Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000870.1 Hibiscus syriacus cultivar Beakdansim tig00001681_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: 122411
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4306 original size:21 final size:20
Alignment explanation
Indices: 4282--4324 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
4272 GATGTAAGCT
*
4282 TTAGGGTTTAAGATTTTGAGA
1 TTAGAGTTTAAGA-TTTGAGA
*
4303 TTAGAGTTTATGATTTGAGA
1 TTAGAGTTTAAGATTTGAGA
4323 TT
1 TT
4325 GGGGGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (20 bp):
TTAGAGTTTAAGATTTGAGA
Found at i:6807 original size:25 final size:26
Alignment explanation
Indices: 6779--6830 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
6769 ATTTATTTTT
*
6779 ATCACCT-CTAAAATTTTATAAGTTC
1 ATCACCTCCTAAAATTTTAAAAGTTC
*
6804 ATCATCTCCTAAAATTTTAAAAGTTC
1 ATCACCTCCTAAAATTTTAAAAGTTC
6830 A
1 A
6831 ACTCCCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (26 bp):
ATCACCTCCTAAAATTTTAAAAGTTC
Found at i:10409 original size:2 final size:2
Alignment explanation
Indices: 10402--10447 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
10392 TATTGACCAC
10402 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
10444 TA TA
1 TA TA
10448 GCGTCTGTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14156 original size:16 final size:17
Alignment explanation
Indices: 14122--14156 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
14112 TTAAAGCCCC
14122 ATCAATTTACTTGATCT
1 ATCAATTTACTTGATCT
*
14139 ATCAATTTA-TTTATCT
1 ATCAATTTACTTGATCT
14155 AT
1 AT
14157 ATGCATACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.51
Consensus pattern (17 bp):
ATCAATTTACTTGATCT
Found at i:15009 original size:19 final size:19
Alignment explanation
Indices: 14985--15021 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
14975 CAAAACTAGA
14985 CATATGTGATAGATTGTTT
1 CATATGTGATAGATTGTTT
15004 CATATGTGATAGATTGTT
1 CATATGTGATAGATTGTT
15022 CTATGAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.46
Consensus pattern (19 bp):
CATATGTGATAGATTGTTT
Found at i:15180 original size:15 final size:15
Alignment explanation
Indices: 15160--15196 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
15150 TCAACACTTC
15160 AAGAATATGCAAAAA
1 AAGAATATGCAAAAA
15175 AAGAATATGCAAAAA
1 AAGAATATGCAAAAA
*
15190 AAAAATA
1 AAGAATA
15197 ATAATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (15 bp):
AAGAATATGCAAAAA
Found at i:18918 original size:15 final size:16
Alignment explanation
Indices: 18898--18927 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18888 AATTTTGATT
18898 TTTAAAAA-TATATAA
1 TTTAAAAATTATATAA
18913 TTTAAAAATTATATA
1 TTTAAAAATTATATA
18928 TATATTCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTAAAAATTATATAA
Found at i:37288 original size:12 final size:12
Alignment explanation
Indices: 37271--37298 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
37261 GCTGTCAATA
37271 TATACGTATATG
1 TATACGTATATG
37283 TATACGTATATG
1 TATACGTATATG
37295 TATA
1 TATA
37299 GTTCTGGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (12 bp):
TATACGTATATG
Found at i:41203 original size:14 final size:15
Alignment explanation
