Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001815.1 Hibiscus syriacus cultivar Beakdansim tig00003674_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: 68595
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2649 original size:371 final size:372
Alignment explanation
Indices: 1942--2672 Score: 1294
Period size: 371 Copynumber: 2.0 Consensus size: 372
1932 TTTTATCCAT
1942 AAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACATCTCAATATTATAATCACTTTTATCAGG
1 AAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACATCTCAATATTATAATCACTTTTATCAGG
*
2007 TTAACTGAAGGGTTCATTTCATCACAAAGTCTTCGACTTGACAATTGCAGTGGAGCAAACACCGA
66 TTAACTGAAGGGTTCATCTCATCACAAAGTCTTCGACTTGACAATTGCAGTGGAGCAAACACCGA
**
2072 ATTGCCAGTGTCCGAGCAATGTCATGGTTTGAACATAATTATTCATAAAGCCAGGGCTTTTGAGT
131 ATTGCCAGTGTCCGAGCAATGTCATGGTTTGAACATAATTATTCATAAAGCCAGGGCAATTGAGT
2137 TTCCTCTATAACCAATTGCCTTATGAATAGCTCAGCTCTATTGTATACGGATTCAATTTTTTAAG
196 TTCCTCTATAACCAATTGCCTTATGAATAGCTCAGCTCTATTGTATACGGATTCAATTTTTTAAG
* *
2202 ATTGTCAAAAAGAACCTGTTATAGTCTAAGTGTTGTTAAAAGTCCAAAAATCTTATCTTTAGAGT
261 ATTGTAAAAAAGAACCTGTTATAGTCTAAGTGTTGTTAAAAGTCCAAAAATCTCATCTTTAGAGT
2267 TCAATTTCCAAGCAACTAACCTAAACTAGATTCACTTTTTCAGGTTA
326 TCAATTTCCAAGCAACTAACCTAAACTAGATTCACTTTTTCAGGTTA
*
2314 AAAGCC-GGGCGTTT-ACCAATTGCTC-AGTGGGACATCTCAATATTATAATCACTTTTATCAGG
1 AAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACATCTCAATATTATAATCACTTTTATCAGG
*
2376 TTAACTGAAGGGTTCATCTCATCACAAAGTCTTCGACTTGACAATTGCAGTGGAGCAAAC-TCGA
66 TTAACTGAAGGGTTCATCTCATCACAAAGTCTTCGACTTGACAATTGCAGTGGAGCAAACACCGA
2440 ATTGGCCAAGTGTCCGAGCAATGTCATGGTTTGAACAT-ATATATTCATAAAGCCAGGGCAATTG
131 ATT-GCC-AGTGTCCGAGCAATGTCATGGTTTGAACATAAT-TATTCATAAAGCCAGGGCAATTG
* *
2504 AG-TTCCTCTATAACCAATTGCCTTAGTGAAATATCTTAGCTCTATTGTATACGGATTCAATTTT
193 AGTTTCCTCTATAACCAATTGCCTTA-TG-AATAGCTCAGCTCTATTGTATACGGATTCAATTTT
2568 TTAAGATTGTAAAAAAGAACCTGTTATAGTCTAAGTGTTGTTAAAAGTCCAAAAATCTCATCTTT
256 TTAAGATTGTAAAAAAGAACCTGTTATAGTCTAAGTGTTGTTAAAAGTCCAAAAATCTCATCTTT
2633 AGAGTTCAATTTCCAAGCAACTAACCTAAACTAGATTCAC
321 AGAGTTCAATTTCCAAGCAACTAACCTAAACTAGATTCAC
2673 CTACTCGACT
Statistics
Matches: 345, Mismatches: 9, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
368 6 0.02
369 123 0.36
370 66 0.19
371 144 0.42
372 6 0.02
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (372 bp):
AAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACATCTCAATATTATAATCACTTTTATCAGG
TTAACTGAAGGGTTCATCTCATCACAAAGTCTTCGACTTGACAATTGCAGTGGAGCAAACACCGA
ATTGCCAGTGTCCGAGCAATGTCATGGTTTGAACATAATTATTCATAAAGCCAGGGCAATTGAGT
TTCCTCTATAACCAATTGCCTTATGAATAGCTCAGCTCTATTGTATACGGATTCAATTTTTTAAG
ATTGTAAAAAAGAACCTGTTATAGTCTAAGTGTTGTTAAAAGTCCAAAAATCTCATCTTTAGAGT
TCAATTTCCAAGCAACTAACCTAAACTAGATTCACTTTTTCAGGTTA
Found at i:6470 original size:36 final size:36
Alignment explanation
Indices: 6427--6633 Score: 344
Period size: 36 Copynumber: 5.8 Consensus size: 36
6417 ATCCATTATT
6427 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
*
6463 AGATTTGATACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
*
