Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007299.1 Hibiscus syriacus cultivar Beakdansim tig00019424_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: 71416
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:142 original size:37 final size:36
Alignment explanation
Indices: 55--326 Score: 289
Period size: 35 Copynumber: 7.6 Consensus size: 36
45 ATTTTGAAAC
55 TATATATATATA-TTTTCAAAATGTTTTCAAAAC--
1 TATATATATATATTTTTCAAAATGTTTTCAAAACTA
88 TAT-TATATATA-TTTTCAAAATG-TTTCAAAAACTA
1 TATATATATATATTTTTCAAAATGTTTTC-AAAACTA
* * *
122 TATATATATTTATGTTTTCAAATTGTTTTAGAAAACTA
1 TATATATATATAT-TTTTCAAAATGTTTT-CAAAACTA
* *
160 TATATTATATATATGTTTTTAGAATGTTTTCAAAAACTA
1 TATA-TATATATAT-TTTTCAAAATGTTTTC-AAAACTA
*
199 TATAGTATATATA--TTTAAAAATGTTTTCAAAACTA
1 TATA-TATATATATTTTTCAAAATGTTTTCAAAACTA
*
234 TAAAT-TATATA-TTTTCAAAAATGTTTTTTCAAAACTA
1 TATATATATATATTTTTC-AAAATG--TTTTCAAAACTA
*
271 TATAT-TATATATTTTTAAAAATGTTTTCAAAACTA
1 TATATATATATATTTTTCAAAATGTTTTCAAAACTA
*
306 TATTTATATATA-TTTTCAAAA
1 TATATATATATATTTTTCAAAA
327 ACCGTTTTTT
Statistics
Matches: 206, Mismatches: 17, Indels: 30
0.81 0.07 0.12
Matches are distributed among these distances:
31 4 0.02
32 24 0.12
33 9 0.04
34 7 0.03
35 47 0.23
36 19 0.09
37 38 0.18
38 18 0.09
39 40 0.19
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (36 bp):
TATATATATATATTTTTCAAAATGTTTTCAAAACTA
Found at i:231 original size:35 final size:34
Alignment explanation
Indices: 51--327 Score: 274
Period size: 37 Copynumber: 7.8 Consensus size: 34
41 AATTATTTTG
*
51 AAACTATATA-TATATATTTTCAAAATGTTTTCA
1 AAACTATATATTATATATTTTAAAAATGTTTTCA
*
84 AAACTAT-TA-TATATATTTTCAAAATG-TTTCAA
1 AAACTATATATTATATATTTTAAAAATGTTTTC-A
* * * *
116 AAACTATATATATATTTATGTTTTCAAATTGTTTTAGA
1 AAACTATATAT-TA--TATATTTTAAAAATGTTTT-CA
* *
154 AAACTATATATTATATATATGTTTTTAGAATGTTTTCAA
1 AAACTATATA-T-TATATA--TTTTAAAAATGTTTTC-A
*
193 AAACTATATAGTATATATATTTAAAAATGTTTTCA
1 AAACTATATATTATATAT-TTTAAAAATGTTTTCA
*
228 AAACTATAAATTATATATTTTCAAAAATGTTTTTTCA
1 AAACTATATATTATATATTTT-AAAAATG--TTTTCA
265 AAACTATATATTATATATTTTTAAAAATGTTTTCA
1 AAACTATATATTATATA-TTTTAAAAATGTTTTCA
*
300 AAACTATATTTATATATATTTTCAAAAA
1 AAACTATATAT-TATATATTTT-AAAAA
328 CCGTTTTTTT
Statistics
Matches: 210, Mismatches: 15, Indels: 35
0.81 0.06 0.13
Matches are distributed among these distances:
31 4 0.02
32 27 0.13
33 9 0.04
34 3 0.01
35 47 0.22
36 24 0.11
37 51 0.24
38 18 0.09
39 27 0.13
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (34 bp):
AAACTATATATTATATATTTTAAAAATGTTTTCA
Found at i:2831 original size:98 final size:99
Alignment explanation
Indices: 2662--2937 Score: 430
Period size: 98 Copynumber: 2.8 Consensus size: 99
2652 CATTGTCTGT
* *
2662 CTAGCTGAATCTTATCAATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGAACAACTTAAGCT
1 CTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGAACAACTCAAGCT
2727 TTATTGTAT-TATATTACAATCACCTTTATCAGG
66 TTATTGTATATATATTACAATCACCTTTATCAGG
* *
2760 CTAGCTGAATTTTATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGAACAACTCAAGCT
1 CTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGAACAACTCAAGCT
* *
2825 TTATTGTATATATATTATAATCACCTTTATTAGG
66 TTATTGTATATATATTACAATCACCTTTATCAGG
* * * * *
2859 CTAGCTGAATCTT-TCCATAAAGTCGGGGTGTTTAACAAATTGCTTTAGAGGGACAACTCAAGCT
1 CTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGAACAACTCAAGCT
*
2923 TTATTGTATACATAT
66 TTATTGTATATATAT
2938 ATCTATAATC
Statistics
Matches: 163, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
98 129 0.79
99 34 0.21
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (99 bp):
CTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGAACAACTCAAGCT
TTATTGTATATATATTACAATCACCTTTATCAGG
Found at i:7008 original size:13 final size:13
Alignment explanation
Indices: 6975--7000 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6965 AGATCGAAAT