Indices: 41178--41206 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41168 CGATACGATA
41178 ATAATATTAAATTAT
1 ATAATATTAAATTAT
41193 ATAAT-TTAAATTAT
1 ATAATATTAAATTAT
41207 TCTAAGTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATATTAAATTAT
Found at i:41537 original size:25 final size:25
Alignment explanation
Indices: 41504--41583 Score: 124
Period size: 25 Copynumber: 3.2 Consensus size: 25
41494 TCATGTTGGG
* *
41504 AGTAGTAGAAGATTGTCCTCACTTT
1 AGTACTAGAAGATTGTCCTCACTTC
*
41529 AGTACTAGAAAATTGTCCTCACTTC
1 AGTACTAGAAGATTGTCCTCACTTC
*
41554 AGTACTAGAAGATTGTTCTCACTTC
1 AGTACTAGAAGATTGTCCTCACTTC
41579 AGTAC
1 AGTAC
41584 AGATTTTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (25 bp):
AGTACTAGAAGATTGTCCTCACTTC
Found at i:43229 original size:31 final size:33
Alignment explanation
Indices: 43182--43242 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 33
43172 AACAAACAAA
*
43182 ATAAATAAAAAGTCTATCGATGTATGTGTTTTG
1 ATAAATAAAAAGTCTATCGATGAATGTGTTTTG
43215 ATAAA-AAAAA-TCTATCGATGAATGTGTT
1 ATAAATAAAAAGTCTATCGATGAATGTGTT
43243 CCACATGGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 17 0.63
32 5 0.19
33 5 0.19
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (33 bp):
ATAAATAAAAAGTCTATCGATGAATGTGTTTTG
Found at i:59302 original size:14 final size:14
Alignment explanation
Indices: 59283--59367 Score: 75
Period size: 14 Copynumber: 6.0 Consensus size: 14
59273 AAACCCTAAG
59283 TTAAGATTTAGGGT
1 TTAAGATTTAGGGT
*
59297 TTAAGATTTAGTAGT
1 TTAAGATTTAG-GGT
* **
59312 TTATGGATTTATAGT
1 TTA-AGATTTAGGGT
*
59327 TTAAGGTTTAGGGT
1 TTAAGATTTAGGGT
59341 TTATA-ATTTAGGGT
1 TTA-AGATTTAGGGT
*
59355 TTACGA-TTAGGGT
1 TTAAGATTTAGGGT
59368 ATAGAATGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.12
14 33 0.57
15 12 0.21
16 6 0.10
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (14 bp):
TTAAGATTTAGGGT
Found at i:64047 original size:59 final size:61
Alignment explanation
Indices: 63948--64066 Score: 147
Period size: 59 Copynumber: 2.0 Consensus size: 61
63938 TGTATAATGC
* * *
63948 GGGATGAAATTGAAATGTTTAAAAAGTTTGGTGACCAATTTAGATTGA-AGATCATAGTTTA
1 GGGATGAAAATGAAATGTTTAAAAAGTTTAGTGACCAATTTAGAATGATA-ATCATAGTTTA
* *
64009 GGGAT-AAAATGAAATG-TTCAAAAGTTTCAG-GACTAATTTAGAATGATAATCATAGTTT
1 GGGATGAAAATGAAATGTTTAAAAAGTTT-AGTGACCAATTTAGAATGATAATCATAGTTT
64067 CATATTGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
59 34 0.67
60 12 0.24
61 5 0.10
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (61 bp):
GGGATGAAAATGAAATGTTTAAAAAGTTTAGTGACCAATTTAGAATGATAATCATAGTTTA
Found at i:64324 original size:20 final size:19
Alignment explanation
Indices: 64299--64350 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
64289 TTGTGTGTGT
*
64299 AAATCAATGATTTTATGATA
1 AAATCAATGA-TTTATAATA
64319 AAATCAAT-A--TATAATA
1 AAATCAATGATTTATAATA
64335 AAATCAATGATATTAT
1 AAATCAATGAT-TTAT
64351 TCTCTTGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
16 14 0.52
17 1 0.04
19 1 0.04
20 11 0.41
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.37
Consensus pattern (19 bp):
AAATCAATGATTTATAATA
Found at i:64337 original size:16 final size:17
Alignment explanation
