Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001415.1 Hibiscus syriacus cultivar Beakdansim tig00002752_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: 68152
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:85 original size:42 final size:42
Alignment explanation
Indices: 34--351 Score: 423
Period size: 42 Copynumber: 7.6 Consensus size: 42
24 GCAATGCGTT
* *
34 TTCCAAATTCTTTGCGATAGTCCAAGTTCGCGTTGCAATTTA
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
76 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TA
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
* * * *
116 GTCCAAGTTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTA
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
158 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TA
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
* * *
198 GTCCAAGTTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1 TTCCAA-ATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
*
241 TTTCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA-TT-
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
* * * *
281 GTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTA
1 TTCCAAATT--CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTA
327 TTCCAAATTCGTTGCGATAGTCCAA
1 TTCCAAATTCGTTGCGATAGTCCAA
352 AATCGCAACG
Statistics
Matches: 239, Mismatches: 26, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
40 48 0.20
41 32 0.13
42 117 0.49
43 6 0.03
44 28 0.12
45 2 0.01
46 6 0.03
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (42 bp):
TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
Found at i:109 original size:21 final size:21
Alignment explanation
Indices: 45--351 Score: 294
Period size: 21 Copynumber: 14.7 Consensus size: 21
35 TCCAAATTCT
45 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* * *
66 TTGCAATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
87 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
108 TTGCGATAGTCCAAGTT--CG
1 TTGCGATAGTCCAAGTTCGCG
* *
127 TTGCGATAGTCGAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCG
* *
148 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
169 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
*
190 TTGCGATAGTCCAAGTT-TCG
1 TTGCGATAGTCCAAGTTCGCG
*
210 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* * *
231 TTGCGATTTATTTCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
252 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
273 TTGCGATTGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
*
294 TTGCGATTTATTCCAAGTTCGCG
1 TTGCGA--TAGTCCAAGTTCGCG
* *
317 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
338 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
352 AATCGCAACG
Statistics
Matches: 240, Mismatches: 29, Indels: 36
0.79 0.10 0.12
Matches are distributed among these distances:
19 51 0.21
20 18 0.08
21 117 0.49
23 54 0.22
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:172 original size:82 final size:82
Alignment explanation
Indices: 35--351 Score: 499
Period size: 82 Copynumber: 3.8 Consensus size: 82
25 CAATGCGTTT
* * *
35 TCCAAATTCTTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATTCGTTGCGATAGTCCA
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
100 AGTTCGCGTTGCGATAG
66 AGTTCGCGTTGCGATAG
* *
117 TCCAAGTTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
182 AGTTCGCGTTGCGATAG
66 AGTTCGCGTTGCGATAG
* *
199 TCCAAGTTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTCAAATTCGTTGCGATAGTCC
1 TCCAAG-TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCC
*
264 AAGTTCGCGTTGCGATTG
65 AAGTTCGCGTTGCGATAG
* *
282 TCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
347 TCCAA
62 TCCAA
352 AATCGCAACG
Statistics
