Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001986.1 Hibiscus syriacus cultivar Beakdansim tig00004047_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: 69274
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3930 original size:20 final size:19
Alignment explanation
Indices: 3905--3958 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
3895 GCGAAATAAA
3905 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
3925 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
3945 AATCGCAACGCGAT
1 AATCGCAACGCGAT
3959 GATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:4092 original size:20 final size:20
Alignment explanation
Indices: 4069--4218 Score: 149
Period size: 20 Copynumber: 7.5 Consensus size: 20
4059 AATTCTGACT
*
4069 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGAATCCGTAA
*
4089 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGAATCCGT-AA
*
4110 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGAATCCGTAA
* * *
4130 TTCGCAACGCGATTACGTAA
1 ATCGCAACGCGAATCCGTAA
* *
4150 ATCGCAACGCGATTACGTAA
1 ATCGCAACGCGAATCCGTAA
* * *
4170 ATCACAATGCGAATCTGTAA
1 ATCGCAACGCGAATCCGTAA
* * *
4190 ATCGCAATGTGAATCTGTAA
1 ATCGCAACGCGAATCCGTAA
4210 ATCGCAACG
1 ATCGCAACG
4219 AGATTCTAAC
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
20 93 0.85
21 17 0.15
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATCCGTAA
Found at i:5122 original size:24 final size:24
Alignment explanation
Indices: 5071--5124 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
5061 GTATTCGAAA
*
5071 TTTGATCTTAGTCAATACCCGGAC
1 TTTGATCTTAGTCAATACCCAGAC
* * *
5095 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTAGTCAATACCCAGAC
5119 TTTGAT
1 TTTGAT
5125 GATTTTTCAG
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:0.19, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATCTTAGTCAATACCCAGAC
Found at i:8055 original size:42 final size:42
Alignment explanation
Indices: 8009--8088 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
7999 TTATGACAGT
* * *
8009 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
8051 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
8089 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:8525 original size:94 final size:94
Alignment explanation
Indices: 8364--8723 Score: 605
Period size: 94 Copynumber: 3.8 Consensus size: 94
8354 TGCATCAGAT
* * * * *
8364 AACAAAGACAAATACTAACTTTAGAGTATTAAAGAATACATAGTTTAGCAGAATTGGCAGCAGCC
1 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
8429 GAACAAATTTACTTTCAACCAAAAGACAA
66 GAACAAATTTACTTTCAACCAAAAGACAA
8458 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
1 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
8523 GAACAAATTTACTTTCAACCAAAAGACAA
66 GAACAAATTTACTTTCAACCAAAAGACAA
*
8552 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGTAGAATTGGCAGCAACC
1 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
*
8617 GAATAAATTTAC-TTCAACCAAAAGACAA
66 GAACAAATTTACTTTCAACCAAAAGACAA
* * *
8645 AACAAACGATAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAAC
1 AACAAA-GACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAC
*
8710 CGAATAAATTTACT
65 CGAACAAATTTACT
8724 AAGCAATCTA
Statistics
Matches: 253, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
93 22 0.09
94 231 0.91
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
GAACAAATTTACTTTCAACCAAAAGACAA
Found at i:9105 original size:21 final size:20
Alignment explanation
Indices: 9081--9155 Score: 50
Period size: 21 Copynumber: 3.8 Consensus size: 20
9071 GTGACGGGAT
9081 AGGTGATGGCTCTCGTTGTAG
1 AGGTGATGGCTCTCG-TGTAG
* * *
9102 AGGTGTATAG-TCTGGTCG-ATC
1 AGGTG-ATGGCTCTCGT-GTA-G
*
9123 AGGTGATGGCTCTAG-GT-G
1 AGGTGATGGCTCTCGTGTAG
9141 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
9156 AAGTGGAGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
18 14 0.33
19 1 0.02
20 5 0.12
21 19 0.45
22 3 0.07
ACGTcount: A:0.16, C:0.15, G:0.39, T:0.31
Consensus pattern (20 bp):
AGGTGATGGCTCTCGTGTAG
Found at i:9564 original size:21 final size:22
