Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003371.1 Hibiscus syriacus cultivar Beakdansim tig00007085_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: 70510
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:4761 original size:21 final size:19
Alignment explanation
Indices: 4735--4773 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
4725 ATTTTTAAGG
4735 ATTAAAAATATAAATAAAATA
1 ATTAAAAAT-TAAA-AAAATA
*
4756 ATTAAATATTAAAAAAAT
1 ATTAAAAATTAAAAAAAT
4774 TAAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTAAAAATTAAAAAAATA
Found at i:4774 original size:16 final size:16
Alignment explanation
Indices: 4749--4781 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4739 AAAATATAAA
*
4749 TAAAATAATTAAATAT
1 TAAAAAAATTAAATAT
4765 TAAAAAAATTAAATAT
1 TAAAAAAATTAAATAT
4781 T
1 T
4782 TTCATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAAAAATTAAATAT
Found at i:8376 original size:7 final size:7
Alignment explanation
Indices: 8364--8446 Score: 51
Period size: 7 Copynumber: 12.0 Consensus size: 7
8354 GTTAGATTAC
8364 ACCCTAA
1 ACCCTAA
8371 ACCCTAA
1 ACCCTAA
*
8378 ACTCTAA
1 ACCCTAA
*
8385 ACTCTAA
1 ACCCTAA
**
8392 ACTATAA
1 ACCCTAA
* *
8399 ACTCTAT
1 ACCCTAA
8406 ACCCTAA
1 ACCCTAA
* *
8413 ATCTTAA
1 ACCCTAA
8420 A-CCTAA
1 ACCCTAA
* *
8426 ATCTTAA
1 ACCCTAA
* *
8433 ATCATAA
1 ACCCTAA
8440 ACCCTAA
1 ACCCTAA
8447 GCCTTAAGTA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
6 5 0.08
7 57 0.92
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.27
Consensus pattern (7 bp):
ACCCTAA
Found at i:8386 original size:14 final size:14
Alignment explanation
Indices: 8364--8426 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
8354 GTTAGATTAC
*
8364 ACCCTAAACCCTAA
1 ACCCTAAACTCTAA
*
8378 ACTCTAAACTCTAA
1 ACCCTAAACTCTAA
** *
8392 ACTATAAACTCTAT
1 ACCCTAAACTCTAA
8406 ACCCTAAA-TCTTAA
1 ACCCTAAACTC-TAA
8420 A-CCTAAA
1 ACCCTAAA
8427 TCTTAAATCA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
13 8 0.20
14 33 0.80
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.25
Consensus pattern (14 bp):
ACCCTAAACTCTAA
Found at i:8393 original size:21 final size:21
Alignment explanation
Indices: 8364--8446 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
8354 GTTAGATTAC
*
8364 ACCCTAAACCCTAAACTCTAA
1 ACCCTAAACCATAAACTCTAA
* * *
8385 ACTCTAAACTATAAACTCTAT
1 ACCCTAAACCATAAACTCTAA
* *
8406 ACCCTAAATCTTAAAC-CTAA
1 ACCCTAAACCATAAACTCTAA
* * * *
8426 ATCTTAAATCATAAACCCTAA
1 ACCCTAAACCATAAACTCTAA
8447 GCCTTAAGTA
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 16 0.33
21 33 0.67
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.27
Consensus pattern (21 bp):
ACCCTAAACCATAAACTCTAA
Found at i:8426 original size:13 final size:13
Alignment explanation
Indices: 8408--8433 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8398 AACTCTATAC
8408 CCTAAATCTTAAA
1 CCTAAATCTTAAA
8421 CCTAAATCTTAAA
1 CCTAAATCTTAAA
8434 TCATAAACCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
CCTAAATCTTAAA
Found at i:8550 original size:7 final size:7
Alignment explanation
Indices: 8538--8628 Score: 53
Period size: 7 Copynumber: 13.4 Consensus size: 7
8528 TAGATTATAG
8538 CCTAAAC
1 CCTAAAC
8545 CCTAAA-
1 CCTAAAC
*
8551 CTTAAAC
1 CCTAAAC
**
8558 TATAAAC
1 CCTAAAC
** *
8565 TATAAAT
1 CCTAAAC
*
8572 CCTAAAT
1 CCTAAAC