6975 AAAGTAAATAAAA
1 AAAGTAAATAAAA
6988 AAAGTAAATAAAA
1 AAAGTAAATAAAA
7001 GGAATAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAGTAAATAAAA
Found at i:7036 original size:15 final size:15
Alignment explanation
Indices: 7016--7050 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
7006 AAAAGAAAAT
*
7016 TTAAATTAAAAAGGA
1 TTAAATTAAAAAGAA
*
7031 TTAAATTAGAAAGAA
1 TTAAATTAAAAAGAA
7046 TTAAA
1 TTAAA
7051 AGTTAAGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (15 bp):
TTAAATTAAAAAGAA
Found at i:8244 original size:16 final size:16
Alignment explanation
Indices: 8225--8259 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
8215 AATAATTAAT
8225 AAAAATAATATTTTCA
1 AAAAATAATATTTTCA
* *
8241 AAAAATACTATTTTTA
1 AAAAATAATATTTTCA
8257 AAA
1 AAA
8260 TTGCATATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAATAATATTTTCA
Found at i:8347 original size:37 final size:37
Alignment explanation
Indices: 8277--8396 Score: 163
Period size: 37 Copynumber: 3.2 Consensus size: 37
8267 TGATATATGC
*
8277 TTTCAAAAATTATTTTC-AAAACTATATAATATATATAT
1 TTTC-AAAA-TATTTTCAAAAACTATATATTATATATAT
*
8315 TTTCGAAATATTTTCAAAAACTATATATTATATATAT
1 TTTCAAAATATTTTCAAAAACTATATATTATATATAT
* *
8352 TTTCAAAATGTTTTCAAAAACTATA-ATATATATATGT
1 TTTCAAAATATTTTCAAAAACTATATAT-TATATATAT
8389 TTTCAAAA
1 TTTCAAAA
8397 CTATATTATA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.12
37 62 0.83
38 4 0.05
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (37 bp):
TTTCAAAATATTTTCAAAAACTATATATTATATATAT
Found at i:8376 original size:26 final size:25
Alignment explanation
Indices: 8357--8423 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
8347 TATATTTTCA
*
8357 AAATGTTTTCAAAAACTATAATATAT
1 AAATGTTTTC-AAAACTATATTATAT
*
8383 ATATGTTTTCAAAACTATATTATAT
1 AAATGTTTTCAAAACTATATTATAT
8408 ATATATGTTTTCAAAA
1 A-A-ATGTTTTCAAAA
8424 TGTTTTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.42
26 9 0.25
27 12 0.33
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (25 bp):
AAATGTTTTCAAAACTATATTATAT
Found at i:8415 original size:27 final size:25
Alignment explanation
Indices: 8359--8423 Score: 103
Period size: 27 Copynumber: 2.5 Consensus size: 25
8349 TATTTTCAAA
8359 ATGTTTTCAAAAACTATAATATATAT
1 ATGTTTTC-AAAACTATAATATATAT
8385 ATGTTTTCAAAACTATATTATATATAT
1 ATGTTTTCAAAACTATA--ATATATAT
8412 ATGTTTTCAAAA
1 ATGTTTTCAAAA
8424 TGTTTTCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
25 9 0.24
26 8 0.22
27 20 0.54
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.45
Consensus pattern (25 bp):
ATGTTTTCAAAACTATAATATATAT
Found at i:8426 original size:64 final size:62
Alignment explanation
Indices: 8325--8484 Score: 236
Period size: 64 Copynumber: 2.5 Consensus size: 62
8315 TTTCGAAATA
8325 TTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATAATA-TATATATG
1 TTTTCAAAAACTATATATTATATAT-TTTTCAAAATGTTTTCAAAAA-TATAATATTATATATG
* *
8388 TTTTC-AAAACTATATTATATATATATGTTTTCAAAATGTTTTCAAAAATTTTATATTATATATG
1 TTTTCAAAAACTATA-TAT-TATATAT-TTTTCAAAATGTTTTCAAAAATATAATATTATATATG
8452 TTTTCAAAAACTATATATTATATA-TTTTCAAAA
1 TTTTCAAAAACTATATATTATATATTTTTCAAAA
8485 CAATATATTA
Statistics
Matches: 90, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
61 9 0.10
62 9 0.10
63 19 0.21
64 44 0.49
65 9 0.10
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (62 bp):
TTTTCAAAAACTATATATTATATATTTTTCAAAATGTTTTCAAAAATATAATATTATATATG
Found at i:8455 original size:37 final size:37
Alignment explanation
Indices: 8385--8460 Score: 118
Period size: 37 Copynumber: 2.0 Consensus size: 37
8375 TAATATATAT
8385 ATGTTTTCAAAACTATATTATATATATATGTTTTCAAA
1 ATGTTTTCAAAAC-ATATTATATATATATGTTTTCAAA
*
8423 ATGTTTTCAAAA-ATTTTATATTATATATGTTTTCAAA
1 ATGTTTTCAAAACATATTATA-TATATATGTTTTCAAA
8460 A
1 A
8461 ACTATATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
36 7 0.19
37 17 0.47
