Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001218.1 Hibiscus syriacus cultivar Beakdansim tig00002406_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: 68557
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:25782 original size:27 final size:27
Alignment explanation
Indices: 25738--25833 Score: 144
Period size: 27 Copynumber: 3.6 Consensus size: 27
25728 CTTGTAGGAA
25738 TTATAGAG--ATGATTTGTTACCATTC
1 TTATAGAGATATGATTTGTTACCATTC
25763 TTATAGAGATATGATTTGTTACCATT-
1 TTATAGAGATATGATTTGTTACCATTC
*
25789 TCTATTGAGATATGATTTGTTACCATTC
1 T-TATAGAGATATGATTTGTTACCATTC
*
25817 CTATAGAGATATGATTT
1 TTATAGAGATATGATTT
25834 TGTAAATAGA
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.12
26 1 0.02
27 55 0.86
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (27 bp):
TTATAGAGATATGATTTGTTACCATTC
Found at i:29547 original size:27 final size:27
Alignment explanation
Indices: 29504--29598 Score: 149
Period size: 27 Copynumber: 3.6 Consensus size: 27
29494 GTGTAGGAAT
*
29504 TATAGAG--ATGATTTGTTACCATTCT
1 TATAGAGATATGATTTGTTACCATTCC
*
29529 TATAGAGATATGATTTGTTATCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
29556 TATAGAGATATGATTTGTTACTATTCC
1 TATAGAGATATGATTTGTTACCATTCC
29583 TATAGAGATATGATTT
1 TATAGAGATATGATTT
29599 TGTAAATAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
25 7 0.11
27 57 0.89
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:30380 original size:54 final size:54
Alignment explanation
Indices: 30303--30606 Score: 448
Period size: 54 Copynumber: 5.6 Consensus size: 54
30293 TTTGCACCTA
* ** * *
30303 AGTGCCGATATGAAAATTTACAAACTCATTATGAATTCTATGGGTTGCACACAT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGCACACAT
* *
30357 AGTGCCGATATGGTAATTCACAAACTCATTATGAATTCTGTGGGTTACACACAT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGCACACAT
* * *
30411 AGTGTCGATACAGTAATTCACAAACTCATTATGAATTCCGTGGGTTGCACACAT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGCACACAT
* *
30465 AGTGCCGATACGATAATTCACAAACTCATTATGAATTCTGTGGGTTGCATACAT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGCACACAT
* ** *
30519 AGTGTCGATACGGTAATTCACAAACTCATTATGAATTCCATGGGTTGCACATAT
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGCACACAT
*
30573 AGTGTCGATACGGTAATTCA-AAACTCATTATGAA
1 AGTGCCGATACGGTAATTCACAAACTCATTATGAA
30607 AATATGTCGA
Statistics
Matches: 229, Mismatches: 21, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
53 14 0.06
54 215 0.94
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (54 bp):
AGTGCCGATACGGTAATTCACAAACTCATTATGAATTCTGTGGGTTGCACACAT
Found at i:30986 original size:22 final size:22
Alignment explanation
Indices: 30955--30997 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
30945 AGTATCAGTA
*
30955 TCTCTGCTATAGTATCGATACT
1 TCTCTGCTATAGTACCGATACT
* *
30977 TCTCTTCTATGGTACCGATAC
1 TCTCTGCTATAGTACCGATAC
30998 CCACTTCAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.40
Consensus pattern (22 bp):
TCTCTGCTATAGTACCGATACT
Found at i:31341 original size:20 final size:21
Alignment explanation
Indices: 31298--31341 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
31288 CAACTAACTT
** *
31298 ACATCCATAAATCTCCTTATA
1 ACATCCATAAATCTCCAAAGA
31319 ACATCCA-AAATCTCCAAAGA
1 ACATCCATAAATCTCCAAAGA
31339 ACA
1 ACA
31342 CTTAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (21 bp):
ACATCCATAAATCTCCAAAGA
Found at i:37092 original size:24 final size:24
Alignment explanation
Indices: 37062--37121 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
37052 TTTAGATGGG
37062 AAATATTCCCAATAGTGAGTAATA
1 AAATATTCCCAATAGTGAGTAATA
37086 AAATATTCCCAATAGTGAGTAATA
1 AAATATTCCCAATAGTGAGTAATA
37110 AAATATTCCCAA
1 AAATATTCCCAA