Matches: 218, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
82 85 0.39
83 78 0.36
84 8 0.04
86 47 0.22
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (82 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
AGTTCGCGTTGCGATAG
Found at i:1102 original size:6 final size:6
Alignment explanation
Indices: 1086--1115 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1076 TCTCGTCTGG
1086 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT G
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT G
1116 TAATATGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:1259 original size:21 final size:21
Alignment explanation
Indices: 1200--1383 Score: 107
Period size: 21 Copynumber: 9.0 Consensus size: 21
1190 ACCAGTCGTT
* *
1200 GCGAACTTCGACTATCGCAA-
1 GCGAACTTGGATTATCGCAAC
* *
1220 -CGAATTTGGATAAATCGCAAC
1 GCGAACTTGGAT-TATCGCAAC
*
1241 GCGAACTTCGATTATCGCAA-
1 GCGAACTTGGATTATCGCAAC
* *
1261 -CGAATTTGGAATAAATCGCAAC
1 GCGAACTTGG-AT-TATCGCAAC
*
1283 GCGAACTTGGACTATCGCAA-
1 GCGAACTTGGATTATCGCAAC
* * * *
1303 -CAAATTTGGAATAAATCGTAAC
1 GCGAACTTGG-AT-TATCGCAAC
*
1325 GCGAACTTGGACTATCGCAA-
1 GCGAACTTGGATTATCGCAAC
* **
1345 -CGAA-TTTGAAAATCGCAAC
1 GCGAACTTGGATTATCGCAAC
*
1364 GCGAACTTGGACTATCGCAA
1 GCGAACTTGGATTATCGCAA
1384 TGTGAATATG
Statistics
Matches: 121, Mismatches: 29, Indels: 27
0.68 0.16 0.15
Matches are distributed among these distances:
18 11 0.09
19 26 0.21
20 14 0.12
21 44 0.36
22 11 0.09
23 15 0.12
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (21 bp):
GCGAACTTGGATTATCGCAAC
Found at i:1288 original size:42 final size:41
Alignment explanation
Indices: 1200--1383 Score: 291
Period size: 42 Copynumber: 4.5 Consensus size: 41
1190 ACCAGTCGTT
*
1200 GCGAACTTCGACTATCGCAACGAATTTGGATAAATCGCAAC
1 GCGAACTTGGACTATCGCAACGAATTTGGATAAATCGCAAC
* *
1241 GCGAACTTCGATTATCGCAACGAATTTGGAATAAATCGCAAC
1 GCGAACTTGGACTATCGCAACGAATTTGG-ATAAATCGCAAC
* *
1283 GCGAACTTGGACTATCGCAACAAATTTGGAATAAATCGTAAC
1 GCGAACTTGGACTATCGCAACGAATTTGG-ATAAATCGCAAC
1325 GCGAACTTGGACTATCGCAACGAATTT-GA-AAATCGCAAC
1 GCGAACTTGGACTATCGCAACGAATTTGGATAAATCGCAAC
1364 GCGAACTTGGACTATCGCAA
1 GCGAACTTGGACTATCGCAA
1384 TGTGAATATG
Statistics
Matches: 135, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
39 29 0.21
40 1 0.01
41 29 0.21
42 76 0.56
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (41 bp):
GCGAACTTGGACTATCGCAACGAATTTGGATAAATCGCAAC
Found at i:1907 original size:18 final size:18
Alignment explanation
Indices: 1884--1924 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1874 TATACACAAG
1884 AAGATGCTAGTAAACATA
1 AAGATGCTAGTAAACATA
1902 AAGATGCTAGTAAACATA
1 AAGATGCTAGTAAACATA
1920 AAGAT
1 AAGAT
1925 CAAGACCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.10, G:0.17, T:0.22
Consensus pattern (18 bp):
AAGATGCTAGTAAACATA
Found at i:2544 original size:21 final size:22
Alignment explanation
Indices: 2520--2562 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2510 TAATGTTTGT
*
2520 TATT-AAAAATCCAATCATTTA
1 TATTAAAAAACCCAATCATTTA
2541 TATTAAAAAACCCAATCATTTA
1 TATTAAAAAACCCAATCATTTA
2563 AGTAAGCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (22 bp):
TATTAAAAAACCCAATCATTTA
Found at i:6224 original size:2 final size:2
Alignment explanation
Indices: 6217--6241 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6207 TGTCAGCTGA
6217 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
6242 CACACACACA
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:6294 original size:3 final size:3
Alignment explanation
Indices: 6286--6330 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
6276 TTATTCCCTT
6286 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6331 CTGCATGAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:6625 original size:2 final size:2
Alignment explanation
