Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006257.1 Hibiscus syriacus cultivar Beakdansim tig00014932_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: 58234
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:7286 original size:24 final size:23
Alignment explanation
Indices: 7259--7346 Score: 104
Period size: 24 Copynumber: 3.7 Consensus size: 23
7249 ATTTCCGACT
*
7259 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATAC-TGATC
*
7283 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGA-TACTGATC
* *
7307 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATA-CTGATC
*
7331 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
7347 TTATGATATT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.02
24 52 0.95
25 2 0.04
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGATC
Found at i:7297 original size:12 final size:12
Alignment explanation
Indices: 7259--7341 Score: 80
Period size: 12 Copynumber: 6.9 Consensus size: 12
7249 ATTTCCGACT
7259 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
7271 TG-ATACATGACC
1 TGAATTC-TGTTC
7283 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
7295 TGATTTCTGATC
1 TGAATTCTGTTC
*
7307 TGGATTCTGTTC
1 TGAATTCTGTTC
7319 TG-ATATCTGTTC
1 TGAAT-TCTGTTC
7331 TGAATTCTGTT
1 TGAATTCTGTT
7342 TTGATTTATG
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
11 5 0.09
12 46 0.82
13 5 0.09
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.47
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:7301 original size:48 final size:48
Alignment explanation
Indices: 7245--7348 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 48
7235 AAATATTTTA
7245 TCTGATTTCCGA-CTTGAATTCTGTTCTGATA-CATGACCTGAATTCTGT
1 TCTGATTTCCGATC-TGAATTCTGTTCTGATATC-TGACCTGAATTCTGT
* * **
7293 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCCGATCTGAATTCTGTTCTGATATCTGACCTGAATTCTGT
*
7341 TTTGATTT
1 TCTGATTT
7349 ATGATATTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
48 47 0.96
49 2 0.04
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCCGATCTGAATTCTGTTCTGATATCTGACCTGAATTCTGT
Found at i:10802 original size:14 final size:14
Alignment explanation
Indices: 10785--10813 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10775 GTTAAAATTA
10785 AAAATAAAGAAAAT
1 AAAATAAAGAAAAT
10799 AAAATAAAGAAAAT
1 AAAATAAAGAAAAT
10813 A
1 A
10814 TTACATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAATAAAGAAAAT
Found at i:11579 original size:25 final size:26
Alignment explanation
Indices: 11518--11580 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
11508 AAAATTTAAT
* *
11518 AAATAAATAAATAATAATAATAATATA
1 AAAT-AATATATAATAATAATAAAATA
**
11545 ACCTAATATATAA-AATAATAAAATA
1 AAATAATATATAATAATAATAAAATA
*
11570 AAATATTATAT
1 AAATAATATAT
11581 TATATTATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
25 19 0.66
26 8 0.28
27 2 0.07
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (26 bp):
AAATAATATATAATAATAATAAAATA
Found at i:11626 original size:28 final size:28
Alignment explanation
Indices: 11576--11629 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
11566 AATAAAATAT
*
11576 TATATTATATTATATTTCCCAAAAACTA
1 TATAATATATTATATTTCCCAAAAACTA
*
11604 TATAATATATTAATATTT-TCAAAAAC
1 TATAATATATT-ATATTTCCCAAAAAC
11630 CGTTTTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (28 bp):
TATAATATATTATATTTCCCAAAAACTA
Found at i:11740 original size:30 final size:30
Alignment explanation
Indices: 11698--11863 Score: 161
Period size: 33 Copynumber: 5.1 Consensus size: 30
11688 AACTATATAC
* *
11698 TATATGTTTTCAAATTTATTTTAAAAACTA
1 TATATATTTTCAAAATTATTTTAAAAACTA
*
11728 TATACATTTTCAAAATTATTTTAAAAACTA
1 TATATATTTTCAAAATTATTTTAAAAACTA
11758 TATTATATGTTTTCAAAATTATTTTAAAAACCATA
1 TA-TATA--TTTTCAAAATTATTTTAAAAA-C-TA
*
11793 TTATATGTTTTCAAAATTATTTTAAAAAACTCTA
1 -TATATATTTTCAAAATTATTTT-AAAAA--CTA
***
11827 TATTATATGTTTTCAAAACCGTTTTAAAAACTA
1 TA-TATA--TTTTCAAAATTATTTTAAAAACTA
11860 TATA
1 TATA
11864 CTATATGTTT
Statistics
Matches: 115, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
30 29 0.25
31 3 0.03
32 2 0.02
33 44 0.38
34 11 0.10
35 11 0.10
36 15 0.13
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (30 bp):
TATATATTTTCAAAATTATTTTAAAAACTA
Found at i:11776 original size:33 final size:33
Alignment explanation
Indices: 11646--11893 Score: 268
Period size: 35 Copynumber: 7.3 Consensus size: 33