37122 CAGTAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (24 bp):
AAATATTCCCAATAGTGAGTAATA
Found at i:37312 original size:14 final size:14
Alignment explanation
Indices: 37275--37313 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
37265 TAATCTTTTG
37275 TTTTCACAAATTTA
1 TTTTCACAAATTTA
*
37289 -TTTCAAAAATTTA
1 TTTTCACAAATTTA
37302 TTTTCACAAATT
1 TTTTCACAAATT
37314 ATCATAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTTCACAAATTTA
Found at i:38391 original size:21 final size:21
Alignment explanation
Indices: 38370--38408 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38360 CTAAAAAATA
*
38370 AATTT-TAGAAAATTAATTAT
1 AATTTATAGAAAATGAATTAT
*
38390 AATTTATGGAAAATGAATT
1 AATTTATAGAAAATGAATT
38409 GTAGAAAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (21 bp):
AATTTATAGAAAATGAATTAT
Found at i:38730 original size:23 final size:23
Alignment explanation
Indices: 38701--38767 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
38691 TTCTATAATC
38701 AACAAACTCAAAGT-ATAACACCA
1 AACAAACTCAAA-TCATAACACCA
* **
38724 AGCAAACTCAAATCATAACATTA
1 AACAAACTCAAATCATAACACCA
38747 AACAAACTCAAATCATAACAC
1 AACAAACTCAAATCATAACAC
38768 TTGTAATAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
22 1 0.03
23 37 0.97
ACGTcount: A:0.55, C:0.25, G:0.03, T:0.16
Consensus pattern (23 bp):
AACAAACTCAAATCATAACACCA
Found at i:41378 original size:37 final size:36
Alignment explanation
Indices: 41328--41480 Score: 128
Period size: 37 Copynumber: 4.4 Consensus size: 36
41318 AAGATATTTG
*
41328 TTGTTTCATGAGAAACGGTCTCAAGGGAGAC-AAGATT
1 TTGTTTCAAGAGAAACGGTCTCAAGGGAGACGAA-A-T
*
41365 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAAT
1 TTGTTTCAAGAGAAACGGTCTCAAGGGAGACGAAAT
* * *
41401 TAGTTTCAA-AGAAACAGAT-TC-A---A-A-G-ATT
1 TTGTTTCAAGAGAAAC-GGTCTCAAGGGAGACGAAAT
* * * *
41429 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAAT
1 TTGTTTCAAGAGAAACGGTCTCAAGGGAGACGAAAT
41465 TTGTTTCAAGAGAAAC
1 TTGTTTCAAGAGAAAC
41481 TGCTTCAAAC
Statistics
Matches: 92, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
28 11 0.12
29 8 0.09
30 2 0.02
31 1 0.01
33 1 0.01
34 2 0.02
35 8 0.09
36 27 0.29
37 30 0.33
38 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACGGTCTCAAGGGAGACGAAAT
Found at i:41452 original size:101 final size:101
Alignment explanation
Indices: 41266--41695 Score: 391
Period size: 101 Copynumber: 4.3 Consensus size: 101
41256 ATGATGCTTT
* * * *
41266 AAGAGAAATTTTCTCGAA-AGAGACAGAATTC-GTTTCAAGGGAAACGATCTCAAAGATATTTGT
1 AAGAGAAACTGTCTC-AAGAGAGACA-AATTCAGTTTCAAGGGAAACGTTTTCAAAG--A-TT-T
* * * *
41329 TGTTTCATGAGAAACGGTCTCAAGGGAGACAAGATTTTGTTTC
60 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAA-AATTTATTTC
* * *
41372 AAGAGAAACTGTCTCAAGGGAGACGAAATT-AGTTTCAA-AGAAACAG-ATTCAAAGATTTTGTT
1 AAGAGAAACTGTCTCAAGAGAGAC-AAATTCAGTTTCAAGGGAAAC-GTTTTCAAAGATTTTGTT
* * * *
41434 TCAAGGGAAACTGTCTCAAGAGAGACTAAATTTGTTTC
64 TCAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTC
** ** *
41472 AAGAGAAACTG-CTTC---A-A-ACATCTTGTGTTTCAAGGGAAACGTTTTCAAAGTTTTATGTT
1 AAGAGAAACTGTC-TCAAGAGAGACAAATTCAGTTTCAAGGGAAACGTTTTCAAAGATTT-TGTT
*
41531 TCAAGAGAAA-TCGTCTCAAGGGAGACAAAATTTATTCC
64 TCAAGAGAAACT-GTCTCAAGGGAGACAAAATTTATTTC
* * * * * *
41569 AAGGGAAACTATCTCAAGAGAGACAAAATTCA-TTTCAAGGGAAATGTTTTCAATGCTTATGTTT
1 AAGAGAAACTGTCTCAAGAGAGAC-AAATTCAGTTTCAAGGGAAACGTTTTCAAAGATTTTGTTT
*
41633 CAAGAAAAACTGTCTCAAGGGAGACAAAATTTATTTC
65 CAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTC
*
41670 AAGGGAAACTGTCTCAAGAGAGACAA
1 AAGAGAAACTGTCTCAAGAGAGACAA
41696 TGGTGAGCAC
Statistics
Matches: 269, Mismatches: 37, Indels: 42
0.77 0.11 0.12
Matches are distributed among these distances:
94 3 0.01
95 10 0.04
