Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004924.1 Hibiscus syriacus cultivar Beakdansim tig00011085_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: 91433
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:915 original size:19 final size:20
Alignment explanation
Indices: 883--920 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
873 TTGCATACGA
883 TTAGTTTAGGTTTA-ATTAT
1 TTAGTTTAGGTTTATATTAT
902 TTAG-TTAGGTTTTATATTA
1 TTAGTTTAGG-TTTATATTA
921 ATAGTTTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (20 bp):
TTAGTTTAGGTTTATATTAT
Found at i:3284 original size:27 final size:27
Alignment explanation
Indices: 3246--3335 Score: 180
Period size: 27 Copynumber: 3.3 Consensus size: 27
3236 AAAACAGTGT
3246 TGAATGATTCAACACAGAAGTACATTC
1 TGAATGATTCAACACAGAAGTACATTC
3273 TGAATGATTCAACACAGAAGTACATTC
1 TGAATGATTCAACACAGAAGTACATTC
3300 TGAATGATTCAACACAGAAGTACATTC
1 TGAATGATTCAACACAGAAGTACATTC
3327 TGAATGATT
1 TGAATGATT
3336 TAGAGTCATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.28
Consensus pattern (27 bp):
TGAATGATTCAACACAGAAGTACATTC
Found at i:7361 original size:21 final size:21
Alignment explanation
Indices: 7322--7362 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7312 GAATTTAATA
*
7322 TAAAATAAAAATTGAAAATTT
1 TAAAATAAAAATGGAAAATTT
* *
7343 TAAAGTAAAAATGGTAAATT
1 TAAAATAAAAATGGAAAATT
7363 AAGGTGCGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (21 bp):
TAAAATAAAAATGGAAAATTT
Found at i:8202 original size:557 final size:559
Alignment explanation
Indices: 7145--8262 Score: 1696
Period size: 557 Copynumber: 2.0 Consensus size: 559
7135 AAGTGTAAAT
* * *
7145 TGAAAACAAAAAATGGGCTAAACGTTAAAAGAAAATTGATATATAAAACATATGAACATATTTGT
1 TGAAAACAAAAAATGGGCTAAACGTTAAAAGAAAAATGATATATAAAAAATATAAACATATTTGT
* * *
7210 AATTAATACAGTATGTATAAAAGTATTTAAAGTATATAAAAAATTTAAAACAAACACACACACAC
66 AATTAATACAATATGTATAAAAGTATGTAAAGTATATAAAAAAATTAAAACAAACACACACACAC
7275 ACATAAGCAAAATAAAATTTAATTTTTTTATTAATTTGAATTTAATATAAAATAAAAATTGAAAA
131 ACA-AAGCAAAATAAAATTTAATTTTTTTATTAATTTGAATTTAATATAAAATAAAAATTGAAAA
*
7340 TTTTAAAGTAAAAATGGTAAATTAAGGTGCGAAAATATAGTATAAACAATATCCATTGACCAATT
195 TTTTAAAGTAAAAATGGTAAATTAAGGTGCGAAAATAAAGTATAAACAATATCCATTGACCAATT
* * *
7405 TAACTCAAACTAGCAAGAAATTAAACCTAAATTAAAAAAAAGGAAAATAGGTTTTAAAATAAATT
260 TAACTCAAACTAGCAAGAAAGTAAACCTAAATTAAAAAAAA-GAAAATAGGTTTTAAAAGAAAAT
7470 TTACCTTGAATCACGATTTGGGATGAAAAGATGATGAATGCACGAATTTGATGAAGTTTGCAGAA
324 TTACCTTGAATCACGATTTGGGATGAAAAGATGATGAATGCACGAATTTGATGAAGTTTGCAGAA
* *
7535 ATCAAGCTTGAAAAAAGATGCGATTTACACCCAAAATCGAGCGATTTGATGAGATTTTAGAGAGA
389 ATAAAACTTGAAAAAAGATGCGATTTACACCCAAAATCGAGCGATTTGATGAGATTTTAGAGAGA
* * * *
7600 AATGAAGGATTTCGTCATTGGCTGCTTTGTTTAGGGTTTGATAAAA-TA-AAAAATGGGAAATTT
454 AAGGAAGGATTTCATCATTGGATGCTTTGTTTAGGCTTTGATAAAATTATAAAAATGGGAAATTT
7663 GACCTTTAAAACGCAAATCTAACCCCGAGTATCAATACTTA
519 GACCTTTAAAACGCAAATCTAACCCCGAGTATCAATACTTA
*
7704 TGAAAACAAAAAATGGGCTAAACGTTAAAAGAAAAATGATATATATAAAAATGTAAACATATTTG
1 TGAAAACAAAAAATGGGCTAAACGTTAAAAGAAAAATGATATATA-AAAAATATAAACATATTTG
* *
7769 TATTTAATACAATATGTATATAAGTATGTAAAGTATATAAAAAAAATTAAAACAAACA-A-ACAC