Indices: 6613--6662 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
6603 AAGAATAACG
6613 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6654 AT AT AT AT A
1 AT AT AT AT A
6663 AGGATACCCC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8514 original size:2 final size:2
Alignment explanation
Indices: 8507--8542 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8497 ATGGATCCTA
8507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8543 GCGCGCGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19318 original size:39 final size:39
Alignment explanation
Indices: 19244--19318 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
19234 AAACAGACAT
*
19244 CAAAATAATCACAAAAACAGAAAAAGAAAAAGAAACCTA
1 CAAAATAATCACAAAAACAGAAAAACAAAAAGAAACCTA
* * * *
19283 CAAAAT-ATTACAAAAACTGTAAAACCAAAATGAAAC
1 CAAAATAATCACAAAAACAG-AAAAACAAAAAGAAAC
19319 AAATCTCTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 11 0.37
39 19 0.63
ACGTcount: A:0.65, C:0.16, G:0.07, T:0.12
Consensus pattern (39 bp):
CAAAATAATCACAAAAACAGAAAAACAAAAAGAAACCTA
Found at i:19939 original size:2 final size:2
Alignment explanation
Indices: 19932--19961 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19922 ATATTTAATA
19932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19962 CAATTATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24628 original size:23 final size:23
Alignment explanation
Indices: 24594--24661 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
24584 CATCTTATAT
24594 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* *
24617 GGCACTAT-GGTGCAATTCTACGT
1 GGCACT-TCGGTGCATTTCTACGC
*
24640 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
24662 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 37 0.95
24 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:24712 original size:16 final size:17
Alignment explanation
Indices: 24691--24724 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
24681 GTGCACAACC
24691 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
24707 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
24724 T
1 T
24725 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:27151 original size:31 final size:31
Alignment explanation
Indices: 27116--27181 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 31
27106 CTTTACCGGA
27116 TCCCTCAACATTTAGT-CTATTTGCAATATGG
1 TCCCTCAACATTTAGTAC-ATTTGCAATATGG
27147 TCCCTCAACATTTAGTACATTTGCAATATGG
1 TCCCTCAACATTTAGTACATTTGCAATATGG
27178 TCCC
1 TCCC
27182 CGATGTAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (31 bp):
TCCCTCAACATTTAGTACATTTGCAATATGG
Found at i:27719 original size:35 final size:35
Alignment explanation
Indices: 27646--27731 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 35
27636 AAAACAGTCA
* * * *
27646 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCACAAATTCCAAAATAAT
* * * *
27681 TCAATTTTATTCTAAACCATAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCACAAATTCCAAAATAAT
*
27716 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
27732 ATACTTCAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCACAAATTCCAAAATAAT
Found at i:27725 original size:21 final size:21
Alignment explanation
Indices: 27700--27742 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
27690 TTCTAAACCA
27700 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
27721 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
27742 T
1 T
27743 TAAGGCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:27898 original size:16 final size:18
Alignment explanation
Indices: 27866--27899 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
27856 TATTAATGTA
27866 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
27884 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
