Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003005.1 Hibiscus syriacus cultivar Beakdansim tig00006222_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: 84685
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:3256 original size:25 final size:24
Alignment explanation
Indices: 3209--3256 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3199 AACCATATTG
*
3209 ATTAATTTAAATCATATTAAATTT
1 ATTAATTTAAATCATATAAAATTT
3233 ATTAATATTATAAT-ATATAAAATT
1 ATTAAT-TTA-AATCATATAAAATT
3257 AATATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 12 0.57
26 3 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTAATTTAAATCATATAAAATTT
Found at i:10423 original size:16 final size:17
Alignment explanation
Indices: 10399--10431 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10389 CGAGGTGTCA
10399 CATTGACTTTT-CAAAG
1 CATTGACTTTTACAAAG
*
10415 CATTTACTTTTACAAAG
1 CATTGACTTTTACAAAG
10432 TAACTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (17 bp):
CATTGACTTTTACAAAG
Found at i:14170 original size:14 final size:14
Alignment explanation
Indices: 14151--14180 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
14141 CCACCTTATT
14151 CCTCCTCTCCCCTC
1 CCTCCTCTCCCCTC
14165 CCTCCTCTCCCCTC
1 CCTCCTCTCCCCTC
14179 CC
1 CC
14181 CCATCATCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.73, G:0.00, T:0.27
Consensus pattern (14 bp):
CCTCCTCTCCCCTC
Found at i:17562 original size:31 final size:30
Alignment explanation
Indices: 17518--17608 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 30
17508 AAAGTTAAGG
*
17518 CCCAATTAAAACCTAAAAATTAATTTACGA
1 CCCAATAAAAACCTAAAAATTAATTTACGA
*
17548 CCCAATAACAAACCTAAATATTAATTTACGA
1 CCCAATAA-AAACCTAAAAATTAATTTACGA
17579 CCCAATAATAAACCTATTAAAATTAATTTA
1 CCCAATAA-AAACCTA--AAAATTAATTTA
17609 AAGAAATACA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
30 7 0.13
31 36 0.67
33 11 0.20
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (30 bp):
CCCAATAAAAACCTAAAAATTAATTTACGA
Found at i:19150 original size:23 final size:23
Alignment explanation
Indices: 19112--19155 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19102 ATTATGTTTA
* *
19112 ATTTAATCCTTATCTTTACAAAT
1 ATTTAATCCATATCTTCACAAAT
*
19135 ATTTAATCCATGTCTTCACAA
1 ATTTAATCCATATCTTCACAA
19156 TTTAAACATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTTAATCCATATCTTCACAAAT
Found at i:22168 original size:19 final size:18
Alignment explanation
Indices: 22133--22168 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22123 GGTATAGATC
22133 AAGAAAAAAAAAATAAAT
1 AAGAAAAAAAAAATAAAT
*
22151 AAGAAAATAAATAATAAA
1 AAGAAAA-AAAAAATAAA
22169 ACTATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (18 bp):
AAGAAAAAAAAAATAAAT
Found at i:23124 original size:2 final size:2
Alignment explanation
Indices: 23117--23153 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
23107 CAATTAGTAA
23117 AT 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 AT A
23154 CACACGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23995 original size:106 final size:106
Alignment explanation
Indices: 23642--24168 Score: 774
Period size: 106 Copynumber: 5.0 Consensus size: 106
23632 TGTTCTGAGT
* * * *
23642 CCAATATCCTTCGCTATGAAGTTGAAATTGGTTCTGGAAA-TGGGAAATTGTATATTGACAACCA
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAACTGGGAAATTGTTTGTTGACAACCA
* * *
23706 GTGGTCCCTTCGTCGTGAAG-TGAACTTGTGCTGTCTCGAGT
65 GTCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGC
* *
23747 CCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAACCAG
* * *
23812 CCGTCCCTTCGTTGTGAAGTTTGAACTTGTGTTGTCTCGAGT
66 TCGTCCCTTCGTCGTGAAG-TTGAACTTGTGTTGTCTCGAGC
