Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001379.1 Hibiscus syriacus cultivar Beakdansim tig00002692_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: 60789
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:19880 original size:19 final size:20
Alignment explanation
Indices: 19838--19886 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
19828 ATCAGCGAGG
* *
19838 GTATCGATACTGGCCCTTGG
1 GTATCGATACTGGACCTTGA
*
19858 GTATCGATACT-TACCTTGA
1 GTATCGATACTGGACCTTGA
*
19877 GTATCAATAC
1 GTATCGATAC
19887 CAAAAATGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (20 bp):
GTATCGATACTGGACCTTGA
Found at i:22449 original size:21 final size:21
Alignment explanation
Indices: 22425--22479 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
22415 CGATTTTCCC
*
22425 AATTCGCAATGCGAATAAGTA
1 AATTCGCAATGCGAATAAGAA
* **
22446 AATT-GCAACGCGAATTGGAA
1 AATTCGCAATGCGAATAAGAA
*
22466 AAATCGCAATGCGA
1 AATTCGCAATGCGA
22480 TAGTGACTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
AATTCGCAATGCGAATAAGAA
Found at i:22493 original size:20 final size:20
Alignment explanation
Indices: 22468--22582 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
22458 AATTGGAAAA
* *
22468 ATCGCAATGCGATAGTGACT
1 ATCGCAACGCGATACTGACT
* *
22488 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
22509 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
22529 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
22549 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
22569 TTCGCAACGAGATA
1 ATCGCAACGCGATA
22583 ATACAGAATC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.77
21 15 0.18
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:22495 original size:41 final size:41
Alignment explanation
Indices: 22465--22596 Score: 151
Period size: 41 Copynumber: 3.2 Consensus size: 41
22455 GCGAATTGGA
* *
22465 AAAATCGCAATGCGATAGTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
22506 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAAT-AC
** * * *
22548 --TTTCGCAACGCGATTCTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
22587 AGAATCGCAA
1 AAAATCGCAA
22597 TGTGATTTTC
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.03
40 32 0.42
41 41 0.53
42 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:22750 original size:12 final size:12
Alignment explanation
Indices: 22731--22764 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
22721 CTCTCCGGCG
22731 ACATCCGTTCCT
1 ACATCCGTTCCT
*
22743 ATATCCGTTCCT
1 ACATCCGTTCCT
22755 ACATCC-TTCC
1 ACATCCGTTCC
22765 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:23347 original size:24 final size:24
Alignment explanation
Indices: 23320--23373 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
23310 GTATTCGAAA
*
23320 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
23344 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
23368 TTTGAT
1 TTTGAT
23374 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:25865 original size:20 final size:20
Alignment explanation
Indices: 25840--25957 Score: 209
Period size: 20 Copynumber: 5.9 Consensus size: 20
25830 ATTCATTTGA
25840 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
25860 CTATCGCAACGCAAAAATGG
1 CTATCGCAACGCGAAAATGG
25880 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
25900 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
25920 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
25940 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
25958 CGTAATGCGA
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 93 1.00
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:26017 original size:19 final size:19
Alignment explanation
Indices: 25976--26040 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
25966 GAAATGAAAA
25976 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
25992 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
26009 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
26028 TCGCATTGCGATT
1 TCGCATTGCGATT
26041 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:26199 original size:14 final size:14
Alignment explanation
Indices: 26180--26216 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
26170 CATCAATTAA
26180 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
26194 ACAAATCATCTTTT
1 ACAAATCAACATTT
26208 ACAAATCAA
1 ACAAATCAA
26217 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:28138 original size:19 final size:20
Alignment explanation
Indices: 28083--28150 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
28073 GAAACTTAAA
**
28083 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
28103 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
* **
28123 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGACT
28142 ATCGCAACG
1 ATCGCAACG
28151 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:28158 original size:14 final size:14
Alignment explanation
Indices: 28139--28197 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
28129 ATGCGAAATG
28139 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
28153 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
28172 AAAATCGCAACGAC
1 AAAATCGCAACGAC
28186 AAAATCGCAACG
1 AAAATCGCAACG
28198 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:28160 original size:33 final size:33
Alignment explanation
Indices: 28123--28214 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
28113 GGAAATGGCT
28123 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
28156 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
28189 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
28215 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:28177 original size:19 final size:19
Alignment explanation
Indices: 28123--28219 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
28113 GGAAATGGCT
28123 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
28142 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
28156 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
28175 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