96 17 0.06
97 46 0.17
98 1 0.00
99 1 0.00
100 25 0.09
101 90 0.33
102 28 0.10
103 4 0.01
105 13 0.05
106 30 0.11
107 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (101 bp):
AAGAGAAACTGTCTCAAGAGAGACAAATTCAGTTTCAAGGGAAACGTTTTCAAAGATTTTGTTTC
AAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTC
Found at i:41465 original size:64 final size:65
Alignment explanation
Indices: 41359--41511 Score: 218
Period size: 64 Copynumber: 2.3 Consensus size: 65
41349 CAAGGGAGAC
* *
41359 AAGATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTAGTTTCAA-AGAAACAGATTCA
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTAGTTTCAAGAGAAACAGATTCA
* * * *
41423 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGAGAAACTGCTTCA
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTAGTTTCAAGAGAAACAGATTCA
*
41488 AACATCTTGTGTTTCAAGGGAAAC
1 AAGAT-TT-TGTTTCAAGGGAAAC
41512 GTTTTCAAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
64 47 0.59
65 15 0.19
66 2 0.03
67 15 0.19
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (65 bp):
AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTAGTTTCAAGAGAAACAGATTCA
Found at i:41480 original size:36 final size:36
Alignment explanation
Indices: 41428--41693 Score: 119
Period size: 36 Copynumber: 7.9 Consensus size: 36
41418 ATTCAAAGAT
41428 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAA
* * *
41464 TTTGTTTCAAGAGAAACTG-CTTCAA-ACA-TCT---
1 TTTGTTTCAAGGGAAACTGTC-TCAAGAGAGACTAAA
* * *
41495 TGTGTTTCAAGGGAAAC-GTTTTC-A-A-AG--T--T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACTAAA
* * *
41524 TTATGTTTCAAGAGAAA-TCGTCTCAAGGGAGACAAAA
1 TT-TGTTTCAAGGGAAACT-GTCTCAAGAGAGACTAAA
* * * *
41561 TTTATTCCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAA
** * *
41597 TTCATTTCAAGGGAAA-TGTTTTC-A-A-TG-CT---
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACTAAA
* ** * *
41626 TATGTTTCAAGAAAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAA
*
41662 TTTATTTCAAGGGAAACTGTCTCAAGAGAGAC
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
41694 AATGGTGAGC
Statistics
Matches: 168, Mismatches: 37, Indels: 50
0.66 0.15 0.20
Matches are distributed among these distances:
28 1 0.01
29 16 0.10
30 22 0.13
31 19 0.11
32 2 0.01
33 4 0.02
34 3 0.02
35 5 0.03
36 93 0.55
37 3 0.02
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAA
Found at i:41645 original size:198 final size:201
Alignment explanation
Indices: 41297--41680 Score: 476
Period size: 198 Copynumber: 1.9 Consensus size: 201
41287 GACAGAATTC
* *
41297 GTTTCAAGGGAAACGATCTCAAAGATATTTGTTGTTTCATGAGAAACGGTCTCAAGGGAGACAAG
1 GTTTCAAGGGAAACGATCTCAAAGATATTTGATGTTTCAAGAGAAACGGTCTCAAGGGAGACAAG
* * * * * *
41362 ATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTAGTTTCAAAGAAACAGATTCAAAGA
66 AATTTATTCCAAGAGAAACTATCTCAAGAGAGACAAAATTAGTTTCAAAGAAACAGATTCAAAGA
* ** * *
41427 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGAGAAACTGCTTCAAACA
131 TTATGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGCTTCAAACA
41492 TCTTGT
196 TCTTGT
* *
41498 GTTTCAAGGGAAACGTTTTCAAAG-T-TTT-ATGTTTCAAGAGAAATC-GTCTCAAGGGAGACAA
1 GTTTCAAGGGAAACGATCTCAAAGATATTTGATGTTTCAAGAGAAA-CGGTCTCAAGGGAGACAA
* * * *
41559 -AATTTATTCCAAGGGAAACTATCTCAAGAGAGACAAAATTCA-TTTCAAGGGAAA-TGTTTTCA
65 GAATTTATTCCAAGAGAAACTATCTCAAGAGAGACAAAATT-AGTTTCAA-AGAAACAG-ATTCA
* * * *
41621 ATGCTTATGTTTCAAGAAAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAACTG
127 AAGATTATGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTG
41681 TCTCAAGAGA
Statistics
Matches: 156, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
197 40 0.26
198 89 0.57
199 4 0.03
200 1 0.01
201 22 0.14
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (201 bp):