* * *
23854 CCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTAAAACTGGGAAATTATTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAACCAG
* *
23919 TCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCGAGC
66 TCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGC
*
23960 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAACTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAACCAG
* * *
24025 -CGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGCCTCAAGC
66 TC-GTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGC
* * *
24066 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCA-
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAACCAG
24130 TCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCG
66 TC-GTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCG
24169 CTTCGAACTA
Statistics
Matches: 388, Mismatches: 29, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
104 4 0.01
105 72 0.19
106 214 0.55
107 98 0.25
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (106 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAACCAG
TCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGC
Found at i:24285 original size:37 final size:37
Alignment explanation
Indices: 24235--24340 Score: 169
Period size: 37 Copynumber: 2.9 Consensus size: 37
24225 TTGCTTCGAG
24235 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCCAAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCCAAA
*
24272 AGAAACTGTCTCAAGGGAGACAAAACTTAG-TTCCAAA
1 AGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCCAAA
* *
24309 AGAAACTATCTCAAGGGAGACAGAATTTGTTT
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTT
24341 TAAGGAAAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
36 3 0.05
37 57 0.90
38 3 0.05
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (37 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCCAAA
Found at i:24440 original size:90 final size:90
Alignment explanation
Indices: 24282--24455 Score: 262
Period size: 90 Copynumber: 1.9 Consensus size: 90
24272 AGAAACTGTC
* *
24282 TCAAGGGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGGAGACAGAATTTGTTTTAAGGA
1 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGGAGACAGAATTAGTTTTAAGGA
24347 AAACATATTCAAAGATTTTTTTGTT
66 AAACATATTCAAAGATTTTTTTGTT
* * *
24372 TCAAGAGAGACAAAACTTTGTTCTAAAAGAAACTGTCTCAAGGGAGAC-GAAATTAG-TTTAATG
1 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGGAGACAG-AATTAGTTTTAA-G
*
24435 TAAAACATATTCAAAGATTTT
64 GAAAACATATTCAAAGATTTT
24456 GTTTCAAGGG
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
89 6 0.08
90 70 0.92
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (90 bp):
TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGGAGACAGAATTAGTTTTAAGGA
AAACATATTCAAAGATTTTTTTGTT
Found at i:24480 original size:30 final size:30
Alignment explanation
Indices: 24444--24502 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
24434 GTAAAACATA
* *
24444 TTCAAAGATTT-TGTTTCAAGGGAAACTGTT
1 TTCAAAG-TTTATGTCTCAAGAGAAACTGTT
24474 TTCAAAGTTTATGTCTCAAGAGAAACTGT
1 TTCAAAGTTTATGTCTCAAGAGAAACTGT
24503 CTCAAGGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (30 bp):
TTCAAAGTTTATGTCTCAAGAGAAACTGTT
Found at i:24536 original size:36 final size:36
Alignment explanation
Indices: 24489--24656 Score: 129
Period size: 36 Copynumber: 4.8 Consensus size: 36
24479 AGTTTATGTC
* *
24489 TCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
* **
24525 TCAAGGGAAACTATCTCAAGAGAGACAAAATTCATT
1 TCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
* * *
24561 TCAAGGGAAA-TGTTTTC-A-A-TG-----TTTATGTT
