Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001513.1 Hibiscus syriacus cultivar Beakdansim tig00002959_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: 66383
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5532 original size:16 final size:17
Alignment explanation
Indices: 5501--5533 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5491 TTTGATTATA
5501 GTTATATAATTATATTT
1 GTTATATAATTATATTT
*
5518 GTTATTTAA-TATATTT
1 GTTATATAATTATATTT
5534 TATCTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
GTTATATAATTATATTT
Found at i:6035 original size:8 final size:8
Alignment explanation
Indices: 6022--6048 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
6012 CAACCAATAT
6022 AAAAATTA
1 AAAAATTA
6030 AAAAATTA
1 AAAAATTA
6038 AAAAATTA
1 AAAAATTA
6046 AAA
1 AAA
6049 CGAAATTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAATTA
Found at i:8025 original size:30 final size:31
Alignment explanation
Indices: 7991--8067 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
7981 ATTGATTTGG
7991 TTTGATTTTATAATTTTTTTA-ATAATTAAA
1 TTTGATTTTATAATTTTTTTACATAATTAAA
* *
8021 TTTGATTTTACAA-TTTTTTACGATAATTAGA
1 TTTGATTTTATAATTTTTTTAC-ATAATTAAA
8052 TTTGATTTT-T-ATTTTT
1 TTTGATTTTATAATTTTT
8068 CTGTCAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 8 0.20
30 16 0.39
31 17 0.41
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (31 bp):
TTTGATTTTATAATTTTTTTACATAATTAAA
Found at i:10325 original size:9 final size:9
Alignment explanation
Indices: 10308--10341 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
10298 CTAAATATTT
10308 AAATAAAATA
1 AAAT-AAATA
10318 AAATAAATA
1 AAATAAATA
10327 AAATAAATA
1 AAATAAATA
*
10336 TAATAA
1 AAATAA
10342 TATTTTCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATAAATA
Found at i:10326 original size:14 final size:15
Alignment explanation
Indices: 10307--10338 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
10297 ACTAAATATT
10307 TAAATAAAATAAA-A
1 TAAATAAAATAAATA
10321 TAAATAAAATAAATA
1 TAAATAAAATAAATA
10336 TAA
1 TAA
10339 TAATATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAATAAAATAAATA
Found at i:11435 original size:21 final size:21
Alignment explanation
Indices: 11409--11448 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11399 GACTATCGCA
11409 TTGCGATTTCCCAAATTCGTG
1 TTGCGATTTCCCAAATTCGTG
* *
11430 TTGCGATTTTCCTAATTCG
1 TTGCGATTTCCCAAATTCG
11449 CAATGCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGTG
Found at i:11455 original size:21 final size:21
Alignment explanation
Indices: 11404--11456 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
11394 ATTCTGACTA
11404 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
** * *
11425 TCGTGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
11446 TCGCAATGCGA
1 TCGCATTGCGA
11457 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:11471 original size:20 final size:20
Alignment explanation
Indices: 11446--11559 Score: 174
Period size: 20 Copynumber: 5.7 Consensus size: 20
11436 TTTTCCTAAT
11446 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
11466 TCGCAACGCGATTACGCAAA
1 TCGCAATGCGAATACGTAAA
* *
11486 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
11507 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
11527 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
11547 TCGCAATGCGAAT
1 TCGCAATGCGAAT
11560 CTGACTATCG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
20 66 0.79
21 18 0.21
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:11477 original size:41 final size:40
Alignment explanation
Indices: 11431--11557 Score: 157
Period size: 41 Copynumber: 3.1 Consensus size: 40
11421 AAATTCGTGT
* *
11431 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGA-TTACCTAAATCGCAATGCGAATACGTAAATCGCAA
* * *
11472 CGCGATTACGC-AAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTAC-CTAAATCGCAATGCGAA-TACGTAAATCGCAA
* *
11513 TGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTACCTAAATCGCAATGCGAATACGTAAATCGCAA
11553 TGCGA
1 TGCGA
11558 ATCTGACTAT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
40 34 0.47
41 39 0.53
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (40 bp):
