Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007157.1 Hibiscus syriacus cultivar Beakdansim tig00018740_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: 86392
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:514 original size:2 final size:2
Alignment explanation
Indices: 507--531 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
497 GATTTTCTGA
507 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 A
532 GATTAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:613 original size:23 final size:22
Alignment explanation
Indices: 575--618 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
565 TTTTTTTTTC
575 TCTTAAAAATTGTATAAGTTCA
1 TCTTAAAAATTGTATAAGTTCA
*
597 TCTTCAAAAATTTTATAAGTTC
1 TCTT-AAAAATTGTATAAGTTC
619 TCTCCTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (22 bp):
TCTTAAAAATTGTATAAGTTCA
Found at i:4256 original size:17 final size:17
Alignment explanation
Indices: 4234--4285 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
4224 TAAAAAATTG
*
4234 AATATTTTTAATTAAAA
1 AATATTTATAATTAAAA
* *
4251 AATATTTACAATTAATAT
1 AATATTTATAATTAA-AA
4269 AATA-TTATAATTAAAA
1 AATATTTATAATTAAAA
4285 A
1 A
4286 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 2 0.07
17 22 0.76
18 5 0.17
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATTTATAATTAAAA
Found at i:8339 original size:10 final size:10
Alignment explanation
Indices: 8310--8376 Score: 89
Period size: 10 Copynumber: 6.4 Consensus size: 10
8300 TTTTTTTTTG
8310 TTATGTTCGT
1 TTATGTTCGT
8320 TTATTGTGTTCGT
1 TTA---TGTTCGT
8333 TTATGTTCGT
1 TTATGTTCGT
**
8343 TCGTGTTCGT
1 TTATGTTCGT
8353 TTATGTTCGT
1 TTATGTTCGT
8363 TTATGTTCGT
1 TTATGTTCGT
8373 TTAT
1 TTAT
8377 TTATTCAATG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
10 40 0.80
13 10 0.20
ACGTcount: A:0.09, C:0.10, G:0.21, T:0.60
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:8982 original size:16 final size:16
Alignment explanation
Indices: 8961--8993 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
8951 AAAAAAAATT
8961 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
8977 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
8993 T
1 T
8994 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:10572 original size:33 final size:33
Alignment explanation
Indices: 10535--10607 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
10525 ATAAAAATGA
* *
10535 ATCATACTAAAAAAATTAGGACTACAAAGACGG
1 ATCATACTAAAAAAATTAAGACTACAAAAACGG
*
10568 ATCATACTAAAAAAATTAAGACTATAAAAACGG
1 ATCATACTAAAAAAATTAAGACTACAAAAACGG
10601 ATCATAC
1 ATCATAC
10608 AAATGGTCCC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (33 bp):
ATCATACTAAAAAAATTAAGACTACAAAAACGG
Found at i:12147 original size:13 final size:13
Alignment explanation
Indices: 12129--12157 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12119 TTTCACTTCT
12129 AAATGCAAGGCCC
1 AAATGCAAGGCCC
12142 AAATGCAAGGCCC
1 AAATGCAAGGCCC
12155 AAA
1 AAA
12158 ATCGTCGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.28, G:0.21, T:0.07
Consensus pattern (13 bp):
AAATGCAAGGCCC
Found at i:16761 original size:38 final size:37
Alignment explanation
Indices: 16705--16776 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
16695 GTTTTCGATT
* *
16705 AACCCGATCCGAACATAATATATTCTTCATCTGATCCG
1 AACCCGATCCGAAAATAATATACT-TTCATCTGATCCG
*
16743 AACCCGA-CCTGAAAATAATATCCTTTCATCTGAT
1 AACCCGATCC-GAAAATAATATACTTTCATCTGAT