27900 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:28568 original size:130 final size:130
Alignment explanation
Indices: 28365--28612 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
28355 AATTTTCTTC
* * *
28365 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
28430 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * * *
28495 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCTTGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
28560 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
28613 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:29955 original size:26 final size:27
Alignment explanation
Indices: 29900--29958 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
29890 TTTAGTCGTT
* *
29900 TATGATTTTTCATTTTTTTTTGTTGAAA
1 TATGATTTTTCATTGTTTTATGTT-AAA
29928 TATGATTTTTCATTGTTTTATGTTAATA
1 TATGATTTTTCATTGTTTTATGTTAA-A
29956 TAT
1 TAT
29959 TAATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.24, C:0.03, G:0.10, T:0.63
Consensus pattern (27 bp):
TATGATTTTTCATTGTTTTATGTTAAA
Found at i:33639 original size:42 final size:41
Alignment explanation
Indices: 33592--33675 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 41
33582 CATTTTTAAG
33592 TTATAGAAATAAACTTCAAACGTTGATATTATTATAGTAAAA
1 TTATAGAAATAAACTTCAAAC-TTGATATTATTATAGTAAAA
*
33634 TTATAGAAATAAACTTCAAACTTGATATTATTATAGTCAAA
1 TTATAGAAATAAACTTCAAACTTGATATTATTATAGTAAAA
33675 T
1 T
33676 AATCAAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 20 0.49
42 21 0.51
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (41 bp):
TTATAGAAATAAACTTCAAACTTGATATTATTATAGTAAAA
Found at i:36031 original size:21 final size:21
Alignment explanation
Indices: 36005--36061 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
35995 AATGCCGGGT
*
36005 AAAATTTTTTAAAATAATCAA
1 AAAATTTATTAAAATAATCAA
36026 AAAATTTATTAAAATAATCAAA
1 AAAATTTATTAAAATAATC-AA
*
36048 AAAAATTATTAAAA
1 AAAATTTATTAAAA
36062 GTATTTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATTTATTAAAATAATCAA
Found at i:36056 original size:22 final size:21
Alignment explanation
Indices: 36013--36061 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 21
36003 GTAAAATTTT
*
36013 TTAAAATAATCAAAAAATTTA
1 TTAAAATAATCAAAAAAATTA
36034 TTAAAATAATCAAAAAAAATTA
1 TTAAAATAATC-AAAAAAATTA
36056 TTAAAA
1 TTAAAA
36062 GTATTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAAATAATCAAAAAAATTA
Found at i:41014 original size:25 final size:26
Alignment explanation
Indices: 40960--41015 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
40950 AATAATCCTT
* **
40960 TTTCACTTTTTACAAATAAATATTTT
1 TTTCACTTTTTACAAATAAATACTAC
40986 TTTCACTTTTTACAAATAAAT-CTAC
1 TTTCACTTTTTACAAATAAATACTAC
41011 TTTCA
1 TTTCA
41016 TGTTATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTCACTTTTTACAAATAAATACTAC
Found at i:47253 original size:29 final size:29
Alignment explanation
Indices: 47211--47270 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
47201 TGCATTGTAC
47211 ATCACCCGTTCAAAGAGAAGCCAAAACAA
1 ATCACCCGTTCAAAGAGAAGCCAAAACAA
47240 ATCACCCGTTCAAAGAGAAGCCAAAACAA
1 ATCACCCGTTCAAAGAGAAGCCAAAACAA
47269 AT
1 AT
47271 GCAACTCGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.27, G:0.13, T:0.12
Consensus pattern (29 bp):
ATCACCCGTTCAAAGAGAAGCCAAAACAA
Found at i:47644 original size:110 final size:110
Alignment explanation
Indices: 47515--47729 Score: 367
Period size: 110 Copynumber: 2.0 Consensus size: 110
47505 CCTAAGGTTA
* * *
47515 ACAAATCAATAATCAAAAACCAGTCAATACAATCATTCGAAAAAGATGAGCAGTTGGGATAAGAC
1 ACAAATCAACAATAAAAAACCAGTCAATACAATCAATCGAAAAAGATGAGCAGTTGGGATAAGAC
*
47580 TACAACAGTATCAGAAAACATTATATAGGTCTACCTTGGATATTG
66 TACAACAGTATCAGAAAACATTATATAGGTATACCTTGGATATTG
47625 ACAAATCAACAATAAAAAACCAGTCAATACAATCAATCGAAAAAGATGAGCAGTTGGGATAAGAC