11636 CAAAAACAAT
* ***
11646 TTTTAAAAACTATATTATATACTTTTTCAAAACCG
1 TTTTAAAAACTATATTATAT--GTTTTCAAAATTA
* *
11681 GTTTAAAAACTATATACTATATGTTTTCAAATTTA
1 TTTTAAAAACTATAT--TATATGTTTTCAAAATTA
*
11716 TTTTAAAAACTATA-TACA--TTTTCAAAATTA
1 TTTTAAAAACTATATTATATGTTTTCAAAATTA
11746 TTTTAAAAACTATATTATATGTTTTCAAAATTA
1 TTTTAAAAACTATATTATATGTTTTCAAAATTA
*
11779 TTTTAAAAACCATATTATATGTTTTCAAAATTA
1 TTTTAAAAACTATATTATATGTTTTCAAAATTA
***
11812 TTTTAAAAAACTCTATATTATATGTTTTCAAAACCG
1 TTTT-AAAAA--CTATATTATATGTTTTCAAAATTA
* *
11848 TTTTAAAAACTATATACTATATGTTTTCAAAACTG
1 TTTTAAAAACTATAT--TATATGTTTTCAAAATTA
*
11883 TTTTCAAAACT
1 TTTTAAAAACT
11894 GTTTTCAAAA
Statistics
Matches: 186, Mismatches: 17, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
30 25 0.13
31 3 0.02
32 3 0.02
33 54 0.29
34 5 0.03
35 67 0.36
36 24 0.13
37 5 0.03
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (33 bp):
TTTTAAAAACTATATTATATGTTTTCAAAATTA
Found at i:11879 original size:23 final size:23
Alignment explanation
Indices: 11847--11928 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
11837 TTTCAAAACC
*
11847 GTTTTAAAAACTATATACTATAT
1 GTTTTCAAAACTATATACTATAT
* * * * *
11870 GTTTTCAAAACTGTTTTCAAAACT
1 GTTTTCAAAACTATATACTATA-T
* *
11894 GTTTTCAAAACTATATATTATAC
1 GTTTTCAAAACTATATACTATAT
11917 GTTTTCAAAACT
1 GTTTTCAAAACT
11929 TATTTTTTTT
Statistics
Matches: 45, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
23 28 0.62
24 17 0.38
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (23 bp):
GTTTTCAAAACTATATACTATAT
Found at i:11886 original size:12 final size:12
Alignment explanation
Indices: 11869--11905 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
11859 ATATACTATA
11869 TGTTTTCAAAAC
1 TGTTTTCAAAAC
11881 TGTTTTCAAAAC
1 TGTTTTCAAAAC
11893 TGTTTTCAAAAC
1 TGTTTTCAAAAC
11905 T
1 T
11906 ATATATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.43
Consensus pattern (12 bp):
TGTTTTCAAAAC
Found at i:11888 original size:47 final size:47
Alignment explanation
Indices: 11834--11928 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
11824 CTATATTATA
*
11834 TGTTTTCAAAACCGTTTTAAAAACTATATACTATATGTTTTCAAAAC
1 TGTTTTCAAAACCGTTTTAAAAACTATATACTATACGTTTTCAAAAC
* * *
11881 TGTTTTCAAAACTGTTTTCAAAACTATATATTATACGTTTTCAAAAC
1 TGTTTTCAAAACCGTTTTAAAAACTATATACTATACGTTTTCAAAAC
11928 T
1 T
11929 TATTTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (47 bp):
TGTTTTCAAAACCGTTTTAAAAACTATATACTATACGTTTTCAAAAC
Found at i:11962 original size:23 final size:24
Alignment explanation
Indices: 11936--11983 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
11926 ACTTATTTTT
11936 TTTAAAAAACTATA-AATTATATA
1 TTTAAAAAACTATATAATTATATA
* *
11959 TTTAAAAAATTATATATTTATATA
1 TTTAAAAAACTATATAATTATATA
11983 T
1 T
11984 ATGCATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTAAAAAACTATATAATTATATA
Found at i:17867 original size:23 final size:24
Alignment explanation
Indices: 17841--17893 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
17831 GTTCATATCT
17841 AAAAAATTAGATG-ATTCTATTG-GA
1 AAAAAATTA-ATGAATTC-ATTGAGA
*
17865 AAAAAATTAATGAATTCATTGATA
1 AAAAAATTAATGAATTCATTGAGA
17889 AAAAA
1 AAAAA
17894 TTCATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (24 bp):
AAAAAATTAATGAATTCATTGAGA
Found at i:17894 original size:23 final size:25
Alignment explanation
Indices: 17840--17895 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
17830 AGTTCATATC
17840 TAAAAAATTAGATGATTCTATTGGA
1 TAAAAAATTAGATGATTCTATTGGA
17865 -AAAAAATTA-ATGAATTC-ATT-GA
1 TAAAAAATTAGATG-ATTCTATTGGA
17887 TAAAAAATT
1 TAAAAAATT
17896 CATAAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 2 0.07
23 14 0.48
24 13 0.45
ACGTcount: A:0.52, C:0.04, G:0.11, T:0.34
Consensus pattern (25 bp):
TAAAAAATTAGATGATTCTATTGGA
Found at i:22578 original size:2 final size:2
Alignment explanation
Indices: 22571--22609 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
22561 ATCCTAACTC
22571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22610 GTTCATTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23227 original size:340 final size:341
Alignment explanation
Indices: 22607--23285 Score: 1315
Period size: 340 Copynumber: 2.0 Consensus size: 341
22597 ATATATATAT
22607 ATAGTTCATTATCTAATGGATTTTTCCGTTCTAATACTCCATCCGAGAGTTATCAGTATTTATCA
1 ATAGTTCATTATCTAATGGATTTTTCCGTTCTAATACTCCATCCGAGAGTTATCAGTATTTATCA