16777 TTAAACTCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 12 0.40
38 18 0.60
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.29
Consensus pattern (37 bp):
AACCCGATCCGAAAATAATATACTTTCATCTGATCCG
Found at i:26035 original size:19 final size:19
Alignment explanation
Indices: 25998--26105 Score: 144
Period size: 19 Copynumber: 5.5 Consensus size: 19
25988 AACACAGAAG
25998 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
26019 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
26038 TCAAATTTGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
26057 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
*
26077 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
*
26097 TCGAATTCG
1 TCAAATTCG
26106 TAATACGAAT
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
19 39 0.48
20 33 0.40
21 10 0.12
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:26143 original size:19 final size:20
Alignment explanation
Indices: 25779--26136 Score: 245
Period size: 20 Copynumber: 18.0 Consensus size: 20
25769 AAATGACCAA
* *
25779 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGAATTT
* * *
25799 CAATTTCGCAAC-CTAGTTT
1 CAAATTCGCAACACGAATTT
*
25818 CCAAATTCGCAACGCGAATTT
1 -CAAATTCGCAACACGAATTT
* *
25839 GTAAA-TCGCAACGCGAATTT
1 -CAAATTCGCAACACGAATTT
* *
25859 GTAAA-TCGCAACGCGAATTT
1 -CAAATTCGCAACACGAATTT
* *
25879 GTAAA-TCGCAACGCGAATTT
1 -CAAATTCGCAACACGAATTT
* *
25899 GTAAA-TCGCAACACTG-ATGT
1 -CAAATTCGCAACAC-GAATTT
* **
25919 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACACGAATTT
*
25939 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACACGAATTT
* **
25959 GTAAA-TCGCAACAC-ATAAGT
1 -CAAATTCGCAACACGA-ATTT
*
25979 CAAATTCGCAACACAGAA-GT
1 CAAATTCGCAACAC-GAATTT
25999 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
*
26020 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* *
26039 CAAATTTGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* *
26058 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
* *
26078 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
* * *
26098 CGAATTCGTAATACGAATTT
1 CAAATTCGCAACACGAATTT
*
26118 -AATTTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
26137 AATTTCGTAA
Statistics
Matches: 286, Mismatches: 40, Indels: 25
0.81 0.11 0.07
Matches are distributed among these distances:
19 60 0.21
20 199 0.70
21 26 0.09
22 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:26148 original size:19 final size:19
Alignment explanation
Indices: 26102--26148 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
26092 GATTTTCGAA
*
26102 TTCGTAATACGAATTTAAT
1 TTCGTAACACGAATTTAAT
*
26121 TTCGCAACACGAATTTAAT
1 TTCGTAACACGAATTTAAT
26140 TTCGTAACA
1 TTCGTAACA
26149 GGTTTTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (19 bp):
TTCGTAACACGAATTTAAT
Found at i:27112 original size:24 final size:24
Alignment explanation
Indices: 27085--27138 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
27075 GTATTCGAAA
**
27085 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTCATCAATACCCGGAC
* *
27109 TTTGATCTTCATCAATACTCGGAT
1 TTTGATCTTCATCAATACCCGGAC
27133 TTTGAT
1 TTTGAT
27139 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATCTTCATCAATACCCGGAC
Found at i:29426 original size:18 final size:18
Alignment explanation
Indices: 29403--29438 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29393 AAGCAAAAGG
*
29403 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