65 TAATTAATACAATATGTATAAAAGTATGTAAAGTATAT-AAAAAAATTAAAACAAACACACACAC
*
7832 ACAC-AAGCAAAATAAAATTTAA-TTTTTTATTACTTTGAATTTAATATAAAATAAAATAAATTG
129 ACACAAAGCAAAATAAAATTTAATTTTTTTATTAATTTGAATTTAATATAAAAT--AA-AAATTG
** * * *
7895 AACAA-TTTGGAGTGAAAATGGTAAATTAGGGTGTGAAAATAAAGTATAAACAATATCCATTGAC
191 AA-AATTTTAAAGTAAAAATGGTAAATTAAGGTGCGAAAATAAAGTATAAACAATATCCATTGAC
* *
7959 CAATTTAACTCAAAGTAGCAAGAAAGTAAACCTAAATTAAAAAATA-AAAATAGGTTTTAAAAGA
255 CAATTTAACTCAAACTAGCAAGAAAGTAAACCTAAATTAAAAAAAAGAAAATAGGTTTTAAAAGA
* *
8023 AAATTTACCTTGAATCATGATTTGGGATGGAAAGATGATGAATGCACGAATTTGATGAAGTTTGC
320 AAATTTACCTTGAATCACGATTTGGGATGAAAAGATGATGAATGCACGAATTTGATGAAGTTTGC
* * *
8088 AGAAATAAAACTTGAAAAACGATGCGATTTACACCCAAAATCGAGCTATTTTATGAGATTTTAGA
385 AGAAATAAAACTTGAAAAAAGATGCGATTTACACCCAAAATCGAGCGATTTGATGAGATTTTAGA
* * *****
8153 GATAAGGGAA-GATTTTCATCATTGGATGCTTTGTTTAGGCTTTGATAAAATTATTTGTTTTTGG
450 GAGAAAGGAAGGA-TTTCATCATTGGATGCTTTGTTTAGGCTTTGATAAAATTA--TAAAAATGG
* * *
8217 GAATTTTGACCTTTAAAATGCAAATCTGACCCCGAGTATCAATACT
512 GAAATTTGACCTTTAAAACGCAAATCTAACCCCGAGTATCAATACT
8263 CATTTAAATG
Statistics
Matches: 506, Mismatches: 42, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
556 31 0.06
557 198 0.39
558 4 0.01
559 156 0.31
560 53 0.10
561 64 0.13
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.30
Consensus pattern (559 bp):
TGAAAACAAAAAATGGGCTAAACGTTAAAAGAAAAATGATATATAAAAAATATAAACATATTTGT
AATTAATACAATATGTATAAAAGTATGTAAAGTATATAAAAAAATTAAAACAAACACACACACAC
ACAAAGCAAAATAAAATTTAATTTTTTTATTAATTTGAATTTAATATAAAATAAAAATTGAAAAT
TTTAAAGTAAAAATGGTAAATTAAGGTGCGAAAATAAAGTATAAACAATATCCATTGACCAATTT
AACTCAAACTAGCAAGAAAGTAAACCTAAATTAAAAAAAAGAAAATAGGTTTTAAAAGAAAATTT
ACCTTGAATCACGATTTGGGATGAAAAGATGATGAATGCACGAATTTGATGAAGTTTGCAGAAAT
AAAACTTGAAAAAAGATGCGATTTACACCCAAAATCGAGCGATTTGATGAGATTTTAGAGAGAAA
GGAAGGATTTCATCATTGGATGCTTTGTTTAGGCTTTGATAAAATTATAAAAATGGGAAATTTGA
CCTTTAAAACGCAAATCTAACCCCGAGTATCAATACTTA
Found at i:14955 original size:18 final size:18
Alignment explanation
Indices: 14932--14971 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
14922 TTGCATTAAT
14932 GGCACCTTTCTGCCAAAA
1 GGCACCTTTCTGCCAAAA
*
14950 GGCACCTTTCTTCCAAAA
1 GGCACCTTTCTGCCAAAA
14968 GGCA
1 GGCA
14972 TCATTAGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.23
Consensus pattern (18 bp):
GGCACCTTTCTGCCAAAA
Found at i:15094 original size:81 final size:81
Alignment explanation
Indices: 14998--15470 Score: 673
Period size: 81 Copynumber: 6.0 Consensus size: 81
14988 CTTTCATCCT
*
14998 AAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGC
1 AAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGC
15063 ATTTAATCTTTTACTC
66 ATTTAATCTTTTACTC
* * * * *
15079 GAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTATGTCAAGTGCAAAGCTAGGC
1 AAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGC
15144 ATTTAATCTTTTACTC
66 ATTTAATCTTTTACTC
* * **
15160 AAAGGTATTTAAACTTTCATCTAA-TTGGCATGATTGACACCTTTCTGTTAAAAACACAGCTAGG
1 AAAGGTATTTAACCTTTCATCTAACTT-GCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
15224 CATTTAATCTTTTACTC
65 CATTTAATCTTTTACTC
* *
15241 AAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCATATGCACAGCTAGGC
1 AAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGC
15306 ATTTAATCTTTTACTC
66 ATTTAATCTTTTACTC
* *
15322 AAAGGTATTTAACCTTTCATCTAAC-TGACATGATTGACACCTTTTTGTCAAATGCACAGCTAGA
1 AAAGGTATTTAACCTTTCATCTAACTTG-CATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
15386 CATTT-A------A---
65 CATTTAATCTTTTACTC
* * * * *
15393 AAAGGTATTTAACCTTTCACCTAACTAGCATGATTGACACATTTATGTCAAATGCACAACTAGGC
1 AAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGC
15458 ATTTAATCTTTTA
66 ATTTAATCTTTTA
15471 TTTTAAAACA
Statistics
Matches: 350, Mismatches: 31, Indels: 25
0.86 0.08 0.06
Matches are distributed among these distances:
71 61 0.17
72 2 0.01
74 1 0.00
78 1 0.00
80 3 0.01
81 281 0.80
82 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (81 bp):
AAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGC
ATTTAATCTTTTACTC
Found at i:15473 original size:71 final size:71
Alignment explanation
Indices: 15322--15463 Score: 223
Period size: 71 Copynumber: 2.0 Consensus size: 71
15312 TCTTTTACTC
* * * *
15322 AAAGGTATTTAACCTTTCATCTAACTGACATGATTGACACCTTTTTGTCAAATGCACAGCTAGAC
1 AAAGGTATTTAACCTTTCACCTAACTGACATGATTGACACATTTATGTCAAATGCACAACTAGAC
15387 ATTTAA
66 ATTTAA
*
15393 AAAGGTATTTAACCTTTCACCTAACT-AGCATGATTGACACATTTATGTCAAATGCACAACTAGG
1 AAAGGTATTTAACCTTTCACCTAACTGA-CATGATTGACACATTTATGTCAAATGCACAACTAGA
15457 CATTTAA
65 CATTTAA
15464 TCTTTTATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
70 1 0.02
71 64 0.98
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (71 bp):
AAAGGTATTTAACCTTTCACCTAACTGACATGATTGACACATTTATGTCAAATGCACAACTAGAC
ATTTAA
Found at i:20054 original size:132 final size:132
Alignment explanation
Indices: 19842--20160 Score: 561
Period size: 132 Copynumber: 2.4 Consensus size: 132
19832 TGCACTGTTC
*
19842 TTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAGAAATGCACCGTTAGACATTTATCTTGCAT
1 TTCATCTAACTTGCATTAGTGGCACCTTTCTGTCAGAAATGCACCGTTAGACATTTATCTTGCAT
19907 TAATGGCACCTTTCTACCAAAAAGCACCGTTAGGTATTTAGTCTTTCATCCCAAAGGTATTTAAC
66 TAATGGCACCTTTCTACCAAAAAGCACCGTTAGGTATTTAGTCTTTCATCCCAAAGGTATTTAAC
19972 CT
131 CT
*
19974 TTCATCTAACTTGCATTAGTGGCACATTTCTGTCAGAAATGCACCGTTAGACATTTATCTTGCAT
1 TTCATCTAACTTGCATTAGTGGCACCTTTCTGTCAGAAATGCACCGTTAGACATTTATCTTGCAT
20039 TAATGGCACCTTTCTACCAAAAAGCACCGTTAGGTATTTAGTCTTTCATCCCAAAGGTATTTAAC
66 TAATGGCACCTTTCTACCAAAAAGCACCGTTAGGTATTTAGTCTTTCATCCCAAAGGTATTTAAC
20104 CT
131 CT
* * * * *
20106 TTCATCTAACTTGCATGATTGACACCTTTCTGTC--AAATGCACAGTTAGGCATTTA
1 TTCATCTAACTTGCATTAGTGGCACCTTTCTGTCAGAAATGCACCGTTAGACATTTA
20161 ATATTTTACT
Statistics
Matches: 179, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
130 19 0.11
132 160 0.89
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (132 bp):
TTCATCTAACTTGCATTAGTGGCACCTTTCTGTCAGAAATGCACCGTTAGACATTTATCTTGCAT
TAATGGCACCTTTCTACCAAAAAGCACCGTTAGGTATTTAGTCTTTCATCCCAAAGGTATTTAAC
CT
Found at i:20186 original size:81 final size:81
Alignment explanation
Indices: 20090--20654 Score: 887
Period size: 81 Copynumber: 7.0 Consensus size: 81
20080 TCTTTCATCC
* *
20090 CAAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
*
20155 CATTTAATATTTTACT
66 CATTTAATCTTTTACT
* * * * *