*
22672 AATATGTTCCTATCTAACGGAAGGCTATTGGATCAAATGACAAAGACATTGTTGAGAAAAAGATG
66 AATATGTTCCTATCTAACAGAAGGCTATTGGATCAAATGACAAAGACATTGTTGAGAAAAAGATG
* *
22737 GCTTTTCCCGGATTAAATGGTTGTTGCTATCTGCTCCAATAACGAATCATTGGTTTAACTGAATA
131 GCTTTTCCCGGATGAAATGGTTGTTGCTATATGCTCCAATAACGAATCATTGGTTTAACTGAATA
22802 ACTAAATAAAATAGATAGACCTTTCTCTTCGTCTCAGGTCGATGGATCTTCTCAACTGGAGGATC
196 ACTAAATAAAATAGATAGACCTTTCTCTTCGTCTCAGGTCGATGGATCTTCTCAACTGGAGGATC
22867 CCCTATATGGATAATATATGGAT-ACACACATTCCAGTTGACCGAGCCTAATTCTAATTGTTCCG
261 CCCTATATGGATAATATATGGATAACACACATTCCAGTTGACCGAGCCTAATTCTAATTGTTCCG
22931 AAGCAAAGATATCCCA
326 AAGCAAAGATATCCCA
22947 ATAGTTCATTATCTAATGGATTTTTCCGTTCTAATACTCCATCCGAGAGTTATCAGTATTTATCA
1 ATAGTTCATTATCTAATGGATTTTTCCGTTCTAATACTCCATCCGAGAGTTATCAGTATTTATCA
*
23012 AATCTGTTCCTATCTAACAGAAGGCTATTGGATCAAATGACAAAGACATTGTTGAGAAAAAGATG
66 AATATGTTCCTATCTAACAGAAGGCTATTGGATCAAATGACAAAGACATTGTTGAGAAAAAGATG
23077 GCTTTTCCCGGATGAAATGGTTGTTGCTATATGCTCCAATAACGAATCATTGGTTTAACTGAATA
131 GCTTTTCCCGGATGAAATGGTTGTTGCTATATGCTCCAATAACGAATCATTGGTTTAACTGAATA
23142 ACTAAATAAAATAGATAGACCTTTCTCTTCGTCTCAGGTCGATGGATCTTCTCAACTGGAGGATC
196 ACTAAATAAAATAGATAGACCTTTCTCTTCGTCTCAGGTCGATGGATCTTCTCAACTGGAGGATC
23207 CCCTATATGGATAATATATGGATAACACACATTCCAGTTGACCGAGCCTAATTCTAATTGTTCCG
261 CCCTATATGGATAATATATGGATAACACACATTCCAGTTGACCGAGCCTAATTCTAATTGTTCCG
23272 AAGCAAAGATATCC
326 AAGCAAAGATATCC
23286 ACGGGGCGGT
Statistics
Matches: 334, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
340 279 0.84
341 55 0.16
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (341 bp):
ATAGTTCATTATCTAATGGATTTTTCCGTTCTAATACTCCATCCGAGAGTTATCAGTATTTATCA
AATATGTTCCTATCTAACAGAAGGCTATTGGATCAAATGACAAAGACATTGTTGAGAAAAAGATG
GCTTTTCCCGGATGAAATGGTTGTTGCTATATGCTCCAATAACGAATCATTGGTTTAACTGAATA
ACTAAATAAAATAGATAGACCTTTCTCTTCGTCTCAGGTCGATGGATCTTCTCAACTGGAGGATC
CCCTATATGGATAATATATGGATAACACACATTCCAGTTGACCGAGCCTAATTCTAATTGTTCCG
AAGCAAAGATATCCCA
Found at i:24082 original size:2 final size:2
Alignment explanation
Indices: 24077--24135 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
24067 ACTGTGTGGT
24077 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
24119 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
24136 TTTATTAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25807 original size:340 final size:339
Alignment explanation
Indices: 25188--25871 Score: 1341
Period size: 340 Copynumber: 2.0 Consensus size: 339
25178 TTATTGGTTG
25188 AAAATCATTAAGTAATTAAATAATTGCGTACGTAATCTTTTTCCCCATAAAAATAAATCAATCTA
1 AAAATCATTAAGTAATTAAATAATTGCGTACGTAATCTTTTTCCCCATAAAAATAAATCAATCTA
25253 TTTTCGGCTTTTTTTTGTCTTATACTTAGGTGACGTTTGGTTGGATGAAATCTATTGGAATTGGT
66 TTTTCGGCTTTTTTTTGTCTTATACTTAGGTGACGTTTGGTTGGATGAAATCTATTGGAATTGGT
25318 GGGAATTGGAATTCAATTCTACCACTTTCTCATGTTTGGTTTAAGTTTTTCAAGGGAATTGGAAT
131 GGGAATTGGAATTCAATTCTACCACTTTCTCATGTTTGGTTTAAGTTTTTCAAGGGAATTGGAAT
25383 CCCTGATGGAATTTAATTCCATCAAATGAGGGAAAGTGAATTCCATCAAAATATGGATGGAATTT
196 CCCTGATGGAATTTAATTCCATCAAATGAGGGAAAGTGAATTCCATCAAAATATGGATGGAATTT
*
25448 AATTTCTTTGTTGGAGAGAATTGAAATTTGACCATATTACCCTCATCAATCGTTTGGTAACTTAT
261 AATTTCCTTGTTGGAGAGAATTGAAATTTGACCATATTACCCTCATCAATCGTTTGGTAACTTAT
25513 TCATATATTGAATA
326 TCATATATTGAATA
25527 AAAATCATTAAGTAATTAAATAATTGCGTACGTAATCTTTTTCCCCATAAAAATAAATCAATCTA
1 AAAATCATTAAGTAATTAAATAATTGCGTACGTAATCTTTTTCCCCATAAAAATAAATCAATCTA
*
25592 TTTTCGGCTTTTTTTTTGTCTTATACTTAGGTGACGTTTGGTTGGATGGAATCTATTGGAATTGG
66 TTTTCGGC-TTTTTTTTGTCTTATACTTAGGTGACGTTTGGTTGGATGAAATCTATTGGAATTGG
25657 TGGGAATTGGAATTCAATTCTACCACTTTCTCATGTTTGGTTTAAGTTTTTCAAGGGAATTGGAA
130 TGGGAATTGGAATTCAATTCTACCACTTTCTCATGTTTGGTTTAAGTTTTTCAAGGGAATTGGAA
25722 TCCCTGATGGAATTTAATTCCATCAAATGAGGGAAAGTGAATTCCATCAAAATATGGATGGAATT
195 TCCCTGATGGAATTTAATTCCATCAAATGAGGGAAAGTGAATTCCATCAAAATATGGATGGAATT
25787 TAATTTCCTTGTTGGAGAGAATTGAAATTTGACCATATTACCCTCATCAATCGTTTGGTAACTTA
260 TAATTTCCTTGTTGGAGAGAATTGAAATTTGACCATATTACCCTCATCAATCGTTTGGTAACTTA
25852 TTCATATATTGAATA
325 TTCATATATTGAATA
25867 AAAAT
1 AAAAT
25872 GTTTTTTTTA
Statistics
Matches: 342, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
339 73 0.21
340 269 0.79
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (339 bp):
AAAATCATTAAGTAATTAAATAATTGCGTACGTAATCTTTTTCCCCATAAAAATAAATCAATCTA
TTTTCGGCTTTTTTTTGTCTTATACTTAGGTGACGTTTGGTTGGATGAAATCTATTGGAATTGGT