1 TCAAGGGAAACTG-TCTCAAGAGAGACAAAATT-TGTT
* * *
24590 TCAAGAGAAAATGTCTCAAGGGAGACAAAATTTTGTT
1 TCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTT
* *
24627 TCAAGGGAAACTATCTCAAGAGAGAAAAAA
1 TCAAGGGAAACTGTCTCAAGAGAGACAAAA
24657 AAATTCATTT
Statistics
Matches: 99, Mismatches: 21, Indels: 23
0.69 0.15 0.16
Matches are distributed among these distances:
28 2 0.02
29 14 0.14
30 3 0.03
32 1 0.01
33 1 0.01
34 1 0.01
35 2 0.02
36 44 0.44
37 29 0.29
38 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.26
Consensus pattern (36 bp):
TCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
Found at i:24598 original size:101 final size:103
Alignment explanation
Indices: 24457--24749 Score: 466
Period size: 105 Copynumber: 2.8 Consensus size: 103
24447 AAAGATTTTG
* *
24457 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTCTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
24521 TGTTTCAAGGGAAACTATCTCAAGAGAG-ACAAAATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGAAAAAAATTCA
*
24559 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
24624 GTTTCAAGGGAAACTATCTCAAGAGAGAAAAAAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAG--AAAAAAATTCA
24664 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA--TT
*
24728 TCTGTTTCGAGGGAAACTATCT
64 T-TGTTTCAAGGGAAACTATCT
24750 TAAGCAAGAT
Statistics
Matches: 178, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
101 46 0.26
102 42 0.24
104 4 0.02
105 64 0.36
106 3 0.02
107 19 0.11
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (103 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGAAAAAAATTCA
Found at i:24644 original size:37 final size:37
Alignment explanation
Indices: 24586--24656 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
24576 TCAATGTTTA
* * *
24586 TGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAAATATCTCAAGAGAGAAAAAATTT
* *
24623 TGTTTCAAGGGAAACTATCTCAAGAGAGAAAAAA
1 TGTTTCAAGAGAAAATATCTCAAGAGAGAAAAAA
24657 AAATTCATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (37 bp):
TGTTTCAAGAGAAAATATCTCAAGAGAGAAAAAATTT
Found at i:26328 original size:183 final size:183
Alignment explanation
Indices: 26020--26373 Score: 636
Period size: 183 Copynumber: 1.9 Consensus size: 183
26010 ATCAGGTTTA
* *
26020 ACTGAAGGGTTCATCTCATCATAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
26085 GCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
26150 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
26203 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
26268 GCCAAGTGTCCGAGTAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
26333 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
26374 TGGATTTAAT
Statistics
Matches: 163, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 163 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:31885 original size:2 final size:2
Alignment explanation
Indices: 31830--31866 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
31820 CAATTAGTAA
31830 AT 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 AT A
31867 CGTTAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35393 original size:24 final size:24
Alignment explanation
Indices: 35366--35411 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
35356 AACGAGGATG
* *
35366 CAAGTTCAACTATGCCTTCTGATT
1 CAAGTTCAACTATACCCTCTGATT
35390 CAAGTTCAACTATACCCTCTGA
1 CAAGTTCAACTATACCCTCTGA
35412 CACGGTTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (24 bp):
CAAGTTCAACTATACCCTCTGATT
Found at i:39440 original size:33 final size:32
Alignment explanation
Indices: 39403--39465 Score: 74
Period size: 33 Copynumber: 1.9 Consensus size: 32
39393 TAAGTTATTA