28189 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
28208 ATCGCAATGCGA
1 ATCGCAATGCGA
28220 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:28308 original size:20 final size:20
Alignment explanation
Indices: 28257--28300 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28247 TTGCGATTTT
* *
28257 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGTGATAGC
*
28276 CATTTCCGCGTTGTGATAGT
1 CATTTCCGCGTTGTGATAGC
28296 CATTT
1 CATTT
28301 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCCGCGTTGTGATAGC
Found at i:30249 original size:20 final size:20
Alignment explanation
Indices: 30201--30259 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
30191 AATAGTTTCT
** *
30201 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
30221 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
30241 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
30260 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:30797 original size:20 final size:20
Alignment explanation
Indices: 30768--30839 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
30758 ATTATGCATT
30768 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
* *
30788 ATCGCATTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
* *
30808 ATCGCGTTGCAAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
30828 ATCTCGTTGCGA
1 ATCGCGTTGCGA
30840 TTTTGTATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:30873 original size:20 final size:20
Alignment explanation
Indices: 30848--30897 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
30838 GATTTTGTAT
30848 TATCGCATTGCGATAGCCAA
1 TATCGCATTGCGATAGCCAA
*
30868 TATCGCATTGCGATAGCCAG
1 TATCGCATTGCGATAGCCAA
30888 TATCGCATTG
1 TATCGCATTG
30898 TGATTTTCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (20 bp):
TATCGCATTGCGATAGCCAA
Found at i:30879 original size:41 final size:41
Alignment explanation
Indices: 30747--30881 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
30737 CGCTTTGAAA
*
30747 ATCGCATTGCGATTATGCATTATCGCGTTGCGAAAGTCAGA-
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCA-AT
* * * *
30788 ATCGCATTGCGA--AAGTCAGTATCGCGTTGCAAAAGTCAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAAT
* * * * * *
30828 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGCCAAT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAAT
30869 ATCGCATTGCGAT
1 ATCGCATTGCGAT
30882 AGCCAGTATC
Statistics
Matches: 73, Mismatches: 17, Indels: 8
0.74 0.17 0.08
Matches are distributed among these distances:
39 2 0.03
40 29 0.40
41 40 0.55
42 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAAT
Found at i:30903 original size:61 final size:61
Alignment explanation
Indices: 30788--30904 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
30778 GAAAGTCAGA
* * * * * *
30788 ATCGCATTGCGAAAGTCAGTATCGCGTTGCAAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGCCAATATCGCATTGCAAAAGCCAGTATCGCATTGCGATTTTGTATT
* * * *
30849 ATCGCATTGCGATAGCCAATATCGCATTGCGATAGCCAGTATCGCATTGTGATTTT
1 ATCGCATTGCGAAAGCCAATATCGCATTGCAAAAGCCAGTATCGCATTGCGATTTT
30905 CCCAATTCGC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGCCAATATCGCATTGCAAAAGCCAGTATCGCATTGCGATTTTGTATT
Found at i:30983 original size:21 final size:22
Alignment explanation
Indices: 30931--30983 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
30921 ATTTACTTAT
30931 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
30952 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
30973 TCGCATTGCGA
1 TCGCATTGCGA
30984 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:34126 original size:22 final size:22
Alignment explanation
Indices: 34101--34151 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
34091 CACCACAGCT
*
34101 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
34123 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
34145 CGTAGAA
1 CGTAGAA
34152 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:34152 original size:22 final size:22
Alignment explanation
Indices: 34109--34153 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
34099 CTCGTATAAA
34109 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
34131 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
34153 T
1 T
34154 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:34421 original size:30 final size:31
Alignment explanation
Indices: 34371--34429 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
34361 TAGACATAGT
*
34371 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
* *
34401 ATTTACATACTTTTATCACATAGTGCATA
1 ATTTACATACCTTTAACACATAGTGCATA
34430 GAACTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:34486 original size:29 final size:29
Alignment explanation
Indices: 34444--34515 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
34434 TTTTCTGCAT
**
34444 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* *
34473 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
34502 ATTCATGTCATGTA
1 ATTCATGTCATGTA
34516 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:34934 original size:66 final size:66
Alignment explanation
Indices: 34819--34967 Score: 210
Period size: 66 Copynumber: 2.2 Consensus size: 66
34809 TTTTCTCATG
* * *
34819 GGGGAATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAATTCATATACGATG
1 GGGGTATCGGTT-CCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
34884 -A
65 AA
* * * *
34885 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
1 GGGGTATCGGTTCCCCCCCT-GGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
34950 AA
65 AA
34952 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
34968 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
65 8 0.11
66 49 0.66
67 17 0.23
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATGA
A
Found at i:34977 original size:21 final size:21
Alignment explanation
Indices: 34947--34989 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34937 ATCATATTCG
* *
34947 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
34968 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
34989 T
1 T