8579 CCTAAAC
1 CCTAAAC
*
8586 CTTAAAC
1 CCTAAAC
8593 CCT-AAC
1 CCTAAAC
8599 CCTAAA-
1 CCTAAAC
**
8605 CCTAAGT
1 CCTAAAC
*
8612 CTTAAAC
1 CCTAAAC
*
8619 TCTAAAC
1 CCTAAAC
8626 CCT
1 CCT
8629 TAATCTAATT
Statistics
Matches: 65, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
6 16 0.25
7 49 0.75
ACGTcount: A:0.43, C:0.31, G:0.01, T:0.25
Consensus pattern (7 bp):
CCTAAAC
Found at i:10009 original size:23 final size:23
Alignment explanation
Indices: 9982--10032 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
9972 CCTTTAGGCC
*
9982 TCGAGCTCAAAATCGAGCTTGAA
1 TCGAGCTCAAAATCGAGCCTGAA
* *
10005 TCGAGTTTAAAATCGAGCCTGAA
1 TCGAGCTCAAAATCGAGCCTGAA
10028 TCGAG
1 TCGAG
10033 TTTAGTCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (23 bp):
TCGAGCTCAAAATCGAGCCTGAA
Found at i:10033 original size:23 final size:23
Alignment explanation
Indices: 9990--10036 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
9980 CCTCGAGCTC
*
9990 AAAATCGAGCTTGAATCGAGTTT
1 AAAATCGAGCCTGAATCGAGTTT
10013 AAAATCGAGCCTGAATCGAGTTT
1 AAAATCGAGCCTGAATCGAGTTT
10036 A
1 A
10037 GTCTTGAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (23 bp):
AAAATCGAGCCTGAATCGAGTTT
Found at i:10130 original size:31 final size:31
Alignment explanation
Indices: 10079--10140 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
10069 AGTTTGAATC
*
10079 TTTTCGAGTTCGAGTCGAGTTTTAATATTTTA
1 TTTTCGAGTTCGAGTCGAGTTATAAT-TTTTA
* *
10111 TTTT-GAGTTTGAGTTGAGTTATAATTTTTA
1 TTTTCGAGTTCGAGTCGAGTTATAATTTTTA
10141 GCTCGTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 5 0.19
31 18 0.67
32 4 0.15
ACGTcount: A:0.23, C:0.05, G:0.19, T:0.53
Consensus pattern (31 bp):
TTTTCGAGTTCGAGTCGAGTTATAATTTTTA
Found at i:11148 original size:28 final size:27
Alignment explanation
Indices: 11088--11148 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
11078 ATCAATAATG
*
11088 AATTTGTTTAATAAAAATGAAATGTTA
1 AATTTTTTTAATAAAAATGAAATGTTA
* *
11115 TATTTTTTTATTAAAAATTGAGAAT-TTA
1 AATTTTTTTAATAAAAA-TGA-AATGTTA
11143 AATTTT
1 AATTTT
11149 GATATTATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 14 0.50
28 11 0.39
29 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (27 bp):
AATTTTTTTAATAAAAATGAAATGTTA
Found at i:13062 original size:2 final size:2
Alignment explanation
Indices: 13055--13095 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
13045 ATCACCAATT
13055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13096 ATTGATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14446 original size:25 final size:25
Alignment explanation
Indices: 14408--14460 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
14398 GGCTCTTCTT
*
14408 GACAGACAAACCCTCGGAGTTATTC
1 GACAGACAAACCCTCGGAGTTATCC
*
14433 GACAGACAAGCCCTCGGAGTTATCC
1 GACAGACAAACCCTCGGAGTTATCC
14458 GAC
1 GAC
14461 TGACGTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (25 bp):
GACAGACAAACCCTCGGAGTTATCC
Found at i:22533 original size:60 final size:60
Alignment explanation
Indices: 22440--22552 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 60
22430 AGTTGGGTGA
* * * * * * *
22440 CTATTTTGTAACTTTTAATAGTTGACTGGCTCAATAAAGCAACATCTTATAGTTGGAGAT
1 CTATTTTATAACTTTTAATAGTCGACAGACTCAAAAAAGCAACACCATATAGTTGGAGAT
* *
22500 CTATTTTATAACTTTTAATAGTCGAGAGACTCAAAAAAGTAACACCATATAGT
1 CTATTTTATAACTTTTAATAGTCGACAGACTCAAAAAAGCAACACCATATAGT