GTTTCAAGGGAAACGATCTCAAAGATATTTGATGTTTCAAGAGAAACGGTCTCAAGGGAGACAAG
AATTTATTCCAAGAGAAACTATCTCAAGAGAGACAAAATTAGTTTCAAAGAAACAGATTCAAAGA
TTATGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGCTTCAAACA
TCTTGT
Found at i:42005 original size:106 final size:106
Alignment explanation
Indices: 41820--42625 Score: 1292
Period size: 106 Copynumber: 7.6 Consensus size: 106
41810 GTATTGCTCC
* * * * * * * *
41820 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATCGGTTCTGGAACTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
41885 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
41926 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
41991 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
42032 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
42097 CCAGCGGTCCCTTCGTCGTGAAGTTGAA-TATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACT-TGCGTTGTCTG
* * * * *
42138 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
42203 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
42244 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * * *
42309 CCAACGGTCCCTTCATTGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
42350 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
42415 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
42456 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
42521 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
42562 GAGTCCACTATCTTTCGCTGTGAAGTTGAAATTGGCTCTAGAAGTGGA-AAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTGAGAAGTTGTTTGTTGACA
42626 GACAACTTTT
Statistics
Matches: 650, Mismatches: 47, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
105 1 0.00
106 642 0.99
107 7 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:43856 original size:165 final size:165
Alignment explanation
Indices: 43669--44732 Score: 1223
Period size: 165 Copynumber: 6.4 Consensus size: 165
43659 ACCTCGAAGT
* * * * *
43669 TGAGTGTAATCGAACCCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
1 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
** * *
43734 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTAGTAGATAACCCTTCTCG
66 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCG
*
43799 ACTTAAGCTATGTTGCAAATGATGTGCCTTGGAGC
131 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
* * * * * * *
43834 TGAGTGTAATCAAACTCAAAGGTC-TTTGTTGACAGATAACCCTTCTAGTCTTGAGTTATGCTGT
1 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * *
43898 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTCTTTGGCAGATAGCCCTTCTC
66 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAA-GGTCTTTGGCAGATAACCCTTCTC
*
43962 GACTTAAGCTATGCTACAAATGATGTGCCGTT-GAGC
130 GACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGC
* * * * *
43998 TTAACGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGC
1 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* *
44063 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCG
66 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCG
* *
44128 ACTTAAGCTATACTGCAAATGATGTGTCGTT-GAGC
131 ACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGC
* * * * * * *
44163 TGAGCGTAGTCGAACTCAAAGCTCTTTTGTAGCCAGACAACCCTTCTAGAATTAAGTTGTGCTGT
1 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * * *
44228 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
66 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTC--T--TTGGCAGATAACCCTT
* * *
44292 CTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGC
127 CTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGC
* * *** * * * *
44332 TGAGTGTAATCGAACTCGGGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGC
1 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * * * * * * * *
44393 AAATGATGTACCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTATTGCCAGACAACCCTT
66 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTT
* * * *
44457 CTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGC
127 CTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
* * *
44496 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
1 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * * ** * *
44561 GAATGAAATACCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCATATAGCCCTTCTCG
66 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCG
44626 ACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGC
131 ACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGC
* * *
44661 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGC
1 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
44726 AAATGAT
66 AAATGAT
44733 TTGTTTTTTT
Statistics
Matches: 760, Mismatches: 121, Indels: 36
0.83 0.13 0.04
Matches are distributed among these distances:
164 196 0.26
165 417 0.55
166 15 0.02
168 89 0.12
169 43 0.06
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (165 bp):
TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCG
ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
Found at i:44086 original size:249 final size:246
Alignment explanation
Indices: 43669--44732 Score: 1404
Period size: 249 Copynumber: 4.3 Consensus size: 246
43659 ACCTCGAAGT
* * *
43669 TGAGTGTAATCGAACCCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
1 TGAGCGTAGTCGAACTCAAAGGTC--TT-TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
* * * * ** *
43734 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTAG-T---AGATAACCCTT
63 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
* * * * * *
43795 CTCGACTTAAGCTATGTTGCAAATGATGTG-CCTTGGAGCTGAGTGTAATCAAACTCAAAGGTCT
127 CTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCT
* * * * * * * *
43859 TTGTTGACAGATAACCCTTCTAGTCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGC
192 TTG--G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGC
* * * * * * * * * *
43918 TGAGTGTAATCGAACTTAAGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAA
1 TGAGCGTAGTCGAACTCAAAGGTCTTTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAA
* * * *
43982 TGATGTGCCGTT-GAGCTTAACGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTC
66 TGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTC
*
44046 GACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTG
130 GACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTG
* *
44111 GCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGTCGTTGAGC
195 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGC
* * *
44163 TGAGCGTAGTCGAACTCAAAGCTCTTTTGTAGCCAGACAACCCTTCTAGAATTAAGTTGTGCTGT
1 TGAGCGTAGTCGAACTCAAAGGTCTTTTG--G-CAGACAACCCTTCTAGACTTAAGTTGTGCTGC
44228 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
63 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
**
44293 TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
128 TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTT
* *
44358 TGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTACCGTTGAGC
193 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGC
*
44412 TGAGCGTAGTCGAACTCAAAGGTCTTTTATTGCCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
1 TGAGCGTAGTCGAACTCAAAGGTC--TT-TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
44477 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
63 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* ** * **
44542 TCGACTTAAGTTATGCTGCGAATGAAATACCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