6499 AGCTTTAATACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
* *
6535 AGCTTTGATACATTCGTGTAGCAATGTTATCATATTT
1 AGCTTTGATACATTCGTGTATCAATGTTATCATA-TC
6572 A-CTTTGATACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
* *
6607 TGCTTTGGTACATTCGTGTATCAATGT
1 AGCTTTGATACATTCGTGTATCAATGT
6634 CCATCACCAT
Statistics
Matches: 159, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
35 1 0.01
36 156 0.98
37 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (36 bp):
AGCTTTGATACATTCGTGTATCAATGTTATCATATC
Found at i:11959 original size:30 final size:30
Alignment explanation
Indices: 11891--11960 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
11881 AAAATGTAAG
* *
11891 TTTTAAAAGTTTAGAGGCTAAAGTATAAAC
1 TTTTAAAAGTTTAGAGGCCAAAATATAAAC
* *
11921 TTTAAAAAGTTTAG-GGACCAAAAT-TGAAAT
1 TTTTAAAAGTTTAGAGG-CCAAAATAT-AAAC
11951 TTTTAAAAGT
1 TTTTAAAAGT
11961 ATATATTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (30 bp):
TTTTAAAAGTTTAGAGGCCAAAATATAAAC
Found at i:14138 original size:36 final size:36
Alignment explanation
Indices: 14092--14194 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
14082 ATTTATCCAT
14092 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
*
14128 TATCAACTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
* *
14164 TATCAGCTTTGGTACATTCATGTATCAATGT
1 TATCAGCTTTGATACATTCGTGTATCAATGT
14195 CCATCACCAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
Found at i:16811 original size:15 final size:17
Alignment explanation
Indices: 16780--16811 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
16770 ATGTATTTTT
16780 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
16797 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
16812 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:18078 original size:17 final size:17
Alignment explanation
Indices: 18057--18101 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
18047 ATGAAAAAAG
18057 AATAATAAAAATATTAA
1 AATAATAAAAATATTAA
* *
18074 TATAATAATAATATTAA
1 AATAATAAAAATATTAA
18091 AATAAATAAAA
1 AAT-AATAAAA
18102 TAGATAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAATAAAAATATTAA
Found at i:18125 original size:57 final size:55
Alignment explanation
Indices: 18064--18183 Score: 125
Period size: 57 Copynumber: 2.1 Consensus size: 55
18054 AAGAATAATA
* * * * * * *
18064 AAAATATTAATATAATAATAATATTAAAATAAATAAAATAGATAAATAAAGAT-AAAT
1 AAAATAGTAATAGAAAAATAATA--AAAATAAAGAAAATA-AAAAACAAAAATGAAAT
18121 AAAATTGAGTAATAGAAAAATAATAAAAATAAAGAAAATAAAAAACAAAAATGAAAT
1 AAAA-T-AGTAATAGAAAAATAATAAAAATAAAGAAAATAAAAAACAAAAATGAAAT
18178 AAAATA
1 AAAATA
18184 AAATAAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
55 1 0.02
56 10 0.19
57 26 0.49
58 1 0.02
59 15 0.28
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.23
Consensus pattern (55 bp):
AAAATAGTAATAGAAAAATAATAAAAATAAAGAAAATAAAAAACAAAAATGAAAT
Found at i:18134 original size:23 final size:22
Alignment explanation
Indices: 18088--18191 Score: 72
Period size: 23 Copynumber: 4.6 Consensus size: 22
18078 ATAATAATAT
18088 TAAAATAAATAAAATAGATAAA