20171 CAAAGGTATTTAACCTTTCATCTAACTAGTATGATTGACACATTTTTGTCAAAAGCACAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
20236 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * * * *
20252 CAAAGATATTTAACCTTTCATCTAATTGGCATGATTGACACCTTTCTGTCAAATACACAGATAGA
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
20317 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * *
20333 CAAAGGTATTTAAGCTTTCATCTAACTGGCATTATTGACACCTTTCTGTCAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
20398 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * *
20414 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTAACACCTTTTTGTCAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
20479 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * *
20495 CAAAGGTAATTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAGCTAGA
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
* *
20560 CATTTAATTTTTTATT
66 CATTTAATCTTTTACT
* * *
20576 CAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
20641 CATTTAATCTTTTA
66 CATTTAATCTTTTA
20655 TTTTAAAATA
Statistics
Matches: 440, Mismatches: 44, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 440 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (81 bp):
CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
CATTTAATCTTTTACT
Found at i:22164 original size:64 final size:64
Alignment explanation
Indices: 22080--22225 Score: 188
Period size: 64 Copynumber: 2.3 Consensus size: 64
22070 CATTCATAAG
* * *
22080 TGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCA-TAGCTA
1 TGCATCGATGCA-TCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACAAG-TA
22143 A
64 A
* * * *
22144 TGCATCGATGCATCCTTTTAAAATAATAACATCGAATGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
22208 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
22226 CATTGAAAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
63 3 0.04
64 63 0.88
65 6 0.08
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
Found at i:24365 original size:22 final size:23
Alignment explanation
Indices: 24324--24366 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
24314 AAAGAAAAAC
24324 TAAATTTACAATTTATATATTTA
1 TAAATTTACAATTTATATATTTA
24347 TAAA-TTA-AATTTAATATATT
1 TAAATTTACAATTT-ATATATT
24367 ATTTTCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TAAATTTACAATTTATATATTTA
Found at i:24507 original size:48 final size:50
Alignment explanation
Indices: 24474--24627 Score: 177
Period size: 51 Copynumber: 3.1 Consensus size: 50
24464 TAATTAATTG
* * *
24474 TTATTAAATTGTGTAGTTCAAAATATATAATTTAATAATTTAATTGATTT
1 TTATTAAATTGTGTAGTTCAAAATGTATAATTTAATATTTTAATTAATTT
** * **
24524 TGTATTTGATTGTGTAGTTAAAAATGTATAATTTGGTATTTTAATT--TTT
1 T-TATTAAATTGTGTAGTTCAAAATGTATAATTTAATATTTTAATTAATTT
* * * *
24573 TTATTGAATTGTGCATTTCAAAATGTGTAATTTAATATTTTAATTAATTT
1 TTATTAAATTGTGTAGTTCAAAATGTATAATTTAATATTTTAATTAATTT
24623 TTATT
1 TTATT
24628 GTGTAATTCA
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
48 36 0.42
49 4 0.05
50 9 0.10
51 37 0.43
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.53
Consensus pattern (50 bp):
TTATTAAATTGTGTAGTTCAAAATGTATAATTTAATATTTTAATTAATTT
