Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006215.1 Hibiscus syriacus cultivar Beakdansim tig00014806_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: 67851
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9606 original size:23 final size:21
Alignment explanation
Indices: 9574--9623 Score: 55
Period size: 25 Copynumber: 2.2 Consensus size: 21
9564 TTTATTTAAT
9574 ATTAATATATTTTAAATTTTAAATA
1 ATTAATATA--TTAAA-TTTAAA-A
*
9599 ATTAATATATTACATTTAAAA
1 ATTAATATATTAAATTTAAAA
9620 ATTA
1 ATTA
9624 TAGATGTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 6 0.25
23 4 0.17
25 9 0.38
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAATATATTAAATTTAAAA
Found at i:12190 original size:21 final size:20
Alignment explanation
Indices: 12164--12244 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 20
12154 AGTCAAGGGT
12164 TTATGTGGTC-CTTCGGGACAA
1 TTATGTGG-CACTTCGGGA-AA
*
12185 TTATGTGGCACTACGGTGTAAA
1 TTATGTGGCACTTCGG-G-AAA
**
12207 TCTATGTGGTC-CTTTAGGATAA
1 T-TATGTGG-CACTTCGGGA-AA
12229 TTATGTGGCACTTCGG
1 TTATGTGGCACTTCGG
12245 TGCAAATTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
20 2 0.04
21 25 0.53
22 8 0.17
23 11 0.23
24 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (20 bp):
TTATGTGGCACTTCGGGAAA
Found at i:12217 original size:44 final size:44
Alignment explanation
Indices: 12165--12251 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
12155 GTCAAGGGTT
* *
12165 TATGTGGTCCTTCGGGACAATTATGTGGCACTACGGTGTAAATC
1 TATGTGGTCCTTCAGGACAATTATGTGGCACTACGGTGCAAATC
* * *
12209 TATGTGGTCCTTTAGGATAATTATGTGGCACTTCGGTGCAAAT
1 TATGTGGTCCTTCAGGACAATTATGTGGCACTACGGTGCAAAT
12252 TACGAGTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.34
Consensus pattern (44 bp):
TATGTGGTCCTTCAGGACAATTATGTGGCACTACGGTGCAAATC
Found at i:17340 original size:20 final size:21
Alignment explanation
Indices: 17303--17342 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17293 ACTGCAGGAA
*
17303 TTTATGGCCTCGACAAAAGAT
1 TTTATGGCCTCGAAAAAAGAT
*
17324 TTTATGGCTTC-AAAAAAGA
1 TTTATGGCCTCGAAAAAAGA
17343 CCTTGATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TTTATGGCCTCGAAAAAAGAT
Found at i:23489 original size:21 final size:21
Alignment explanation
Indices: 23463--23506 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
23453 CAATTAAGAA
* *
23463 TCAAGGAGCTTTACTTCATAG
1 TCAAGGAGCCTTACTTCAAAG
*
23484 TCAAGGCGCCTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
23505 TC
1 TC
23507 CTAGCTCGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (21 bp):
TCAAGGAGCCTTACTTCAAAG
Found at i:28062 original size:20 final size:20
Alignment explanation
Indices: 28039--28083 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
28029 TTAACTTTTT
*
28039 CTTTTCTCTTTC-TTCCTTAA
1 CTTTTCTATTTCATT-CTTAA
*
28059 CTTTTCTATTTCATTTTTAA
1 CTTTTCTATTTCATTCTTAA
28079 CTTTT
1 CTTTT
28084 ACTTTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTCTATTTCATTCTTAA
Found at i:32905 original size:23 final size:23
Alignment explanation
Indices: 32878--32939 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
32868 ATTTTATATG
32878 GCACTTCGGTGCATTTCTACGCA
1 GCACTTCGGTGCATTTCTACGCA
* **
32901 GCACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCATTTCTACGCA
*
32924 GCACTTCAGTGCATTT
1 GCACTTCGGTGCATTT
32940 ATTCGAGCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCA
Found at i:37522 original size:23 final size:23
Alignment explanation
Indices: 37479--37522 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
37469 ATTTATCTTT
*
37479 TAAATTTTATAAAACATTATACA
1 TAAATTTTATAAAACAGTATACA
37502 TAAATTTTATTAAAA-AGTATA
1 TAAATTTTA-TAAAACAGTATA
37523 TATATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAATTTTATAAAACAGTATACA
Found at i:37940 original size:20 final size:20
Alignment explanation
Indices: 37917--37964 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
37907 GCAAGAACAA
* * *
37917 TATCGGTATTTTTCATGCAG
1 TATCGATATTGTTCATACAG
*
37937 TATCGATATTGTTCTTACAG
1 TATCGATATTGTTCATACAG
37957 TATCGATA
1 TATCGATA
37965 CTACTTACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.44
Consensus pattern (20 bp):
TATCGATATTGTTCATACAG
Found at i:39015 original size:2 final size:2
Alignment explanation
Indices: 39010--39049 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
39000 TAAAAAAGAA
39010 AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- 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
39050 TACCTTACCG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40051 original size:19 final size:19