22553 CGGGGTACCA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (60 bp):
CTATTTTATAACTTTTAATAGTCGACAGACTCAAAAAAGCAACACCATATAGTTGGAGAT
Found at i:29458 original size:31 final size:32
Alignment explanation
Indices: 29393--29471 Score: 124
Period size: 33 Copynumber: 2.5 Consensus size: 32
29383 CGAACCCGAG
*
29393 CCGACCTGACCCGAATATCACACTTAAAAAAAC
1 CCGACCCGACCCGAATATCACACTT-AAAAAAC
*
29426 CCGACCCGACTCGAATATCACACTT-AAAAAC
1 CCGACCCGACCCGAATATCACACTTAAAAAAC
29457 CCGACCCGACCCGAA
1 CCGACCCGACCCGAA
29472 CAAAATAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 20 0.47
33 23 0.53
ACGTcount: A:0.38, C:0.38, G:0.11, T:0.13
Consensus pattern (32 bp):
CCGACCCGACCCGAATATCACACTTAAAAAAC
Found at i:29503 original size:62 final size:61
Alignment explanation
Indices: 29426--29541 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 61
29416 TTAAAAAAAC
* *
29426 CCGACCCGACTCGAATATCA-CACTTAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCAT
1 CCGACCCGACCCGAATAT-ATCAATTAAAAACCCGACCCGACCCGAA-AAAATAAAGTTTCAT
* * * *
29488 CCGACCCGACCCGAATATATGAATTAGAAATCCGACCCGACCCGAAATAATAAA
1 CCGACCCGACCCGAATATATCAATTAAAAACCCGACCCGACCCGAAAAAATAAA
29542 AAAATATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 8 0.17
62 39 0.83
ACGTcount: A:0.40, C:0.32, G:0.13, T:0.16
Consensus pattern (61 bp):
CCGACCCGACCCGAATATATCAATTAAAAACCCGACCCGACCCGAAAAAATAAAGTTTCAT
Found at i:39839 original size:23 final size:23
Alignment explanation
Indices: 39807--39851 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
39797 CATGCATGCG
*
39807 TTGCATCCATAGCTGGGAGATTC
1 TTGCACCCATAGCTGGGAGATTC
*
39830 TTGCACCCATAGTTGGGAGATT
1 TTGCACCCATAGCTGGGAGATT
39852 GCAGCCAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (23 bp):
TTGCACCCATAGCTGGGAGATTC
Found at i:39936 original size:83 final size:83
Alignment explanation
Indices: 39773--39939 Score: 246
Period size: 83 Copynumber: 2.0 Consensus size: 83
39763 AAGCTGGCGA
*
39773 CCAAACTTTAACCCTCTGCTCCCTCATGCATGCGTTGCATCCATAGCTGGGAGATTCTTGCACCC
1 CCAAACTTTAACCCTCTGCTCCCTCATGCATGCGTTGCATCCATAGCTGGGAGATTCCTGCACCC
* **
39838 ATAGTTGGGAGATTGCAG
66 ATAGCTGACAGATTGCAG
* * *
39856 CCAAGCTTTAACCCTCTGCTCCGTCATGCATGCGTTGCATCCATAGCTGGGAGATTCCTGCATCC
1 CCAAACTTTAACCCTCTGCTCCCTCATGCATGCGTTGCATCCATAGCTGGGAGATTCCTGCACCC
*
39921 ATAGCT-ACATTATTGCAG
66 ATAGCTGACA-GATTGCAG
39939 C
1 C
39940 GTTAATTTAG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
82 1 0.01
83 74 0.99
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (83 bp):
CCAAACTTTAACCCTCTGCTCCCTCATGCATGCGTTGCATCCATAGCTGGGAGATTCCTGCACCC
ATAGCTGACAGATTGCAG
Found at i:40302 original size:21 final size:21
Alignment explanation
Indices: 40277--40320 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
40267 AATTTAGTTA
40277 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
40298 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
40319 AT
1 AT
40321 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:40321 original size:28 final size:28
Alignment explanation
Indices: 40290--40355 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
40280 AGTTTGTTAG
40290 TATAAATTATTAGTTTGTTAGTTTAAGT
1 TATAAATTATTAGTTTGTTAGTTTAAGT
*
40318 TAT-ATTATATTAGTTTGTTAGTTTAAGT
1 TATAAAT-TATTAGTTTGTTAGTTTAAGT
*
40346 TATATATTAT
1 TATAAATTAT