Indices: 64316--64347 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
64306 TGATTTTATG
64316 ATAAAATCAAT-ATATA
1 ATAAAATCAATGATATA
64332 ATAAAATCAATGATAT
1 ATAAAATCAATGATAT
64348 TATTCTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAAAATCAATGATATA
Found at i:65228 original size:26 final size:24
Alignment explanation
Indices: 65199--65277 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 24
65189 TTTATGATAT
65199 AAAATTAAATATCTAATATAATATTAA
1 AAAATT-AATATCT-ATATAATATT-A
* *
65226 AAAATTAATATTTCAT-TTAT-TTA
1 AAAATTAATATCT-ATATAATATTA
65249 AAAATTAATATCTATAATAATATTA
1 AAAATTAATATCTAT-ATAATATTA
65274 AAAA
1 AAAA
65278 AATAATATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 2 0.05
23 13 0.30
24 5 0.11
25 10 0.23
26 8 0.18
27 6 0.14
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
AAAATTAATATCTATATAATATTA
Found at i:65251 original size:23 final size:23
Alignment explanation
Indices: 65220--65309 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 23
65210 TCTAATATAA
*
65220 TATTAAAAAATTAATATTTCATT
1 TATTAAAAAATTAATATTTAATT
* *
65243 TATTTAAAAATTAATATCTATAATAA
1 TATTAAAAAATTAATAT-T-TAAT-T
*
65269 TATTAAAAAAATAATATTTAATT
1 TATTAAAAAATTAATATTTAATT
* *
65292 TATTTAAAAACTAATATT
1 TATTAAAAAATTAATATT
65310 AAAATTAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
23 32 0.57
24 5 0.09
25 4 0.07
26 15 0.27
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTAAAAAATTAATATTTAATT
Found at i:65259 original size:49 final size:49
Alignment explanation
Indices: 65199--65308 Score: 168
Period size: 49 Copynumber: 2.2 Consensus size: 49
65189 TTTATGATAT
* *
65199 AAAATTAAATATCTA-ATATAATATTAAAAAATTAATATTTCATTTATTTA
1 AAAATT-AATATCTATA-ATAATATTAAAAAAATAATATTTAATTTATTTA
65249 AAAATTAATATCTATAATAATATTAAAAAAATAATATTTAATTTATTTA
1 AAAATTAATATCTATAATAATATTAAAAAAATAATATTTAATTTATTTA
*
65298 AAAACTAATAT
1 AAAATTAATAT
65309 TAAAATTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
49 49 0.88
50 7 0.12
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (49 bp):
AAAATTAATATCTATAATAATATTAAAAAAATAATATTTAATTTATTTA
Found at i:65283 original size:26 final size:26
Alignment explanation
Indices: 65199--65285 Score: 92
Period size: 26 Copynumber: 3.4 Consensus size: 26
65189 TTTATGATAT
65199 AAAATTAAATATCTA-ATATAATATTAA
1 AAAATT-AATATCTATA-ATAATATTAA
* * *
65226 AAAATTAATAT-T-TCAT-TTATTTA
1 AAAATTAATATCTATAATAATATTAA
65249 AAAATTAATATCTATAATAATATTAA
1 AAAATTAATATCTATAATAATATTAA
*
65275 AAAAATAATAT
1 AAAATTAATAT
65286 TTAATTTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
23 16 0.33
24 3 0.06
25 4 0.08
26 20 0.41
27 6 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAATTAATATCTATAATAATATTAA
Found at i:65307 original size:26 final size:25
Alignment explanation
Indices: 65222--65307 Score: 74
Period size: 24 Copynumber: 3.5 Consensus size: 25
65212 TAATATAATA
* *
65222 TTAAAAA-ATTAATATTTCATTTAT
1 TTAAAAATAATAATATTTAATTTAT
*
65246 TTAAAAAT--TAATATCTATAA-TAAT
1 TTAAAAATAATAATAT-T-TAATTTAT
65270 ATTAAAAA-AATAATATTTAATTTAT
1 -TTAAAAATAATAATATTTAATTTAT
65295 TTAAAAACTAATA
1 TTAAAAA-TAATA
65308 TTAAAATTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
23 6 0.12
24 21 0.42
25 13 0.26