128 TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTT
*
44607 TGGCATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGC
193 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGC
*
44661 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGC
1 TGAGCGTAGTCGAACTCAAAGGTC--TT-TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
44726 AAATGAT
63 AAATGAT
44733 TTGTTTTTTT
Statistics
Matches: 728, Mismatches: 73, Indels: 28
0.88 0.09 0.03
Matches are distributed among these distances:
244 26 0.04
245 63 0.09
246 43 0.06
247 1 0.00
248 41 0.06
249 549 0.75
251 2 0.00
252 3 0.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (246 bp):
TGAGCGTAGTCGAACTCAAAGGTCTTTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAA
TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
ACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGG
CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGC
Found at i:50986 original size:18 final size:18
Alignment explanation
Indices: 50958--51003 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
50948 GAATTTGTGA
50958 AGGAA-TTGAAATCTGTC
1 AGGAATTTGAAATCTGTC
50975 AGGAATTTGAAATCTGTC
1 AGGAATTTGAAATCTGTC
50993 AGGAATTTGAA
1 AGGAATTTGAA
51004 TCCAATTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (18 bp):
AGGAATTTGAAATCTGTC
Found at i:51617 original size:31 final size:33
Alignment explanation
Indices: 51547--51629 Score: 125
Period size: 32 Copynumber: 2.5 Consensus size: 33
51537 TAAACCCGAC
*
51547 CCCGACCCGACCCGAATATCACACTTAAAAAAA
1 CCCGACCCGACCCAAATATCACACTTAAAAAAA
51580 CCCGA-CCGACCCAAATATCACACTT-AAAAAA
1 CCCGACCCGACCCAAATATCACACTTAAAAAAA
*
51611 CTCGACCCGACCCGAAATA
1 CCCGACCCGACCC-AAATA
51630 ATAAAAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 10 0.22
32 26 0.57
33 10 0.22
ACGTcount: A:0.41, C:0.37, G:0.10, T:0.12
Consensus pattern (33 bp):
CCCGACCCGACCCAAATATCACACTTAAAAAAA
Found at i:52769 original size:30 final size:30
Alignment explanation
Indices: 52703--52771 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
52693 TTGGAGAGAT
* * *
52703 TCTAGAAAATTCTAAAGCTTTCTAGAGAAG
1 TCTAGAAAATTCTAAAGCATTCCAGAGAAC
* ** *
52733 TTTAGAATTTTCTAAAGCATTCCGGAGAAC
1 TCTAGAAAATTCTAAAGCATTCCAGAGAAC
52763 TCTAGAAAA
1 TCTAGAAAA
52772 GTGTAAAACT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (30 bp):
TCTAGAAAATTCTAAAGCATTCCAGAGAAC
Found at i:53751 original size:29 final size:28
Alignment explanation
Indices: 53709--53774 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
53699 TATAAAGAAT
* *
53709 GAATCAAAAGTTTGTTTTTTTACTTTCAA
1 GAATCAAAACTTTG-ATTTTTACTTTCAA
* *
53738 GAATCAAGACTTTGATTTTTCCTTTCAA
1 GAATCAAAACTTTGATTTTTACTTTCAA
*
53766 GAATAAAAA
1 GAATCAAAA
53775 AGAAAAAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
28 19 0.61
29 12 0.39
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (28 bp):
GAATCAAAACTTTGATTTTTACTTTCAA
Found at i:56859 original size:38 final size:33
Alignment explanation
Indices: 56779--56844 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
56769 AGTTGGCAAG
*
56779 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCAAACTTA
*
56812 TTGGAAATTTTATCTTGGTTGGTGGCTAAACTT
1 TTGGAAATTTCATCTTGGTTGGTGGC-AAACTT
56845 TGAATATGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.42
Consensus pattern (33 bp):
TTGGAAATTTCATCTTGGTTGGTGGCAAACTTA
Found at i:64691 original size:21 final size:20
Alignment explanation
Indices: 64651--64692 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
64641 CCAACTTACA
*
64651 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
64671 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
64692 A
1 A
64693 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Done.