34990 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:34980 original size:67 final size:65
Alignment explanation
Indices: 34819--34989 Score: 193
Period size: 66 Copynumber: 2.6 Consensus size: 65
34809 TTTTCTCATG
* * *
34819 GGGGAATCGGTTCCCCCCCCT-GGGGTATCGATTCCCCTCAAGCAATCTGGAATTCATATACGAT
1 GGGGTATCGGTT--CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
34883 GA
64 GA
* * * *
34885 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
34950 AA
65 -A
* *
34952 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
34990 AACCCAGAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
65 14 0.15
66 49 0.53
67 29 0.32
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.27
Consensus pattern (65 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATGA
Found at i:41033 original size:22 final size:22
Alignment explanation
Indices: 41016--41082 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
41006 CTCGTATAAA
41016 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
41038 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
41060 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
41082 T
1 T
41083 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:41352 original size:30 final size:31
Alignment explanation
Indices: 41302--41360 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
41292 TAGACATAGT
*
41302 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
* *
41332 ATTTACATACTTTTATCACATAGTGCATA
1 ATTTACATACCTTTAACACATAGTGCATA
41361 GAACTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:41417 original size:29 final size:29
Alignment explanation
Indices: 41375--41446 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
41365 TTTTCTGCAT
**
41375 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* *
41404 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
41433 ATTCATGTCATGTA
1 ATTCATGTCATGTA
41447 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:41866 original size:67 final size:66
Alignment explanation
Indices: 41749--41899 Score: 212
Period size: 67 Copynumber: 2.3 Consensus size: 66
41739 TTTTTCTCAT
* * *
41749 GGGGGAATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAATTCATATACGAT
1 GGGGGTATCGGTT-CCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
41814 GA
65 GA
* * * *
41816 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTT
1 GGGGGTATCGGTTCCCCCCCT-GGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
41881 GA
65 GA
*
41883 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
41900 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
66 8 0.11
67 67 0.89
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.26
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
A
Found at i:41909 original size:21 final size:21
Alignment explanation
Indices: 41879--41921 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41869 ATCATATTCG
* *
41879 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
41900 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
41921 T
1 T
41922 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:41910 original size:67 final size:66
Alignment explanation
Indices: 41750--41921 Score: 195
Period size: 67 Copynumber: 2.6 Consensus size: 66
41740 TTTTCTCATG
* * *
41750 GGGGAATCGGTTCCCCCCCCT-GGGGTATCGATTCCCCTCAAGCAATCTGGAATTCATATACGAT
1 GGGGTATCGGTT--CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
*
41814 GAG
64 GAA
* * * *
41817 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTTG
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATG
41882 AA
65 AA
* *
41884 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
41922 AACCCAGAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
65 6 0.07
66 8 0.09
67 78 0.85
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGATGA
A
Found at i:44789 original size:19 final size:20
Alignment explanation
Indices: 44761--44798 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
44751 ACACACAAAA
*
44761 CAACTTTTTTTC-TCTCAAT
1 CAACTGTTTTTCTTCTCAAT
44780 CAACTGTTTTTCTTCTCAA
1 CAACTGTTTTTCTTCTCAA
44799 CAAATCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.21, C:0.26, G:0.03, T:0.50
Consensus pattern (20 bp):
CAACTGTTTTTCTTCTCAAT
Found at i:52511 original size:26 final size:26
Alignment explanation
Indices: 52475--52526 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
52465 ATGCCAATTC
52475 TTGAAGTCCTTGTAGATATTTATGCT
1 TTGAAGTCCTTGTAGATATTTATGCT
52501 TTGAAGTCCTTGTAGATATTTATGCT
1 TTGAAGTCCTTGTAGATATTTATGCT
52527 GTATGTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (26 bp):
TTGAAGTCCTTGTAGATATTTATGCT
Found at i:60051 original size:3 final size:3
Alignment explanation
Indices: 60038--60104 Score: 99
Period size: 3 Copynumber: 24.0 Consensus size: 3
60028 TTGTTTGGAG
60038 ATA AT- ATA ATA ATA ATA AT- ATA AT- ATA ATA ATA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
60082 ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
60105 GTTGAGGCAG
Statistics
Matches: 59, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
2 10 0.17
3 49 0.83
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:60054 original size:11 final size:11
Alignment explanation
Indices: 60046--60101 Score: 80
Period size: 11 Copynumber: 5.1 Consensus size: 11
60036 AGATAATATA
60046 ATAATAATAAT
1 ATAATAATAAT
60057 ATAAT-ATAAT
1 ATAATAATAAT
60067 AATAA-AATAAT
1 -ATAATAATAAT
60078 AATAATAATAAT
1 -ATAATAATAAT
60090 ATAATAATAAT
1 ATAATAATAAT
60101 A
1 A
60102 ATAGTTGAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.12
11 31 0.74
12 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:60057 original size:14 final size:14
Alignment explanation
Indices: 60038--60104 Score: 95
Period size: 14 Copynumber: 4.9 Consensus size: 14
60028 TTGTTTGGAG
60038 ATAAT-ATAATAATA
1 ATAATAATAAT-ATA
60052 ATAAT-ATAATATA
1 ATAATAATAATATA
60065 ATAATAA-AATAATA
1 ATAATAATAAT-ATA
60079 ATAATAATAATATA
1 ATAATAATAATATA
60093 ATAATAATAATA
1 ATAATAATAATA
60105 GTTGAGGCAG
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
13 11 0.22
14 36 0.72
15 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATATA
Done.