40356 ATTATATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.91
29 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (28 bp):
TATAAATTATTAGTTTGTTAGTTTAAGT
Found at i:40902 original size:22 final size:23
Alignment explanation
Indices: 40877--40920 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40867 AATTAAGTTT
40877 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
40899 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
40921 GTATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:40922 original size:10 final size:10
Alignment explanation
Indices: 40907--40931 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40897 AATAATTTTA
40907 CAAAGTATTT
1 CAAAGTATTT
40917 CAAAGTATTT
1 CAAAGTATTT
40927 CAAAG
1 CAAAG
40932 CCAAAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (10 bp):
CAAAGTATTT
Found at i:40985 original size:22 final size:21
Alignment explanation
Indices: 40959--41012 Score: 92
Period size: 20 Copynumber: 2.6 Consensus size: 21
40949 CTCAGAGGGA
40959 ACCGATTCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCAA-GGGGT
40981 ACCGATT-CCCCCCAAGGGGT
1 ACCGATTCCCCCCCAAGGGGT
41001 ACCGATTCCCCC
1 ACCGATTCCCCC
41013 TGAATGGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.39
21 12 0.39
22 7 0.23
ACGTcount: A:0.19, C:0.44, G:0.22, T:0.15
Consensus pattern (21 bp):
ACCGATTCCCCCCCAAGGGGT
Found at i:42199 original size:21 final size:21
Alignment explanation
Indices: 42155--42199 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42145 GATTTCTGGG
* * *
42155 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
42176 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
42197 CAA
1 CAA
42200 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:42272 original size:23 final size:22
Alignment explanation
Indices: 42224--42272 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
42214 ACAGAATGTC
42224 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
42245 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
42268 AAGGA
1 AAGGA
42273 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:43916 original size:103 final size:103
Alignment explanation
Indices: 43737--43949 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
43727 GGGTCTACGC
*
43737 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
43802 CCTTGGCATATGTATATGATTCTTTAGGAATGATATAT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATAT
43840 GGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
43905 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATAT
43943 GGTCCTT
1 GGTCCTT
43950 ATGGACATTA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATAT
Found at i:43992 original size:23 final size:23
Alignment explanation
Indices: 43966--44025 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
43956 ATTATTATAT
*
43966 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTACGC
*
43989 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
44012 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
44026 TTTATATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:50599 original size:20 final size:21
Alignment explanation
Indices: 50564--50604 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
50554 GAATTTTCCA
*
50564 AAAAAAATTAATTTTTGAAAT
1 AAAAAAATTAATTTTTCAAAT
*
50585 AAAAAAATTGA-TTTTCAAAT
1 AAAAAAATTAATTTTTCAAAT