29421 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
29439 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:29886 original size:64 final size:66
Alignment explanation
Indices: 29731--29874 Score: 238
Period size: 66 Copynumber: 2.2 Consensus size: 66
29721 AATTTAAAAC
* *
29731 AACAAATCAACTTTTACAAATCAATTAAACAAGCAATAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATAAATTAAACAAACAATAAAATAATTCTTATTTACACATCAAATT
29796 A
66 A
* *
29797 AACAAATCAACTTTTACAAATAAATTAAACAAACAA-AAAATAATTCTTATTTCCTCATC-AATT
1 AACAAATCAACTTTTACAAATAAATTAAACAAACAATAAAATAATTCTTATTTACACATCAAATT
29860 A
66 A
29861 AACAAATCAACTTT
1 AACAAATCAACTTT
29875 CAATGTAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
64 19 0.26
65 21 0.28
66 34 0.46
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (66 bp):
AACAAATCAACTTTTACAAATAAATTAAACAAACAATAAAATAATTCTTATTTACACATCAAATT
A
Found at i:31281 original size:21 final size:20
Alignment explanation
Indices: 31257--31328 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
31247 GATTGACCCA
* *
31257 TTGAACGATGACTATGGCCTC
1 TTGAACGATGA-GAAGGCCTC
* * *
31278 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGAGA-AGGCCTC
31299 TTGAACGATGAGAAGAGCCTC
1 TTGAACGATGAGAAG-GCCTC
31320 TTGAACGAT
1 TTGAACGAT
31329 AGGAGATGCC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.05
21 40 0.95
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (20 bp):
TTGAACGATGAGAAGGCCTC
Found at i:31303 original size:42 final size:42
Alignment explanation
Indices: 31233--31326 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 42
31223 GTGAATCGGG
** * *
31233 CTCTTGAACGGTGGGATTGACCCATTGAACGATGACTATG-GC
1 CTCTTGAACGGTGGGAGGGACCCATTGAACGATGA-GAAGAGC
*
31275 CTCTTGAACGGTGGGAGGGGCCTC-TTGAACGATGAGAAGAGC
1 CTCTTGAACGGTGGGAGGGACC-CATTGAACGATGAGAAGAGC
31317 CTCTTGAACG
1 CTCTTGAACG
31327 ATAGGAGATG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
41 2 0.04
42 42 0.93
43 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCCATTGAACGATGAGAAGAGC
Found at i:31339 original size:21 final size:20
Alignment explanation
Indices: 31273--31346 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
31263 GATGACTATG
* * *
31273 GCCTCTTGAACGGTGGGAGGG
1 GCCTCTTGAACGATAGGA-GA
*
31294 GCCTCTTGAACGATGAGAAGA
1 GCCTCTTGAACGAT-AGGAGA
31315 GCCTCTTGAACGATAGGAGA
1 GCCTCTTGAACGATAGGAGA
*
31335 TGCCTATTGAAC
1 -GCCTCTTGAAC
31347 AATGACAAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 5 0.11
21 38 0.84
22 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (20 bp):
GCCTCTTGAACGATAGGAGA
Found at i:31345 original size:42 final size:42
Alignment explanation
Indices: 31256--31352 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
31246 GGATTGACCC
* * * * *
31256 ATTGAACGATGACTATGGCCTCTTGAACGGTGGGAGGGGCCT
1 ATTGAACGATGACGAAGGCCTCTTGAACGATAGGAGAGGCCT
* *
31298 CTTGAACGATGA-GAAGAGCCTCTTGAACGATAGGAGATGCCT
1 ATTGAACGATGACGAAG-GCCTCTTGAACGATAGGAGAGGCCT
*
31340 ATTGAACAATGAC
1 ATTGAACGATGAC
31353 AAGTGAATCA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 2 0.05
42 42 0.95
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.23
Consensus pattern (42 bp):
ATTGAACGATGACGAAGGCCTCTTGAACGATAGGAGAGGCCT
Found at i:33917 original size:22 final size:22
Alignment explanation
Indices: 33887--33937 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
33877 GATGGAGATA
* * *
33887 GACGAATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGAG
*