Found at i:24539 original size:51 final size:50
Alignment explanation
Indices: 24455--24627 Score: 178
Period size: 48 Copynumber: 3.5 Consensus size: 50
24445 TGTATGAATC
* * *
24455 ATTT-ATA-TTTAATTAATTGTTA-TTAAATTGTGTAGTTCAAAATATATA
1 ATTTAATATTTTAATT-ATTTTTATTTGAATTGTGTAGTTCAAAATGTATA
* *
24503 ATTTAATAATTTAATTGATTTTGTATTTG-ATTGTGTAGTTAAAAATGTATA
1 ATTTAATATTTTAATT-ATTTT-TATTTGAATTGTGTAGTTCAAAATGTATA
** * * *
24554 ATTTGGTATTTTAATT-TTTTTA-TTGAATTGTGCATTTCAAAATGTGTA
1 ATTTAATATTTTAATTATTTTTATTTGAATTGTGTAGTTCAAAATGTATA
24602 ATTTAATATTTTAATTAATTTTTATT
1 ATTTAATATTTTAATT-ATTTTTATT
24628 GTGTAATTCA
Statistics
Matches: 103, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
47 3 0.03
48 38 0.37
49 7 0.07
50 17 0.17
51 36 0.35
52 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (50 bp):
ATTTAATATTTTAATTATTTTTATTTGAATTGTGTAGTTCAAAATGTATA
Found at i:25199 original size:34 final size:32
Alignment explanation
Indices: 25146--25208 Score: 99
Period size: 34 Copynumber: 1.9 Consensus size: 32
25136 AACAAGCCTA
*
25146 TGTTCGTGTTTGTTTGTTTATTTTTTTAAAGG
1 TGTTCGTGTTTGTTTGTTTAATTTTTTAAAGG
25178 TGTTCGTGTTCGTGTTTGTTTAATTTTTTAA
1 TGTTCGTGTT--TGTTTGTTTAATTTTTTAA
25209 TATCATGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 10 0.36
34 18 0.64
ACGTcount: A:0.13, C:0.05, G:0.21, T:0.62
Consensus pattern (32 bp):
TGTTCGTGTTTGTTTGTTTAATTTTTTAAAGG
Found at i:25281 original size:24 final size:24
Alignment explanation
Indices: 25245--25292 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
25235 GTGTTCATTT
* *
25245 AATGTTTATGAACATATTTGTTTA
1 AATGTTCACGAACATATTTGTTTA
* *
25269 AATGTTCACGAACGTGTTTGTTTA
1 AATGTTCACGAACATATTTGTTTA
25293 GCGTTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (24 bp):
AATGTTCACGAACATATTTGTTTA
Found at i:25326 original size:34 final size:34
Alignment explanation
Indices: 25278--25401 Score: 149
Period size: 34 Copynumber: 3.6 Consensus size: 34
25268 AAATGTTCAC
* *
25278 GAACGTGTTTGTTTAGCGTTCATTTAACGTTCGT
1 GAACATGTTCGTTTAGCGTTCATTTAACGTTCGT
* *
25312 GAACATGTTCGTTTAGCGTTCATTCAACGTTCGC
1 GAACATGTTCGTTTAGCGTTCATTTAACGTTCGT
** * * **
25346 GAACATGTTTTTTTAGCGTTCATATAATGTTATT
1 GAACATGTTCGTTTAGCGTTCATTTAACGTTCGT
*
25380 GAACATGTTCATTTAGCGTTCA
1 GAACATGTTCGTTTAGCGTTCA
25402 CGAACATGTT
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 76 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (34 bp):
GAACATGTTCGTTTAGCGTTCATTTAACGTTCGT
Found at i:25386 original size:68 final size:68
Alignment explanation
Indices: 25272--25401 Score: 188
Period size: 68 Copynumber: 1.9 Consensus size: 68
25262 TTGTTTAAAT
* * * *
25272 GTTCACGAACGTGTTTGTTTAGCGTTCATTTAACGTTCGTGAACATGTTCGTTTAGCGTTCATTC
1 GTTCACGAACATGTTTGTTTAGCGTTCATATAACGTTAGTGAACATGTTCATTTAGCGTTCATTC
25337 AAC
66 AAC
* * * *
25340 GTTCGCGAACATGTTTTTTTAGCGTTCATATAATGTTATTGAACATGTTCATTTAGCGTTCA
1 GTTCACGAACATGTTTGTTTAGCGTTCATATAACGTTAGTGAACATGTTCATTTAGCGTTCA
25402 CGAACATGTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 54 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (68 bp):
GTTCACGAACATGTTTGTTTAGCGTTCATATAACGTTAGTGAACATGTTCATTTAGCGTTCATTC
AAC
Found at i:26073 original size:19 final size:20