TGCGATTACCTAAATCGCAATGCGAATACGTAAATCGCAA
Found at i:12146 original size:14 final size:14
Alignment explanation
Indices: 12127--12180 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
12117 GGAAATGACT
12127 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
12141 ATCGCAACGGGAAATGAAA
1 ATCGCAAC--G--A-GAGA
12160 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
12174 ATCGCAA
1 ATCGCAA
12181 TGCGAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 18 0.55
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.33
ACGTcount: A:0.44, C:0.20, G:0.26, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:12164 original size:19 final size:18
Alignment explanation
Indices: 12100--12201 Score: 67
Period size: 19 Copynumber: 5.9 Consensus size: 18
12090 TAGTTTCGAG
12100 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAA--CGGA
**
12120 AATGACTATCGCAAC-G-
1 AATGAAAATCGCAACGGA
*
12136 -A-GAGAATCGCAACGGGA
1 AATGAAAATCGCAAC-GGA
12153 AATGAAAATCGCAAC-G-
1 AATGAAAATCGCAACGGA
* *
12169 -A-GAGAATCGCAATGCGA
1 AATGAAAATCGCAACG-GA
12186 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
12202 CGTCGCGTTG
Statistics
Matches: 63, Mismatches: 9, Indels: 21
0.68 0.10 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 2 0.03
17 2 0.03
18 3 0.05
19 22 0.35
20 12 0.19
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.12
Consensus pattern (18 bp):
AATGAAAATCGCAACGGA
Found at i:12164 original size:33 final size:33
Alignment explanation
Indices: 12106--12201 Score: 147
Period size: 33 Copynumber: 2.9 Consensus size: 33
12096 CGAGAATGAA
**
12106 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACG-GGAAATGAAAATCGCAACGAGAG
12140 AATCGCAACGGGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGGGAAATGAAAATCGCAACGAGAG
* *
12173 AATCGCAATGCGAAATGAAAATCGCAACG
1 AATCGCAACGGGAAATGAAAATCGCAACG
12202 CGTCGCGTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (33 bp):
AATCGCAACGGGAAATGAAAATCGCAACGAGAG
Found at i:12289 original size:20 final size:19
Alignment explanation
Indices: 12221--12297 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 19
12211 GCGATTCTCT
12221 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
**
12240 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
* *
12260 CGTTACGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
12280 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
12298 AACCAAAAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
19 17 0.35
20 31 0.63
21 1 0.02
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:14146 original size:94 final size:93
Alignment explanation
Indices: 13959--14334 Score: 582
Period size: 94 Copynumber: 4.1 Consensus size: 93
13949 TAGATTGCTT
* *
13959 AGTAAATTTATTCGGTTGCTGCCAATACTTCTAAAC----TATT-TATTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCT-TTAACACTGTGAAGTTAG
14019 TATTTGTCTTTTGTTTTGTCTTTTGGTTGA
65 TATTTGTC-TTTGTTTTGTCTTTTGGTTGA
* *
14049 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
14114 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
14143 AGTAAATTTGTTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
14208 ATTTGTCTTTGTTTTGTATTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
14237 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
14302 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
14330 AGTAA
1 AGTAA
14335 TGCAATCCAT
Statistics
Matches: 266, Mismatches: 14, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
90 33 0.12
93 26 0.10
94 206 0.77
95 1 0.00
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:14496 original size:19 final size:19
Alignment explanation
Indices: 14425--14487 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
14415 TCTTTTGGTT
* *
14425 GAAATGAAAATCGCAACGA
1 GAAACGAAAATCGCAACGC
*
14444 GAGAATGAAAATCGCAACGC
1 GA-AACGAAAATCGCAACGC
14464 GAAACGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
14483 GAAAC
1 GAAAC
14488 TATAATCGCG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 23 0.56
20 18 0.44
ACGTcount: A:0.49, C:0.21, G:0.22, T:0.08
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:15057 original size:21 final size:21