33909 GACGGATTTCGTCAGAGATGAG
1 GACGGATTTCGCCAGAGATGAG
33931 GACGGAT
1 GACGGAT
33938 GTCACCCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.39, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGAG
Found at i:34122 original size:20 final size:20
Alignment explanation
Indices: 34097--34368 Score: 229
Period size: 20 Copynumber: 13.6 Consensus size: 20
34087 TAAACGCGCT
34097 TTGCGAATTTGACTATTGCG
1 TTGCGAATTTGACTATTGCG
34117 TTGCGAATTTGACTATTGCG
1 TTGCGAATTTGACTATTGCG
34137 TTGCGAATTTGACTATTGCG
1 TTGCGAATTTGACTATTGCG
* *
34157 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATTGCG
* *
34177 TTGCGAATTTGA-AATTCAGTG
1 TTGCGAATTTGACTATT--GCG
* *
34198 TTGCGAATTTGACTATCGCT
1 TTGCGAATTTGACTATTGCG
* * *
34218 TTGCGATTTTGACTTTTGTG
1 TTGCGAATTTGACTATTGCG
*
34238 TTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC-TATT-GCG
* *
34258 CTGC-AATTT-ACAGATTTGCG
1 TTGCGAATTTGAC-TA-TTGCG
* *
34278 TTGCGAATTTGACT-TCAGTG
1 TTGCGAATTTGACTAT-TGCG
*
34298 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTATTGCG
* *
34318 TTGTGAATTTGACT-TATGTG
1 TTGCGAATTTGACTAT-TGCG
*
34338 TTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC-TATT-GCG
34358 TTGCGAATTTG
1 TTGCGAATTTG
34369 TTGGTCATTT
Statistics
Matches: 205, Mismatches: 30, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
18 4 0.02
19 14 0.07
20 156 0.76
21 27 0.13
22 4 0.02
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (20 bp):
TTGCGAATTTGACTATTGCG
Found at i:34200 original size:21 final size:21
Alignment explanation
Indices: 34156--34209 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
34146 TGACTATTGC
* **
34156 GTTGCGAATTTG-ACTTTTGT
1 GTTGCGAATTTGAAATTCAGT
34176 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAATTCAGT
34197 GTTGCGAATTTGA
1 GTTGCGAATTTGA
34210 CTATCGCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (21 bp):
GTTGCGAATTTGAAATTCAGT
Found at i:34341 original size:60 final size:60
Alignment explanation
Indices: 34097--34343 Score: 256
Period size: 60 Copynumber: 4.1 Consensus size: 60
34087 TAAACGCGCT
* *
34097 TTGCGAATTTGACTATTGCGTTGCGAATTTGACTATT-GCGTTGCGAATTTGACTATTGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTA-TGCG
* * *
34157 TTGCGAATTTGACTTTTGTGTTGCGAATTTGA-AATTCAGTGTTGCGAATTTGACTATCGCT
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATTC-GCGTTGCGAATTTGACTAT-GCG
* * * *
34218 TTGCGATTTTGACTTTTGTGTTGCG-ATTT-ACAGATTCGCGCTGC-AATTT-ACAGATTTGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGAC-TATTCGCGTTGCGAATTTGAC---TATGCG
** * *
34278 TTGCGAATTTGACTTCAGTGTTGCGAATTTGACTA-TCGCGTTGTGAATTTGACTTATGTG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATTCGCGTTGCGAATTTGAC-TATGCG
34338 TTGCGA
1 TTGCGA
34344 TTTACAGATT
Statistics
Matches: 155, Mismatches: 20, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
58 2 0.01
59 9 0.06
60 81 0.52
61 59 0.38
62 4 0.03
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (60 bp):
TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATTCGCGTTGCGAATTTGACTATGCG
Found at i:43640 original size:2 final size:2
Alignment explanation
Indices: 43633--43667 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
43623 AACCAGAATA
43633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43668 GATTTACCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46254 original size:97 final size:95
Alignment explanation
Indices: 46139--46320 Score: 301
Period size: 97 Copynumber: 1.9 Consensus size: 95