38 12 0.33
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (37 bp):
ATGTTTTCAAAACATATTATATATATATGTTTTCAAA
Found at i:8459 original size:26 final size:26
Alignment explanation
Indices: 8423--8507 Score: 106
Period size: 26 Copynumber: 3.4 Consensus size: 26
8413 TGTTTTCAAA
* *
8423 ATGTTTTCAAAAATTTTATATTATAT
1 ATGTTTTCAAAAACTATATATTATAT
8449 ATGTTTTCAAAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATATTATAT
*
8475 A--TTTTC-AAAACAATATATTA-AT
1 ATGTTTTCAAAAACTATATATTATAT
*
8497 ATATTTTCAAA
1 ATGTTTTCAAA
8508 GATGTTTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
22 3 0.06
23 13 0.25
24 10 0.19
25 2 0.04
26 25 0.47
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (26 bp):
ATGTTTTCAAAAACTATATATTATAT
Found at i:8541 original size:21 final size:23
Alignment explanation
Indices: 8512--8565 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
8502 TTCAAAGATG
*
8512 TTTTCAAAACTATA-TAT-TATA
1 TTTTCAAAAATATATTATATATA
*
8533 TTTTTAAAAATATATTATATATA
1 TTTTCAAAAATATATTATATATA
8556 TTTTCAAAAA
1 TTTTCAAAAA
8566 CCGTTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 12 0.43
22 3 0.11
23 13 0.46
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTTCAAAAATATATTATATATA
Found at i:8552 original size:85 final size:88
Alignment explanation
Indices: 8367--8564 Score: 234
Period size: 85 Copynumber: 2.3 Consensus size: 88
8357 AAATGTTTTC
* * *
8367 AAAAACTATAATATATATATGTTTTCAAAACTATATTATATATATATGTTTTCAAAATGTTTTCA
1 AAAAACTAT-ATAT-TATATATTTTCAAAACAATATTATATATATATATTTTCAAAATGTTTTCA
* * **
8432 AAAATTTTATATTATATATGTTTTC
64 AAAACTATATATTATATATGTTTAA
8457 AAAAACTATATATTATATATTTTCAAAACAATA-TAT-TA-ATATATTTTCAAAGATGTTTTC-A
1 AAAAACTATATATTATATATTTTCAAAACAATATTATATATATATATTTTCAAA-ATGTTTTCAA
8518 AAACTATATATTATAT-T-TTTAA
65 AAACTATATATTATATATGTTTAA
*
8540 AAATA-TAT-TA-TATATATTTTCAAAA
1 AAAAACTATATATTATATATTTTCAAAA
8565 ACCGTTTTTT
Statistics
Matches: 99, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
80 15 0.15
81 2 0.02
82 3 0.03
83 7 0.07
84 1 0.01
85 27 0.27
86 10 0.10
87 3 0.03
88 18 0.18
89 4 0.04
90 9 0.09
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (88 bp):
AAAAACTATATATTATATATTTTCAAAACAATATTATATATATATATTTTCAAAATGTTTTCAAA
AACTATATATTATATATGTTTAA
Found at i:9393 original size:30 final size:31
Alignment explanation
Indices: 9315--9422 Score: 128
Period size: 31 Copynumber: 3.5 Consensus size: 31
9305 TAGTTACGTC
*
9315 AGGGATCATATTGCGAACGGACTAAATGTTG
1 AGGGATCATATTGCAAACGGACTAAATGTTG
* *
9346 TGGGATCATATTGCAAACGGAGTAAAT-TTG
1 AGGGATCATATTGCAAACGGACTAAATGTTG
* * **
9376 AGGGACCATATTACAAACAAACTAAATGTTG
1 AGGGATCATATTGCAAACGGACTAAATGTTG
* *
9407 GGGGATTATATTGCAA
1 AGGGATCATATTGCAA
9423 GTTTTAAAAG
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
30 24 0.38
31 39 0.62
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (31 bp):
AGGGATCATATTGCAAACGGACTAAATGTTG
Found at i:9511 original size:2 final size:2
Alignment explanation
Indices: 9504--9530 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9494 AAATAAATTT
9504 TA TA TA 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 T
9531 TTAGAGTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9600 original size:26 final size:27
Alignment explanation
Indices: 9570--9623 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
9560 ATTTTAGGGG
* *
9570 TGAATTTTTAAAATTTTAGGAGA-AAA
1 TGAATTTATAAAATTTTAAGAGATAAA
9596 TGAATTTATAAAATTTTAAGAGATAAA
1 TGAATTTATAAAATTTTAAGAGATAAA
9623 T
1 T
9624 TTTTTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (27 bp):
TGAATTTATAAAATTTTAAGAGATAAA
Found at i:9763 original size:16 final size:17
Alignment explanation
Indices: 9742--9778 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
9732 CGGTTTTCTT
*
9742 AAATA-GTCTATTTTGC
1 AAATAGGTCAATTTTGC
9758 AAATAGGTCAATTTTGC
1 AAATAGGTCAATTTTGC
9775 AAAT
1 AAAT