26 10 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAAAAATAATAATATTTAATTTAT
Found at i:66603 original size:30 final size:30
Alignment explanation
Indices: 66567--66634 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
66557 CGTTTTTGCT
* *
66567 ATGGATTCAATCTCTGGGTTTAGAAATTTA
1 ATGGATTCAATCTCTGGGTTTACAAATTCA
* *
66597 ATGGATTTAATCTTTGGGTTTACAAATTCA
1 ATGGATTCAATCTCTGGGTTTACAAATTCA
66627 ATGGATTC
1 ATGGATTC
66635 TGAAATCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.41
Consensus pattern (30 bp):
ATGGATTCAATCTCTGGGTTTACAAATTCA
Found at i:68821 original size:30 final size:30
Alignment explanation
Indices: 68785--68851 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
68775 ATGAAATCCG
* *
68785 CATTCCCTCATTTGGTTAGCACGAGAATCT
1 CATTCCCCCATTTGGTTAGCAAGAGAATCT
* *
68815 CATTCCCCCGTTTGGTTAGCAAGGGAATCT
1 CATTCCCCCATTTGGTTAGCAAGAGAATCT
68845 CATTCCC
1 CATTCCC
68852 GGTAATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.31
Consensus pattern (30 bp):
CATTCCCCCATTTGGTTAGCAAGAGAATCT
Found at i:76077 original size:86 final size:86
Alignment explanation
Indices: 75960--76142 Score: 267
Period size: 86 Copynumber: 2.1 Consensus size: 86
75950 TCAAATTCCA
* * *
75960 TACATAAAATGTTACAAACTGTTTATATACCCCTAACATCACAAATTACTTTAGTTCTAAAAACA
1 TACATAAAA-GTTACAAACTGTTTACATACCCCTAACATCACAAAATACTTTAGTTCCAAAAACA
* *
76025 ACATATTGTAGTTCCACAAAGT
65 ACATATTGTAGTTCAACAAAGC
** * *
76047 TACATAAAAGTTACAATTTTTTTACATACCCCTGACATCACAAAATACTTTAGTTCCAAAAACAA
1 TACATAAAAGTTACAAACTGTTTACATACCCCTAACATCACAAAATACTTTAGTTCCAAAAACAA
76112 CATATTGTAGTTCAACAAAGC
66 CATATTGTAGTTCAACAAAGC
*
76133 TACACAAAAG
1 TACATAAAAG
76143 ATTGTTTGAG
Statistics
Matches: 86, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 77 0.90
87 9 0.10
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (86 bp):
TACATAAAAGTTACAAACTGTTTACATACCCCTAACATCACAAAATACTTTAGTTCCAAAAACAA
CATATTGTAGTTCAACAAAGC
Found at i:76348 original size:21 final size:21
Alignment explanation
Indices: 76322--76383 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
76312 GGATATGTTT
* *
76322 GTGTTGTAGGCTAAGATGAAG
1 GTGTTGTAGGCTGAGATGAAA
*
76343 GTGTTGTAGGCTGCGATGAAA
1 GTGTTGTAGGCTGAGATGAAA
* *
76364 GTGCTGTAGGATGAGATGAA
1 GTGTTGTAGGCTGAGATGAA
76384 TCTGTTACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.27, C:0.06, G:0.39, T:0.27
Consensus pattern (21 bp):
GTGTTGTAGGCTGAGATGAAA
Found at i:80677 original size:18 final size:18
Alignment explanation
Indices: 80642--80737 Score: 84
Period size: 21 Copynumber: 4.9 Consensus size: 18
80632 CGAGGGTTAC
*
80642 AGTGGTCCTACGGGGACAT
1 AGTGGTCCTTC-GGGACAT
*
80661 AGTGGTCATTCGGGACAAT
1 AGTGGTCCTTCGGGAC-AT
*
80680 ACAATGGTCCTTCGGGACAATAT
1 --AGTGGTCCTTCGGGAC---AT
*
80703 AGTGGTCCTACGGGACAT
1 AGTGGTCCTTCGGGACAT
*
80721 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
80738 AATTTCAATG
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
18 22 0.35
19 11 0.17
21 28 0.44
23 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:81445 original size:21 final size:22
Alignment explanation
Indices: 81415--81459 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
81405 TGTAGCAGTA
*
81415 CTGTAACA-GGGTATCGGTTCC