GGGAATTGGAATTCAATTCTACCACTTTCTCATGTTTGGTTTAAGTTTTTCAAGGGAATTGGAAT
CCCTGATGGAATTTAATTCCATCAAATGAGGGAAAGTGAATTCCATCAAAATATGGATGGAATTT
AATTTCCTTGTTGGAGAGAATTGAAATTTGACCATATTACCCTCATCAATCGTTTGGTAACTTAT
TCATATATTGAATA
Found at i:26229 original size:37 final size:38
Alignment explanation
Indices: 26177--26249 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
26167 TTTTGTTCAG
*
26177 GTCGGGTTGG-GTTTTTTAAGTGTGATATTCGGGTCTA
1 GTCGGGTTGGATTTTTTTAAGTGTGATATTCGGGTCTA
26214 GTCGGGTTGGATTTTTTTAAGTGTGATATTCGGGTC
1 GTCGGGTTGGATTTTTTTAAGTGTGATATTCGGGTC
26250 GGGTTCGGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 10 0.29
38 24 0.71
ACGTcount: A:0.14, C:0.08, G:0.34, T:0.44
Consensus pattern (38 bp):
GTCGGGTTGGATTTTTTTAAGTGTGATATTCGGGTCTA
Found at i:35132 original size:21 final size:20
Alignment explanation
Indices: 35046--35203 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
35036 AAATGACCAA
**
35046 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
35065 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
35085 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
35105 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
35126 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
35147 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
35167 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
35188 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
35204 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:35232 original size:20 final size:20
Alignment explanation
Indices: 35170--35363 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
35160 CGATTTTCCA
* ** *
35170 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
35190 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
35210 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
35230 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
35250 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
35270 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
35290 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
35310 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
35330 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
35351 AAATCGCAACGCG
1 AAATCGCAACGCG
35364 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:35254 original size:60 final size:60
Alignment explanation
Indices: 35170--35363 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
35160 CGATTTTCCA
* ** * *
35170 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
35230 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
35290 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
35351 AAATCGCAACGCG
1 AAATCGCAACGCG
35364 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:35785 original size:33 final size:33
Alignment explanation
Indices: 35746--35816 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
35736 TTCACTTAGA
*
35746 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
35779 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
35812 TTTCA
1 TTTCA
35817 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:35921 original size:20 final size:19
Alignment explanation
Indices: 35896--36000 Score: 87
Period size: 20 Copynumber: 5.6 Consensus size: 19
35886 TGCAGAAGAG
35896 TCGCAACGAGATAAATGAAA
1 TCGCAACGAGA-AAATGAAA
* **
35916 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGA-AA
35936 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATG-AAA
35957 TCGCAACGAG---A-G-AA
1 TCGCAACGAGAAAATGAAA
*
35971 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATG-AAA
35990 TCGCAACGAGA
1 TCGCAACGAGA
36001 GAATCGCAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 16 0.24
20 22 0.32
21 14 0.21
22 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (19 bp):
TCGCAACGAGAAAATGAAA
Found at i:35952 original size:40 final size:41
Alignment explanation
Indices: 35895--36004 Score: 139
Period size: 33 Copynumber: 2.9 Consensus size: 41
35885 TTGCAGAAGA
*
35895 GTCGCAACGAGATAAATG-AAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
35935 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAG-A--A--
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
*
35971 -TCGCAAC--GCGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
36005 CGCAACGTGA
Statistics
Matches: 65, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