46129 CATGAATCTC
* *
46139 ATAAGAAATGAAGGCAATAAGATGTACATCAAGCAAATAGACTACGGATGAATCCATGAATGACA
1 ATAAGAAATGAAGGCAATAAGATGAACATCAAGCAAATAGAC-ACGGATGAATCCATGAATCACA
*
46204 GGCAAATGGATTATGGATGAACAAGACACCTG
65 GGCAAATGGA-CATGGATGAACAAGACACCTG
* *
46236 ATAAGAAATGAAGGCAATAAGATGAACATCAAGCAAATGGACATGGATGAATCCATGAATCACAG
1 ATAAGAAATGAAGGCAATAAGATGAACATCAAGCAAATAGACACGGATGAATCCATGAATCACAG
46301 GCAAATGGACATGGATGAAC
66 GCAAATGGACATGGATGAAC
46321 CCATGAATCA
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
95 10 0.12
96 30 0.38
97 40 0.50
ACGTcount: A:0.45, C:0.14, G:0.23, T:0.18
Consensus pattern (95 bp):
ATAAGAAATGAAGGCAATAAGATGAACATCAAGCAAATAGACACGGATGAATCCATGAATCACAG
GCAAATGGACATGGATGAACAAGACACCTG
Found at i:46305 original size:33 final size:33
Alignment explanation
Indices: 46268--46354 Score: 138
Period size: 33 Copynumber: 2.6 Consensus size: 33
46258 TGAACATCAA
*
46268 GCAAATGGACATGGATGAATCCATGAATCACAG
1 GCAAATGGACATGGATGAACCCATGAATCACAG
46301 GCAAATGGACATGGATGAACCCATGAATCACAG
1 GCAAATGGACATGGATGAACCCATGAATCACAG
* *
46334 ACAAATGGACTATGAATGAAC
1 GCAAATGGAC-ATGGATGAAC
46355 AAGACACCTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
33 41 0.82
34 9 0.18
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.17
Consensus pattern (33 bp):
GCAAATGGACATGGATGAACCCATGAATCACAG
Found at i:46341 original size:129 final size:130
Alignment explanation
Indices: 46171--46450 Score: 413
Period size: 129 Copynumber: 2.2 Consensus size: 130
46161 TGTACATCAA
* * * * * * *
46171 GCAAATAGACTACGGATGAATCCATGAATGACAGGCAAATGGATTATGGATGAACAAGACACCTG
1 GCAAATGGACTATGGATGAACCCATGAATCACAGACAAATGGACTATGAATGAACAAGACACCTG
* * *
46236 ATAAGAAATGAAGGCAATAAGATGAA-CATCAAGCAAATGGAC-ATGGATGAATCCATGAATCAC
66 ATAAGAAATGAAGGC-ATAAGAT-AAGCATCAAGCAAAAGGACTATGGACGAATCCATGAATAAC
46299 AG
129 AG
46301 GCAAATGGAC-ATGGATGAACCCATGAATCACAGACAAATGGACTATGAATGAACAAGACACCTG
1 GCAAATGGACTATGGATGAACCCATGAATCACAGACAAATGGACTATGAATGAACAAGACACCTG
*
46365 ATAAGAAATGAAGGCATAAGATAAGCATCAAGCAAAAGGGCTATGGACGAATCCATGAATAACAG
66 ATAAGAAATGAAGGCATAAGATAAGCATCAAGCAAAAGGACTATGGACGAATCCATGAATAACAG
*
46430 GCAAATGGACTATGAATGAAC
1 GCAAATGGACTATGGATGAAC
46451 AAGACATCTG
Statistics
Matches: 135, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
127 2 0.01
128 21 0.16
129 94 0.70
130 18 0.13
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (130 bp):
GCAAATGGACTATGGATGAACCCATGAATCACAGACAAATGGACTATGAATGAACAAGACACCTG
ATAAGAAATGAAGGCATAAGATAAGCATCAAGCAAAAGGACTATGGACGAATCCATGAATAACAG
Found at i:46536 original size:97 final size:97
Alignment explanation
Indices: 46311--46588 Score: 416
Period size: 97 Copynumber: 2.9 Consensus size: 97
46301 GCAAATGGAC
* * *
46311 ATGGATGAACCCATGAATCACAGACAAATGGACTATGAATGAACAAGACACCTGATAAGAAATGA
1 ATGGATGAATCCATGAATAACAGGCAAATGGACTATGAATGAACAAGACACCTGATAAGAAATGA
* ***
46376 AGGC-ATAAGAT-AAGCATCAAGCAAAAGGGCT
66 AGGCAATAACATGAA-CATCAAGCAAAAGAAAT
* * *
46407 ATGGACGAATCCATGAATAACAGGCAAATGGACTATGAATGAACAAGACATCTGATAAGAGATGA
1 ATGGATGAATCCATGAATAACAGGCAAATGGACTATGAATGAACAAGACACCTGATAAGAAATGA
*
46472 AGGCAATAACATGAACATCAAGCAAATGAAAT
66 AGGCAATAACATGAACATCAAGCAAAAGAAAT
*
46504 ATGGATGAATCCATGAATAACAGGCAAATGGACTATGGATGAACAAGACACCTGATAAGAAATGA
1 ATGGATGAATCCATGAATAACAGGCAAATGGACTATGAATGAACAAGACACCTGATAAGAAATGA
*
46569 AGACAATAACATGAACATCA
66 AGGCAATAACATGAACATCA
46589 GACCAGGTTC
Statistics
Matches: 164, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