Alignment explanation
Indices: 9522--9564 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
9512 AATAACAAAT
*
9522 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
9544 ATTA-TAATT-TTAAAAACATTA
1 ATTAGTAATTGTTAAAAA-ATTA
9565 TATCGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:10437 original size:20 final size:20
Alignment explanation
Indices: 10414--10456 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
10404 ATGAAAATCA
10414 CAACGA-GAGAATGACTATCG
1 CAACGAGGA-AATGACTATCG
*
10434 CAACGCGGAAATGACTATCG
1 CAACGAGGAAATGACTATCG
10454 CAA
1 CAA
10457 TGCGAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (20 bp):
CAACGAGGAAATGACTATCG
Found at i:10465 original size:19 final size:19
Alignment explanation
Indices: 10401--10499 Score: 108
Period size: 19 Copynumber: 5.1 Consensus size: 19
10391 TCTTTTGGTT
* *
10401 GAAATGAAAATCACAACGA
1 GAAATGAAAATCGCAACGC
**
10420 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
10440 GGAAATGACTATCGCAATGC
1 -GAAATGAAAATCGCAACGC
10460 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
10479 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
10498 GA
1 GA
10500 TTTTGGTTTC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 38 0.55
20 29 0.42
21 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:10492 original size:38 final size:40
Alignment explanation
Indices: 10401--10499 Score: 121
Period size: 38 Copynumber: 2.5 Consensus size: 40
10391 TCTTTTGGTT
* * * **
10401 GAAATGAAAATCACAACGAGAGAATGACTATCGCAACGCG
1 GAAATGAAAATCGCAATGCGAGAATGAAAATCGCAACGCG
**
10441 GAAATGACTATCGCAATGCGA-AATGAAAATCGCAACGC-
1 GAAATGAAAATCGCAATGCGAGAATGAAAATCGCAACGCG
10479 GAAATGAAAATCGCAATGCGA
1 GAAATGAAAATCGCAATGCGA
10500 TTTTGGTTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 19 0.38
39 15 0.30
40 16 0.32
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (40 bp):
GAAATGAAAATCGCAATGCGAGAATGAAAATCGCAACGCG
Found at i:10560 original size:21 final size:21
Alignment explanation
Indices: 10519--10562 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
10509 CGCGTTGCGA
**
10519 TTCTCTCATTGCGATTTTCAT
1 TTCTCTCATTGCGATAGTCAT
*
10540 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCATTGCGATAGTCAT
10561 TT
1 TT
10563 ACATGTTGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.50
Consensus pattern (21 bp):
TTCTCTCATTGCGATAGTCAT
Found at i:10597 original size:20 final size:20
Alignment explanation
Indices: 10527--10597 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
10517 GATTCTCTCA
10527 TTGCGATTTTCATTTCTC-TCG
1 TTGCGATTTTCATTT-TCAT-G
** *
10548 TTGCGATAGTCATTTACATG
1 TTGCGATTTTCATTTTCATG
*
10568 TTGCGGTTTTCATTTTCATG
1 TTGCGATTTTCATTTTCATG
10588 TTGCGATTTT
1 TTGCGATTTT
10598 AAGTTTAGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (20 bp):
TTGCGATTTTCATTTTCATG
Found at i:11159 original size:20 final size:20
Alignment explanation
Indices: 11134--11326 Score: 192
Period size: 20 Copynumber: 9.6 Consensus size: 20
11124 CTTTAAAAAT
11134 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
11154 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
11174 TGTCGTTGCAATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * * *
11195 CACATTGCGATTTATGTATT
1 CGCGTTGCGATTTACGGATA
* *
11215 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
11235 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
11255 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
11275 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
11295 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
11316 CTCGTTGCGAT
1 CGCGTTGCGAT
11327 AGTCAGAATC
Statistics
Matches: 137, Mismatches: 30, Indels: 12
0.77 0.17 0.07
Matches are distributed among these distances:
20 106 0.77
21 31 0.23
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:11228 original size:40 final size:40
Alignment explanation
Indices: 11136--11326 Score: 292
Period size: 40 Copynumber: 4.7 Consensus size: 40
11126 TTAAAAATCG
*
11136 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