Alignment explanation
Indices: 40027--40064 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40017 ACAGGTAACG
40027 TGATCAGCAGGACAAATAA
1 TGATCAGCAGGACAAATAA
* *
40046 TGATCAGCGGGACACATAA
1 TGATCAGCAGGACAAATAA
40065 CGTTAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (19 bp):
TGATCAGCAGGACAAATAA
Found at i:45809 original size:38 final size:39
Alignment explanation
Indices: 45766--45843 Score: 149
Period size: 38 Copynumber: 2.0 Consensus size: 39
45756 TGACCGTCAG
45766 TATCTGTGTTTTTCCTTTGCTTTATGATAATGTA-TATT
1 TATCTGTGTTTTTCCTTTGCTTTATGATAATGTATTATT
45804 TATCTGTGTTTTTCCTTTGCTTTATGATAATGTATTATT
1 TATCTGTGTTTTTCCTTTGCTTTATGATAATGTATTATT
45843 T
1 T
45844 TTTCCTTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
38 34 0.87
39 5 0.13
ACGTcount: A:0.18, C:0.10, G:0.13, T:0.59
Consensus pattern (39 bp):
TATCTGTGTTTTTCCTTTGCTTTATGATAATGTATTATT
Found at i:46037 original size:21 final size:21
Alignment explanation
Indices: 46011--46108 Score: 69
Period size: 21 Copynumber: 4.7 Consensus size: 21
46001 ATCAGTTCCC
46011 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATGA
*
46032 AGAATCGCAATGCGA-TA-GTA
1 AGAATCGCAACGCGATTATG-A
** ** * *
46052 CA-AATTAACATTGCGATTTTTA
1 -AGAA-TCGCAACGCGATTATGA
*
46074 AGAATCGCAACGCGAATATGA
1 AGAATCGCAACGCGATTATGA
46095 A-AATCGCAACGCGA
1 AGAATCGCAACGCGA
46109 ACATATAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
19 1 0.02
20 18 0.31
21 35 0.60
22 4 0.07
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.21
Consensus pattern (21 bp):
AGAATCGCAACGCGATTATGA
Found at i:46182 original size:20 final size:20
Alignment explanation
Indices: 46076--46351 Score: 181
Period size: 20 Copynumber: 13.6 Consensus size: 20
46066 GATTTTTAAG
* * *
46076 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCTGTA
* *
46096 AATCGCAACGCG-AACATATAA
1 AATCGCAACGCGTATC-TGT-A
*
46117 AATCACAACGC-TATTCTG-A
1 AATCGCAACGCGTA-TCTGTA
* * *
46136 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGTATCTGT-A
* *
46158 AATCGTAATGCGTATCTGTA
1 AATCGCAACGCGTATCTGTA
* *
46178 AATCGCAACGAC-AATATGTAA
1 AATCGCAACG-CGTATCTGT-A
*
46199 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCTGTA
* *
46219 AATCGCAACGAGAATAC-GTA
1 AATCGCAACGCGTAT-CTGTA
*
46239 AATCGCAATGCGTATCTGTA
1 AATCGCAACGCGTATCTGTA
* *
46259 AATCGCAACGAGAATAC-GTA
1 AATCGCAACGCGTAT-CTGTA
* *
46279 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCTGTA
*
46299 AATCGCAACGAC-AATAC-GTAA
1 AATCGCAACG-CGTAT-CTGT-A
*
46320 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCTGTA
46340 AATCGCAACGCG
1 AATCGCAACGCG
46352 ATTTTTAAAG
Statistics
Matches: 199, Mismatches: 37, Indels: 40
0.72 0.13 0.14
Matches are distributed among these distances:
19 4 0.02
20 129 0.65
21 64 0.32
22 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCTGTA
Found at i:46253 original size:40 final size:41
Alignment explanation
Indices: 46138--46349 Score: 320
Period size: 41 Copynumber: 5.2 Consensus size: 41
46128 TATTCTGACT
* * * *
46138 ATCGCAACGAGTATCCGTAAAATCGTAATGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAATGCGTATCCGTAA
* * *
46179 ATCGCAACGACAATATGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAATGCGTATCCGTAA
*
46220 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAATGCGTATCCGTAA
46260 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAATGCGTATCCGTAA
* *
46300 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAATGCGTATCCGTAA
46341 ATCGCAACG
1 ATCGCAACG
46350 CGATTTTTAA
Statistics
Matches: 156, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 76 0.49
41 80 0.51
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAATGCGTATCCGTAA
Found at i:46971 original size:21 final size:21
Alignment explanation
Indices: 46910--46988 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
46900 TTCTAAACTT
46910 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
46930 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
46950 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
46971 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
46989 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:47006 original size:33 final size:33
Alignment explanation
Indices: 46965--47048 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
46955 CGCAACGAGA
*
46965 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCACAACGC
*
46998 GAAATGAAAATCGCAACGAGATAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCACAACGC
**
47031 GAAACCAAAATCGCAACG
1 GAAATGAAAATCGCAACG
47049 CGATTTTCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAACGC
Found at i:47063 original size:19 final size:19
Alignment explanation
Indices: 47041--47082 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
47031 GAAACCAAAA
47041 TCGCAACGCGATTTTCATT
1 TCGCAACGCGATTTTCATT
***
47060 TCGCGTTGCGATTTTCATT
1 TCGCAACGCGATTTTCATT
47079 TCGC
1 TCGC
47083 GTTGCGATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.40
Consensus pattern (19 bp):
TCGCAACGCGATTTTCATT
Found at i:47136 original size:20 final size:19
Alignment explanation
Indices: 47048--47139 Score: 112
Period size: 19 Copynumber: 4.7 Consensus size: 19
47038 AAATCGCAAC
47048 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
47067 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
**
47086 GCGATAGTCATTTCTGCGTT
1 GCGATTTTCATTTC-GCGTT
** *
47106 GCGATAGTCATTCTCTCGTT
1 GCGATTTTCATT-TCGCGTT
*
47126 GCAATTTTCATTTC
1 GCGATTTTCATTTC
47140 AACCAAAAGA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 33 0.51
20 30 0.46
21 2 0.03
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:48996 original size:94 final size:94
Alignment explanation
Indices: 48835--49214 Score: 647
Period size: 94 Copynumber: 4.1 Consensus size: 94
48825 TAGATTGCTT
* * * * *
48835 AGTAAATTTATTCAGTTGTTGCCAATACTGCTAAACTGTTTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
48900 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
48929 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
48994 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
49023 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
49088 ATTTGTCGTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
49117 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
49182 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
49210 AGTAA
1 AGTAA
49215 TGCAATCCAT
Statistics
Matches: 275, Mismatches: 10, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
93 26 0.09
94 249 0.91
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:49390 original size:19 final size:19
Alignment explanation
Indices: 49270--49399 Score: 122
Period size: 19 Copynumber: 6.8 Consensus size: 19
49260 TTTCGTAACA
49270 CGAAACTTAAAATCGCAACG
1 CGAAAC-TAAAATCGCAACG
* * **
49290 TGAAAAATGACTATCGCAACG
1 CG-AAACT-AAAATCGCAACG
*
49311 CGAAA-T-GAATCGCAACG
1 CGAAACTAAAATCGCAACG
*
49328 AGAAA-TGAAAATCGCAACG
1 CGAAACT-AAAATCGCAACG
*
49347 CGAAACCAAAATCGCAACG
1 CGAAACTAAAATCGCAACG
*
49366 CGAAACTATAATCGCAACG
1 CGAAACTAAAATCGCAACG
*
49385 CGAAACTATAATCGC
1 CGAAACTAAAATCGC
49400 GTTACGATTT
Statistics
Matches: 92, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
17 14 0.15
19 59 0.64
20 5 0.05
21 14 0.15
ACGTcount: A:0.45, C:0.24, G:0.18, T:0.14
Consensus pattern (19 bp):
CGAAACTAAAATCGCAACG
Found at i:49461 original size:20 final size:20
Alignment explanation
Indices: 49432--49520 Score: 133
Period size: 20 Copynumber: 4.5 Consensus size: 20
49422 GCGATTCTCT
* **
49432 CATTGTGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
49452 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
49472 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
49492 TATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
49512 CGTTGCGAT
1 CATTGCGAT
49521 TTTAAGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:50095 original size:21 final size:21
Alignment explanation
Indices: 50004--50108 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
49994 AACTCACCTG
*
50004 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
50026 T-ATCATTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
50046 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
50067 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
50088 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
50109 CCAACATTCT
Statistics
Matches: 62, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
20 3 0.05
21 58 0.94
22 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:50101 original size:42 final size:42
Alignment explanation
Indices: 50031--50111 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
50021 TCCCCTATCA
*
50031 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCG
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCACCG
* ** *
50073 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
50112 ACATTCTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.21
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACCG
Found at i:51473 original size:14 final size:14
