Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002372.1 Hibiscus syriacus cultivar Beakdansim tig00004845_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: 133374
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:104274 original size:41 final size:43
Alignment explanation
Indices: 104186--104274 Score: 121
Period size: 41 Copynumber: 2.1 Consensus size: 43
104176 CGACTCACCT
** *
104186 GTCATCCCTCAAGAGTCCCCTCCAATTGTTCAAGAGGCCCCTA
1 GTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
*
104229 -TCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCAC-A
1 GTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
104269 GTCATC
1 GTCATC
104275 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 1 0.02
41 21 0.51
42 19 0.46
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (43 bp):
GTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:105719 original size:14 final size:14
Alignment explanation
Indices: 105685--105723 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
105675 TTGATTGTTT
105685 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
105699 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
105713 TGTTGATTTGT
1 AATTGATTTGT
105724 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:105979 original size:34 final size:34
Alignment explanation
Indices: 105936--106002 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
105926 GCGATTTTCA
* *
105936 TTTCGCATTGCCATTTTCGCGTTGCGATAGTCAT
1 TTTCGCATTGCCATTTCCCCGTTGCGATAGTCAT
*
105970 TTTCGCATTGCGATTTCCCCGTTGCGATAGTCA
1 TTTCGCATTGCCATTTCCCCGTTGCGATAGTCA
106003 AATGAATGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (34 bp):
TTTCGCATTGCCATTTCCCCGTTGCGATAGTCAT
Found at i:106231 original size:20 final size:20
Alignment explanation
Indices: 106206--106282 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
106196 ATTGTGATTT
*
106206 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
106226 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
106246 TCAGTATCGCGTTGCGAAAA
1 TCAGAATCGCGTTGCGAAAG
* *
106266 TAAGTATCGCGTTGCGA
1 TCAGAATCGCGTTGCGA
106283 TTTTGTATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:106313 original size:41 final size:41
Alignment explanation
Indices: 106250--106327 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
106240 CGAAAGTCAG
* *
106250 TATCGCGTTGCGAAAATAAGTATCGCGTTGCGATTTTGTAT
1 TATCGCATTGCGAAAATAAGTATCGCATTGCGATTTTGTAT
* * *
106291 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAATAAGTATCGCATTGCGATTTT
106328 CCAAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (41 bp):
TATCGCATTGCGAAAATAAGTATCGCATTGCGATTTTGTAT
Found at i:106324 original size:20 final size:20
Alignment explanation
Indices: 106215--106323 Score: 112
Period size: 20 Copynumber: 5.4 Consensus size: 20
106205 TTCAGAATCT
*
106215 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
106235 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
* *
106255 CGTTGCGAAAATAAGTATCG
1 CGTTGCGAAAGTCAGTATCG
** *
106275 CGTTGCGATTTTGT-ATTATCG
1 CGTTGCGA--AAGTCAGTATCG
* *
106296 CATTGCGATAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
*
106316 CATTGCGA
1 CGTTGCGA
106324 TTTTCCAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
19 3 0.04
20 59 0.78
21 13 0.17
22 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCG
Found at i:106339 original size:21 final size:20
Alignment explanation
Indices: 106313--106364 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
106303 ATAGTCAGTA
*
106313 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
* **
106334 TCGCATTGTGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
106354 TCGCATTGCGA
1 TCGCATTGCGA
106365 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:106400 original size:20 final size:20
Alignment explanation
Indices: 106375--106467 Score: 105
Period size: 20 Copynumber: 4.7 Consensus size: 20
106365 ATTGGGAAAA
** *
106375 TCGCAACGTTATACTTACTT
1 TCGCAACGCGATACTGACTT
106395 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
106415 TTGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
* * *
106435 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATACTGACTT
*
106455 TCGCAACGAGATA
1 TCGCAACGCGATA
106468 ATACAGAATC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:106622 original size:12 final size:12
Alignment explanation
Indices: 106603--106643 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
106593 CTCTCCGGTG
106603 ACATCCGTTCCT
1 ACATCCGTTCCT
* *
106615 ATATCCGTTCAT
1 ACATCCGTTCCT
106627 ACATCC-TTCCT
