTCTGAAAACATATA
36098 TAATATAATG
Statistics
Matches: 95, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
69 5 0.05
70 21 0.22
71 16 0.17
72 44 0.46
73 5 0.05
74 4 0.04
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (69 bp):
ATATAATATATAGTTTTATAAACGGTTCTGAAAACATATAATAAATAGTTTTTAAAATAATTTTG
AAAA
Found at i:36291 original size:17 final size:16
Alignment explanation
Indices: 36269--36314 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 16
36259 TTTTCGTTAT
36269 TATTATTATATTATTTA
1 TATTATTAT-TTATTTA
36286 TATTATTATTTA-TTA
1 TATTATTATTTATTTA
36301 T-TT-TTATTTATTTA
1 TATTATTATTTATTTA
36315 ATCATTTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.25
14 5 0.18
15 4 0.14
16 3 0.11
17 9 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTATTATTTATTTA
Found at i:36312 original size:20 final size:20
Alignment explanation
Indices: 36266--36308 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
36256 AGTTTTTCGT
36266 TATTATTATTATATTATTTA
1 TATTATTATTATATTATTTA
*
36286 TATTATTATT-TATTATTTT
1 TATTATTATTATATTATTTA
36305 TATT
1 TATT
36309 TATTTAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTATTATTATATTATTTA
Found at i:38360 original size:21 final size:20
Alignment explanation
Indices: 38323--38403 Score: 135
Period size: 20 Copynumber: 4.0 Consensus size: 20
38313 CCGTTAGACA
38323 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
38343 GGGGGAATCGGTACCCCCTAG
1 GGGGGAATCGGTACCCCCT-G
*
38364 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
*
38384 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
38404 AACAATCTGA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
20 40 0.68
21 19 0.32
ACGTcount: A:0.16, C:0.30, G:0.37, T:0.17
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:38378 original size:41 final size:41
Alignment explanation
Indices: 38323--38402 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
38313 CCGTTAGACA
38323 GGGGGAATCGGTACCCCCTGGGGGGAATCGGTACCCCCTAG
1 GGGGGAATCGGTACCCCCTGGGGGGAATCGGTACCCCCTAG
* *
38364 GGGGGAATCTGTACCCCCTGGGGGGAATCTGTACCCCCT
1 GGGGGAATCGGTACCCCCTGGGGGGAATCGGTACCCCCT
38403 GAACAATCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.16, C:0.30, G:0.36, T:0.17
Consensus pattern (41 bp):
GGGGGAATCGGTACCCCCTGGGGGGAATCGGTACCCCCTAG
Found at i:41353 original size:32 final size:34
Alignment explanation
Indices: 41317--41386 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
41307 CCTTACAAAC
*
41317 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
*
41349 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
41383 TCCC
1 TCCC
41387 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
Found at i:41694 original size:21 final size:21
Alignment explanation
Indices: 41668--41720 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
41658 TTGGAGCATG
41668 GGGGAATCGGTACCCCCTCAT
1 GGGGAATCGGTACCCCCTCAT
41689 GGGGAATCGGTACCCCCTCAT
1 GGGGAATCGGTACCCCCTCAT
41710 GGGGAATCGGT
1 GGGGAATCGGT
41721 TCCCTAAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.28, G:0.34, T:0.19
Consensus pattern (21 bp):
GGGGAATCGGTACCCCCTCAT
Found at i:41817 original size:21 final size:21
Alignment explanation
Indices: 41755--41818 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
41745 CCGTTAGACA
* * *
41755 GGGGGTAATCGGTACCCCCTA
1 GGGGGGAATCTGTACCCCCTG
*
41776 GGGGGGAATCTGTTCCCCCTG
1 GGGGGGAATCTGTACCCCCTG
41797 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
41818 G
1 G
41819 ACAATTTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:43095 original size:18 final size:18
Alignment explanation
Indices: 43068--43105 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
43058 TGGGGTAGGA
*
43068 ATTTTTATTTT-ATTTATT
1 ATTTTGATTTTGATTT-TT
43086 ATTTTGATTTTGATTTTT
1 ATTTTGATTTTGATTTTT
43104 AT
1 AT
43106 CTTACTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (18 bp):
ATTTTGATTTTGATTTTT
Found at i:50751 original size:53 final size:53
Alignment explanation
Indices: 50652--51069 Score: 599
Period size: 53 Copynumber: 7.9 Consensus size: 53