39403 TTATCCTCTT-TTATCCATTGTATTTATTTCTCC
1 TTATCCTCTTATTATCC-TTGT-TTTATTTCTCC
* * *
39436 TTATCTTTTTATTATCCTTGTTTTTTTTCT
1 TTATCCTCTTATTATCCTTGTTTTATTTCT
39466 TGTCTTAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 8 0.31
33 12 0.46
34 6 0.23
ACGTcount: A:0.13, C:0.19, G:0.03, T:0.65
Consensus pattern (32 bp):
TTATCCTCTTATTATCCTTGTTTTATTTCTCC
Found at i:41418 original size:29 final size:29
Alignment explanation
Indices: 41363--41418 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
41353 AGAAACCTCG
* **
41363 ACTACACACCACACATAATGAGGCAAAGC
1 ACTACACACCACACATAAAGACACAAAGC
*
41392 ACTACACACCACACATAAAGCCACAAA
1 ACTACACACCACACATAAAGACACAAA
41419 ATCCATAGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.48, C:0.34, G:0.09, T:0.09
Consensus pattern (29 bp):
ACTACACACCACACATAAAGACACAAAGC
Found at i:43052 original size:41 final size:41
Alignment explanation
Indices: 42946--43052 Score: 119
Period size: 41 Copynumber: 2.6 Consensus size: 41
42936 AATATGTATG
* * *
42946 TACCTTAGCGGCGTTTTTTCGTAAACGCCATGATTGACCTG
1 TACCTTAGCGGCGTTTTTTCGTAAACGCCACGAATGACCTA
** *
42987 TAATTTAGCGGC-TCTTTTTCGTAAACGTCACGAATGACCTA
1 TACCTTAGCGGCGT-TTTTTCGTAAACGCCACGAATGACCTA
*
43028 TACCTTAGTGGCGTTTTATT-GTAAA
1 TACCTTAGCGGCGTTTT-TTCGTAAA
43053 TGCCGCAACT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
40 1 0.02
41 50 0.93
42 3 0.06
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (41 bp):
TACCTTAGCGGCGTTTTTTCGTAAACGCCACGAATGACCTA
Found at i:47937 original size:21 final size:21
Alignment explanation
Indices: 47912--47969 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
47902 TGGCCCACAA
*
47912 AATAATTATAATATATAA-ATT
1 AATAATAATAATA-ATAATATT
*
47933 AATAATGATAATAATAATATT
1 AATAATAATAATAATAATATT
47954 AATAATAATAAGTAAT
1 AATAATAATAA-TAAT
47970 TATTATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
AATAATAATAATAATAATATT
Found at i:47946 original size:3 final size:3
Alignment explanation
Indices: 47912--47979 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
47902 TGGCCCACAA
* * * *
47912 AAT AAT TAT AAT ATAT AA- ATT AAT AAT GAT AAT AAT AAT ATT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
47957 AAT AAT AAGT AAT TAT TAT AAT A
1 AAT AAT AA-T AAT AAT AAT AAT A
47980 TTTTTTTAAG
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 1 0.02
3 45 0.87
4 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:48404 original size:84 final size:84
Alignment explanation
Indices: 48286--48582 Score: 342
Period size: 84 Copynumber: 3.5 Consensus size: 84
48276 AGTCGACGGA
* * * * * * **
48286 TTTTATTGACATATAACCCTTCTTGCCTTGAGCTAAGCTGTAAATGATGTGCCTTTCAGCTGAGT
1 TTTTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGT
*
48351 GTAATCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * *
48370 TTTGGTTGACAGATAGCCCTTTTCGCCTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGT
1 TTTTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGT
* * *
48435 GTTGTCCAACTCGAAGATC
66 GTAGTCGAACTCGAAGGTC
** * * * * * * *
48454 TTTTGTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGAAAATGACGTGCCTTGGAGCTGAGC
1 TTTTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGT
48519 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * *
48538 TTTTGTTGGCAGATAGCCCTTCTCACCTTAAACTATGCTGCAAAT
1 TTTTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGCAAAT
48583 AAACACGATA
Statistics
Matches: 175, Mismatches: 38, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
84 175 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (84 bp):
TTTTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGT
GTAGTCGAACTCGAAGGTC