* * * *
11177 CGTTGCAATTTACGGATACACATTGCGATTTATGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
*
11217 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
*
11257 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
*
11298 CGTTGCGATTTACGGATACTCGTTGCGAT
1 CGTTGCGATTTACGGATACGCGTTGCGAT
11327 AGTCAGAATC
Statistics
Matches: 136, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
40 73 0.54
41 63 0.46
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:11360 original size:81 final size:81
Alignment explanation
Indices: 11136--11367 Score: 231
Period size: 81 Copynumber: 2.9 Consensus size: 81
11126 TTAAAAATCG
* * * * * * *
11136 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGT-ATTGTCGTTGCAATTTACGGATACACAT
1 CGTTGCGATTTACAGATACGCGTTGCGA-TTCACGTAATCG-CGTTGCGATTTAAGGATACGCGT
*
11200 TGCGA-TTTATGTATTCT
64 TGCGATTTTACGTATTCT
* * * *
11217 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTG
1 CGTTGCGATTTACAGATACGCGTTGCGATTCACGTAATCGCGTTGCGATTTAAGGATACGCGTTG
*
11282 CGATTTTACGTATTGT
66 CGATTTTACGTATTCT
* * * *
11298 CGTTGCGATTTACGGATACTCGTTGCGATAGTCA-G-AATCGCGTTGCGATTTATATG-TTCGCG
1 CGTTGCGATTTACAGATACGCGTTGCGAT--TCACGTAATCGCGTTGCGATTTA-AGGATACGCG
11360 TTGCGATT
63 TTGCGATT
11368 CTGGAAAATC
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
80 32 0.25
81 93 0.72
82 2 0.02
83 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (81 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTCACGTAATCGCGTTGCGATTTAAGGATACGCGTTG
CGATTTTACGTATTCT
Found at i:11360 original size:121 final size:121
Alignment explanation
Indices: 11136--11367 Score: 344
Period size: 121 Copynumber: 1.9 Consensus size: 121
11126 TTAAAAATCG
11136 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCAATTTACGGATACACATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCAATTTACGGATACACATT
* * *
11201 GCGATTTATGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
66 GCGATTCATGTAATCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
* * *
11257 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACTCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCAATTTACGGATACACATT
* *
11322 GCGATAGTCA-G-AATCGCGTTGCGATTTATATG-TTCGCGTTGCGATT
66 GCGAT--TCATGTAATCGCGTTGCGATTTACA-GATACGCGTTGCGATT
11368 CTGGAAAATC
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
121 96 0.96
122 2 0.02
123 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (121 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCAATTTACGGATACACATT
GCGATTCATGTAATCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
Found at i:11466 original size:20 final size:20
Alignment explanation
Indices: 11416--11470 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
11406 GATTCTTCAT
11416 AATCGCGTTGCGATTCTGGG
1 AATCGCGTTGCGATTCTGGG
* **
11436 AATTGATTTGCGATTCT-GG
1 AATCGCGTTGCGATTCTGGG
11455 AGATCGCGTTGCGATT
1 A-ATCGCGTTGCGATT
11471 TTTATTTCGC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.35
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTGGG
Found at i:14951 original size:54 final size:54
Alignment explanation
Indices: 14835--14980 Score: 161
Period size: 54 Copynumber: 2.6 Consensus size: 54
14825 TGTAAGGGTA
* * *
14835 GTATCTATACCTGAAGGATGGTATTGATACCCTTAAAACATTCGAATGCCAGATTG
1 GTATCGATACCTG-AGGAT-GTATCGATACCCTTGAAACATTCGAATGCCAGATTG
** *
14891 GTATCGATACCTTGAGGATGTATCGATACCCTTGAAACA-TCGAATGTTA-TTTCG
1 GTATCGATACC-TGAGGATGTATCGATACCCTTGAAACATTCGAATGCCAGATT-G
* *
14945 GTATCGATACCATGAGGAGGTATCTATACCCTTGAA
1 GTATCGATACC-TGAGGATGTATCGATACCCTTGAA
14981 GGGTAGTATC
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
53 2 0.03
54 42 0.53
55 18 0.23
56 15 0.19
57 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (54 bp):
GTATCGATACCTGAGGATGTATCGATACCCTTGAAACATTCGAATGCCAGATTG
Found at i:20821 original size:22 final size:23
Alignment explanation
Indices: 20791--20837 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
20781 TTAAAATATT
20791 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