50605 TATTGTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (21 bp):
AAAAAAATTAATTTTTCAAAT
Found at i:51359 original size:24 final size:23
Alignment explanation
Indices: 51309--51382 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
51299 GCTTCAACTT
* *
51309 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
51332 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
*
51356 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTGTGAA
51379 TTTG
1 TTTG
51383 TTTGGATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 12 0.27
24 12 0.27
25 12 0.27
26 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.27, T:0.55
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:53150 original size:23 final size:26
Alignment explanation
Indices: 53119--53169 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 26
53109 TAAATCATTA
*
53119 AATATTTAT-AATAAAT-A-ATTATT
1 AATAATTATGAATAAATCATATTATT
53142 AATAATTATGAATAAATCATATTATT
1 AATAATTATGAATAAATCATATTATT
53168 AA
1 AA
53170 ATCATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 7 0.29
25 1 0.04
26 8 0.33
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
AATAATTATGAATAAATCATATTATT
Found at i:56404 original size:30 final size:31
Alignment explanation
Indices: 56368--56442 Score: 57
Period size: 30 Copynumber: 2.4 Consensus size: 31
56358 TTATAATAAT
*
56368 TATTTAATAATGATTTAATAATGAT-TAA-AA
1 TATTTAATAATGA-TTAATAATCATATAATAA
*
56398 TATTTAATGATTTGA-TAATAATCATTATAATAA
1 TATTTAAT-A-ATGATTAATAATCA-TATAATAA
*
56431 TGATTTAGTAAT
1 T-ATTTAATAAT
56443 AATCATTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
30 16 0.46
31 2 0.06
32 7 0.20
33 4 0.11
34 6 0.17
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.45
Consensus pattern (31 bp):
TATTTAATAATGATTAATAATCATATAATAA
Found at i:56417 original size:64 final size:67
Alignment explanation
Indices: 56338--56532 Score: 188
Period size: 64 Copynumber: 2.9 Consensus size: 67
56328 TATGATTTAA
* *
56338 TAATGATTTAGTAATAATCATTATAATAATTA-TT-TAATAATGATT-TAATAATGATTAAAATA
1 TAATGATTTAGTAATAATCATTATAATAATGATTTATAATAATCATTATAATAATGATTAAAATA
56400 TT
66 TT
56402 TAATGATTT-GATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTAAT
1 TAATGATTTAG-TAATAATCATTATAATAATGATTTA-TAATAATCATTATAATAATGA-TTAA-
56466 AATTATT
62 AA-TATT
* * * * * *
56473 AAAAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGA-AATAATCATTATAATAATGATT
1 -TAATGATTTAGT-A-ATAATCATTATAATAATGATTT-ATAATAATCATTATAATAATGATT
56533 TAGTAATAAT
Statistics
Matches: 110, Mismatches: 8, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
63 1 0.01
64 29 0.26
65 2 0.02
67 10 0.09
68 9 0.08
69 4 0.04
70 4 0.04
71 29 0.26
72 15 0.14
73 7 0.06
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (67 bp):
TAATGATTTAGTAATAATCATTATAATAATGATTTATAATAATCATTATAATAATGATTAAAATA
TT
Found at i:56442 original size:26 final size:26
Alignment explanation
Indices: 56335--56559 Score: 161
Period size: 26 Copynumber: 8.9 Consensus size: 26
56325 TATTATGATT
* *
56335 TAATAATGATTTAGTAATAATCA-TTA-
1 TAATAATCA-TTA-TAATAATGATTTAG
* *
56361 TAATAATTATT-TAATAATGATTTAA
1 TAATAATCATTATAATAATGATTTAG
* * ** *
56386 TAATGATTAAAATATTTAATGATTT-G
1 TAATAATCATTATA-ATAATGATTTAG
56412 ATAATAATCATTATAATAATGATTTAG
1 -TAATAATCATTATAATAATGATTTAG
56439 TAATAATCATTATAATAATGA-TT--
1 TAATAATCATTATAATAATGATTTAG