9779 CGAAAGTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (17 bp):
AAATAGGTCAATTTTGC
Found at i:10373 original size:18 final size:17
Alignment explanation
Indices: 10347--10382 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
10337 ATTTTGTAGT
*
10347 AATTTTAAATTATTTAAA
1 AATTATAAATT-TTTAAA
10365 AATTATAAATTTTTAAA
1 AATTATAAATTTTTAAA
10382 A
1 A
10383 TAATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTATAAATTTTTAAA
Found at i:10920 original size:31 final size:31
Alignment explanation
Indices: 10870--10977 Score: 164
Period size: 31 Copynumber: 3.5 Consensus size: 31
10860 CTTTTAAAAC
**
10870 TTGCAATATAATCCC-CAACATTTAGTCCGT
1 TTGCAATATGGTCCCTCAACATTTAGTCCGT
*
10900 TTGCATTATGGTCCCTCAACATTTAGTCCGT
1 TTGCAATATGGTCCCTCAACATTTAGTCCGT
*
10931 TTGCAATATGGTTCCTCAACATTTAGTCCGT
1 TTGCAATATGGTCCCTCAACATTTAGTCCGT
*
10962 TTGCAATAAGGTCCCT
1 TTGCAATATGGTCCCT
10978 GGCGTAACTG
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 12 0.17
31 58 0.83
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (31 bp):
TTGCAATATGGTCCCTCAACATTTAGTCCGT
Found at i:17731 original size:20 final size:20
Alignment explanation
Indices: 17662--17731 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
17652 ATAAGTTCAA
17662 AATGTAAAA-ATAATAAAATT
1 AATGTAAAATATAA-AAAATT
* *
17682 TATGAAAAATATATAAAAATT
1 AATGTAAAATATA-AAAAATT
* *
17703 AAGGATAAAATATAAATAATT
1 AATG-TAAAATATAAAAAATT
17724 AATGTAAA
1 AATGTAAA
17732 TAATTAGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
20 11 0.28
21 20 0.50
22 9 0.22
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (20 bp):
AATGTAAAATATAAAAAATT
Found at i:19192 original size:3 final size:3
Alignment explanation
Indices: 19184--19242 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
19174 TTTATTTATT
* *
19184 TAA TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA TGA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
19230 TAA TTAA -AA TAA T
1 TAA -TAA TAA TAA T
19243 TTTAATGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 41 0.84
4 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:19196 original size:22 final size:23
Alignment explanation
Indices: 19184--19243 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 23
19174 TTTATTTATT
19184 TAATAATAATAA-TAATAATATA
1 TAATAATAATAATTAATAATATA
*
19206 TAATAATAATAATGATAAAAATA-A
1 TAATAATAATAAT--TAATAATATA
19230 TAATTAA-AATAATT
1 TAA-TAATAATAATT
19244 TTAATGAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 13 0.39
24 10 0.30
25 10 0.30
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
TAATAATAATAATTAATAATATA
Found at i:19555 original size:73 final size:73
Alignment explanation
Indices: 19401--19991 Score: 903
Period size: 73 Copynumber: 8.0 Consensus size: 73
19391 GGTCTTATGA
* * * * *
19401 ATGACTCTGAGGCTTTAAAATAAAAAAACTCCCGAAGGTTTTTTTTTGAAAATATCATGCACTGT
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGG---CTTTTTGAAAACATCATGCACTGT
*
19466 CGGTCTTACAG
63 AGGTCTTACAG
* * *
19477 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCAGAAGGATTTTTGAAAACATCATGCACTATAGG
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
*
19542 TCTTACAT
66 TCTTACAG
**
19550 ATGACCCTGAGGCTTTAGGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
19615 TCTTACAG
66 TCTTACAG
* * *
19623 ATGACCCTGAGGCTTTAGAATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATACACTGTAGG
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
19688 TCTTACAG
66 TCTTACAG
* * * *
19696 ATGACCCTGAGGCTTTAGAATAAAAAAGCTCCCAAACGCTTTTTGAAAACATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
19761 TCTTACAG
66 TCTTACAG
* **
19769 ATGACCCTGAGGATTTAGGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
*
19834 TCTTATAG
66 TCTTACAG
* *
19842 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCAAGCATTGTAGG
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