50642 TGTTAAATGG
* *
50652 CTAAATGTCCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
* * * * * *
50705 CTAACTATGCATATTGGTAGAAAGGTATCAATAATGTAAGTAAGATGAAAGAC
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
* * *
50758 CTAACTGTGCAT-TTGACAGAAAGGTGTCAATAATGCAAGTTAGATAAAAGGT
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
* * * * *
50810 TTAACTGTGCATATTGGCATAAATGTGTCAATAATGTAAGTTAGATGAAAGGT
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
* *
50863 CGAGCTGTGCAT-TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
* *
50915 CTAACTGTGCATATTGGCATAAAGGTGTCGATAATGCAAGTTAGATGAAAGGC
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
* *
50968 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAATGC
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
* *
51021 CTAACTGTGCAT-TTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAA
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
51070 AGTTAAATGC
Statistics
Matches: 322, Mismatches: 41, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
52 123 0.38
53 199 0.62
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (53 bp):
CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGC
Found at i:50856 original size:105 final size:105
Alignment explanation
Indices: 50665--51069 Score: 596
Period size: 105 Copynumber: 3.9 Consensus size: 105
50655 AATGTCCATA
* *
50665 TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTATGCATATTGGTAGAAAGG
1 TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATATTGGCAGAAAGG
* * * *
50730 TATCAATAATGTAAGTAAGATGAAAGACCTAACTGTGCAT
66 TGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCAT
* * ** * *
50770 TTGACAGAAAGGTGTCAATAATGCAAGTTAGATAAAAGGTTTAACTGTGCATATTGGCATAAATG
1 TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATATTGGCAGAAAGG
* * * *
50835 TGTCAATAATGTAAGTTAGATGAAAGGTCGAGCTGTGCAT
66 TGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCAT
*
50875 TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATATTGGCATAAAGG
1 TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATATTGGCAGAAAGG
*
50940 TGTCGATAATGCAAGTTAGATGAAAGGCCTAACTGTGCAT
66 TGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCAT
* * *
50980 ATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAATGCCTAACTGTGCAT-TTGGCAGAAAT
1 -TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATATTGGCAGAAAG
*
51044 GTGCCAATAATGCAAGTTAGATGAAA
65 GTGTCAATAATGCAAGTTAGATGAAA
51070 AGTTAAATGC
Statistics
Matches: 269, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
105 219 0.81
106 50 0.19
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (105 bp):
TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATATTGGCAGAAAGG
TGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCAT
Found at i:50949 original size:158 final size:157
Alignment explanation
Indices: 50652--51069 Score: 611
Period size: 158 Copynumber: 2.6 Consensus size: 157
50642 TGTTAAATGG
* * * *
50652 CTAAATGTCCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTATGCAT
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAGGCCTAACTGTGCAT
* * * *
50717 ATTGGTAGAAAGGTATCAATAATGTAAGTAAGATGAAAGACCTAACTGTGCATTTGACAGAAAGG
66 -TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGACCTAACTGTGCATTTGACAGAAAGG
*
50782 TGTCAATAATGCAAGTTAGATAAAAGGT
130 TGTCAATAATGCAAGTTAGATAAAAGGC
* * * * * *
50810 TTAACTGTGCATATTGGCATAAATGTGTCAATAATGTAAGTTAGATGAAAGGTCGAGCTGTGCAT
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAGGCCTAACTGTGCAT
* * *
50875 TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATATTGGCATAAAGG
66 TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGACCTAACTGTGCAT-TTGACAGAAAGG
* *
50940 TGTCGATAATGCAAGTTAGATGAAAGGC
130 TGTCAATAATGCAAGTTAGATAAAAGGC
*
50968 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAATGCCTAACTGTGCAT
1 CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAGGCCTAACTGTGCAT
* *
51033 TTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAA
66 TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
51070 AGTTAAATGC
Statistics