20814 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
20836 TA
1 TA
20838 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:20844 original size:30 final size:33
Alignment explanation
Indices: 20786--20861 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 33
20776 AATATTTAAA
* *
20786 ATATTTATTAATATTTCTAATAATATAAT-ATT
1 ATATTTATTAATATTTATAATAAAATAATAATT
20818 ATATTT-TTAATA-TTATAATAAAATAATCAATT
1 ATATTTATTAATATTTATAATAAAATAAT-AATT
20850 ATA-TTA-TAATAT
1 ATATTTATTAATAT
20862 AATATAAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 13 0.34
31 13 0.34
32 12 0.32
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (33 bp):
ATATTTATTAATATTTATAATAAAATAATAATT
Found at i:20873 original size:20 final size:23
Alignment explanation
Indices: 20827--20877 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
20817 TATATTTTTA
*
20827 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAATG
*
20850 ATATTATAATATAAT-AT-AA-G
1 ATATTATAATAAAATAATCAATG
20870 ATATTATA
1 ATATTATA
20878 TTTTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 8 0.31
21 2 0.08
22 2 0.08
23 14 0.54
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAATG
Found at i:20997 original size:10 final size:9
Alignment explanation
Indices: 20944--20999 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 9
20934 TTCATAAAAA
20944 TAATATTAT
1 TAATATTAT
20953 TAA-ATTAT
1 TAATATTAT
* *
20961 TAATAATGAC
1 TAAT-ATTAT
20971 TAATATTAT
1 TAATATTAT
20980 ATATATATATAT
1 -TA-ATAT-TAT
20992 TAATATTA
1 TAATATTA
21000 ATATAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
8 8 0.21
9 8 0.21
10 13 0.34
11 6 0.16
12 3 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (9 bp):
TAATATTAT
Found at i:21269 original size:15 final size:15
Alignment explanation
Indices: 21245--21274 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21235 TCGTAAAACG
*
21245 TTTTCCAAAAAATGT
1 TTTTCAAAAAAATGT
21260 TTTTCAAAAAAATGT
1 TTTTCAAAAAAATGT
21275 AATCCATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (15 bp):
TTTTCAAAAAAATGT
Found at i:23989 original size:16 final size:16
Alignment explanation
Indices: 23968--24006 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
23958 ATCCTCGTGC
23968 ACAAACAATCACTATT
1 ACAAACAATCACTATT
23984 ACAAACAATCACTATT
1 ACAAACAATCACTATT
24000 ACAAACA
1 ACAAACA
24007 TCAGACATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.21
Consensus pattern (16 bp):
ACAAACAATCACTATT
Found at i:29375 original size:2 final size:2
Alignment explanation
Indices: 29370--29427 Score: 59
Period size: 2 Copynumber: 30.0 Consensus size: 2
29360 ATTTGTTTTT
* *
29370 TA TA TA TA T- TA TC TA T- TT TA T- TA TA TA TA TA TA 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
*
29409 AA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA -TA TA
29428 ATTTTTGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
1 3 0.06
2 42 0.89
3 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29482 original size:38 final size:38
Alignment explanation
Indices: 29414--29697 Score: 126
Period size: 36 Copynumber: 7.3 Consensus size: 38
29404 ATATAAATAT
* *
29414 ATATATATAGTATAATTTTTGAAAATA-TTTTTGAAAAA
1 ATATATATA-TATAATTTTAGAAAAGATTTTTTGAAAAA
29452 ATATA-ATATATAATTTTCAGAAAACGATTTTTTGAATATATA
1 ATATATATATATAATTTT-AGAAAA-GATTTTTTGAA-A-A-A
* *
29494 TATATATATATTATATAGTTTTTGAAAACA-TTTTT-AAAATA
1 -ATATATATA-TATA-A-TTTTAGAAAAGATTTTTTGAAAA-A
* *
29535 GATATA-ATATATAGTTTT-GAAAACA--TTTTGAAAACA
1 -ATATATATATATAATTTTAGAAAAGATTTTTTGAAAA-A
* ** * *
29571 CTTATATATTATATATATTTTTTAAAA-ATATTTTGAAAAT
1 -ATATATA-TATATA-ATTTTAGAAAAGATTTTTTGAAAAA
* ** **
29611 ATATAT-TATATAGTTTTTTAAAA-ACATTTTG-AAAA
1 ATATATATATATAATTTTAGAAAAGATTTTTTGAAAAA
* * * *
29646 ATATATAATATATAGTTTT-TAAAACATTTTTTGAAAAC
1 ATATAT-ATATATAATTTTAGAAAAGATTTTTTGAAAAA
*
29684 TTATATATAATATA
1 ATATATAT-ATATA
29698 TAGTTTTTAA
Statistics
Matches: 203, Mismatches: 20, Indels: 46
0.75 0.07 0.17
Matches are distributed among these distances:
35 13 0.06
36 47 0.23
37 38 0.19
38 25 0.12
39 22 0.11
40 8 0.04