Alignment explanation
Indices: 15033--15099 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
15023 TCATTCCTCG
15033 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
15054 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
15075 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
15096 AGAG
1 AGAG
15100 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:15057 original size:42 final size:42
Alignment explanation
Indices: 14981--15099 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
14971 GACTCGCCTG
* * * *
14981 TCATCCCTC-AAGA-GTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCATTCAAGAGGCCACTA
* *
15023 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAGAGGCCACTA
* *
15065 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
15100 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 54 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCACTA
Found at i:16469 original size:14 final size:14
Alignment explanation
Indices: 16450--16485 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
16440 ATTGTTTAAT
16450 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
16464 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
16478 TGATTTGT
1 TGATTTGT
16486 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:16606 original size:19 final size:19
Alignment explanation
Indices: 16590--16636 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
16580 AAAAATGACT
*
16590 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
16609 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
16628 ATCGCAACG
1 ATCGCAACG
16637 ACAAAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:16683 original size:19 final size:19
Alignment explanation
Indices: 16661--16778 Score: 67
Period size: 19 Copynumber: 6.7 Consensus size: 19
16651 CGAAACTAAA
16661 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
16680 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * *
16695 -CCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
* *
16713 TTCACATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
16728 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
16746 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
16765 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
16779 AGACATTAAG
Statistics
Matches: 72, Mismatches: 16, Indels: 21
0.66 0.15 0.19
Matches are distributed among these distances:
14 17 0.24
16 5 0.07
17 5 0.07
19 35 0.49
20 10 0.14
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:16707 original size:33 final size:33
Alignment explanation
Indices: 16665--16758 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
16655 ACTAAATTCG
*
16665 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* * *
16698 CGTTGCGATTTTTATTTCACATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
16731 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
16759 AGTCATTTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:16777 original size:20 final size:20
Alignment explanation
Indices: 16731--16824 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
16721 GCGATTCTCT
**
16731 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
16750 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
16770 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
16789 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
16811 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
16825 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:19083 original size:14 final size:14
Alignment explanation
Indices: 19064--19100 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
19054 TCCCGTGGCA
19064 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAT
*
19078 TTTTCTTTGGGGAT
1 TTTTCTTCGGGGAT
19092 TTCTTCTTC
1 TT-TTCTTC
19101 TTCTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.05, C:0.16, G:0.22, T:0.57
Consensus pattern (14 bp):
TTTTCTTCGGGGAT
Found at i:20336 original size:61 final size:60
Alignment explanation
Indices: 20204--20399 Score: 191
Period size: 61 Copynumber: 3.2 Consensus size: 60
20194 CAGAATCTCG
* * * * * *
20204 TTGCGATTTAC-TAAATCGCAATGCAATTACGTAAATCGAAGTGCGAATTAGGAAAATCGCA