* *
56462 TAATAATTA-T-TAA-AAT-ATTTAA
1 TAATAATCATTATAATAATGATTTAG
* * * *
56484 TGATTTGATGATT-TAGTAATGATTT-G
1 T-A-ATAATCATTATAATAATGATTTAG
*
56510 AAATAATCATTATAATAATGATTTAG
1 TAATAATCATTATAATAATGATTTAG
56536 TAATAATCATTATAATAATGATTT
1 TAATAATCATTATAATAATGATTT
56560 TAATATTTAA
Statistics
Matches: 159, Mismatches: 24, Indels: 32
0.74 0.11 0.15
Matches are distributed among these distances:
19 1 0.01
20 5 0.03
21 3 0.02
22 2 0.01
23 17 0.11
24 13 0.08
25 27 0.17
26 67 0.42
27 24 0.15
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
TAATAATCATTATAATAATGATTTAG
Found at i:56735 original size:14 final size:14
Alignment explanation
Indices: 56661--56737 Score: 85
Period size: 14 Copynumber: 5.9 Consensus size: 14
56651 ATAATGATAA
56661 TAATGATTTAATAG
1 TAATGATTTAATAG
56675 TAATGATTT-A-A-
1 TAATGATTTAATAG
56686 TAATGA-TT--TAG
1 TAATGATTTAATAG
* *
56697 TAATGATTTTATAA
1 TAATGATTTAATAG
*
56711 TAATGATTTAATAC
1 TAATGATTTAATAG
56725 TAATGATTTAATA
1 TAATGATTTAATA
56738 TTTATTACTA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
10 3 0.05
11 12 0.22
12 3 0.05
13 1 0.02
14 36 0.65
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.45
Consensus pattern (14 bp):
TAATGATTTAATAG
Found at i:56907 original size:17 final size:17
Alignment explanation
Indices: 56867--56908 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
56857 AATGTTTTAC
56867 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
56884 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
56901 TAATTATT
1 TAATTATT
56909 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:56913 original size:59 final size:56
Alignment explanation
Indices: 56824--56944 Score: 152
Period size: 59 Copynumber: 2.1 Consensus size: 56
56814 TCGAATTTAT
* * * *
56824 TAATGATTTTTAAATATTTAATGAATTGATATTAATGTTTTACTAATTATTATTAA
1 TAATGATTTTTAAATATTTAATGAATTGATACTAATGATTTACTAATAATTACTAA
* * *
56880 TAATGATTTATTATTAATATTTAATTATTTGATACTAATGATTTACTAATAATTACTAG
1 TAATGATTT-TTA--AATATTTAATGAATTGATACTAATGATTTACTAATAATTACTAA
56939 TAATGA
1 TAATGA
56945 AATTATAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
56 9 0.16
57 3 0.05
59 43 0.78
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (56 bp):
TAATGATTTTTAAATATTTAATGAATTGATACTAATGATTTACTAATAATTACTAA
Found at i:59673 original size:13 final size:13
Alignment explanation
Indices: 59634--59681 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
59624 CTCACAAGAG
59634 CCTTATCTCCCTTT
1 CCTT-TCTCCCTTT
* *
59648 CTTCTTCTTCCTTT
1 CCT-TTCTCCCTTT
59662 CCTTTCTCCCTTT
1 CCTTTCTCCCTTT
59675 -CTTTCTC
1 CCTTTCTC
59682 GGCTGTAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 7 0.24
13 9 0.31
14 12 0.41
15 1 0.03
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (13 bp):
CCTTTCTCCCTTT
Found at i:59680 original size:12 final size:12
Alignment explanation
Indices: 59639--59709 Score: 52
Period size: 13 Copynumber: 5.2 Consensus size: 12
59629 AAGAGCCTTA
59639 TCTCCCTTTCTTCT
1 TCTCCCTTTC-T-T
*
59653 TCTTCCTTTCCTT
1 TCTCCCTTT-CTT
59666 TCTCCCTTTCTT
1 TCTCCCTTTCTT
*
59678 TCTCGGCTGTAATCTCT
1 TCTC-CCT-T--TCT-T
59695 TCTCCCTTTCTT
1 TCTCCCTTTCTT
59707 TCT
1 TCT
59710 TTTATGTTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
12 11 0.23
13 14 0.30
14 10 0.21
15 2 0.04
16 5 0.11
17 5 0.11
ACGTcount: A:0.03, C:0.38, G:0.04, T:0.55