1 TAAAATAAATAAAATAGATAAA
*
18110 TAAAGATAAATAAAATTGAGT-AA
1 TAAA-ATAAATAAAATAGA-TAAA
* *
18133 TAGAA-AAATAATAA-AAATAAA
1 TAAAATAAATAA-AATAGATAAA
* * *
18154 GAAAATAAA-AAACAAAAATGAAA
1 TAAAATAAATAAA-ATAGAT-AAA
18177 TAAAATAAAATAAAA
1 TAAAAT-AAATAAAA
18192 AAGGTTAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
20 2 0.03
21 15 0.23
22 14 0.22
23 26 0.40
24 5 0.08
25 3 0.05
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (22 bp):
TAAAATAAATAAAATAGATAAA
Found at i:18193 original size:23 final size:23
Alignment explanation
Indices: 18137--18193 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
18127 GAGTAATAGA
*
18137 AAAATAATAAAAATAAAGAAAAT
1 AAAATAACAAAAATAAAGAAAAT
*
18160 AAAA-AACAAAAATGAAATAAAAT
1 AAAATAACAAAAAT-AAAGAAAAT
18183 AAAATAA-AAAA
1 AAAATAACAAAA
18194 GGTTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 8 0.27
23 20 0.67
24 2 0.07
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.14
Consensus pattern (23 bp):
AAAATAACAAAAATAAAGAAAAT
Found at i:18876 original size:16 final size:16
Alignment explanation
Indices: 18855--18914 Score: 84
Period size: 16 Copynumber: 3.7 Consensus size: 16
18845 TCCTTTGTGC
18855 TTGTTGTGGTTCAATG
1 TTGTTGTGGTTCAATG
18871 TTGTTGTGGTTTCAATG
1 TTGTTGTGG-TTCAATG
* * *
18888 TTGTCGGGGTTCGATG
1 TTGTTGTGGTTCAATG
18904 TTGTTGTGGTT
1 TTGTTGTGGTT
18915 GGTTCTCCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
16 24 0.63
17 14 0.37
ACGTcount: A:0.08, C:0.07, G:0.35, T:0.50
Consensus pattern (16 bp):
TTGTTGTGGTTCAATG
Found at i:19214 original size:3 final size:3
Alignment explanation
Indices: 19206--19252 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
19196 GAATAAGAAT
* *
19206 TAA TAA TAA TAA TAA TAAA TAA TAA AAA TAA AAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19251 TA
1 TA
19253 TTACTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:19315 original size:38 final size:37
Alignment explanation
Indices: 19266--19503 Score: 143
Period size: 36 Copynumber: 6.6 Consensus size: 37
19256 CTTAAATATA
* * * *
19266 TATATATTATATTTATTTTCCCAAAATGTTTTTAAAATC
1 TATATATTATATATAATTT--CAAAATGTTTTCAAAAAC
19305 -ATATATTATATATAATTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATAATTTCAAAATGTTTTCAAAAAC
19341 TATATATT-T-TCA-AA----AATAA--TTTTC-AAAAC
1 TATATATTATAT-ATAATTTCAA-AATGTTTTCAAAAAC
* *
19370 TATATATTATATATATGTTTTTAAAATGTTTTCAAAAAC
1 TATATATTATATATA--ATTTCAAAATGTTTTCAAAAAC
*
19409 -ATATATTATATAT--TTTCAAAAATAATTTTC-AAAAC
1 TATATATTATATATAATTTC-AAAAT-GTTTTCAAAAAC
* *
19444 TATA-A-TATATATATTTTCAAAAATCATTTTC-AAAAC
1 TATATATTATATATAATTTC-AAAAT-GTTTTCAAAAAC
* * * *
19480 CATATAATATATGTATTTTCAAAA
1 TATATATTATATATAATTTCAAAA
19504 ATAATTTTCA
Statistics
Matches: 167, Mismatches: 10, Indels: 46
0.75 0.04 0.21
Matches are distributed among these distances:
29 13 0.08
30 7 0.04
31 4 0.02
32 2 0.01
34 10 0.06
35 14 0.08
36 52 0.31
37 14 0.08
38 46 0.28
39 5 0.03
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (37 bp):
TATATATTATATATAATTTCAAAATGTTTTCAAAAAC
Found at i:19347 original size:30 final size:29