Alignment explanation
Indices: 26049--26094 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
26039 GAACAATCAA
*
26049 ATTAAATAA-TATATCAAAT
1 ATTAAATAAGTATAACAAAT
26068 ATTAAATAAGTATAACAAAT
1 ATTAAATAAGTATAACAAAT
26088 ACTTAAA
1 A-TTAAA
26095 AAAATACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 9 0.38
20 10 0.42
21 5 0.21
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (20 bp):
ATTAAATAAGTATAACAAAT
Found at i:27605 original size:15 final size:15
Alignment explanation
Indices: 27585--27621 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
27575 TAAGACATTA
*
27585 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
27600 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
27615 CCCGCCC
1 CCCGCCC
27622 AGCTAAATAT
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:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:32801 original size:23 final size:23
Alignment explanation
Indices: 32771--32840 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
32761 AGTACCCATG
32771 CACT-AATGTGGTTGTATCGGTA
1 CACTCAATGTGGTTGTATCGGTA
32793 CACTCAATGTGGTTGTATCGGTA
1 CACTCAATGTGGTTGTATCGGTA
** * *
32816 TGCTCAATCTGGCTGTATCGGTA
1 CACTCAATGTGGTTGTATCGGTA
32839 CA
1 CA
32841 TTACCCATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 4 0.10
23 37 0.90
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (23 bp):
CACTCAATGTGGTTGTATCGGTA
Found at i:35079 original size:15 final size:15
Alignment explanation
Indices: 35059--35087 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35049 ACTCTATTAG
35059 ATCAAATAAAGGATC
1 ATCAAATAAAGGATC
35074 ATCAAATAAAGGAT
1 ATCAAATAAAGGAT
35088 GAGAAGTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.14, T:0.21
Consensus pattern (15 bp):
ATCAAATAAAGGATC
Found at i:37219 original size:28 final size:28
Alignment explanation
Indices: 37157--37220 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
37147 TGGTGTAAAT
* *
37157 ATTTCAAGTTTTCATGCTTGGAGTGTAG
1 ATTTCATGTTTTAATGCTTGGAGTGTAG
*
37185 ATTTCATGTTTTAATGCTTGGAGTGTTG
1 ATTTCATGTTTTAATGCTTGGAGTGTAG
37213 ATTTCATG
1 ATTTCATG
37221 AAAATGGGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.20, C:0.09, G:0.23, T:0.47
Consensus pattern (28 bp):
ATTTCATGTTTTAATGCTTGGAGTGTAG
Found at i:43177 original size:19 final size:20
Alignment explanation
Indices: 43134--43177 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
43124 TTTATTTTTG
*
43134 ATAAATTTTTATCTATGAAA
1 ATAAATTTTTATCTATCAAA
* *
43154 TTAAATTTTTAT-TTTCAAA
1 ATAAATTTTTATCTATCAAA
43173 ATAAA
1 ATAAA
43178 ATATTAAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (20 bp):
ATAAATTTTTATCTATCAAA
Found at i:50265 original size:28 final size:28
Alignment explanation
Indices: 50223--50419 Score: 268
Period size: 28 Copynumber: 7.0 Consensus size: 28
50213 TCCAAAAAAG
* ** *
50223 AAAATAACACATTTTTTTAAATAATTACA
1 AAAATATCAC-TTTTTCGAAATAATTACC
50252 AAAATATCACTTTTTCGAAATAATTACC
1 AAAATATCACTTTTTCGAAATAATTACC
* * *
50280 ATAATATCATTTTTTTGAAATAATTACC
1 AAAATATCACTTTTTCGAAATAATTACC
50308 AAAATATCACTTTTTCGAAATAATTACC
1 AAAATATCACTTTTTCGAAATAATTACC
* * *
50336 AAAATATTATTTTTTTCAAAATAATTACC