1 ACATCCGTTCCT
106638 -CATCCG
1 ACATCCG
106644 GCAACATGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
10 5 0.21
11 4 0.17
12 15 0.62
ACGTcount: A:0.20, C:0.39, G:0.07, T:0.34
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:107242 original size:24 final size:24
Alignment explanation
Indices: 107191--107244 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
107181 GTATTCAAAA
* *
107191 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* *
107215 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
107239 TTTGAT
1 TTTGAT
107245 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:107436 original size:12 final size:12
Alignment explanation
Indices: 107419--107443 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
107409 ATATAATCCT
107419 GAAGAAGAAAAA
1 GAAGAAGAAAAA
107431 GAAGAAGAAAAA
1 GAAGAAGAAAAA
107443 G
1 G
107444 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:110024 original size:21 final size:21
Alignment explanation
Indices: 109958--110024 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
109948 GTGAATCGGG
*
109958 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
109978 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
110000 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
110021 CTCT
1 CTCT
110025 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:110043 original size:42 final size:41
Alignment explanation
Indices: 109958--110080 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
109948 GTGAATCGGG
* * * *
109958 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
110000 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * * *
110042 CTATTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
110081 CGAGTTGAGC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 4 0.06
42 56 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:110405 original size:91 final size:91
Alignment explanation
Indices: 110298--110481 Score: 270
Period size: 92 Copynumber: 2.0 Consensus size: 91
110288 ATTTCAAACT
110298 TTCAACCAAAAGAC-AAAC-AAAGACAAATA-TAACTTC-ACAGTGTTAA-AGAATACACAGTTT
1 TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCAACAGTGTTAATA-AAT----AGTTT
110358 AGCAGAATTGGCAGCAACCGAATAAATTTAC
61 AGCAGAATTGGCAGCAACCGAATAAATTTAC
110389 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCAACAGTGTTAATAAATAGTTTAGCA
1 TTCAACCAAAAGACAAAAC-AAAAGACAAATACTAACTTCAACAGTGTTAATAAATAGTTTAGCA
*
110454 GTATTGGCAGCAACCGAATAAATTTAC
65 GAATTGGCAGCAACCGAATAAATTTAC
110481 T
1 T
110482 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 1, Indels: 11
0.88 0.01 0.11
Matches are distributed among these distances:
91 14 0.16
92 40 0.47
94 11 0.13
95 7 0.08
96 13 0.15
97 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (91 bp):
TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCAACAGTGTTAATAAATAGTTTAGCAG
AATTGGCAGCAACCGAATAAATTTAC
Found at i:112192 original size:20 final size:19
Alignment explanation
Indices: 112167--112286 Score: 89
Period size: 20 Copynumber: 6.7 Consensus size: 19
112157 TTTTGGTTGC
112167 AATGAAAATCGCAACGAGA
1 AATGAAAATCGCAACGAGA
*
112186 TAATGAAAATCGCAACGCGGA
1 -AATGAAAATCGCAACG-AGA
**
112207 AATGACTATCGCAACGAG-
1 AATGAAAATCGCAACGAGA
*
112225 -A-G--AATCGCAACGCGA
1 AATGAAAATCGCAACGAGA
**
112240 AATGACTATCGCAACGAG-
1 AATGAAAATCGCAACGAGA
*
112258 -A-G--AATCGCAACGCGA
1 AATGAAAATCGCAACGAGA
112273 AATGAAAATCGCAA
1 AATGAAAATCGCAA
112287 TGCGATTTGG
Statistics
Matches: 79, Mismatches: 10, Indels: 23
0.71 0.09 0.21
Matches are distributed among these distances:
14 20 0.25
16 4 0.05
17 4 0.05
19 19 0.24
20 30 0.38
21 2 0.03
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
AATGAAAATCGCAACGAGA
Found at i:112233 original size:14 final size:14
Alignment explanation
Indices: 112214--112269 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
112204 GGAAATGACT
112214 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
112228 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
112245 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
112261 ATCGCAACG
1 ATCGCAACG
112270 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:112247 original size:33 final size:33
Alignment explanation
Indices: 112193--112286 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
112183 AGATAATGAA
112193 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACGAGAG
112227 AATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
**
112260 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGACTATCGCAA
112287 TGCGATTTGG