19907 TCTTACAG
66 TCTTACAG
* *
19915 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCTCGAAGGCTTTTTTAAAAACATCATGCACTGTAG
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCATGCACTGTAG
19980 GTCTTACAG
65 GTCTTACAG
19989 ATG
1 ATG
19992 TGAGAAATAA
Statistics
Matches: 477, Mismatches: 37, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
73 409 0.86
74 34 0.07
76 34 0.07
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (73 bp):
ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
TCTTACAG
Found at i:20372 original size:22 final size:22
Alignment explanation
Indices: 20342--20396 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
20332 AATAAGGTTT
20342 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* **
20364 TCATATTTGAGGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
20386 TCATCTTTGAA
1 TCATCTTTGAA
20397 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:24565 original size:32 final size:32
Alignment explanation
Indices: 24524--24585 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
24514 GAAGAAATGA
* *
24524 TTGTTATGCTTATCTGGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTCGTAGAGATACTTCTCG
24556 TTGTTATGCTCATCTCGTAGAGATACTTCT
1 TTGTTATGCTCATCTCGTAGAGATACTTCT
24586 TGTTTACAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTCGTAGAGATACTTCTCG
Found at i:33388 original size:7 final size:7
Alignment explanation
Indices: 33368--33436 Score: 61
Period size: 7 Copynumber: 10.1 Consensus size: 7
33358 TCATGAAGAG
*
33368 AAAGAAG
1 AAAGAAA
33375 AAA-AAA
1 AAAGAAA
33381 AAAGAAA
1 AAAGAAA
* *
33388 AAATAGA
1 AAAGAAA
33395 AAA-AAA
1 AAAGAAA
*
33401 ATAGAAA
1 AAAGAAA
*
33408 AAAGATA
1 AAAGAAA
*
33415 GAAGAAA
1 AAAGAAA
*
33422 AAAGAGA
1 AAAGAAA
33429 AAAGAAA
1 AAAGAAA
33436 A
1 A
33437 TTGGAAATGA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
6 9 0.19
7 39 0.81
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (7 bp):
AAAGAAA
Found at i:33399 original size:11 final size:11
Alignment explanation
Indices: 33373--33437 Score: 73
Period size: 11 Copynumber: 6.0 Consensus size: 11
33363 AAGAGAAAGA
33373 AGAAAAAAAA-
1 AGAAAAAAAAT
33383 AG--AAAAAAT
1 AGAAAAAAAAT
33392 AGAAAAAAAAT
1 AGAAAAAAAAT
*
33403 AGAAAAAAGAT
1 AGAAAAAAAAT
*
33414 AGAAGAAAAAAG
1 AGAA-AAAAAAT
33426 AGAAAAGAAAAT
1 AGAAAA-AAAAT
33438 TGGAAATGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 6 0.13
9 2 0.04
10 2 0.04
11 23 0.50
12 13 0.28
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.06
Consensus pattern (11 bp):
AGAAAAAAAAT
Found at i:33431 original size:22 final size:20
Alignment explanation
Indices: 33363--33433 Score: 83
Period size: 19 Copynumber: 3.5 Consensus size: 20
33353 TGACATCATG
*
33363 AAGAGAAAGA-AGAAAAAAA
1 AAGAAAAAGATAGAAAAAAA
33382 AAGAAAAA-ATAGAAAAAAA
1 AAGAAAAAGATAGAAAAAAA
*
33401 ATAGAAAAAAGATAGAAGAAAA
1 A-AG-AAAAAGATAGAAAAAAA
33423 AAGAGAAAAGA
1 AAGA-AAAAGA
33434 AAATTGGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
18 1 0.02
19 17 0.38
20 3 0.07
21 13 0.29
22 11 0.24
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.04
Consensus pattern (20 bp):
AAGAAAAAGATAGAAAAAAA
Found at i:35705 original size:36 final size:36
Alignment explanation
Indices: 35658--35767 Score: 166
Period size: 36 Copynumber: 3.0 Consensus size: 36
35648 GATTAGGGTA
* *
35658 AGTCATTCTTAAGCCTTCACCGAAGAGGAGTGAAGC
1 AGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGC
*
35694 AGTCAATCTTAAGCCTTCACCAAAGAGTAGTGAAGC
1 AGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGC
* *
35730 AACTCAATCTTAAGCCTTCACCGAATAGTAGTGAAGC
1 -AGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGC
35767 A
1 A
35768 AATCCATCCG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 34 0.51
37 33 0.49
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (36 bp):
AGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGC
Found at i:35746 original size:37 final size:37
Alignment explanation
Indices: 35664--35768 Score: 167
Period size: 37 Copynumber: 2.9 Consensus size: 37
35654 GGTAAGTCAT
* *
35664 TCTTAAGCCTTCACCGAAGAGGAGTGAAGC-AGTCAA
1 TCTTAAGCCTTCACCGAAGAGTAGTGAAGCAACTCAA
*
35700 TCTTAAGCCTTCACCAAAGAGTAGTGAAGCAACTCAA
1 TCTTAAGCCTTCACCGAAGAGTAGTGAAGCAACTCAA
*
35737 TCTTAAGCCTTCACCGAATAGTAGTGAAGCAA
1 TCTTAAGCCTTCACCGAAGAGTAGTGAAGCAA
35769 ATCCATCCGT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
36 28 0.44
37 35 0.56
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (37 bp):
TCTTAAGCCTTCACCGAAGAGTAGTGAAGCAACTCAA
Found at i:36137 original size:207 final size:207
Alignment explanation
Indices: 35779--36910 Score: 1783
Period size: 207 Copynumber: 5.4 Consensus size: 207
35769 ATCCATCCGT
35779 ATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCA
1 ATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCA
* *
35844 TCCATAAAACTTTCGGGTAGGATATTTTCACATGAATTTGAGAATGAAAAAAATGATGTTGG-AA
66 TCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATG-AAAAAATGATGTTGGAAA
*
35908 TTTTTTGAAAACGAAAAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGT
130 TTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGT
35973 AAGTCTTTCGAGC
195 AAGTCTTTCGAGC
* *
35986 ATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTAGAGCAAGATGATAAGTCCTTTGGGCCA
1 ATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCA
36051 TCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTGGAAAT
66 TCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTGGAAAT
* *
36116 TTTTTTAAAATGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTA
131 TTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTA
36181 AGTCTTTCGAGC
196 AGTCTTTCGAGC
* *
36193 ATGAAGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGAAAGATGATAAGTCCTTCGGGCCA
1 ATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCA
* *
36258 TCCATAAAACCTTAGGGTAGAATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTGG-AAT
66 TCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTGGAAAT
*
36322 TTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGACATCAGTA
131 TTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTA
36387 AGTCTTTCGAGC
196 AGTCTTTCGAGC
*
36399 ATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCA
1 ATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCA
*
36464 TCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATG-AAAAATGGTGTT-GAAA-
66 TCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTGGAAAT
*
36526 TTTTTGAAAACGAAGAATGCGAGTTTCAGAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTA
131 TTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTA
36591 AGTCTTTCGAGC
196 AGTCTTTCGAGC
* * *
36603 ATGATGCTTAAATCCTTCGGGTCGTCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGACCA
1 ATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCA
* * * * *
36668 TCCGTAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGA-AATGAAGAAATGGTGTTTTAAGA
66 TCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATG--TT----
* * * *
36732 AGATGAAATTTTTT-AAAACAAAGAATGCAATTTTCAAAATTTCACAATTTATAAGTCTTTCGGG
125 -G--GAAATTTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
36796 CCATCAGTAAGTCTTTCGAGC
187 CCATCAGTAAGTCTTTCGAGC
* * * * * * *
36817 ATGATGCTTAAATCCTTCGGCTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTC
1 ATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATG-ATAAGTCCTTCGGGCC
** *
36882 ATCCATAAGGCCTTCGGGCAGGATGTTTT
65 ATCCATAAAACCTTCGGGTAGGATGTTTT
36911 TCACCAAGAT
Statistics
Matches: 860, Mismatches: 50, Indels: 22
0.92 0.05 0.02
Matches are distributed among these distances:
203 4 0.00
204 184 0.21
205 13 0.02
206 200 0.23
207 304 0.35
214 112 0.13
215 43 0.05
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (207 bp):
ATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCA
TCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTGGAAAT
TTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTA
AGTCTTTCGAGC
Found at i:36634 original size:42 final size:41
Alignment explanation
Indices: 36568--36680 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 41
36558 TTCACAATTT
* * * *
36568 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * * *
36609 CTTAAATCCTTCGGGTCGTCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * *
36651 ATAAGTCCTTCGGACCATCCGTAAGACCTT
1 ATAAATCCTTCGGGCCATCAGTAAG-CCTT
36681 CGGGTAGGAT
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 19 0.34
42 37 0.66
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:36849 original size:42 final size:42
Alignment explanation
Indices: 36797--36884 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
36787 TCTTTCGGGC
36797 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGCT
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGCT
*
36839 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGCT
36881 CATC
1 CATC
36885 CATAAGGCCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGCT
Found at i:45011 original size:2 final size:2
Alignment explanation
Indices: 45004--45054 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
44994 ATTTAAACAA
*
45004 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45046 AT AT AT AT A
1 AT AT AT AT A
45055 GATACTTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:45236 original size:21 final size:20
Alignment explanation
Indices: 45201--45259 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
45191 TTCAAAATGT
* *
45201 AAAAATA-ATAAAATTTATG
1 AAAAATATATAAAATTAAGG
45220 AAAAATATATAAAAATTAAGG
1 AAAAATATAT-AAAATTAAGG
45241 ATAAAATATA-AATAATTAA
1 A-AAAATATATAA-AATTAA
45260 TGTACAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 7 0.21
20 4 0.12
21 15 0.44
22 8 0.24
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAATATATAAAATTAAGG
Found at i:46715 original size:15 final size:14
Alignment explanation
Indices: 46692--46730 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
46682 TATTTATTTA
*
46692 ATAATAATAATAAT
1 ATAAAAATAATAAT
46706 GATAAAAATAATAAT
1 -ATAAAAATAATAAT
46721 -TAAAAATAAT
1 ATAAAAATAAT
46731 TTTAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
15 13 0.57
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
ATAAAAATAATAAT
Found at i:49722 original size:46 final size:46
Alignment explanation
Indices: 49614--49883 Score: 362
Period size: 46 Copynumber: 5.9 Consensus size: 46
49604 ATGAGTCGCA
* * * ** *
49614 CCTTTTATGCCGTTAATGCACCCCTATGCATTTTCATTTGTGGCAT
1 CCTTTCATGCCGATAATGCATCGTTATGCATTTTCATTTATGGCAT
* * * * * *
49660 CATTTCTTGTCTATAATTCATCGTTATGCATTTTCATTTATGGTAT
1 CCTTTCATGCCGATAATGCATCGTTATGCATTTTCATTTATGGCAT
*
49706 CCTTTCATGCCGATAATGCATCGTTATGCATTTTCATTTATGGTAT
1 CCTTTCATGCCGATAATGCATCGTTATGCATTTTCATTTATGGCAT
*
49752 CCTTTCATGCCGATAATGCATCGTTATGCATTTTCATTTATGACAT
1 CCTTTCATGCCGATAATGCATCGTTATGCATTTTCATTTATGGCAT
* *
49798 CCTTTCATGCCGATAATGCACCGTTATGCATTTTCATTTATGGAAT
1 CCTTTCATGCCGATAATGCATCGTTATGCATTTTCATTTATGGCAT
* * *
49844 CC-GTCATGTCGATAATGCACCGTTATGCATTTTCATTTAT
1 CCTTTCATGCCGATAATGCATCGTTATGCATTTTCATTTAT
49884 TCATTCATTT
Statistics
Matches: 200, Mismatches: 24, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
45 36 0.18
46 164 0.82
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (46 bp):
CCTTTCATGCCGATAATGCATCGTTATGCATTTTCATTTATGGCAT
Found at i:56737 original size:46 final size:46
Alignment explanation
Indices: 56670--56881 Score: 293
Period size: 46 Copynumber: 4.6 Consensus size: 46
56660 TTAATACTGT
* * *
56670 TAATGCACCGTCATGCATTTTCATTTGTGGCATCATTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCATTTCATACCGA
*