Matches: 230, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
157 47 0.20
158 183 0.80
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (157 bp):
CTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAGGCCTAACTGTGCAT
TTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGACCTAACTGTGCATTTGACAGAAAGGT
GTCAATAATGCAAGTTAGATAAAAGGC
Found at i:51115 original size:61 final size:61
Alignment explanation
Indices: 51015--51678 Score: 960
Period size: 61 Copynumber: 11.0 Consensus size: 61
51005 AAGTTAGATG
* *
51015 AAATGCCTAACTG-TGCA--TTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAAGTT
1 AAATGCCTAAC-GATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTT
* * **
51074 AAATGCCTAACGATGCATTTTTGGCAAAAAGGTGCCAATAATATAAGTTAGATGAAAAGTT
1 AAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTT
* * * * *
51135 AAATACCTAACGATGCATTTTTGGCAGTAAGGTGCCACTAATGTAAGCTAGATGAACAGTT
1 AAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTT
* * *
51196 AAATGCCTAACGATGCATTTTTAGTAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATT
1 AAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTT
* *
51257 AAATGCCTAACGATGCATTTTTGGCATAAAGGTGCCACTAATGCAAGTTAGATGAAAAGCT
1 AAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTT
* **
51318 AAATGCCTAACGATGTATTTTTGGCAGAAAAATGCCACTAATGCAAGTTAGATGAAAAGTT
1 AAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTT
* * *
51379 AAATGCCTAACGATGTATTTTTGGCATAAAGGTGCCACTAATGCAAGTTAGAT-TAAAGTT
1 AAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTT
* *
51439 AAATGCCTAACGATGCATTTTTGGCATAAAGGTACCACTAATGCAAGTTAGATGAAAAGTT
1 AAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTT
* * * **
51500 AAATGCCTAATGATGCATATTTGGCTGAAAGGTGCCACTAATGCAAGTTAGATGAAAAAAT
1 AAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTT
* * *
51561 AAATGCCTAACGATGCATTTTTGACAGAAAGGTGCCACTAATGCAAGTGAGATGAAACGTT
1 AAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTT
* * * *
51622 AAATGCCTATCGGTGCA-TTTTGGCAGAAAGATGCCACTAATGCAATTTAGATGAAAA
1 AAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAA
51679 ACAGTGCATA
Statistics
Matches: 543, Mismatches: 58, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
58 1 0.00
59 15 0.03
60 92 0.17
61 435 0.80
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (61 bp):
AAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTT
Found at i:56774 original size:52 final size:53
Alignment explanation
Indices: 56679--57112 Score: 549
Period size: 53 Copynumber: 8.3 Consensus size: 53
56669 AATGTTAAAT
* * * * *
56679 GCCTAACTCTGCATATTGACAGAAATGTGTCAATAATGCAAGTTATATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
* * * *
56732 GCGTAACTCTGCATATTGGCA-TAAGGTGTCAATAATGTAAGTTAAATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
* * *
56784 ACCTAACTATGCAT-TTGGCAGAAATGTGTCAATAATG-ACAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTA-AGTTAGATGAAAG
* * *
56836 GCTTAACTTTGCATATTGGTAGAAAGGTGTCAATAATGTAAGTTAGATG-AAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
* *
56888 GCCTAACTATGCAT-TTGGCAGAAA-GTGTCAATAATGCAAGTTAGATGAAA-
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
* ** *
56938 GCCTAATTGTGCATATTGGCAGAAAGGTGTCAATAATACATGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
* * **
56991 ACCTAACTGTGCATATTGACAGAAATATGTCAATAATGTAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
*
57044 GCCTAACTGTGCATATTGGCAGAAAGGTGTTAATAATGTAAGTTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAG-TTAGATGAAAG
* *
57098 ACCTAATTGTGCATA
1 GCCTAACTGTGCATA
57113 GATGAAAAGT
Statistics
Matches: 332, Mismatches: 40, Indels: 17
0.85 0.10 0.04
Matches are distributed among these distances:
50 34 0.10
51 28 0.08
52 114 0.34
53 131 0.39
54 25 0.08
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (53 bp):
GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTTAGATGAAAG
Found at i:56968 original size:155 final size:158
Alignment explanation
Indices: 56680--57112 Score: 615
Period size: 155 Copynumber: 2.8 Consensus size: 158
56670 ATGTTAAATG
* * * *