Alignment explanation
Indices: 51454--51489 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
51444 ATTGTTTAAT
51454 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
51468 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
51482 TGATTTGT
1 TGATTTGT
51490 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:51628 original size:33 final size:34
Alignment explanation
Indices: 51591--51666 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
51581 AAAACAGACT
51591 ATCGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
*
51624 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
51658 ATCGCAACG
1 ATCGCAACG
51667 CGAAACTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 24 0.59
34 17 0.41
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:51662 original size:20 final size:19
Alignment explanation
Indices: 51604--51671 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
51594 GCAACGAGAG
51604 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
51623 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
51637 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
51657 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
51672 CTAATTTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.08
19 11 0.28
20 11 0.28
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:51738 original size:33 final size:34
Alignment explanation
Indices: 51681--51759 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 34
51671 ACTAATTTCG
51681 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
51715 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
51748 CGTTGCGATTTT
1 CGTTGCGATTTT
51760 ATACAGTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 30 0.68
34 14 0.32
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:53376 original size:20 final size:20
Alignment explanation
Indices: 53351--53499 Score: 172
Period size: 20 Copynumber: 7.3 Consensus size: 20
53341 CAAAATCGCA
* *
53351 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACTCG
* *
53371 TTGCGATTTACAGATACGCG
1 TTGCGATTTACGGATACTCG
* *
53391 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACTCG
* *
53411 TTGTGATTTACGGATACGCG
1 TTGCGATTTACGGATACTCG
* **
53431 TTGCGATTTTACGTATTGTCG
1 TTGCGA-TTTACGGATACTCG
*
53452 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACTCG
53472 TTGCGATTTTACGGATACTCG
1 TTGCGA-TTTACGGATACTCG
53493 TTGCGAT
1 TTGCGAT
53500 AGTCAGAATC
Statistics
Matches: 105, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
20 70 0.67
21 35 0.33
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGGATACTCG
Found at i:53395 original size:40 final size:40
Alignment explanation
Indices: 53351--53560 Score: 235
Period size: 40 Copynumber: 5.2 Consensus size: 40
53341 CAAAATCGCA
53351 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
* *
53391 TTGCGATTTACGTATTCTCGTTGTGATTTACGGATACGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
* *
53431 TTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCG
1 TTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATACGCG
* * * *
53472 TTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCACG
1 TTGCGA-TTTACGTATTCTCGTTGCGAT-TTACAGATA-CGCG
** * * * * *
53513 TTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
53553 TTGCGATT
1 TTGCGATT
53561 CTGGAAAACC
Statistics
Matches: 145, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 74 0.51
41 69 0.48
42 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
Found at i:53454 original size:41 final size:40
Alignment explanation
Indices: 53351--53499 Score: 235
Period size: 41 Copynumber: 3.7 Consensus size: 40
53341 CAAAATCGCA
*
53351 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
*
53391 TTGCGATTTACGTATTCTCGTTGTGATTTACGGATACGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
*
53431 TTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCG
1 TTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCG
* *
53472 TTGCGATTTTACGGATACTCGTTGCGAT
1 TTGCGA-TTTACGTATTCTCGTTGCGAT
53500 AGTCAGAATC
Statistics
Matches: 101, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 44 0.44
41 57 0.56
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
Found at i:53534 original size:20 final size:20
Alignment explanation
Indices: 53511--53560 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
53501 GTCAGAATCA
*
53511 CGTTGCGATTTAT-ATGTTCG
1 CGTTGCGATTT-TCATATTCG
53531 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTTCATATTCG
53551 CGTTGCGATT
1 CGTTGCGATT
53561 CTGGAAAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATATTCG
Found at i:53535 original size:81 final size:81
Alignment explanation
Indices: 53351--53560 Score: 212
Period size: 81 Copynumber: 2.6 Consensus size: 81
53341 CAAAATCGCA
** * * * * *
53351 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGT
1 TTGCGATTTATATGTTCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATACTCGTTGC
* * *
53415 GATTTACGGATACGCG
66 GATTCACGAATACACG
* * *
53431 TTGCGATTT-TACGTATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTT
1 TTGCGATTTATATGT-TCG-CGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATACTCGTT
53495 GCGATAGTCA-GAAT-CACG
64 GCGAT--TCACGAATACACG
* * *
53513 TTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TTGCGATTTATATGTTCGCGTTGCGATTTACAGATACGCGTTGCGATT
53561 CTGGAAAACC
Statistics
Matches: 105, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
79 1 0.01
80 10 0.10
81 53 0.50
82 32 0.30
83 7 0.07
84 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (81 bp):
TTGCGATTTATATGTTCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATACTCGTTGC
GATTCACGAATACACG
Found at i:55747 original size:22 final size:21
Alignment explanation
Indices: 55720--55761 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
55710 ATTTATTAAG
55720 AATAATAGTTTATAAACTATTA
1 AATAATAGTTTA-AAACTATTA
* *
55742 AATAATATTTTAAAATTATT
1 AATAATAGTTTAAAACTATT
55762 TTTTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
AATAATAGTTTAAAACTATTA
Found at i:58315 original size:21 final size:21
Alignment explanation
Indices: 58289--58329 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
58279 TTTGAATTTA
* *
58289 ATGAAGGTGTATCGATACCCT
1 ATGAAGGGGTACCGATACCCT
58310 ATGAAGGGGTACCGATACCC
1 ATGAAGGGGTACCGATACCC
58330 CATGTTATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (21 bp):
ATGAAGGGGTACCGATACCCT
Found at i:58595 original size:20 final size:20
Alignment explanation
Indices: 58556--58594 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
58546 CCAACAATTG
58556 GTAACAATTGGTATCCTTTT
1 GTAACAATTGGTATCCTTTT
58576 GTAACAATTGGTAT-CTTTT
1 GTAACAATTGGTATCCTTTT
58595 TCATTAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (20 bp):
GTAACAATTGGTATCCTTTT
Found at i:59036 original size:19 final size:19
Alignment explanation
Indices: 59012--59058 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
59002 TTTGAATTTA
59012 ATGAAGGTA-TCGATACCCT
1 ATGAAGGTACT-GATACCCT
59031 ATGAAGGGGTACTGATACCCT
1 ATGAA--GGTACTGATACCCT
59052 ATGAAGG
1 ATGAAGG
59059 GGTACCGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.28
21 17 0.68
22 1 0.04
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (19 bp):
ATGAAGGTACTGATACCCT
Found at i:59047 original size:21 final size:21
Alignment explanation
Indices: 59017--59071 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
59007 ATTTAATGAA
*
59017 GGTATCGATACCCTATGAAGG
1 GGTACCGATACCCTATGAAGG
*
59038 GGTACTGATACCCTATGAAGG
1 GGTACCGATACCCTATGAAGG
59059 GGTACCGATACCC
1 GGTACCGATACCC
59072 AATGTTATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (21 bp):
GGTACCGATACCCTATGAAGG
Found at i:60948 original size:19 final size:19
Alignment explanation
Indices: 60924--60972 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
60914 AAAGATGGAT
60924 TGATTTTGAAAGGAAAAGA
1 TGATTTTGAAAGGAAAAGA
*
60943 TGATTTTGAAAGGAAAAGT
1 TGATTTTGAAAGGAAAAGA
60962 TGATTTTGAAA
1 TGATTTTGAAA
60973 ATCAAAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (19 bp):
TGATTTTGAAAGGAAAAGA
Found at i:62103 original size:20 final size:20
Alignment explanation
Indices: 62080--62124 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
62070 TTTTCATATA
62080 TTTTCCAACAATTGGTATCC
1 TTTTCCAACAATTGGTATCC
** *
62100 TTTTGTAACAATTGGTATCT
1 TTTTCCAACAATTGGTATCC
62120 TTTTC
1 TTTTC
62125 ATTAAGCATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (20 bp):
TTTTCCAACAATTGGTATCC
Found at i:62500 original size:20 final size:19
Alignment explanation
Indices: 62441--62503 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
62431 AAGAGTACCG
62441 ATACCCCTATGAGTGTATCC
1 ATACCCCT-TGAGTGTATCC
*
62461 ATA-CAC-TG-GTGTA-CC
1 ATACCCCTTGAGTGTATCC
62476 GATACCCCTTGCAGTGTATCC
1 -ATACCCCTTG-AGTGTATCC
62497 ATACCCC
1 ATACCCC
62504 CTGGCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
15 2 0.06
16 8 0.23
17 4 0.11
18 2 0.06
19 2 0.06
20 15 0.43
21 2 0.06
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (19 bp):
ATACCCCTTGAGTGTATCC
Done.