1 TTGCGATTTACGTAAATCGCAATGCGATTACGT-AATCGAATTGTGATTTACG-TAATCGCA
* * * *
20265 ATGCGA-TTACGTAAATCGCAATGCGATTACGTAATCGCATTGTGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAAATCGCAATGCGATTACGTAATCGAATTGTGATTTACGTAA-TCGCA
* * * * *
20325 TTGCGATTTACGT-AATCGCATTGCGATTTTCCTAATTCGTATTGTGATTTACGTAATCGTA
1 TTGCGATTTACGTAAATCGCAATGCGA-TTACGTAA-TCGAATTGTGATTTACGTAATCGCA
20386 TTGCGATTTACGTA
1 TTGCGATTTACGTA
20400 TTCGCATTGC
Statistics
Matches: 111, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
59 2 0.02
60 38 0.34
61 54 0.49
62 17 0.15
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (60 bp):
TTGCGATTTACGTAAATCGCAATGCGATTACGTAATCGAATTGTGATTTACGTAATCGCA
Found at i:20343 original size:41 final size:41
Alignment explanation
Indices: 20258--20411 Score: 188
Period size: 41 Copynumber: 3.8 Consensus size: 41
20248 GAATTAGGAA
* * * * *
20258 AATCGCAATGCGA-TTACGTAAATCGCAATGCGA-TTACGT
1 AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
*
20297 AATCGCATTGTGATTTTCCTAATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
* *
20338 AATCGCATTGCGATTTTCCTAATTCGTATTGTGATTTACGT
1 AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
* * *
20379 AATCGTATTGCGATTTACGT-ATTCGCATTGCGA
1 AATCGCATTGCGATTTTCCTAATTCGCATTGCGA
20412 ATTAGGAAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 11 0.11
40 27 0.27
41 61 0.62
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (41 bp):
AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
Found at i:20345 original size:20 final size:20
Alignment explanation
Indices: 20204--20411 Score: 172
Period size: 20 Copynumber: 10.3 Consensus size: 20
20194 CAGAATCTCG
20204 TTGCGATTTAC-TAAATCGCA
1 TTGCGATTTACGT-AATCGCA
* * *
20224 ATGC-AATTACGTAAATCGAA
1 TTGCGATTTACGT-AATCGCA
* * * *
20244 GTGCGAATTAGGAAAATCGCA
1 TTGCGATTTACG-TAATCGCA
*
20265 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
*
20285 ATGCGA-TTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
* * *
20304 TTGTGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAA-TCGCA
20325 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
* * *
20345 TTGCGATTTTCCTAATTCGTA
1 TTGCGATTTACGTAA-TCGCA
* *
20366 TTGTGATTTACGTAATCGTA
1 TTGCGATTTACGTAATCGCA
*
20386 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
20406 TTGCGA
1 TTGCGA
20412 ATTAGGAAAA
Statistics
Matches: 155, Mismatches: 26, Indels: 14
0.79 0.13 0.07
Matches are distributed among these distances:
19 16 0.10
20 89 0.57
21 50 0.32
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:20424 original size:41 final size:41
Alignment explanation
Indices: 20258--20433 Score: 178
Period size: 41 Copynumber: 4.3 Consensus size: 41
20248 GAATTAGGAA
* * * *
20258 AATCGCAATGCGA-TTACGTAAATCGCAATGCG-ATTACGT
1 AATCGCATTGCGATTTACCTAATTCGCATTGCGAATTACGT
* * *
20297 AATCGCATTGTGATTTTCCTAATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACCTAATTCGCATTGCGAATTACGT
* * * *
20338 AATCGCATTGCGATTTTCCTAATTCGTATTGTGATTTACGT
1 AATCGCATTGCGATTTACCTAATTCGCATTGCGAATTACGT
* * * *
20379 AATCGTATTGCGATTTACGT-ATTCGCATTGCGAATTAGGAA
1 AATCGCATTGCGATTTACCTAATTCGCATTGCGAATTACG-T
*
20420 AATCGCAATGCGAT
1 AATCGCATTGCGAT
20434 AGTCAGAATC
Statistics
Matches: 114, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
39 11 0.10
40 30 0.26
41 73 0.64
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (41 bp):
AATCGCATTGCGATTTACCTAATTCGCATTGCGAATTACGT
Found at i:22238 original size:41 final size:41
Alignment explanation
Indices: 22193--22369 Score: 324
Period size: 41 Copynumber: 4.4 Consensus size: 41
22183 ATTCGCGTTG
*
22193 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
22234 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
22275 CATTTCGCGTTGCGATAGTTGAAAATCGC---GCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
22313 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
22354 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
22370 TTTCCAAATT
Statistics
Matches: 132, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
38 38 0.29
41 94 0.71
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:22243 original size:20 final size:20
Alignment explanation
Indices: 22218--22375 Score: 124