56680 CCTAACTCTGCATATTGACAGAAATGTGTCAATAATGCAAGTTATATGAAAGGCGTAACTCTGCA
1 CCTAACTCTGCATATTGACAGAAATGTGTCAATAATGTAAGTTAGATGAAAGGCCTAACTATGCA
* * * * * *
56745 TATTGGCATAAGGTGTCAATAATGTAAGTTAAATGAAAGACCTAACTATGCAT-TTGGCAGAAAT
66 TATTGGCAGAAAGTGTCAATAATGTAAGTTAGATGAAAGACCTAATTGTGCATATTGGCAGAAAG
*
56809 GTGTCAATAATGACA-GTTAGATGAAAGG
131 GTGTCAATAAT-ACATGTTAGATGAAAGA
* * ** *
56837 CTTAACTTTGCATATTGGTAGAAAGGTGTCAATAATGTAAGTTAGATG-AAGGCCTAACTATGCA
1 CCTAACTCTGCATATTGACAGAAATGTGTCAATAATGTAAGTTAGATGAAAGGCCTAACTATGCA
*
56901 T-TTGGCAGAAAGTGTCAATAATGCAAGTTAGATGAAAG-CCTAATTGTGCATATTGGCAGAAAG
66 TATTGGCAGAAAGTGTCAATAATGTAAGTTAGATGAAAGACCTAATTGTGCATATTGGCAGAAAG
56964 GTGTCAATAATACATGTTAGATGAAAGA
131 GTGTCAATAATACATGTTAGATGAAAGA
* * *
56992 CCTAACTGTGCATATTGACAGAAATATGTCAATAATGTAAGTTAGATGAAAGGCCTAACTGTGCA
1 CCTAACTCTGCATATTGACAGAAATGTGTCAATAATGTAAGTTAGATGAAAGGCCTAACTATGCA
*
57057 TATTGGCAGAAAGGTGTTAATAATGTAAGTTTAGATGAAAGACCTAATTGTGCATA
66 TATTGGCAGAAA-GTGTCAATAATGTAAG-TTAGATGAAAGACCTAATTGTGCATA
57113 GATGAAAAGT
Statistics
Matches: 243, Mismatches: 26, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
154 14 0.06
155 108 0.44
156 31 0.13
157 51 0.21
158 14 0.06
159 11 0.05
160 14 0.06
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (158 bp):
CCTAACTCTGCATATTGACAGAAATGTGTCAATAATGTAAGTTAGATGAAAGGCCTAACTATGCA
TATTGGCAGAAAGTGTCAATAATGTAAGTTAGATGAAAGACCTAATTGTGCATATTGGCAGAAAG
GTGTCAATAATACATGTTAGATGAAAGA
Found at i:57211 original size:61 final size:61
Alignment explanation
Indices: 57111--57659 Score: 775
Period size: 61 Copynumber: 9.1 Consensus size: 61
57101 TAATTGTGCA
* * * * *
57111 TAGATGAAAAG-TAAATGCCTAACGGT-TA-TTTTGGCAGAAAGCTTCCACTGATGCAAGT
1 TAGATGAAAAGTTAAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
* * * * * *
57169 TAGATGAAAATTTAAATGCCAAACAATACATTTTTGGAAGAAATGTGCCACTAATGCAAGT
1 TAGATGAAAAGTTAAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
*
57230 TAGATGAAAAGTTAAATGCCTAACGATGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGT
1 TAGATGAAAAGTTAAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
*
57291 TAGATGAAAAGTTAAATGCCTAACGATGCATTTTTGGCAGAAATGTGCCACTAATGCAAGT
1 TAGATGAAAAGTTAAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
* * * *
57352 TAGATGAAAAGTTAAATGCGTAACAATGCATTTTTGGTAGAAAGTTGCCACTAATGCAAGT
1 TAGATGAAAAGTTAAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
* ** *
57413 TAGATGAAAAGTTAAATGCCTAACGATGTATTTTTGGCAGAAAAATGCCACTAATACAAGT
1 TAGATGAAAAGTTAAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
* * * *
57474 TAGATGAAATGTTAAATGTCTAACGATGCATTTTTTGCAGAAAGGTGCCAATAATGCAAGT
1 TAGATGAAAAGTTAAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
* * *
57535 TAGATGAAACA-TTAAATGCCTAACAATGCATTTTTGGCAGAAAGGTGCCACTATTACAAGT
1 TAGATGAAA-AGTTAAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
* * *
57596 GAAATGAAAAGTTAAATGCCTAACGGTGCA-TTTTGGCAGAAAGGTGCCACTAATGCAAGT
1 TAGATGAAAAGTTAAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
57656 TAGA
1 TAGA
57660 AGATAAACGG
Statistics
Matches: 433, Mismatches: 53, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
58 10 0.02
59 12 0.03
60 32 0.07
61 379 0.88
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (61 bp):
TAGATGAAAAGTTAAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGT
Found at i:57259 original size:33 final size:33
Alignment explanation
Indices: 57222--57320 Score: 77
Period size: 33 Copynumber: 3.2 Consensus size: 33
57212 TGTGCCACTA
57222 ATGCAAGTTAGATGAAAAGTTAAATGCCTAACG
1 ATGCAAGTTAGATGAAAAGTTAAATGCCTAACG
** * * * *
57255 ATGCATTTTTGGT-AGAAAG----GTGCC--ACTA
1 ATGCAAGTTAGATGA-AAAGTTAAATGCCTAAC-G
57283 ATGCAAGTTAGATGAAAAGTTAAATGCCTAACG
1 ATGCAAGTTAGATGAAAAGTTAAATGCCTAACG
57316 ATGCA
1 ATGCA
57321 TTTTTGGCAG
Statistics
Matches: 45, Mismatches: 12, Indels: 18
0.60 0.16 0.24
Matches are distributed among these distances:
27 2 0.04
28 13 0.29
29 5 0.11
32 5 0.11
33 18 0.40
34 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.26
Consensus pattern (33 bp):
ATGCAAGTTAGATGAAAAGTTAAATGCCTAACG
Done.