Alignment explanation
Indices: 19313--19377 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
19303 TCATATATTA
* *
19313 TATATAATTTC-AAAAT-GTTTTCAAAAAC
1 TATATATTTTCAAAAATAATTTTC-AAAAC
19341 TATATATTTTCAAAAATAATTTTCAAAAC
1 TATATATTTTCAAAAATAATTTTCAAAAC
19370 TATATATT
1 TATATATT
19378 ATATATATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 10 0.30
29 18 0.55
30 5 0.15
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (29 bp):
TATATATTTTCAAAAATAATTTTCAAAAC
Found at i:19352 original size:17 final size:16
Alignment explanation
Indices: 19330--19377 Score: 66
Period size: 13 Copynumber: 3.1 Consensus size: 16
19320 TTTCAAAATG
19330 TTTTCAAAAACTATATA
1 TTTTC-AAAACTATATA
19347 TTTTCAAAA--ATA-A
1 TTTTCAAAACTATATA
19360 TTTTCAAAACTATATA
1 TTTTCAAAACTATATA
19376 TT
1 TT
19378 ATATATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 10 0.36
14 3 0.11
15 3 0.11
16 7 0.25
17 5 0.18
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTTCAAAACTATATA
Found at i:19438 original size:74 final size:75
Alignment explanation
Indices: 19341--19528 Score: 267
Period size: 74 Copynumber: 2.5 Consensus size: 75
19331 TTTCAAAAAC
** *
19341 TATATATTTTCAAAAATAATTTTCAAAACTATATATTATATATATGTTTTTAAAAT-GTTTTCAA
1 TATATATTTTCAAAAATAATTTTCAAAACTATATA-TATATATAT-TTTCAAAAATCATTTTCAA
19405 AAACATAT-AT-
64 AAACATATAATA
19415 TATATATTTTCAAAAATAATTTTCAAAACTATA-ATATATATATTTTCAAAAATCATTTTCAAAA
1 TATATATTTTCAAAAATAATTTTCAAAACTATATATATATATATTTTCAAAAATCATTTTCAAAA
*
19479 CCATATAATA
66 ACATATAATA
* *
19489 TATGTATTTTCAAAAATAATTTTCAAAATTATATGATATA
1 TATATATTTTCAAAAATAATTTTCAAAACTATAT-ATATA
19529 CTTTCAAAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
71 8 0.08
72 23 0.22
73 3 0.03
74 64 0.62
76 5 0.05
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (75 bp):
TATATATTTTCAAAAATAATTTTCAAAACTATATATATATATATTTTCAAAAATCATTTTCAAAA
ACATATAATA
Found at i:19528 original size:38 final size:37
Alignment explanation
Indices: 19341--19528 Score: 240
Period size: 38 Copynumber: 5.1 Consensus size: 37
19331 TTTCAAAAAC
19341 TATATATTTTCAAAAATAATTTTCAAAACTATATATTA
1 TATATATTTTCAAAAATAATTTTCAAAACTATATA-TA
** *
19379 TATATATGTTTTTAAAAT-GTTTTCAAAAAC-ATATAT-
1 TATATAT-TTTCAAAAATAATTTTC-AAAACTATATATA
19415 TATATATTTTCAAAAATAATTTTCAAAACTATA-ATA
1 TATATATTTTCAAAAATAATTTTCAAAACTATATATA
* *
19451 TATATATTTTCAAAAATCATTTTCAAAACCATATAATA
1 TATATATTTTCAAAAATAATTTTCAAAACTATAT-ATA
* *
19489 TATGTATTTTCAAAAATAATTTTCAAAATTATATGATA
1 TATATATTTTCAAAAATAATTTTCAAAACTATAT-ATA
19527 TA
1 TA
19529 CTTTCAAAAA
Statistics
Matches: 130, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
35 15 0.12
36 46 0.35
37 1 0.01
38 55 0.42
39 13 0.10
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (37 bp):
TATATATTTTCAAAAATAATTTTCAAAACTATATATA
Found at i:20096 original size:2 final size:2
Alignment explanation
Indices: 20089--20115 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20079 GGCTCAATTA
20089 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 A
20116 ACGTTTAAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28542 original size:20 final size:21