1 AAAATATCA-CTTTTTCGAAATAATTACC
*
50365 AAAATATCACTTTTTCGAAATAATTATC
1 AAAATATCACTTTTTCGAAATAATTACC
*
50393 AAAATATCACTTTTTCGAAATATTTAC
1 AAAATATCACTTTTTCGAAATAATTAC
50420 GAAACTAACA
Statistics
Matches: 148, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
28 114 0.77
29 34 0.23
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.40
Consensus pattern (28 bp):
AAAATATCACTTTTTCGAAATAATTACC
Found at i:50371 original size:85 final size:84
Alignment explanation
Indices: 50223--50419 Score: 268
Period size: 85 Copynumber: 2.3 Consensus size: 84
50213 TCCAAAAAAG
* ** * *
50223 AAAATAACACATTTTTTTAAATAATTACAAAAATATCACTTTTTCGAAATAATTACCATAATATC
1 AAAATATCAC-TTTTTCGAAATAATTACAAAAATATCACTTTTTCAAAATAATTACCAAAATATC
* *
50288 ATTTTTTTGAAATAATTACC
65 ACTTTTTCGAAATAATTACC
* * *
50308 AAAATATCACTTTTTCGAAATAATTACCAAAATATTATTTTTTTCAAAATAATTACCAAAATATC
1 AAAATATCACTTTTTCGAAATAATTACAAAAATATCA-CTTTTTCAAAATAATTACCAAAATATC
*
50373 ACTTTTTCGAAATAATTATC
65 ACTTTTTCGAAATAATTACC
*
50393 AAAATATCACTTTTTCGAAATATTTAC
1 AAAATATCACTTTTTCGAAATAATTAC
50420 GAAACTAACA
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
84 23 0.23
85 76 0.77
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.40
Consensus pattern (84 bp):
AAAATATCACTTTTTCGAAATAATTACAAAAATATCACTTTTTCAAAATAATTACCAAAATATCA
CTTTTTCGAAATAATTACC
Found at i:50415 original size:16 final size:16
Alignment explanation
Indices: 50366--50415 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
50356 ATAATTACCA
50366 AAATATCACTTTTTCG
1 AAATATCACTTTTTCG
* *
50382 AAATA--A--TTATCA
1 AAATATCACTTTTTCG
50394 AAATATCACTTTTTCG
1 AAATATCACTTTTTCG
50410 AAATAT
1 AAATAT
50416 TTACGAAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
12 9 0.35
14 2 0.08
16 15 0.58
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.40
Consensus pattern (16 bp):
AAATATCACTTTTTCG
Found at i:50475 original size:28 final size:29
Alignment explanation
Indices: 50411--50476 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
50401 ACTTTTTCGA
50411 AATATTTACGAAACTAACACATTCTTAAC
1 AATATTTACGAAACTAACACATTCTTAAC
* * * *
50440 AGTATTTATGAAACTAACA-TTTTTTAAC
1 AATATTTACGAAACTAACACATTCTTAAC
50468 AATATTTAC
1 AATATTTAC
50477 AAAAATACCA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (29 bp):
AATATTTACGAAACTAACACATTCTTAAC
Found at i:53664 original size:31 final size:31
Alignment explanation
Indices: 53601--53664 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
53591 TAGGTCCATA
* * *
53601 AGGAATTACCAATCGGTGCTGAACCTATCAG
1 AGGAATTACCAATCAGCGCTGAACCTACCAG
*
53632 AGGAATTACCAA-CAGCGACTGAACCTGCCAG
1 AGGAATTACCAATCAGCG-CTGAACCTACCAG
53663 AG
1 AG
53665 TCTTCATACC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.17
Consensus pattern (31 bp):
AGGAATTACCAATCAGCGCTGAACCTACCAG
Found at i:54609 original size:28 final size:28
Alignment explanation
Indices: 54571--54782 Score: 286
Period size: 28 Copynumber: 7.6 Consensus size: 28
54561 CAATAACATT
*
54571 TTTTTTG--ATAATTACAAAAATATCAC
1 TTTTTTGAAATAATTACCAAAATATCAC
* * * *
54597 TTTTTAGAAATAATTACTAAAATAACAT
1 TTTTTTGAAATAATTACCAAAATATCAC
54625 TTTTTTCGAAATAATTACCAAAATATCA-
1 TTTTTT-GAAATAATTACCAAAATATCAC