Period size: 20 Copynumber: 7.9 Consensus size: 20
22208 TAGTTGAAAA
*
22218 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
22238 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
22259 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
22279 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
22300 TCGC---GCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
22317 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
22338 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
22358 TCGCGTTGCGATTTTCCA
1 TCGCGTTGCGATTTTCCA
22376 AATTTGTTGA
Statistics
Matches: 102, Mismatches: 30, Indels: 12
0.71 0.21 0.08
Matches are distributed among these distances:
17 7 0.07
18 5 0.05
20 53 0.52
21 37 0.36
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:22339 original size:79 final size:80
Alignment explanation
Indices: 22193--22369 Score: 320
Period size: 79 Copynumber: 2.2 Consensus size: 80
22183 ATTCGCGTTG
*
22193 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGC--TGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
22258 ATCGCGTTGCGATTTTC
64 ATCGCGTTGCGATTTTC
22275 CATTTCGCGTTGCGATAGTTGAAAATCGC-GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAAT
22339 CGCGTTGCGATTTTC
66 CGCGTTGCGATTTTC
22354 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
22370 TTTCCAAATT
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
79 65 0.69
82 29 0.31
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (80 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAAT
CGCGTTGCGATTTTC
Found at i:22511 original size:5 final size:6
Alignment explanation
Indices: 22460--22508 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
22450 GACACGTATT
*
22460 ACCACG ACCACA ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
22506 ACC
1 ACC
22509 CGAGACGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 10 0.24
6 31 0.76
ACGTcount: A:0.33, C:0.53, G:0.14, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:22884 original size:14 final size:14
Alignment explanation
Indices: 22865--22920 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
22855 CGTTCGTGAA
22865 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
22879 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
22892 --TT-GTTTATGTT
1 CGTTCGATTATGTT
22903 CGTTCGATTATGTT
1 CGTTCGATTATGTT
22917 CGTT
1 CGTT
22921 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:22899 original size:24 final size:24
Alignment explanation
Indices: 22872--22941 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
22862 GAACGTTCGA
*
22872 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
22896 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
22920 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
22942 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:23688 original size:16 final size:16
Alignment explanation
Indices: 23667--23733 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
23657 GTCTCCAACG
23667 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
23683 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
23699 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
23715 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
23729 TTTAT
1 TTTAT
23734 TAAATGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:23706 original size:32 final size:32
Alignment explanation
Indices: 23665--23725 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
23655 GGGTCTCCAA
23665 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
*
23697 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
23726 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:24221 original size:6 final size:6
Alignment explanation
Indices: 24200--24314 Score: 216
Period size: 6 Copynumber: 19.5 Consensus size: 6
24190 GTCCGTCTCG
24200 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
24246 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
24294 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
24315 AATACGTGTC
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.09
6 99 0.91
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:24445 original size:21 final size:21