Alignment explanation
Indices: 28506--28566 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
28496 TTTTGGTGCA
*
28506 GAGGGAA-TCGATACCCCC-AT
1 GAGGGAACT-GATTCCCCCTAT
*
28526 GAGGGAACTGATTCCCCCTTT
1 GAGGGAACTGATTCCCCCTAT
*
28547 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACTGATTCCCCC
28567 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 15 0.44
21 3 0.09
22 1 0.03
23 15 0.44
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACTGATTCCCCCTAT
Found at i:28575 original size:21 final size:21
Alignment explanation
Indices: 28549--28588 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28539 CCCCCTTTGA
*
28549 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
28570 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
28589 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:31179 original size:22 final size:23
Alignment explanation
Indices: 31154--31197 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
31144 AATTAAGTTT
31154 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
31176 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
31198 GCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:33852 original size:3 final size:3
Alignment explanation
Indices: 33844--33870 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
33834 AATAAACATT
33844 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
33871 TATAGTATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:33959 original size:21 final size:22
Alignment explanation
Indices: 33926--33978 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
33916 AATTTATGTA
*
33926 ATATGTATGTTATAAAAAAATAC
1 ATAT-TATATTATAAAAAAATAC
* *
33949 AT-TTATATTATATAAAATTAC
1 ATATTATATTATAAAAAAATAC
33970 ATATTATAT
1 ATATTATAT
33979 AATGGGGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 17 0.65
22 7 0.27
23 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATTATATTATAAAAAAATAC
Found at i:34508 original size:85 final size:85
Alignment explanation
Indices: 34365--35208 Score: 1151
Period size: 85 Copynumber: 9.9 Consensus size: 85
34355 TACCATGTGG
* * * *
34365 TTGATAGGCCCTCGAGCTAAATAG-AATCGAACTCGAAGGTGTTTGTTGACAGATAGCCCTTCTT
1 TTGATATGCCCTTGAGCTGAAT-GTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTC-T
*
34429 C-CCTTGAGCTATGCTATAAAT
64 CGCCTTGAGCTATGCTGTAAAT
* *
34450 TTGATAAGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTTG
1 TTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
34515 CCTTGAGCTATGCTGTAAAT
66 CCTTGAGCTATGCTGTAAAT
* * *
34535 TTGATATACCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTTGTTGACAAATAACCCTTCT
1 TTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGG--TTTTTGTTGACAGATAGCCCTTCT
34600 CGCCTTGAGCTATGCTGTAAAT
64 CGCCTTGAGCTATGCTGTAAAT
* * *
34622 TTGATATGCCCTTGAGTTGAATGTAATCGAACTTGAAGGTTTTCGTTGACAGATAGCCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
* *
34687 CCTTGAGCTATGCTATAAAC
66 CCTTGAGCTATGCTGTAAAT
* * * * * *
34707 TTGATATG-ACTTGAGCTAAATGCAATCGAACTTGAAGGTTTTCGTTGACATATAGCCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