41 18 0.09
42 2 0.01
43 7 0.03
44 8 0.04
45 5 0.02
46 6 0.03
47 4 0.02
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (38 bp):
ATATATATATATAATTTTAGAAAAGATTTTTTGAAAAA
Found at i:29501 original size:45 final size:46
Alignment explanation
Indices: 29452--29547 Score: 113
Period size: 47 Copynumber: 2.1 Consensus size: 46
29442 TTTTGAAAAA
* ** *
29452 ATATAATATATAATTTTCAGAAAACGATTTTTTGAATATATAT-ATAT
1 ATATATTATATAATTTT-AGAAAAC-ATTTTTAAAATAGATATAATAT
* *
29499 ATATATTATATAGTTTTTGAAAACATTTTTAAAATAGATATAATAT
1 ATATATTATATAATTTTAGAAAACATTTTTAAAATAGATATAATAT
29545 ATA
1 ATA
29548 GTTTTGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
45 14 0.33
46 13 0.31
47 15 0.36
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (46 bp):
ATATATTATATAATTTTAGAAAACATTTTTAAAATAGATATAATAT
Found at i:29503 original size:47 final size:44
Alignment explanation
Indices: 29452--29547 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 44
29442 TTTTGAAAAA
** *
29452 ATATAATATATAATTTTCAGAAAACGATTTTTTGAATATATATATAT
1 ATATAATATATAATTTT-AGAAAAC-ATTTTTAAAATAGATATA-AT
* * *
29499 ATATATTATATAGTTTTTGAAAACATTTTTAAAATAGATATAAT
1 ATATAATATATAATTTTAGAAAACATTTTTAAAATAGATATAAT
29543 ATATA
1 ATATA
29548 GTTTTGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
44 7 0.16
45 15 0.35
46 6 0.14
47 15 0.35
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (44 bp):
ATATAATATATAATTTTAGAAAACATTTTTAAAATAGATATAAT
Found at i:29593 original size:77 final size:76
Alignment explanation
Indices: 29411--29755 Score: 309
Period size: 77 Copynumber: 4.4 Consensus size: 76
29401 TATATATAAA
* * *
29411 TATATATATATAGTATAATTTTTGAAAATATTTTTGAAAA-AATATAATATATAATTTTCAGAAA
1 TATATATATATA-TATAGTTTTTGAAAACATTTTTGAAAATAATATAATATATAGTTTT--GAAA
*
29475 ACGATTTTTTGAATATAT
63 AC-A--TTTTGAA-AAAT
29493 ATATATATATATTATATAGTTTTTGAAAACATTTTT-AAAATAGATATAATATATAGTTTTGAAA
1 -TATATATATA-TATATAGTTTTTGAAAACATTTTTGAAAATA-ATATAATATATAGTTTTGAAA
29557 ACATTTTGAAAACACT
63 ACATTTTGAAAA-A-T
* * *
29573 TATATAT-TATATATA-TTTTTTAAAA-ATATTTTGAAAAT-ATATATTATATAGTTTTTTAAAA
1 TATATATATATATATAGTTTTTGAAAACAT-TTTTGAAAATAATATAATATATAG--TTTTGAAA
29634 ACATTTTG-AAAA-
63 ACATTTTGAAAAAT
*
29646 -ATATATA-ATATATAGTTTTT-AAAACATTTTTTGAAAACTTATATATAATATATAGTTTTTAA
1 TATATATATATATATAGTTTTTGAAAACA-TTTTTGAAAA--TA-ATATAATATATAGTTTTGAA
* *
29708 AACATTTTTGATATA-
62 AACA-TTTTGAAAAAT
* *
29723 TATATATATATTATATAGTTTTTAAAAATATTT
1 TATATATATA-TATATAGTTTTTGAAAACATTT
29756 ATTTATTTAT
Statistics
Matches: 227, Mismatches: 12, Indels: 49
0.79 0.04 0.17
Matches are distributed among these distances:
72 17 0.07
73 15 0.07
74 1 0.00
75 26 0.11
76 21 0.09
77 40 0.18
78 10 0.04
79 16 0.07
80 16 0.07
81 6 0.03
82 10 0.04
83 31 0.14
84 18 0.08
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (76 bp):
TATATATATATATATAGTTTTTGAAAACATTTTTGAAAATAATATAATATATAGTTTTGAAAACA
TTTTGAAAAAT
Found at i:29652 original size:112 final size:115
Alignment explanation
Indices: 29491--29755 Score: 364
Period size: 112 Copynumber: 2.3 Consensus size: 115
29481 TTTTGAATAT
* *
29491 ATATATATATATATTATATAGTTTTTGAAAACATTTTTAAAATAGATATAATATATAGTTTTGAA
1 ATATATATATATATTATATAGTTTTTAAAAACATTTTGAAAATAGATATAATATATAGTTTTGAA
* *
29556 AACA-TTTTGAAAACACTTATATATTATATATATTTTTTAAAA-ATATTTTG-
66 AACATTTTTG-AAA-ACTTATATATAATATATAGTTTTTAAAACAT-TTTTGA
* *
29606 A-A-A-ATATATATTATATAGTTTTTTAAAAACATTTTGAAAA-ATATATAATATATAGTTTTTA
1 ATATATATATATATTATATAG-TTTTTAAAAACATTTTGAAAATAGATATAATATATAGTTTTGA
29667 AAACATTTTTTGAAAACTTATATATAATATATAGTTTTTAAAACATTTTTGA
65 AAACA-TTTTTGAAAACTTATATATAATATATAGTTTTTAAAACATTTTTGA
*
29719 TATATATATATATATTATATAGTTTTTAAAAATATTT
1 -ATATATATATATATTATATAGTTTTTAAAAACATTT
29756 ATTTATTTAT
Statistics
Matches: 134, Mismatches: 7, Indels: 17
0.85 0.04 0.11
Matches are distributed among these distances:
112 70 0.52
113 25 0.19
114 7 0.05
115 2 0.01
116 15 0.11
117 15 0.11
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (115 bp):
ATATATATATATATTATATAGTTTTTAAAAACATTTTGAAAATAGATATAATATATAGTTTTGAA