1 CTGTAACAGGGGAATCGGTTCC
*
81436 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAACAGGGGAATCGGTTCC
81458 CT
1 CT
81460 CCTGACATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (22 bp):
CTGTAACAGGGGAATCGGTTCC
Found at i:81559 original size:19 final size:20
Alignment explanation
Indices: 81511--81559 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
81501 GGTATTGTTC
* *
81511 ATTACTATTTATATGGTATT
1 ATTACTGTTTATATCGTATT
81531 ATTCACTGTTTATATCGTATT
1 ATT-ACTGTTTATATCGTATT
81552 -TTACTGTT
1 ATTACTGTT
81560 CATAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 6 0.23
20 5 0.19
21 15 0.58
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.55
Consensus pattern (20 bp):
ATTACTGTTTATATCGTATT
Found at i:94418 original size:165 final size:164
Alignment explanation
Indices: 94091--94483 Score: 421
Period size: 165 Copynumber: 2.4 Consensus size: 164
94081 GATTAAATTG
* * * * *
94091 AAAAATAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTACTCATGTATTCTATTATGGTTTAGG
1 AAAAATAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTACACATGTACTCTACTATGGTTTAGG
** * * * ** * *
94156 AGCATGTGGCTCAAGTTTCATAAAAAATAGAGTTAAAATAAATGACGAATTGAATAAATAAGGAG
66 AGCATGTAACTCAAATTTCATAAAAAACAGACTTAAAATAAATGAAAAAGTGAAGAAATAAGGAG
94221 ATTATGAAAAATCAAAGGACTAAATAAAAAATAA
131 ATTATGAAAAATCAAAGGACTAAATAAAAAATAA
* *
94255 AAAAATAAAAAAATTGTTATAAAAAATATGAATTGAAAGTACACATGTACTCTACTATGGTTTAG
1 AAAAAT-AAAAAATTGTTATAAAAAAGAGGAATTGAAAGTACACATGTACTCTACTATGGTTTAG
* * *
94320 TAGCATGTAACTCAAATTT-AGT-GAAAACGGACTTAAAATAAATGAAAAAGTGAAGAAATAAGG
65 GAGCATGTAACTCAAATTTCA-TAAAAAACAGACTTAAAATAAATGAAAAAGTGAAGAAATAAGG
* **
94383 AGATTATGAAAAATTGAAA-GACT---T----AATTG
129 AGATTATGAAAAA-TCAAAGGACTAAATAAAAAATAA
* * * * * *
94412 AAAAATAAAAATTTGTTATCAAAAAGCA-TAATTGAAAGTAAACATGTATTCTACTATGGTTTAA
1 AAAAATAAAAAATTGTTATAAAAAAG-AGGAATTGAAAGTACACATGTACTCTACTATGGTTTAG
94476 GAGCATGT
65 GAGCATGT
94484 TGTTCAAATT
Statistics
Matches: 195, Mismatches: 30, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
156 56 0.29
157 10 0.05
161 1 0.01
164 57 0.29
165 71 0.36
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (164 bp):
AAAAATAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTACACATGTACTCTACTATGGTTTAGG
AGCATGTAACTCAAATTTCATAAAAAACAGACTTAAAATAAATGAAAAAGTGAAGAAATAAGGAG
ATTATGAAAAATCAAAGGACTAAATAAAAAATAA
Found at i:94465 original size:156 final size:155
Alignment explanation
Indices: 94011--94514 Score: 532
Period size: 156 Copynumber: 3.2 Consensus size: 155
94001 CATGTGGTTT
* * ** *
94011 AAATTTGGTGAAAA-ACGAACTTAAAATAAATGATAAATTGAAGGGATAAGGAAATTATGAAAAA
1 AAATTTAGTGAAAACA-G-ACTTAAAATAAATGAAAAATTGAAGAAATAAGGAGATTATGAAAAA
* *
94075 TTGAAAGA-TTAAATTGAAAAATAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTACTCATGTA
64 TTGAAAGACTTAAATTGAAAAATAAAAATTTGTTATCAAAAAGA-TAATTGAAAGTACACATGTA
* *
94139 TTCTATTATGGTTTAGGAGCATGTGGCTC
128 TTCTACTATGGTTTA-GAGCATGTAGCTC
* * * * ** *
94168 AAGTTTCA-TAAAAAATAGAGTTAAAATAAATGACGAATTGAATAAATAAGGAGATTATGAAAAA
1 AAATTT-AGT-GAAAACAGACTTAAAATAAATGAAAAATTGAAGAAATAAGGAGATTATGAAAAA
* ** * * *
94232 -TCAAAGGACTAAATAAAAAATAAAAAAATAAAAAAATTGTTATAAAAAATATGAATTGAAAGTA