Consensus pattern (12 bp):
TCTCCCTTTCTT
Found at i:59969 original size:29 final size:29
Alignment explanation
Indices: 59927--60032 Score: 149
Period size: 29 Copynumber: 3.7 Consensus size: 29
59917 GAGACAAGGT
*
59927 CGGAGTGCATGGCGACCTAGAAGGTCGCC
1 CGGAGTGCATGGCGACCTACAAGGTCGCC
59956 CGGAGTGCATGGCGACCTACAAGGTCGCC
1 CGGAGTGCATGGCGACCTACAAGGTCGCC
* * *
59985 CGGACTGCCTGGCGACCTTCAAGGTCGCC
1 CGGAGTGCATGGCGACCTACAAGGTCGCC
* * *
60014 CAGAGGGCATGACGACCTA
1 CGGAGTGCATGGCGACCTA
60033 TGGGTTGGGT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.21, C:0.31, G:0.34, T:0.14
Consensus pattern (29 bp):
CGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:64750 original size:145 final size:145
Alignment explanation
Indices: 64601--64887 Score: 565
Period size: 145 Copynumber: 2.0 Consensus size: 145
64591 AATAATATTT
64601 AATTTTAAGTTATTAAAAATACATATTATTCATTAAAAGATAATATATTTATCTACTCGATATTA
1 AATTTTAAGTTATTAAAAATACATATTATTCATTAAAAGATAATATATTTATCTACTCGATATTA
64666 CAATATCATTTTACATATTATATTATATTTTATATAAATAAATATGATACTTATGAAGATTATTT
66 CAATATCATTTTACATATTATATTATATTTTATATAAATAAATATGATACTTATGAAGATTATTT
64731 AAAAATATAAGTATA
131 AAAAATATAAGTATA
*
64746 AATTTTAAGTTATTAAAAATAGATATTATTCATTAAAAGATAATATATTTATCTACTCGATATTA
1 AATTTTAAGTTATTAAAAATACATATTATTCATTAAAAGATAATATATTTATCTACTCGATATTA
64811 CAATATCATTTTACATATTATATTATATTTTATATAAATAAATATGATACTTATGAAGATTATTT
66 CAATATCATTTTACATATTATATTATATTTTATATAAATAAATATGATACTTATGAAGATTATTT
64876 AAAAATATAAGT
131 AAAAATATAAGT
64888 TTGATATACT
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 141 1.00
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (145 bp):
AATTTTAAGTTATTAAAAATACATATTATTCATTAAAAGATAATATATTTATCTACTCGATATTA
CAATATCATTTTACATATTATATTATATTTTATATAAATAAATATGATACTTATGAAGATTATTT
AAAAATATAAGTATA
Found at i:65888 original size:42 final size:42
Alignment explanation
Indices: 65658--66093 Score: 471
Period size: 43 Copynumber: 10.2 Consensus size: 42
65648 TGAGAACAAA
* * *
65658 AAACGCCGCAATAGGTTAAGATCTATCGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAAC
* * *
65701 ACACGCCGCAAAAGGTTGC-TATCTCTAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGG-T-CAGATCTATAGCGGCGTTTTTGGAAC
** * *
65744 AAACGCTACAAAAGGTCAATATCTATAGCGACGTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* * *
65787 AAACGCCGCAAAAGGTTGATATCTATAGCGGCGTTTTAGGATAC
1 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGA-AC
* * * *
65831 AAACGCCGCAAAAGGTAAAATCTATAGCTGCGTTTTTTGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* * * * **
65873 AAACGCTGCAAAAGGTTGATATCTATAGCGGC-ATTTTGGAGT
1 AAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAAC
* * *
65915 AAACGTCGTAAAAGGTCAGATCTATAGCGGCGTTTTTGTAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* *
65957 AAACGCCCCAAAAGGTCAGATCTATAGCGGCGTTTTTGTAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
*
65999 AAACGCCGCAAAAGGTCAGATCTATGGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
* ** * *
66042 AAAAGCCGCAAAATATCAGATCTATAGCGGCATTTTTTGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
66085 AAACGCCGC
1 AAACGCCGC
66094 TAATTACCTT
Statistics
Matches: 334, Mismatches: 51, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
41 15 0.04
42 117 0.35
43 184 0.55
44 18 0.05
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Done.