AACATTTTTGAAAACTTATATATAATATATAGTTTTTAAAACATTTTTGA
Found at i:29776 original size:13 final size:13
Alignment explanation
Indices: 29758--29803 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
29748 AAATATTTAT
29758 TTATTTATTATTA
1 TTATTTATTATTA
*
29771 TTATTTATTATTT
1 TTATTTATTATTA
29784 TTA-TTACTTATTA
1 TTATTTA-TTATTA
29797 CTTATTT
1 -TTATTT
29804 TTGTTTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 20 0.71
14 3 0.11
15 2 0.07
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:31090 original size:24 final size:24
Alignment explanation
Indices: 31057--31105 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
31047 ATTATTCTTA
*
31057 TTTTCTTTTTGTTTTAT-TTATATT
1 TTTTCATTTTGTTTTATGTT-TATT
31081 TTTTCATTTTGTTTTATGTTTATT
1 TTTTCATTTTGTTTTATGTTTATT
31105 T
1 T
31106 ATTTTACCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.12, C:0.04, G:0.06, T:0.78
Consensus pattern (24 bp):
TTTTCATTTTGTTTTATGTTTATT
Found at i:31096 original size:20 final size:20
Alignment explanation
Indices: 31073--31110 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31063 TTTTGTTTTA
31073 TTTATATTT-TTTCATTTTGT
1 TTTATATTTATTT-ATTTTGT
*
31093 TTTATGTTTATTTATTTT
1 TTTATATTTATTTATTTT
31111 ACCATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTATATTTATTTATTTTGT
Found at i:31117 original size:28 final size:25
Alignment explanation
Indices: 31057--31135 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 25
31047 ATTATTCTTA
*
31057 TTTTCTTTTTGTTTTA-TTTATATT
1 TTTTCATTTTGTTTTATTTTATATT
31081 TTTTCATTTTGTTTTATGTTTAT-TT
1 TTTTCATTTTGTTTTAT-TTTATATT
*
31106 ATTTTACCATTTTATTTTATTCCTTATATT
1 -TTTT--CATTTTGTTTTATT--TTATATT
31136 ATTTATATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
24 15 0.33
25 2 0.04
26 9 0.20
27 1 0.02
28 12 0.27
29 4 0.09
30 2 0.04
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (25 bp):
TTTTCATTTTGTTTTATTTTATATT
Found at i:31807 original size:6 final size:6
Alignment explanation
Indices: 31798--31859 Score: 61
Period size: 6 Copynumber: 10.0 Consensus size: 6
31788 AATAAAAAGG
* * * * *
31798 AATAAA AATACA AATAAA AATAGA AATAAA ATTAAA ACTAAA AACATAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATA-AA
31847 AATAATA AATAAA
1 AATAA-A AATAAA
31860 GTATTAATAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
6 34 0.76
7 11 0.24
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:31923 original size:6 final size:7
Alignment explanation
Indices: 31906--31932 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
31896 TCAAGAATAA
31906 AAAAATG
1 AAAAATG
31913 AAAAATG
1 AAAAATG
31920 AAAAATG
1 AAAAATG
31927 AAAAAT
1 AAAAAT
31933 AAAGTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:33729 original size:15 final size:15
Alignment explanation
Indices: 33706--33736 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33696 TTTGTGTGTT
*
33706 TCAAGAGAAACTATC
1 TCAAAAGAAACTATC
33721 TCAAAAGAAACTATC
1 TCAAAAGAAACTATC
33736 T
1 T
33737 TGAGTGAGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (15 bp):
TCAAAAGAAACTATC
Found at i:33828 original size:102 final size:102
Alignment explanation
Indices: 33722--33920 Score: 251
Period size: 102 Copynumber: 2.0 Consensus size: 102
33712 GAAACTATCT
** *
33722 CAAAAGAAACTATCTTGAGTGAGACGA-AATTTGTTT-AATGGAAAACAGATTCAAAGATTTTAT
1 CAAAAGAAACTATCTCAAGGGAGAC-ACAATTTGTTTCAA-GGAAAACAGATTCAAAGATTTTAT
* * *
33785 TTCAAG-GAAAATTGTATTAAGAGAGACAAAATTTAGTTC
64 TTCAAGAG-AAACTGTATCAAGAAAGACAAAATTTAGTTC
* * * *
33824 CAAAAGAAACTGTCTCAAGGGAGACACAATTTGTTTCAAGGAAAGCATATTCAGAGATTTTATTT
1 CAAAAGAAACTATCTCAAGGGAGACACAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTATTT
*
33889 CAAGAGAAACTGTCTCAAGAAAGACAAAATTT
66 CAAGAGAAACTGTATCAAGAAAGACAAAATTT
33921 GTTTTACGGG
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
101 1 0.01
102 79 0.95
103 3 0.04
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.28
Consensus pattern (102 bp):
CAAAAGAAACTATCTCAAGGGAGACACAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTATTT
CAAGAGAAACTGTATCAAGAAAGACAAAATTTAGTTC