33 23 0.35
34 1 0.02
35 7 0.11
38 1 0.02
40 18 0.28
41 15 0.23
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:35974 original size:14 final size:14
Alignment explanation
Indices: 35955--36011 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
35945 GAGAAATGAA
35955 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
35969 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
35988 AATCGCAACGAGAG
1 AATCGCAACGAGAG
36002 AATCGCAACG
1 AATCGCAACG
36012 TGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:35987 original size:33 final size:33
Alignment explanation
Indices: 35947--36027 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
35937 CGCAACGAGA
35947 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
35980 GAAATGAAAATCGCAACGAGAGAATCGCAACGT
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
36013 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
36028 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:36045 original size:19 final size:19
Alignment explanation
Indices: 36023--36128 Score: 106
Period size: 19 Copynumber: 6.1 Consensus size: 19
36013 GAAACCAAAA
*
36023 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
36042 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
36056 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
36075 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
36089 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
36108 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
36127 TC
1 TC
36129 AACCAAAAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
14 20 0.29
16 5 0.07
17 6 0.09
19 39 0.56
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:36064 original size:14 final size:14
Alignment explanation
Indices: 36045--36101 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
36035 TTTCATTTCG
36045 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
36059 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
36078 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
36092 CGTTGCGATT
1 CGTTGCGATT
36102 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:36070 original size:33 final size:33
Alignment explanation
Indices: 36028--36120 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
36018 CAAAATCGCA
36028 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
36061 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
36094 TTGCGATTGTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
36121 TTCATTTCAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:37986 original size:93 final size:93
Alignment explanation
Indices: 37827--38387 Score: 1090
Period size: 93 Copynumber: 6.1 Consensus size: 93
37817 TAGATTGCTT
*
37827 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37892 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37920 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37985 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38013 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38078 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38106 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38171 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38199 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38264 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
38291 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38356 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38383 AGTAA
1 AGTAA
38388 TGCAATCCAT
Statistics
Matches: 465, Mismatches: 2, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
92 97 0.21
93 368 0.79
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:38475 original size:19 final size:19
Alignment explanation
Indices: 38435--38563 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
38425 TAGTTTACTT
* *
38435 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
38455 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
38474 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
38493 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
38507 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
38526 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
38540 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
38559 TCGCA
1 TCGCA
38564 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:38514 original size:33 final size:32
Alignment explanation