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 47 0.81
34 11 0.19
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAG
Found at i:112334 original size:33 final size:33
Alignment explanation
Indices: 112297--112378 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
112287 TGCGATTTGG
*
112297 TTTCGCGTTGCGATTATCTCGTTGCAAT-TTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCAATAGTT-A
* *
112330 TTTCGCGTTGCGATTCTCTCGTTGCGATAGTTA
1 TTTCGCGTTGCGATTATCTCGTTGCAATAGTTA
112363 TTTCTGCGTTGCGATT
1 TTTC-GCGTTGCGATT
112379 TTCATTCTCG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 31 0.70
34 13 0.30
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCTCGTTGCAATAGTTA
Found at i:112950 original size:20 final size:20
Alignment explanation
Indices: 112909--113020 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
112899 GCTATGTAAA
* *
112909 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
*
112929 TCACATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
112949 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
112970 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
112990 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
113010 TCGCATTGCGA
1 TCGCATTGCGA
113021 ATTATGAAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 56 0.73
21 18 0.23
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:112984 original size:41 final size:40
Alignment explanation
Indices: 112927--113020 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
112917 CGATAGTAAG
* * *
112927 ATTCACATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
112967 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
113008 ATTCGCATTGCGA
1 ATTCGCATTGCGA
113021 ATTATGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:113033 original size:41 final size:42
Alignment explanation
Indices: 112949--113083 Score: 134
Period size: 41 Copynumber: 3.3 Consensus size: 42
112939 ATTTACGTAT
* * * *
112949 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACT--TAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTA-TGAAAA
*
112990 TCGCGTTGCGATTTACGT-ATTCGCATTGCGAATTATGAAAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
** * * * *
113031 TCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
113072 TCGCATTGCGAT
1 TCGCATTGCGAT
113084 AGTCATAATC
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
39 1 0.01
40 21 0.28
41 54 0.71
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (42 bp):
TCGCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAA
Found at i:113041 original size:21 final size:21
Alignment explanation
Indices: 113017--113076 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
113007 TATTCGCATT
*
113017 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
113038 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
113058 GCGAATTAGGAAAATCGCA
1 GCGAATTACGAAAATCGCA
113077 TTGCGATAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:113053 original size:61 final size:61
Alignment explanation
Indices: 112934--113054 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 61
112924 AAGATTCACA
* * * ** * *
112934 TTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTTAATCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAATCGCG
*
112995 TTGCGATTTACGTATTCGCATTGCGAATTAT-GAAAATCGCAACGCGA-ATACGTAAATCGC
1 TTGCGATTTACGTATTCGCATTGCG-ATTATCCAAAATCGCAACGCGATATAC-TAAATCGC
113055 AATGCGAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 3 0.06
61 43 0.86
62 4 0.08
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (61 bp):
TTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAATCGCG
Found at i:113081 original size:21 final size:21
Alignment explanation
Indices: 113010--113082 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
113000 ATTTACGTAT
* *
113010 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
113031 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
113051 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
*
113072 TCGCATTGCGA
1 TCGCAATGCGA
113083 TAGTCATAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:113449 original size:31 final size:31
Alignment explanation
Indices: 113398--113523 Score: 139
Period size: 31 Copynumber: 4.1 Consensus size: 31
113388 AAATATGTGC
* * *
113398 CTAAAGTTTACGACGTTATACTTTTAAGTGT
1 CTAACGTTTCCGACGTTATACTTTTAGGTGT
* *
113429 CTAACGTTTCTGGCGTTATACTTTTAGGTGT
1 CTAACGTTTCCGACGTTATACTTTTAGGTGT
* * *
113460 TTAATGTTTCCGACGTTATACTTTTTAGGTAT
1 CTAACGTTTCCGACGTTATAC-TTTTAGGTGT
* *
113492 CTAACGTTT-CAAC-TTACACTTTTAGGTGT