Found at i:33954 original size:36 final size:36
Alignment explanation
Indices: 33890--34137 Score: 179
Period size: 36 Copynumber: 7.0 Consensus size: 36
33880 ATTTTATTTC
* * *
33890 AAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTT
1 AAGAGAAAATGTCTCAAGAGAGAAAAAATTTGTTTT
* * *
33926 ACGGGAAAATGTCTCAAGAGAGAAAAAATTTAGTTAT
1 AAGAGAAAATGTCTCAAGAGAGAAAAAATTT-GTTTT
* * * * *
33963 AAAAGAAACTGTCTCGAGAGAGACAAAACTTTGTTTC
1 AAGAGAAAATGTCTCAAGAGAGA-AAAAATTTGTTTT
*** ** *
34000 AAG-GAAAA-----CAA-A-TTCAAAGTTTCTGTTTC
1 AAGAGAAAATGTCTCAAGAGAGAAAAAATT-TGTTTT
* ** *
34029 AAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTT
1 AAGAGAAAATGTCTCAAGAGAGAAAAAATTTGTTTT
* *
34065 AAGAGAATATGTCTCAAGAGAGACAAAATTTGTTTT
1 AAGAGAAAATGTCTCAAGAGAGAAAAAATTTGTTTT
* *
34101 AAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTT
1 AAGAGAAAATGTCTCAAGAGAGA-AAAAATTTGTTTT
34138 GAGTAAATTA
Statistics
Matches: 162, Mismatches: 38, Indels: 23
0.73 0.17 0.10
Matches are distributed among these distances:
28 5 0.03
29 9 0.06
30 5 0.03
31 2 0.01
35 3 0.02
36 89 0.55
37 42 0.26
38 7 0.04
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (36 bp):
AAGAGAAAATGTCTCAAGAGAGAAAAAATTTGTTTT
Found at i:34043 original size:139 final size:139
Alignment explanation
Indices: 33803--34136 Score: 467
Period size: 139 Copynumber: 2.4 Consensus size: 139
33793 AAATTGTATT
** * *
33803 AAGAGAGACAAAATTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACACAA-TTTGTTTCAAGGAA
1 AAGAGAGACAAAATTTAGTTATAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAA
* * * * * *
33867 AGCATATTCAGAGATTTTATTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTTACGGGA
66 AACAAATTCAAAGATTTTATTTCAAGAGAAACCGTCTCAAGAAAGACAAAATTTGTTTTAAGAGA
33932 AAATGTCTC
131 AAATGTCTC
* *
33941 AAGAGAGAAAAAATTTAGTTATAAAAGAAACTGTCTCGAGAGAGACAAAACTTTGTTTCAAGGAA
1 AAGAGAGACAAAATTTAGTTATAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAA
* * *
34006 AACAAATTCAAAG-TTTCTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTTAAGAG
66 AACAAATTCAAAGATTT-TATTTCAAGAGAAACCGTCTCAAGAAAGACAAAATTTGTTTTAAGAG
*
34070 AATATGTCTC
130 AAAATGTCTC
* * *
34080 AAGAGAGACAAAATTT-GTTTTAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTT
1 AAGAGAGACAAAATTTAGTTATAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
34137 TGAGTAAATT
Statistics
Matches: 173, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
138 84 0.49
139 89 0.51
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (139 bp):
AAGAGAGACAAAATTTAGTTATAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAA
AACAAATTCAAAGATTTTATTTCAAGAGAAACCGTCTCAAGAAAGACAAAATTTGTTTTAAGAGA
AAATGTCTC
Found at i:34070 original size:21 final size:21
Alignment explanation
Indices: 34044--34106 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
34034 AAACCGTCTC
34044 AAGAGAGACAAAATTTGTTTT
1 AAGAGAGACAAAATTTGTTTT
* * *
34065 -A-AGAG----AATATGTCTC
1 AAGAGAGACAAAATTTGTTTT
34080 AAGAGAGACAAAATTTGTTTT
1 AAGAGAGACAAAATTTGTTTT
34101 AAGAGA
1 AAGAGA
34107 AATTGTCTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
15 7 0.23
16 1 0.03
17 4 0.13
19 4 0.13
20 1 0.03
21 13 0.43
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (21 bp):
AAGAGAGACAAAATTTGTTTT
Found at i:34146 original size:36 final size:34
Alignment explanation
Indices: 34039--34151 Score: 154
Period size: 36 Copynumber: 3.1 Consensus size: 34
34029 AAGGGAAACC
*
34039 GTCTCAAGAGAGACAAAATTTGTTTTAAGAGAATAT
1 GTCTCAAGAGAGACAAAATTTGTTTTGAGA-AAT-T
34075 GTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAATT
1 GTCTCAAGAGAGACAAAATTTGTTTT--GAGAAATT
34111 GTCTCAAGAGAGACAAAACTTTGTTTTGAGTAAATT
1 GTCTCAAGAGAGACAAAA-TTTGTTTTGAG-AAATT
34147 AGTCT
1 -GTCT
34152 TGAGCGAGGC
Statistics
Matches: 71, Mismatches: 1, Indels: 9
0.88 0.01 0.11
Matches are distributed among these distances:
35 3 0.04
36 50 0.70
37 15 0.21
38 3 0.04
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (34 bp):
GTCTCAAGAGAGACAAAATTTGTTTTGAGAAATT
Found at i:39681 original size:6 final size:6