Alignment explanation
Indices: 24405--24445 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24395 AATTTGGAAA
** *
24405 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
24426 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
24446 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:25527 original size:37 final size:36
Alignment explanation
Indices: 25452--25529 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 36
25442 TTTTTATATT
* *
25452 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTATTTTTGTAAAAAAATTATATAAATATTATCAA
* *
25488 TTTATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTATTTTTGTAAA-AAAATTATATAAATATTAT-CAA
25525 TTTAT
1 TTTAT
25530 AATATTATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 25 0.69
37 11 0.31
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTATTTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:25548 original size:18 final size:18
Alignment explanation
Indices: 25504--25551 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
25494 TTTTTAAAGA
*
25504 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
*
25523 -AATTTATAATATTATAC
1 AAATATATAATATTATAC
25540 AAATATATAATA
1 AAATATATAATA
25552 AGGACATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:26551 original size:20 final size:20
Alignment explanation
Indices: 26463--26573 Score: 84
Period size: 20 Copynumber: 5.5 Consensus size: 20
26453 AAAATACCAA
* *
26463 CAAATTCGCAACGC-GAACT
1 CAAATTCGCAACACAGAAGT
* **
26482 CCAATTTCGCAACACAG-TTT
1 -CAAATTCGCAACACAGAAGT
*
26502 CCAAATTCGCAACACA-AATT
1 -CAAATTCGCAACACAGAAGT
* *
26522 TATAAATCGCAACACAGAAGT
1 CA-AATTCGCAACACAGAAGT
*
26543 CAAATTCGCAACACATAAGT
1 CAAATTCGCAACACAGAAGT
*
26563 CAAATTGGCAA
1 CAAATTCGCAA
26574 ATCGCGTTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.01
20 68 0.92
21 5 0.07
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:26692 original size:20 final size:19
Alignment explanation
Indices: 26656--26710 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
26646 TAAACAGTAA
26656 TGCGATTTTAGTTTCGCGT
1 TGCGATTTTAGTTTCGCGT
*
26675 TGCGATTTTCATTTTCGCGT
1 TGCGATTTT-AGTTTCGCGT
*
26695 TGCGAATTTAAGTTTC
1 TGCG-ATTTTAGTTTC
26711 AGAAACTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.29
20 18 0.58
21 4 0.13
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.47
Consensus pattern (19 bp):
TGCGATTTTAGTTTCGCGT
Found at i:28565 original size:21 final size:21
Alignment explanation
Indices: 28523--28571 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
28513 AATGGTGCGC
* * *
28523 TACGTGGTGAGGTATCTACTT
1 TACGTGATGAGGTAGCCACTT
*
28544 TACGTGATGAGGTAGCCGCTT
1 TACGTGATGAGGTAGCCACTT
*
28565 TATGTGA
1 TACGTGA
28572 GATTGTTTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (21 bp):
TACGTGATGAGGTAGCCACTT
Found at i:28677 original size:4 final size:4
Alignment explanation
Indices: 28668--28713 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
28658 TTTTTCGGCA
* * *
28668 TTAT TTAT TTAT TTAT TTAT TTAC TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
28714 TCAGCGGCCC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:28927 original size:21 final size:21
Alignment explanation
Indices: 28858--28933 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
28848 ATTCACCTGT
*
28858 CATCGTTCAAGAGGCATCTCC
1 CATCGTTCAAGAGGCCTCTCC
* * *
28879 TATCATTCAAGAGGCC-CATCT
1 CATCGTTCAAGAGGCCTC-TCC
28900 CATCGTTCAAGAGGCCTCTCC
1 CATCGTTCAAGAGGCCTCTCC
*
28921 CACCGTTCAAGAG
1 CATCGTTCAAGAG
28934 CCCGATTCAC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.02
21 43 0.96
22 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCTCTCC
Found at i:30419 original size:64 final size:65
Alignment explanation
Indices: 30286--30441 Score: 244
Period size: 64 Copynumber: 2.4 Consensus size: 65
30276 TTAATTGAAT
*
30286 TTTACATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATTATTTTTTGCTT
1 TTTA-ATTGATTTGTAAAAGTTGATTTATTTAATTTGATGAGGAAATAAGAATTATTTTTTGCTT
30351 G
65 G
* *
30352 TTTAATTGATTTATAAAAGTTGATTTATTTAA-TTGATGTA-TAAATAAGAATTATTTTTTGCTT
1 TTTAATTGATTTGTAAAAGTTGATTTATTTAATTTGATG-AGGAAATAAGAATTATTTTTTGCTT