Found at i:48804 original size:123 final size:123
Alignment explanation
Indices: 48586--48822 Score: 368
Period size: 123 Copynumber: 1.9 Consensus size: 123
48576 TGCAAATAAA
* * * *
48586 CACGATATCCTTCATCGTGAAGTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGATCCTAGAA
1 CACGATATCCTTCATCGTGAAGTGAAACCGTGGATAGCCCATTCGTCGTGAAGTTGAGCCTAGAA
* *
48651 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATG-ATGTTATTGGTGAG
66 TTGGATATCCTTCATCGTGAACTTGAAATCCAATCTAAAGATGAATGTTATTGGTGAG
* * * *
48708 CACGATTTCCTTCATTGTGAAGTTGAAACCGTGGATAGCCCATTCGTTGTGAAGTTGAGCCTTGA
1 CACGATATCCTTCATCGTGAAG-TGAAACCGTGGATAGCCCATTCGTCGTGAAGTTGAGCCTAGA
48773 ATTGGATATCCTTCATCGTGAACTTGAAATCCAATCTAAAGATGAATGTT
65 ATTGGATATCCTTCATCGTGAACTTGAAATCCAATCTAAAGATGAATGTT
48823 GCTTCGAGTC
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
122 20 0.19
123 78 0.76
124 5 0.05
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (123 bp):
CACGATATCCTTCATCGTGAAGTGAAACCGTGGATAGCCCATTCGTCGTGAAGTTGAGCCTAGAA
TTGGATATCCTTCATCGTGAACTTGAAATCCAATCTAAAGATGAATGTTATTGGTGAG
Found at i:48850 original size:123 final size:122
Alignment explanation
Indices: 48602--48858 Score: 322
Period size: 123 Copynumber: 2.1 Consensus size: 122
48592 ATCCTTCATC
* * * * *
48602 GTGAAG-TGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGATCCTAGAATTGGATATCCTTCGT
1 GTGAAGTTGAAACCGTGGATAGCCCATTCGTCGTGAAGTTGAGCCTAGAATTGGATATCCTTCAT
* * * * * *
48666 CGTGAAGTTGAAATCCAATCTAAAGATGATGTTATTGGTGAGCACGATTTCCTTCATT
66 CGTGAACTTGAAATCCAATCTAAAGATGATGTTATT-GCGAGCACAATATCCCTCACT
* *
48724 GTGAAGTTGAAACCGTGGATAGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCAT
1 GTGAAGTTGAAACCGTGGATAGCCCATTCGTCGTGAAGTTGAGCCTAGAATTGGATATCCTTCAT
* *
48789 CGTGAACTTGAAATCCAATCTAAAGATGAATGTTGCTT-CGAGTC-CAATATCCCTCGCT
66 CGTGAACTTGAAATCCAATCTAAAGATG-ATGTT-ATTGCGAG-CACAATATCCCTCACT
48847 GTGAAGTTGAAA
1 GTGAAGTTGAAA
48859 TTGGCTCTGA
Statistics
Matches: 116, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
122 6 0.05
123 102 0.88
124 6 0.05
125 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (122 bp):
GTGAAGTTGAAACCGTGGATAGCCCATTCGTCGTGAAGTTGAGCCTAGAATTGGATATCCTTCAT
CGTGAACTTGAAATCCAATCTAAAGATGATGTTATTGCGAGCACAATATCCCTCACT
Found at i:49013 original size:110 final size:111
Alignment explanation
Indices: 48882--49293 Score: 379
Period size: 110 Copynumber: 3.6 Consensus size: 111
48872 AAATTGGGAA
*
48882 GCCCCTTCGTTGTGAAGTTGAGCTTTGAATTGAATAT-ATTTCATCGTGAAGTTGAAATCCAATC
1 GCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGAATATCATTTCATCGTGAAGTTGAAATCCAATC
48946 TAGAGTTGGCACGATATCCATT-GTCGTGAAGTTGAAATCGTGGGTG
66 TAGAGTTGGCACGATATCC-TTCGTCGTGAAGTTGAAATCGTGGGTG
* * *
48992 GCCCCTTCGTTGTGAAGTTGAGCCTTGACTTGAATATC-CTTCGTCGTGAAGTTGAAATCCAAGC
1 GCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGAATATCATTTCATCGTGAAGTTGAAATCCAA--
* * * * *
49056 TTGTATTATTTCGAGTC-CAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGA
64 -TCTA-GAGTT-G-G-CACGATATCCTTCGTCGTGAAGTTGAAA-----TC-G--TG-----GG-
**
49120 AA
110 TG
* * ** * *
49122 GCCCCTTC-TCCGTGAAGTTAAGTTTTGAATTGGATATCA-TTCGTCGTGAAGTTGAAATCCAAT
1 GCCCCTTCGT-TGTGAAGTTGAGCCTTGAATTGAATATCATTTCATCGTGAAGTTGAAATCCAAT
*
49185 CTAGAGTTGACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGGTG
65 CTAGAGTTGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGGTG
* * *
49232 GCCCCTTCGTTGTGAAGTTGAGCCTTGACTTGAGTATCCTTT-ATCGTGAAGTTGAAATCCAA
1 GCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGAATATCATTTCATCGTGAAGTTGAAATCCAA
49294 GCTTGTATTG
Statistics
Matches: 240, Mismatches: 34, Indels: 56
0.73 0.10 0.17
Matches are distributed among these distances:
110 105 0.44