Indices: 38471--38563 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
38461 CGCGAAACCA
**
38471 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
38503 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
38536 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
38564 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:38561 original size:52 final size:52
Alignment explanation
Indices: 38435--38563 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
38425 TAGTTTACTT
**
38435 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
38487 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
38540 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
38564 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:38581 original size:19 final size:19
Alignment explanation
Indices: 38559--38693 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
38549 GAAACCAAAA
*
38559 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
38578 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
38594 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
38611 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
38627 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
38644 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
38663 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
38683 TCGTGTTGCGA
1 TCGCGTTGCGA
38694 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:38600 original size:14 final size:14
Alignment explanation
Indices: 38581--38637 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
38571 TTTCATTTCG
38581 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
38595 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
38612 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
38628 CGTTGCGATT
1 CGTTGCGATT
38638 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:38606 original size:33 final size:33
Alignment explanation
Indices: 38564--38656 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
38554 CAAAATCGCA
*
38564 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
38597 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
38630 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
38657 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:40635 original size:14 final size:14
Alignment explanation
Indices: 40616--40651 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
40606 ATTGTTTAAT
40616 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
40630 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
40644 TGATTTGT
1 TGATTTGT
40652 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:40774 original size:19 final size:19
Alignment explanation
Indices: 40758--40855 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
40748 AAAAATGACT
40758 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
40777 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
40796 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
40810 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
40829 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
40849 ATCGCAA
1 ATCGCAA
40856 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:40887 original size:53 final size:53
Alignment explanation
Indices: 40758--40873 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
40748 AAAAATGACT
40758 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
40810 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
40863 ATCGCAATGCG
1 ATCGCAATGCG
40874 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:40926 original size:19 final size:19
Alignment explanation
Indices: 40902--41136 Score: 278
Period size: 19 Copynumber: 13.4 Consensus size: 19
40892 GATTCTCTCG
40902 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
40921 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
40940 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
40959 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
40978 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
40997 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
41011 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41029 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
41043 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41062 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