1 CTAACGTTTCCGACGTTATACTTTTAGGTGT
113521 CTA
1 CTA
113524 GACCATAATT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
29 12 0.15
30 5 0.06
31 46 0.58
32 16 0.20
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (31 bp):
CTAACGTTTCCGACGTTATACTTTTAGGTGT
Found at i:116960 original size:12 final size:12
Alignment explanation
Indices: 116943--116969 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
116933 AATCTCCTTG
116943 TCATCATTGCCA
1 TCATCATTGCCA
116955 TCATCATTGCCA
1 TCATCATTGCCA
116967 TCA
1 TCA
116970 GTTGCTGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.33, G:0.07, T:0.33
Consensus pattern (12 bp):
TCATCATTGCCA
Found at i:117075 original size:36 final size:36
Alignment explanation
Indices: 117023--117094 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
117013 GGCAACCAAC
* * *
117023 TTTGGAAAATATTTTTTTAAAGTTTGGTAAATATTTT
1 TTTGAAAAATATTTTTTCAAAGTTTGATAAA-ATTTT
117060 TTTGAAAAATA-TTTTTCAAAGTTTGATAAAATTTT
1 TTTGAAAAATATTTTTTCAAAGTTTGATAAAATTTT
117095 GGTAGATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 5 0.16
36 17 0.53
37 10 0.31
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.51
Consensus pattern (36 bp):
TTTGAAAAATATTTTTTCAAAGTTTGATAAAATTTT
Found at i:123374 original size:41 final size:43
Alignment explanation
Indices: 123322--123516 Score: 161
Period size: 41 Copynumber: 4.7 Consensus size: 43
123312 ACTTCGACTA
*
123322 TCGCATTGCGATTTTCCAAATTCGCGTTGCGAT-TTACATA-T
1 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATAGTACATAGT
** ** * *
123363 TCGCATTGCGATAGTCGGAGTTCGCGTTGCGATAGTCCA-AGT
1 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATAGTACATAGT
* * * * * * *
123405 TCACGTTGTGA-TTTACATATTCGCATTGCGATAGT-CAAAGT
1 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATAGTACATAGT
* * *
123446 TCGCGTTGCGATTTTCCAAATTCACGTTGCGAT-TTACATA-T
1 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATAGTACATAGT
** *
123487 TCGCATTGCGATAGTCGAAATTCGCGTTGC
1 TCGCATTGCGATTTTCCAAATTCGCGTTGC
123517 CCAAAATCGC
Statistics
Matches: 118, Mismatches: 31, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
40 2 0.02
41 84 0.71
42 32 0.27
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (43 bp):
TCGCATTGCGATTTTCCAAATTCGCGTTGCGATAGTACATAGT
Found at i:123412 original size:62 final size:62
Alignment explanation
Indices: 123322--123516 Score: 309
Period size: 62 Copynumber: 3.1 Consensus size: 62
123312 ACTTCGACTA
* * *
123322 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACATATTCGCATTGCGATAGTCGGAGT
1 TCGCGTTGCGATTTTCCAAATTCACGTTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
** * * *
123384 TCGCGTTGCGATAGTCCAAGTTCACGTTGTGATTTACATATTCGCATTGCGATAGTCAAAGT
1 TCGCGTTGCGATTTTCCAAATTCACGTTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
*
123446 TCGCGTTGCGATTTTCCAAATTCACGTTGCGATTTACATATTCGCATTGCGATAGTCGAAAT
1 TCGCGTTGCGATTTTCCAAATTCACGTTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
123508 TCGCGTTGC
1 TCGCGTTGC
123517 CCAAAATCGC
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 119 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (62 bp):
TCGCGTTGCGATTTTCCAAATTCACGTTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
Found at i:123620 original size:6 final size:6
Alignment explanation
Indices: 123609--123640 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
123599 AGACACATAT
123609 GACCAC GACCAC GACCAC GACCAC GACCAC GA
1 GACCAC GACCAC GACCAC GACCAC GACCAC GA
123641 GACGCGACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.47, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:124352 original size:6 final size:6
Alignment explanation
Indices: 124341--124367 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
124331 TCTCGTCTCG
124341 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
124368 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:124525 original size:21 final size:21
Alignment explanation
Indices: 124465--124577 Score: 108
Period size: 21 Copynumber: 5.5 Consensus size: 21
124455 TTTGGACTAT
*
124465 CGCGAACTTCGACTATCGCAA
1 CGCGAACTTGGACTATCGCAA
* * *
124486 TGCGAA-TATGTA-AATCGCAA
1 CGCGAACT-TGGACTATCGCAA
124506 CGCGAACTTGGACTATCGCAA
1 CGCGAACTTGGACTATCGCAA
*
124527 CGTGAACTTGGACTATCGCAA
1 CGCGAACTTGGACTATCGCAA
* * **
124548 --CGAATTTGAAAAATCGCAA
1 CGCGAACTTGGACTATCGCAA
124567 CGCGAACTTGG
1 CGCGAACTTGG
124578 TCATCTTGAC
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
19 14 0.19
20 16 0.22
21 42 0.58
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (21 bp):
CGCGAACTTGGACTATCGCAA
Done.