64 TTGAAA-GACT---T---AAATTGAAAAAT-AAAAATTTGTTATCAAAAAGAT-AATTGAAAGTA
* *
94296 CACATGTACTCTACTATGGTTTAGTAGCATGTAACTC
120 CACATGTATTCTACTATGGTTTAG-AGCATGTAGCTC
* *
94333 AAATTTAGTGAAAACGGACTTAAAATAAATGAAAAAGTGAAGAAATAAGGAGATTATGAAAAATT
1 AAATTTAGTGAAAACAGACTTAAAATAAATGAAAAATTGAAGAAATAAGGAGATTATGAAAAATT
*
94398 GAAAGACTT-AATTGAAAAATAAAAATTTGTTATCAAAAAGCATAATTGAAAGTAAACATGTATT
66 GAAAGACTTAAATTGAAAAATAAAAATTTGTTATCAAAAAG-ATAATTGAAAGTACACATGTATT
* *
94462 CTACTATGGTTTAAGAGCATGTTGTTC
130 CTACTATGGTTT-AGAGCATGTAGCTC
* *
94489 AAATTTGGTGAAAACATACTTAAAAT
1 AAATTTAGTGAAAACAGACTTAAAAT
94515 GGAGGAGGAA
Statistics
Matches: 284, Mismatches: 45, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
156 84 0.30
157 60 0.21
158 6 0.02
159 1 0.00
161 2 0.01
164 62 0.22
165 69 0.24
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (155 bp):
AAATTTAGTGAAAACAGACTTAAAATAAATGAAAAATTGAAGAAATAAGGAGATTATGAAAAATT
GAAAGACTTAAATTGAAAAATAAAAATTTGTTATCAAAAAGATAATTGAAAGTACACATGTATTC
TACTATGGTTTAGAGCATGTAGCTC
Found at i:94776 original size:22 final size:22
Alignment explanation
Indices: 94724--94768 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
94714 TTTTGCTCAC
94724 CACTACCTTCCGGTTCAAAAGG
1 CACTACCTTCCGGTTCAAAAGG
*
94746 CACTACCTTCCTGTTCAAAAGG
1 CACTACCTTCCGGTTCAAAAGG
94768 C
1 C
94769 TCTGCCTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (22 bp):
CACTACCTTCCGGTTCAAAAGG
Found at i:101593 original size:17 final size:17
Alignment explanation
Indices: 101571--101604 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
101561 TACTCATTTT
* *
101571 TCCGAATCGTCGGTAAA
1 TCCGAAGCGCCGGTAAA
101588 TCCGAAGCGCCGGTAAA
1 TCCGAAGCGCCGGTAAA
101605 AATGAGAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (17 bp):
TCCGAAGCGCCGGTAAA
Found at i:105806 original size:2 final size:2
Alignment explanation
Indices: 105799--105829 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
105789 CTTTTACATG
*
105799 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
105830 TATTTGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:107540 original size:29 final size:30
Alignment explanation
Indices: 107459--107546 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 30
107449 TAGACCTCTA
* ****
107459 ATAATAAATATTAGAAAAAATTGAACCCACA
1 ATAATAAATATTAGAAAAAATTCAA-CTTTT
*
107490 ATAATAAATATTAGAGAAAATT-AACTTTT
1 ATAATAAATATTAGAAAAAATTCAACTTTT
*
107519 ATAATAAGTATTA-AAAATAATTCAACTT
1 ATAATAAATATTAGAAAA-AATTCAACTT
107547 ATAACTTATA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.06
29 17 0.35
30 7 0.15
31 21 0.44
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.32
Consensus pattern (30 bp):
ATAATAAATATTAGAAAAAATTCAACTTTT
Found at i:117416 original size:21 final size:21
Alignment explanation
Indices: 117385--117447 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
117375 TGTAATGTTA
117385 TCAACCATTATGAACTACCACG
1 TCAA-CATTATGAACTACCACG
* *
117407 TCAACATTATGTACAACCACG
1 TCAACATTATGAACTACCACG
* *
117428 TCAATATCATGAACTACCAC
1 TCAACATTATGAACTACCAC
117448 ATCATCACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 31 0.89
22 4 0.11
ACGTcount: A:0.38, C:0.30, G:0.08, T:0.24
Consensus pattern (21 bp):
TCAACATTATGAACTACCACG
Done.