*
34771 CCTTGAGCTATGCTGTAAAC
66 CCTTGAGCTATGCTGTAAAT
* * * * * *
34791 TTGATATG-ACTTGAGCTAAATGCAATCGAACTTGAAGGTTTTCGTTGACATATAGCCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
34855 CCTTGAGCTATGCTGTAAAT
66 CCTTGAGCTATGCTGTAAAT
* * * * *
34875 TTGATATGCTCTTGAGTTGAATGTAATCGAACTTGAAGGTTTTATGCTGACAGATAACCCTTCTC
1 TTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTT-TGTTGACAGATAGCCCTTCTC
* *
34940 GCCTTGAGCTATGTTATAAAT
65 GCCTTGAGCTATGCTGTAAAT
* * * ** *
34961 TTGATATGCCTTTGAGCTGAATGTAATTGAACTCGATGGTTTTCATTGACAGATAGCCCTTCTCT
1 TTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
*
35026 CATTGAGCTATGCTAG-AAAT
66 CCTTGAGCTATGCT-GTAAAT
*
35046 TTGATATG-ACTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
35110 CCTTGAGCTATGCTGTAAAT
66 CCTTGAGCTATGCTGTAAAT
* * * * *
35130 TTGATATGCCCTTGAGCTGAATCTAATCAAACTCGAAGGTTTTTGTTGACAGATAGACCTTATCT
1 TTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
*
35195 CCTTGAGATATGCT
66 CCTTGAGCTATGCT
35209 TCGAAAAGTT
Statistics
Matches: 685, Mismatches: 65, Indels: 18
0.89 0.08 0.02
Matches are distributed among these distances:
83 1 0.00
84 237 0.35
85 295 0.43
86 73 0.11
87 79 0.12
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (85 bp):
TTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
CCTTGAGCTATGCTGTAAAT
Found at i:35053 original size:339 final size:339
Alignment explanation
Indices: 34378--35208 Score: 1229
Period size: 339 Copynumber: 2.4 Consensus size: 339
34368 ATAGGCCCTC
34378 GAGCTAAATAGAATCGAACTCGAAGGTGTTTGTTGACAGATAGCCCTTCTTC-CCTTGAGCTATG
1 GAGCTAAAT-GAATCGAACTCGAAGGT-TTTGTTGACAGATAGCCCTTC-TCGCCTTGAGCTATG
* * *
34442 CTATAAATTTGATAAGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGC
63 CTGTAAATTTGATATGCCCTTGAGCTGAATGCAATCGAACTCGAAGGTTTTTGTTGACAGATAGC
*
34507 CCTTCTTGCCTTGAGCTATGCTGTAAATTTGATATACCCTTGAGCTGAATGTAATCGAACTCGAA
128 CCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATACCCTTGAGCTGAATGTAATCGAACTCGAA
* * *
34572 GGTTTTTTTGTTGACAAATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGA
193 GGTTTTTATGCTGACAAATAACCCTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCCTTGA
* * * *
34637 GTTGAATGTAATCGAACTTGAAGGTTTTCGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTA
258 GCTGAATGTAATCGAACTCGAAGGTTTTCATTGACAGATAGCCCTTCTCGCATTGAGCTATGCTA
*
34702 TAAACTTGATATGACTT
323 GAAACTTGATATGACTT
* *
34719 GAGCTAAATGCAATCGAACTTGAAGGTTTTCGTTGACATATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTAAATG-AATCGAACTCGAAGGTTTT-GTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* * * * * *
34784 TGTAAACTTGATATG-ACTTGAGCTAAATGCAATCGAACTTGAAGGTTTTCGTTGACATATAGCC
64 TGTAAATTTGATATGCCCTTGAGCTGAATGCAATCGAACTCGAAGGTTTTTGTTGACAGATAGCC
* * * *
34848 CTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCTCTTGAGTTGAATGTAATCGAACTTGAAG
129 CTTCTCGCCTTGAGCTATGCTGTAAATTTGATATACCCTTGAGCTGAATGTAATCGAACTCGAAG
* * *
34913 G-TTTTATGCTGACAGATAACCCTTCTCGCCTTGAGCTATGTTATAAATTTGATATGCCTTTGAG
194 GTTTTTATGCTGACAAATAACCCTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCCTTGAG
* * *
34977 CTGAATGTAATTGAACTCGATGGTTTTCATTGACAGATAGCCCTTCTCTCATTGAGCTATGCTAG
259 CTGAATGTAATCGAACTCGAAGGTTTTCATTGACAGATAGCCCTTCTCGCATTGAGCTATGCTAG
*
35042 AAATTTGATATGACTT
324 AAACTTGATATGACTT
*
35058 GAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTAAATG-AATCGAACTCGAAGG-TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* *
35123 TGTAAATTTGATATGCCCTTGAGCTGAAT-CTAATCAAACTCGAAGGTTTTTGTTGACAGATAGA
64 TGTAAATTTGATATGCCCTTGAGCTGAATGC-AATCGAACTCGAAGGTTTTTGTTGACAGATAGC
* * *
35187 CCTTATCTCCTTGAGATATGCT
128 CCTTCTCGCCTTGAGCTATGCT
35209 TCGAAAAGTT
Statistics
Matches: 438, Mismatches: 46, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
339 200 0.46
340 172 0.39
341 66 0.15
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (339 bp):
GAGCTAAATGAATCGAACTCGAAGGTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTG
TAAATTTGATATGCCCTTGAGCTGAATGCAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCT
TCTCGCCTTGAGCTATGCTGTAAATTTGATATACCCTTGAGCTGAATGTAATCGAACTCGAAGGT
TTTTATGCTGACAAATAACCCTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCCTTGAGCT
GAATGTAATCGAACTCGAAGGTTTTCATTGACAGATAGCCCTTCTCGCATTGAGCTATGCTAGAA
ACTTGATATGACTT
Found at i:35677 original size:16 final size:16
Alignment explanation
Indices: 35656--35700 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
35646 ACTCTAAAAT
35656 TGCAAAAAATTATGTA
1 TGCAAAAAATTATGTA
35672 TGCAAAAAATTATGTA
1 TGCAAAAAATTATGTA
*
35688 TGCGAAAAATTAT
1 TGCAAAAAATTAT
35701 AAATGTGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (16 bp):
TGCAAAAAATTATGTA
Found at i:36988 original size:13 final size:13
Alignment explanation
Indices: 36972--37007 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
36962 TAAGATTTTC
36972 TTTTTGAAAATCA
1 TTTTTGAAAATCA
36985 TTTTTG-AAATCA
1 TTTTTGAAAATCA
36997 TTTTTGAAAAT
1 TTTTTGAAAAT
37008 TACTCCCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:38863 original size:20 final size:19
Alignment explanation
Indices: 38838--38879 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
38828 TATAGTTTTC
*
38838 AAAACAACATAATTAAATCA
1 AAAACAACA-AATTAAAACA
*
38858 AAAACAACAATTTAAAACA
1 AAAACAACAAATTAAAACA
38877 AAA
1 AAA
38880 CATTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAACAACAAATTAAAACA
Found at i:39332 original size:21 final size:22
Alignment explanation
Indices: 39288--39338 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
39278 CTAGGGGTAC
39288 CGATACACATTCAAGGAATGTAT
1 CGATACACATTCAAGG-ATGTAT
*
39311 CGGTACACATTCAAGG-TGTAT
1 CGATACACATTCAAGGATGTAT
39332 CGATACA
1 CGATACA
39339 TAACAGGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 11 0.42
23 15 0.58
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (22 bp):
CGATACACATTCAAGGATGTAT
Found at i:41372 original size:12 final size:12
Alignment explanation
Indices: 41355--41379 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41345 ATGATGGTTC
41355 TCCAACGTCATG
1 TCCAACGTCATG
41367 TCCAACGTCATG
1 TCCAACGTCATG
41379 T
1 T
41380 GTATTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCAACGTCATG
Found at i:46262 original size:99 final size:99
Alignment explanation
Indices: 46090--46275 Score: 311
Period size: 99 Copynumber: 1.9 Consensus size: 99
46080 TTTTAATTTT
46090 CCTTTATCAGGCTAGCTGAATCTTATCCATAAAGATGGGGCGTTTAACCAATTGCTCTAGAGGGA
1 CCTTTATCAGGCTAGCTGAATCTTATCCATAAAGATGGGGCGTTTAACCAATTGCTCTAGAGGGA
*
46155 CAGCTCAAGGTTTATTGTATATGTATTATAATCA
66 CAGCTCAAGCTTTATTGTATATGTATTATAATCA
* * *
46189 CCTTTATCAGGCTAGCTTAATCTTATCCATAAAG-TCGGGGCGTTTAATCAATTGCTCTAGAGTG
1 CCTTTATCAGGCTAGCTGAATCTTATCCATAAAGAT-GGGGCGTTTAACCAATTGCTCTAGAGGG
*
46253 ACAGTTCAAGCTTTATTGTATAT
65 ACAGCTCAAGCTTTATTGTATAT
46276 ATATATGATT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 1 0.01
99 80 0.99
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (99 bp):
CCTTTATCAGGCTAGCTGAATCTTATCCATAAAGATGGGGCGTTTAACCAATTGCTCTAGAGGGA
CAGCTCAAGCTTTATTGTATATGTATTATAATCA
Found at i:50782 original size:17 final size:16
Alignment explanation
Indices: 50762--50804 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
50752 ATAAAAATTA
*
50762 TTAAATTAAAATGTGAC
1 TTAAATTAAAAAG-GAC
*
50779 TTAAATAAAAAAGGAC
1 TTAAATTAAAAAGGAC
50795 -TAAATTAAAA
1 TTAAATTAAAA
50805 GAAAGATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 9 0.39
16 3 0.13
17 11 0.48
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (16 bp):
TTAAATTAAAAAGGAC
Found at i:51861 original size:22 final size:22
Alignment explanation
Indices: 51835--51876 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
51825 ATATGTATGT
51835 TATAAAAAATACAT-TTATATTA
1 TATAAAAAA-ACATATTATATTA
*
51857 TATAAAATAACATATTATAT
1 TATAAAAAAACATATTATAT
51877 AATTGGGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
TATAAAAAAACATATTATATTA
Found at i:51863 original size:20 final size:22
Alignment explanation
Indices: 51825--51876 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
51815 AATATACGTA
*
51825 ATATGTATGTTATAAAAAAT-AC
1 ATAT-TATATTATAAAAAATAAC
*
51847 AT-TTATATTATATAAAATAAC
1 ATATTATATTATAAAAAATAAC
51868 ATATTATAT
1 ATATTATAT
51877 AATTGGGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 13 0.50
21 5 0.19
22 8 0.31
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (22 bp):
ATATTATATTATAAAAAATAAC
Found at i:52875 original size:12 final size:11
Alignment explanation
Indices: 52855--52886 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
52845 TTTTTTATAT
52855 TTGCATTCACA
1 TTGCATTCACA
52866 TTGACATTCACA
1 TTG-CATTCACA
52878 TTGCATTCA
1 TTGCATTCA
52887 ATTATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.38
Consensus pattern (11 bp):
TTGCATTCACA
Found at i:54646 original size:19 final size:19
Alignment explanation
Indices: 54624--54673 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
54614 ACCTAACTCA
* *
54624 TTGACTTTGACCTGACCCG
1 TTGACTTTGACCCGACCAG
*
54643 TTGA-TTATGACCCGACTAG
1 TTGACTT-TGACCCGACCAG
54662 TTGACTTTGACC
1 TTGACTTTGACC
54674 AAAGTTGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 22 0.85
20 2 0.08
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (19 bp):
TTGACTTTGACCCGACCAG
Done.