111 5 0.02
113 3 0.01
114 3 0.01
115 3 0.01
116 24 0.10
117 1 0.00
118 1 0.00
119 2 0.01
121 2 0.01
122 1 0.00
123 1 0.00
124 26 0.11
125 1 0.00
126 3 0.01
127 3 0.01
129 3 0.01
130 53 0.22
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (111 bp):
GCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGAATATCATTTCATCGTGAAGTTGAAATCCAATC
TAGAGTTGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGGTG
Found at i:49151 original size:240 final size:238
Alignment explanation
Indices: 48707--49468 Score: 1042
Period size: 240 Copynumber: 3.1 Consensus size: 238
48697 TTATTGGTGA
* * * * * * *
48707 GCACGATTTCCTTCATTGTGAAGTTGAAACCGTGGATAGCCCATTCGTTGTGAAGTTGAGCCTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGGTGGCCCCTTCGTTGTGAAGTTGAGCCTTG
* * * * *
48772 AATTGGATATCCTTCATCGTGAACTTGAAATCCAATCTAAAGATGAATGTTGCTTCGAGTCCAAT
66 ACTTGAATATCCTTCATCGTGAAGTTGAAATCCAAGCT-----TGTAT-TT--TTCGAGTCCAAT
* * *
48837 ATCCCTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAATTGGGAAGCCCCTTCGT-TGTGAAGTT
123 ATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAATTGGGAAGCCCCTTC-TCCGTGAAGTT
* *
48901 GAGCTTTGAATTGAATATATTTCATCGTGAAGTTGAAATCCAATCTAGAGTTG
187 GAGCTTTGAATTGGATATA-TTCGTCGTGAAGTTGAAATCCAATCTAGAGTTG
48954 GCACGATATCCATT-GTCGTGAAGTTGAAATCGTGGGTGGCCCCTTCGTTGTGAAGTTGAGCCTT
1 GCACGATATCC-TTCGTCGTGAAGTTGAAATCGTGGGTGGCCCCTTCGTTGTGAAGTTGAGCCTT
*
49018 GACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTATTTCGAGTCCAATATCCTT
65 GACTTGAATATCCTTCATCGTGAAGTTGAAATCCAAGCTTGTATT-TTTCGAGTCCAATATCCTT
* * * *
49083 CGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGAAAGCCCCTTCTCCGTGAAGTTAAGTTTT
129 CGCCGTGAAGTTGAAATTGGCTCTGAATGAAATTGGGAAGCCCCTTCTCCGTGAAGTTGAGCTTT
49148 GAATTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTAGAGTTG
194 GAATTGGATAT-ATTCGTCGTGAAGTTGAAATCCAATCTAGAGTTG
*
49194 ACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGGTGGCCCCTTCGTTGTGAAGTTGAGCCTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGGTGGCCCCTTCGTTGTGAAGTTGAGCCTTG
* * **
49259 ACTTGAGTATCCTTTATCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATATTTC
66 ACTTGAATATCCTTCATCGTGAAGTTGAAATCCAAGCTTGTATT-TTTCGAGTCCAATATCCTTC
* * *
49324 GCCGTGAAGCTGAAATTAGCTCTGAATGAAATTGGGAAGCCCCTTCGCCGTGAAGTTGAGCTTTG
130 GCCGTGAAGTTGAAATTGGCTCTGAATGAAATTGGGAAGCCCCTTCTCCGTGAAGTTGAGCTTTG
* *
49389 AATTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCTAGAGTTG
195 AATTGGATAT-ATTCGTCGTGAAGTTGAAATCCAATCTAGAGTTG
* * * * *
49434 GAACAATATTCTTCGTTGTAAAGTTGAAATCGTGG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGG
49469 ATTTATGGGT
Statistics
Matches: 466, Mismatches: 44, Indels: 17
0.88 0.08 0.03
Matches are distributed among these distances:
239 3 0.01
240 366 0.79
241 2 0.00
242 5 0.01
247 88 0.19
248 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (238 bp):
GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGGTGGCCCCTTCGTTGTGAAGTTGAGCCTTG
ACTTGAATATCCTTCATCGTGAAGTTGAAATCCAAGCTTGTATTTTTCGAGTCCAATATCCTTCG
CCGTGAAGTTGAAATTGGCTCTGAATGAAATTGGGAAGCCCCTTCTCCGTGAAGTTGAGCTTTGA
ATTGGATATATTCGTCGTGAAGTTGAAATCCAATCTAGAGTTG
Found at i:49167 original size:130 final size:127
Alignment explanation
Indices: 49003--49420 Score: 408
Period size: 130 Copynumber: 3.4 Consensus size: 127
48993 CCCCTTCGTT
* * *
49003 GTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTATTTC
1 GTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTATTTC
49068 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGAAAGCCCCTTCTCC
66 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATT-GCTCTGAATGAAA-TGG-AAGCCCCTTCTCC
* * * * * *