54653 TTTTTTGAAATAATTACCAAAATATCAC
1 TTTTTTGAAATAATTACCAAAATATCAC
* *
54681 ATTTTTGAAATAATTACCAAAATATCATT
1 TTTTTTGAAATAATTACCAAAATATCA-C
54710 TTTTTTGAAATAATTACCAAAATATCAC
1 TTTTTTGAAATAATTACCAAAATATCAC
* * *
54738 TTTTTCGAAATAATTATCAAAATATAAC
1 TTTTTTGAAATAATTACCAAAATATCAC
*
54766 TTTTTTGAAATATTTAC
1 TTTTTTGAAATAATTAC
54783 GAAACTAAAA
Statistics
Matches: 164, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
26 6 0.04
27 21 0.13
28 92 0.56
29 45 0.27
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (28 bp):
TTTTTTGAAATAATTACCAAAATATCAC
Found at i:54648 original size:57 final size:57
Alignment explanation
Indices: 54562--54782 Score: 281
Period size: 57 Copynumber: 3.9 Consensus size: 57
54552 TCAAAAGTCC
* * * *
54562 AATAACATTTTTTTTG--ATAATTACAAAAATATCACTTTTTAGAAATAATTACTAA
1 AATAACATTTTTTTCGAAATAATTACCAAAATATCACTTTTTTGAAATAATTACCAA
54617 AATAACATTTTTTTCGAAATAATTACCAAAATATCA-TTTTTTGAAATAATTACCAA
1 AATAACATTTTTTTCGAAATAATTACCAAAATATCACTTTTTTGAAATAATTACCAA
* ** *
54673 AATATCACATTTTT-GAAATAATTACCAAAATATCATTTTTTTTGAAATAATTACCAA
1 AATAACATTTTTTTCGAAATAATTACCAAAATATCA-CTTTTTTGAAATAATTACCAA
* * * * *
54730 AATATCA-CTTTTTCGAAATAATTATCAAAATATAACTTTTTTGAAATATTTAC
1 AATAACATTTTTTTCGAAATAATTACCAAAATATCACTTTTTTGAAATAATTAC
54783 GAAACTAAAA
Statistics
Matches: 149, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
55 36 0.24
56 50 0.34
57 63 0.42
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (57 bp):
AATAACATTTTTTTCGAAATAATTACCAAAATATCACTTTTTTGAAATAATTACCAA
Found at i:89064 original size:13 final size:16
Alignment explanation
Indices: 89034--89063 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
89024 AATTTATCAA
89034 TTAATTATTATTTGTG
1 TTAATTATTATTTGTG
89050 TTAATTA-TATTTGT
1 TTAATTATTATTTGT
89064 TTGTCTACCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (16 bp):
TTAATTATTATTTGTG
Found at i:90184 original size:17 final size:17
Alignment explanation
Indices: 90162--90197 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
90152 GCTTGATATA
90162 ATTAGAA-TATTATATTT
1 ATTAGAATTA-TATATTT
90179 ATTAGAATTATATATTT
1 ATTAGAATTATATATTT
90196 AT
1 AT
90198 GTTTCAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTAGAATTATATATTT
Found at i:90859 original size:42 final size:42
Alignment explanation
Indices: 90757--90848 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
90747 AATGCCACAG
* *
90757 GGGTACATGCCCACCCCACCAGTTCAAATACCATCTCCGCAA
1 GGGTACATGCCAAGCCCACCAGTTCAAATACCATCTCCGCAA
* * **
90799 GGGTATATGCCAAGCCCACCAGTTCATATTTCATCTCCGC-A
1 GGGTACATGCCAAGCCCACCAGTTCAAATACCATCTCCGCAA
90840 GGGTTACAT
1 GGG-TACAT
90849 TCCTAACCCA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (42 bp):
GGGTACATGCCAAGCCCACCAGTTCAAATACCATCTCCGCAA
Found at i:90889 original size:21 final size:21
Alignment explanation
Indices: 90865--90907 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
90855 CCCACAGGGG
90865 TACATACCCAGCCCGCAAGGT
1 TACATACCCAGCCCGCAAGGT
* *
90886 TACATGCCCATCCCGCAAGGT
1 TACATACCCAGCCCGCAAGGT
90907 T
1 T
90908 TTATGACACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.37, G:0.19, T:0.19
Consensus pattern (21 bp):
TACATACCCAGCCCGCAAGGT
Done.