1 ACAAATCAACAATAAAAAACCAGTCAATACAATCAATCGAAAAAGATGAGCAGTTGGGATAAGAC
* * *
47690 TACGACATTATCGGAAAACATTATATAGGTATACCTTGGA
66 TACAACAGTATCAGAAAACATTATATAGGTATACCTTGGA
47730 AACATTGGGC
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 98 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (110 bp):
ACAAATCAACAATAAAAAACCAGTCAATACAATCAATCGAAAAAGATGAGCAGTTGGGATAAGAC
TACAACAGTATCAGAAAACATTATATAGGTATACCTTGGATATTG
Found at i:51923 original size:14 final size:14
Alignment explanation
Indices: 51904--51930 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51894 TAAATTTTAA
51904 ATATATAATATATT
1 ATATATAATATATT
51918 ATATATAATATAT
1 ATATATAATATAT
51931 GATCTCAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATAATATATT
Found at i:57711 original size:3 final size:3
Alignment explanation
Indices: 57703--57743 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
57693 ATATGTTATC
* *
57703 ATA ATA ATA ATC ATT AT- ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
57744 TTTAAAATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:61388 original size:32 final size:32
Alignment explanation
Indices: 61301--61406 Score: 101
Period size: 30 Copynumber: 3.4 Consensus size: 32
61291 AAAATCATAT
* *
61301 CTAATATTT-ACTTTTTATTTTATTTTAGTAC
1 CTAATTTTTAACTTCTTATTTTATTTTAGTAC
* ** * *
61332 C-CATCGTT-ACTTCTTGTTTCATTTTAGTAC
1 CTAATTTTTAACTTCTTATTTTATTTTAGTAC
* *
61362 CTTATTTTTAACTTCTTATTTTATTTTAGTGC
1 CTAATTTTTAACTTCTTATTTTATTTTAGTAC
61394 CTAAATTTTTAAC
1 CT-AATTTTTAAC
61407 GGTAGGGTAC
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
30 24 0.41
31 5 0.08
32 21 0.36
33 9 0.15
ACGTcount: A:0.23, C:0.15, G:0.06, T:0.57
Consensus pattern (32 bp):
CTAATTTTTAACTTCTTATTTTATTTTAGTAC
Found at i:62828 original size:16 final size:16
Alignment explanation
Indices: 62807--62861 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
62797 CATTTAATAA
*
62807 ATAAACGAACACAAAC
1 ATAAACGAACACGAAC
62823 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
62839 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
62855 ATAAACG
1 ATAAACG
62862 TTGGAGACCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:64133 original size:27 final size:29
Alignment explanation
Indices: 64068--64133 Score: 73
Period size: 33 Copynumber: 2.2 Consensus size: 29
64058 AAGGGAAAGT
*
64068 GATGAAGCTCTGTCGAATCGTTGCAGTTGAA
1 GATGAAGCTCCGTCGAATCGTTGCA--TGAA
64099 GACTTGAAGCTCCGTCGAATCGTTGCA-GAA
1 GA--TGAAGCTCCGTCGAATCGTTGCATGAA
64129 -ATGAA
1 GATGAA
64134 AATTGTGGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
27 4 0.12
29 1 0.03
30 3 0.09
31 2 0.06
33 22 0.69
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (29 bp):
GATGAAGCTCCGTCGAATCGTTGCATGAA
Found at i:64416 original size:24 final size:24
Alignment explanation
Indices: 64355--64416 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
64345 TATTAGGTTA
*
64355 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
* *
64379 AACATAACTAAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
64403 AACATAACCGAACG
1 AACATAACTGAACG
64417 TTCACGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:65427 original size:2 final size:2
Alignment explanation
Indices: 65416--65455 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
65406 TCATTTAATA
65416 AT AT -T 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 AT AT A
65456 AATTATACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65546 original size:19 final size:18
Alignment explanation
Indices: 65505--65545 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
65495 CCCATAATTA
*
65505 AAAATTAATATATGTTTT
1 AAAATTAATATATATTTT
65523 AAAATTAATTATATATTTGT
1 AAAATTAA-TATATATTT-T
65543 AAA
1 AAA
65546 TCATACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
AAAATTAATATATATTTT
Done.