49133 GTGAAGTTAAGTTTTGAATTGGATATCATTCGTCGTGAAGTTGAAATCCAA---TCTA-GAGTT-
1 GTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTATTTC
* * ** *
49193 GA--CACGATATCCTTCGTCGTGAAGTTGAAA----TC-G--TG----GGTGGCCCCTTCGT-T
66 GAGTC-CAATATCCTTCGCCGTGAAGTTGAAATTGCTCTGAATGAAATGGAAGCCCCTTC-TCC
* * ** *
49243 GTGAAGTTGAGCCTTGACTT-GAGTATCCTTTATCGTGAAGTTGAAATCCAAGCTTGTATTGTTT
1 GTGAAGTTGAGCTTTGAATTGGA-TATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTATTT
** * *
49307 CGAGTCCAATATATTTCGCCGTGAAGCTGAAATTAGCTCTGAATGAAATTGGGAAGCCCCTTCGC
65 CGAGTCCAATATCCTTCGCCGTGAAGTTGAAATT-GCTCTGAATGAAA-T-GGAAGCCCCTTCTC
49372 C
127 C
49373 GTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
1 GTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
49421 TAATCTAGAG
Statistics
Matches: 224, Mismatches: 38, Indels: 52
0.71 0.12 0.17
Matches are distributed among these distances:
109 2 0.01
110 49 0.22
111 3 0.01
113 3 0.01
114 2 0.01
115 2 0.01
116 23 0.10
117 1 0.00
118 1 0.00
119 2 0.01
121 2 0.01
122 1 0.00
123 1 0.00
124 26 0.12
125 2 0.01
126 3 0.01
127 3 0.01
130 96 0.43
131 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (127 bp):
GTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTATTTC
GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGCTCTGAATGAAATGGAAGCCCCTTCTCC
Found at i:62901 original size:21 final size:21
Alignment explanation
Indices: 62875--62918 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
62865 GCATCAAGGT
62875 TTTTGTAGACG-CCATGAAATC
1 TTTTGTAGA-GACCATGAAATC
* *
62896 TTTTGTCGAGACCATGAATTC
1 TTTTGTAGAGACCATGAAATC
62917 TT
1 TT
62919 GCAATGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (21 bp):
TTTTGTAGAGACCATGAAATC
Found at i:64496 original size:21 final size:19
Alignment explanation
Indices: 64458--64503 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
64448 AATTAATCCT
64458 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
64478 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
64499 A-TAAT
1 ACTAAT
64504 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:66752 original size:3 final size:3
Alignment explanation
Indices: 66720--66779 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
66710 ATAGTGGCCC
* *
66720 ATA A-A ATA ATT ATA ATA TATA A-A TTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
66764 AGTA ATT ATT ATA ATA
1 A-TA ATA ATA ATA ATA
66780 TTTTTTTAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 3 0.06
3 38 0.81
4 6 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:76511 original size:17 final size:17
Alignment explanation
Indices: 76476--76515 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
76466 AAAAAGTTCA
*
76476 ATTAAAACATTTTAGTT
1 ATTAAAACATTTTACTT
76493 ATTAAAACA-TTTATCTT
1 ATTAAAACATTTTA-CTT
76510 ATTAAA
1 ATTAAA
76516 TATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTAAAACATTTTACTT
Found at i:77672 original size:21 final size:23
Alignment explanation
Indices: 77642--77688 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
77632 ATTACCTTGT
*
77642 AAAATGTTAAAAATTA-AATTAA
1 AAAATGTTAAAAATTACAAGTAA
*
77664 AAAAT-TTAAAACTTACAAGTAA
1 AAAATGTTAAAAATTACAAGTAA
77686 AAA
1 AAA
77689 TAACAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAATGTTAAAAATTACAAGTAA
Found at i:83989 original size:21 final size:20
Alignment explanation
Indices: 83963--84003 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
83953 GATCATATAG
83963 CCATTGAGAAGAAGGTTAAAA
1 CCATTG-GAAGAAGGTTAAAA
* *
83984 CCATTGGAGGATGGTTAAAA
1 CCATTGGAAGAAGGTTAAAA
84004 GGTTTTGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.22
Consensus pattern (20 bp):
CCATTGGAAGAAGGTTAAAA
Done.