30415 G
65 G
*
30416 TTTAATTGATTTGTAAAAGTTAATTT
1 TTTAATTGATTTGTAAAAGTTGATTT
30442 GTTGTTTTAA
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
64 53 0.63
65 27 0.32
66 4 0.05
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.51
Consensus pattern (65 bp):
TTTAATTGATTTGTAAAAGTTGATTTATTTAATTTGATGAGGAAATAAGAATTATTTTTTGCTTG
Found at i:31482 original size:83 final size:83
Alignment explanation
Indices: 31338--31508 Score: 279
Period size: 83 Copynumber: 2.1 Consensus size: 83
31328 GATAATATCC
* * *
31338 GAAAGGCATTCTTCGGATATCCAATCTTCCTACTTGTTAACCAAAAATTACGATGGTCGGGATTT
1 GAAAAGCATTCTTCGGATATCCAATCTTCCTACTTGTTAACAAAAAATTACAATGGTCGGGATTT
*
31403 CCCTCGTGTTTAAAGTTG
66 CCCTCGCGTTTAAAGTTG
* *
31421 GAAAAGCATTCTTCGGATATCCAATCTTCCTGCTTGTTAATAAAAAATTACAATGGTCGGGATTT
1 GAAAAGCATTCTTCGGATATCCAATCTTCCTACTTGTTAACAAAAAATTACAATGGTCGGGATTT
*
31486 CCCTCGCGTTTAGAGTTG
66 CCCTCGCGTTTAAAGTTG
31504 GAAAA
1 GAAAA
31509 AAACAATGGA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (83 bp):
GAAAAGCATTCTTCGGATATCCAATCTTCCTACTTGTTAACAAAAAATTACAATGGTCGGGATTT
CCCTCGCGTTTAAAGTTG
Found at i:31660 original size:18 final size:18
Alignment explanation
Indices: 31637--31673 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31627 ATTTATATAT
31637 ATTGAAATTTAAACTCAA
1 ATTGAAATTTAAACTCAA
*
31655 ATTGAAATTTAAATTCAA
1 ATTGAAATTTAAACTCAA
31673 A
1 A
31674 CTCCAATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (18 bp):
ATTGAAATTTAAACTCAA
Found at i:32091 original size:25 final size:25
Alignment explanation
Indices: 32063--32112 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
32053 TATTATTTTC
* *
32063 CAAATAATGTACCTATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
32088 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
32113 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:32234 original size:20 final size:20
Alignment explanation
Indices: 32186--32227 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
32176 GTACACTTTT
32186 GCAACGCGAAAGTCAAATTC
1 GCAACGCGAAAGTCAAATTC
32206 GCAACGCGAAAGTCAAATTC
1 GCAACGCGAAAGTCAAATTC
32226 GC
1 GC
32228 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.14
Consensus pattern (20 bp):
GCAACGCGAAAGTCAAATTC
Found at i:34840 original size:24 final size:24
Alignment explanation
Indices: 34813--34866 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
34803 TTGAAACGTT
*
34813 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
34837 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
34861 ATCAAA
1 ATCAAA
34867 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:34880 original size:24 final size:24
Alignment explanation
Indices: 34829--34880 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
34819 ATCTGAGTAT
* *
34829 TGACCAAGATCAAAGTCCGAGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
34853 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
34877 TGAC
1 TGAC
34881 TAGTACCCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:35857 original size:19 final size:19
Alignment explanation
Indices: 35816--35878 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
35806 TTAAATTCGT
* *
35816 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTC-A
35836 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
35855 GTTGCGAAATTGAAATTCA
1 GTTGCGAATTTGAAATTCA
35874 GTTGC
1 GTTGC
35879 AAGTGTTGCG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:44375 original size:18 final size:18
Alignment explanation
Indices: 44349--44399 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
44339 CAGTGTAAAC
44349 AAATGAAAATGTAAAAGCA
1 AAAT-AAAATGTAAAAGCA
44368 AAATAAAATGTAAAAGCA
1 AAATAAAATGTAAAAGCA
44386 AAATAAAATGTAAA
1 AAATAAAATGTAAA
44400 GGTTGGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.18
Consensus pattern (18 bp):
AAATAAAATGTAAAAGCA
Found at i:51694 original size:16 final size:15
Alignment explanation
Indices: 51669--51698 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
51659 AATTATTTAC
51669 AAAATAAAATAAAAA
1 AAAATAAAATAAAAA
51684 AAAATTAAAATAAAA
1 AAAA-TAAAATAAAA
51699 GGAAAAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATAAAATAAAAA
Done.