96 63 0.38
97 99 0.60
98 2 0.01
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.17
Consensus pattern (97 bp):
ATGGATGAATCCATGAATAACAGGCAAATGGACTATGAATGAACAAGACACCTGATAAGAAATGA
AGGCAATAACATGAACATCAAGCAAAAGAAAT
Found at i:49683 original size:21 final size:21
Alignment explanation
Indices: 49657--49706 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
49647 CACTCTCGTT
49657 CTCTTCCTTCGGTGGTTCTGA
1 CTCTTCCTTCGGTGGTTCTGA
*
49678 CTCTTCCTTTGGTGGTTCTGA
1 CTCTTCCTTCGGTGGTTCTGA
49699 CTCTTCCT
1 CTCTTCCT
49707 CATTGGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.04, C:0.30, G:0.20, T:0.46
Consensus pattern (21 bp):
CTCTTCCTTCGGTGGTTCTGA
Found at i:64772 original size:25 final size:25
Alignment explanation
Indices: 64738--64785 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
64728 AATGATATCC
64738 CGACTTTAGCGTACTACTTTATTCT
1 CGACTTTAGCGTACTACTTTATTCT
64763 CGACTTTAGCGTACTACTTTATT
1 CGACTTTAGCGTACTACTTTATT
64786 AAGTCATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (25 bp):
CGACTTTAGCGTACTACTTTATTCT
Found at i:65888 original size:42 final size:42
Alignment explanation
Indices: 65829--65944 Score: 160
Period size: 42 Copynumber: 2.8 Consensus size: 42
65819 ATCAAATAAT
* *
65829 TCATCTATACAAGATCCGGGTGTTCGATGAAAGCACATAACA
1 TCATCTATACAAGATCCGGGTGTACGACGAAAGCACATAACA
* *
65871 TCATCTGTAGAAGATCCGGGTGTACGACGAAAGCACATAACA
1 TCATCTATACAAGATCCGGGTGTACGACGAAAGCACATAACA
* * * *
65913 TCATCTACAAAAGATACGGGTTTACGACGAAA
1 TCATCTATACAAGATCCGGGTGTACGACGAAA
65945 AGAACATATA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (42 bp):
TCATCTATACAAGATCCGGGTGTACGACGAAAGCACATAACA
Found at i:75655 original size:29 final size:29
Alignment explanation
Indices: 75613--75668 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
75603 TCTCTCTCTC
*
75613 TCTATTTTAATCACTGAAATTTT-AATTTT
1 TCTAATTTAATCACTG-AATTTTGAATTTT
*
75642 TCTAATTTACTCACTGAATTTTGAATT
1 TCTAATTTAATCACTGAATTTTGAATT
75669 ACTCTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.52
Consensus pattern (29 bp):
TCTAATTTAATCACTGAATTTTGAATTTT
Found at i:76733 original size:23 final size:22
Alignment explanation
Indices: 76707--76773 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 22
76697 AAAATAATTT
*
76707 CAGAATCGAAAAACACTGTTTAC
1 CAGAA-CGAAAAACTCTGTTTAC
* *
76730 CAGAACTGAAAAACTTTATTTAC
1 CAGAAC-GAAAAACTCTGTTTAC
76753 CAGAACCGAAAAACTCTGTTT
1 CAGAA-CGAAAAACTCTGTTT
76774 CTATATGGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (22 bp):
CAGAACGAAAAACTCTGTTTAC
Found at i:83287 original size:17 final size:18
Alignment explanation
Indices: 83261--83296 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
83251 ATTTATTAAA
83261 ATTTTAATTTTAATTTAG
1 ATTTTAATTTTAATTTAG
83279 ATTTT-ATTTTAATTTAG
1 ATTTTAATTTTAATTTAG
83296 A
1 A
83297 GTGAAATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
ATTTTAATTTTAATTTAG
Found at i:86331 original size:36 final size:36
Alignment explanation
Indices: 86257--86331 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
86247 TTTTTATATT
* *
86257 TTTAATTTTATAAAAAAAATTATATAATATTATGAA
1 TTTAATTTTATAAAAAAAATAATATAATATTATCAA
* * *
86293 TTTAATTTTTTAAAGAAAATAATA-AATATTTTACAA
1 TTTAATTTTATAAAAAAAATAATATAATATTAT-CAA
86329 TTT
1 TTT
86332 GTAATATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
35 7 0.21
36 26 0.79
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (36 bp):
TTTAATTTTATAAAAAAAATAATATAATATTATCAA
Done.