56716 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATACCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCATTTCATACCGA
*
56762 TAATGCACTGTTATGCAATTTT-ATTTATGGCATCATTTCATACCGA
1 TAATGCACCGTTATGC-ATTTTCATTTATGGCATCATTTCATACCGA
* * * * *
56808 TAATGCCCCATTATGCATTTTCATTTATGGAATCCTTTCA-AGTCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCATTTCATA-CCGA
*
56854 TAATGCATCGTTATGCATTTTCATTTAT
1 TAATGCACCGTTATGCATTTTCATTTAT
56882 TCATTCATTT
Statistics
Matches: 148, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
45 6 0.04
46 137 0.93
47 5 0.03
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.41
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTATGGCATCATTTCATACCGA
Found at i:57982 original size:31 final size:31
Alignment explanation
Indices: 57940--57999 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
57930 AACTTAAAAG
* *
57940 AGTTTTTCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
57971 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
58000 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:58485 original size:19 final size:20
Alignment explanation
Indices: 58455--58507 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
58445 TATTTAAACT
58455 TAAATAAAAAATAATTAA-AA
1 TAAAT-AAAAATAATTAATAA
*
58475 TAAATAAAAAT-TTTAATAA
1 TAAATAAAAATAATTAATAA
*
58494 TATAT-AAAATAATT
1 TAAATAAAAATAATT
58508 TATATGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.32
19 14 0.50
20 5 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAATAAAAATAATTAATAA
Found at i:58588 original size:64 final size:62
Alignment explanation
Indices: 58516--58670 Score: 237
Period size: 64 Copynumber: 2.5 Consensus size: 62
58506 TTTATATGAT
58516 TTAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTACAAAATTAATA
1 TTAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTT--AAAATTAATA
58580 TTAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAATTAATA
1 TTAAAATTAAATATCTATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAATTAATA
* *
58642 CTAAAATTAAA-A--TATAATATAAAATTAAA
1 TTAAAATTAAATATCTATAATATAATATTAAA
58671 TATAAACCTC
Statistics
Matches: 87, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
59 3 0.03
60 13 0.15
62 18 0.21
63 22 0.25
64 31 0.36
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (62 bp):
TTAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAATTAATA
Found at i:58605 original size:26 final size:23
Alignment explanation
Indices: 58572--58641 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 23
58562 TTATTTACAA
58572 AATTAATATTAAAATTAATATCTAT
1 AATTAATATTAAAATTAATAT-T-T
58597 AATATAATATTAAAAAATTAATATTT
1 AAT-TAATATT--AAAATTAATATTT
*
58623 AATTTAT-TTAAAATTAATA
1 AATTAATATTAAAATTAATA
58642 CTAAAATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 10 0.24
24 2 0.05
25 6 0.15
26 11 0.27
27 1 0.02
28 11 0.27
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTAATATTAAAATTAATATTT
Found at i:58620 original size:40 final size:37
Alignment explanation
Indices: 58538--58621 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 37
58528 ATCTATAATA
* *
58538 TAATATTAAAAATTAATATTTAATTTATTTACAAAAT
1 TAATATTAAAAATTAATATTTAATTAATTTAAAAAAT
58575 TAATATT-AAAATTAATATCTATAATATAATATTAAAAAAT
1 TAATATTAAAAATTAATAT-T-TAAT-TAAT-TTAAAAAAT
58615 TAATATT
1 TAATATT
58622 TAATTTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
36 11 0.27
37 8 0.20
38 4 0.10
39 3 0.07
40 15 0.37
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (37 bp):
TAATATTAAAAATTAATATTTAATTAATTTAAAAAAT
Found at i:68103 original size:12 final size:12
Alignment explanation
Indices: 68086--68116 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
68076 CATTATAGAC
68086 TTATAATATGAA
1 TTATAATATGAA
68098 TTATAATATGAA
1 TTATAATATGAA
68110 TTATAAT
1 TTATAAT
68117 CTTAAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (12 bp):
TTATAATATGAA
Done.