41076 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
41096 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
41110 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41129 TTGCGATT
1 TTGCGATT
41137 CTCTCGTTGC
Statistics
Matches: 188, Mismatches: 8, Indels: 40
0.80 0.03 0.17
Matches are distributed among these distances:
14 29 0.15
15 3 0.02
16 24 0.13
17 16 0.09
18 9 0.05
19 95 0.51
20 12 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:41158 original size:33 final size:33
Alignment explanation
Indices: 40880--41150 Score: 384
Period size: 33 Copynumber: 7.9 Consensus size: 33
40870 TGCGTTTATA
40880 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
40913 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
*
40951 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
40989 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
41021 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
41054 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
41087 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
41121 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
41151 GTAATTTCCG
Statistics
Matches: 223, Mismatches: 6, Indels: 18
0.90 0.02 0.07
Matches are distributed among these distances:
32 33 0.15
33 83 0.37
34 29 0.13
35 8 0.04
36 7 0.03
38 63 0.28
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:43664 original size:24 final size:24
Alignment explanation
Indices: 43630--43676 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43620 CTGAAACATC
43630 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
43654 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
43677 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:44387 original size:20 final size:20
Alignment explanation
Indices: 44359--44588 Score: 230
Period size: 20 Copynumber: 11.5 Consensus size: 20
44349 AAATTTCAGT
* * *
44359 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
44379 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
44399 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
44419 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
44439 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
44459 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
44479 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
44499 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
44519 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
44539 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
**
44559 GTTGCGATTTTA-ATATTCGC
1 GTTGCGA-TTTACGGATTCGC
44579 GTTGCGATTT
1 GTTGCGATTT
44589 TGGAAAATCG
Statistics
Matches: 183, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
19 3 0.02
20 175 0.96
21 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:44589 original size:20 final size:20
Alignment explanation
Indices: 44555--44652 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
44545 ATTTATGTGT
*
44555 TCGCGTTGCGATTTTAATAT
1 TCGCGTTGCGATTTTAATAA
44575 TCGCGTTGCGATTTTGGAA-AA
1 TCGCGTTGCGATTTT--AATAA
** *
44596 TCGCAATGCGAATTTGTACT-A
1 TCGCGTTGCG-ATTT-TAATAA
* *
44617 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTT-AATAA
44638 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
44653 GGAAACTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 20 0.32
21 35 0.56
22 6 0.10
23 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTAATAA
Found at i:44648 original size:42 final size:43
Alignment explanation
Indices: 44555--44653 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
44545 ATTTATGTGT
* *
44555 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
** *
44596 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAA-AA
*
44638 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
44654 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 10 0.21
42 33 0.70
43 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
Found at i:49321 original size:23 final size:23
Alignment explanation
Indices: 49295--49373 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
49285 GTTTGTATTC
*
49295 ATTCGTTTAATATTCGTGAACAT
1 ATTCGTTTAATGTTCGTGAACAT
* *
49318 ATTCGTTTAACGTTCGAGAACAT
1 ATTCGTTTAATGTTCGTGAACAT
* * * *
49341 GTTTGTTTAGTGTTCATGAACAT
1 ATTCGTTTAATGTTCGTGAACAT
49364 ATTCGTTTAA
1 ATTCGTTTAA
49374 CGATAGTTTA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (23 bp):
ATTCGTTTAATGTTCGTGAACAT
Done.