Alignment explanation
Indices: 39672--39747 Score: 62
Period size: 6 Copynumber: 12.0 Consensus size: 6
39662 AATAAAAAGG
* * * **
39672 AATAAA AATACA AATAAA AATAAA ATTAAA ATTAAA GCTAAA AACTAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AA-TAAA
*
39721 AACTAAA AACATAA AATAATA AATAAA
1 AA-TAAA AATA-AA AATAA-A AATAAA
39748 GTACTAATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
6 34 0.59
7 24 0.41
ACGTcount: A:0.72, C:0.07, G:0.01, T:0.20
Consensus pattern (6 bp):
AATAAA
Found at i:39796 original size:20 final size:20
Alignment explanation
Indices: 39773--39829 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
39763 ATACAAGTAA
* * *
39773 AAAAAATGAACATCAAGAAT
1 AAAAAATGAAAATAAAAAAT
39793 AAAAAATGAAAATAAAAAAT
1 AAAAAATGAAAATAAAAAAT
*
39813 AAAAAAT-AAAGTAAAAA
1 AAAAAATGAAAATAAAAA
39830 GTAGAAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 9 0.27
20 24 0.73
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (20 bp):
AAAAAATGAAAATAAAAAAT
Found at i:39808 original size:13 final size:14
Alignment explanation
Indices: 39790--39822 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39780 GAACATCAAG
*
39790 AATAAAAAAT-GAA
1 AATAAAAAATAAAA
39803 AATAAAAAATAAAA
1 AATAAAAAATAAAA
39817 AATAAA
1 AATAAA
39823 GTAAAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (14 bp):
AATAAAAAATAAAA
Found at i:39811 original size:7 final size:7
Alignment explanation
Indices: 39790--39822 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
39780 GAACATCAAG
39790 AATAAAA
1 AATAAAA
*
39797 AAT-GAA
1 AATAAAA
39803 AATAAAA
1 AATAAAA
39810 AATAAAA
1 AATAAAA
39817 AATAAA
1 AATAAA
39823 GTAAAAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (7 bp):
AATAAAA
Found at i:43842 original size:95 final size:95
Alignment explanation
Indices: 43714--43976 Score: 341
Period size: 95 Copynumber: 2.7 Consensus size: 95
43704 AGATTATAAT
* * * *
43714 ATTATATATATACAATAAAGCTTGAGCTT-TCCCTCTAAAGCAATTGGTTAAACGTCTTGGCTTT
1 ATTATA-ATATACAATAAAGCTTGAG-TTGTCCCTATAGAGCAATTGGTTAAACGCCCTGGCTTT
43778 ATGGATAAGATTCAGCTAGCCTGATAAAGGTG
64 ATGGATAAGATTCAGCTAGCCTGATAAAGGTG
* * *
43810 ATTATAATATACAATAAAGCTTGAGTTGTCCCTATAGAGCAATTAGTTAAACACCCTGCCTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTATAGAGCAATTGGTTAAACGCCCTGGCTTTAT
43875 GGATAAGATTCAGCTAGCCTGATAAAGGTG
66 GGATAAGATTCAGCTAGCCTGATAAAGGTG
* * * * * *
43905 ATTATAATAT-CTATACAATGATATTGAGTTGTCCCTTTAGAGAAATTGATTAAACGCCCTGGAT
1 ATTATAATATACAATA-AA-G--CTTGAGTTGTCCCTATAGAGCAATTGGTTAAACGCCCTGGCT
43969 TTATGGAT
62 TTATGGAT
43977 CAAGCTAGCA
Statistics
Matches: 146, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
94 6 0.04
95 91 0.62
96 7 0.05
98 42 0.29
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGTTGTCCCTATAGAGCAATTGGTTAAACGCCCTGGCTTTAT
GGATAAGATTCAGCTAGCCTGATAAAGGTG
Found at i:44907 original size:85 final size:83
Alignment explanation
Indices: 44761--45768 Score: 1067
Period size: 85 Copynumber: 12.0 Consensus size: 83
44751 AAAAGCACCT
* * * *
44761 TCAACAAAGACCTTCGAGTTTGATTCCATTCAGCTCAAAGGCATATCCAATTTACAGCATAACTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-C-ATTTACAGCATAACTC
* ** *
44826 AAGGCAAGAATAGTTATTTG
64 AAGGCGAGAAGGGTTATCTG
* * *
44846 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAACATAACTT
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-C-ATTTACAGCATAACTC
44911 AAGGCGAGAAGGGTTATCTG
64 AAGGCGAGAAGGGTTATCTG
* * *** * * *
44931 TCAACCAAGACCTTCGAGTTCAATTACACTCAGCTCAAATATACATCATTTGCAGTATAGCTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
44996 GGCGAGAAGGGTTATCTG
66 GGCGAGAAGGGTTATCTG
* * * * * *
45014 CCAATAAAAGACCTTCGAGATCGATTACACTTAGCTCAAAGGCACATCCAATTTAAAACATAACT
1 TCAA-CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-C-ATTTACAGCATAACT
*
45079 CAAGGTGAGAAGGGTTATCTG
63 CAAGGCGAGAAGGGTTATCTG
* * * ** *
45100 TCAACCAAGACCTTCAAATTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
* *
45165 GGTGAGAAGGGTTATCTA
66 GGCGAGAAGGGTTATCTG
* * * * * ** *
45183 CCAATAAAAGATCTTCGAGTTCGATTACACTCAGCTTAAAGACACATCATTTGTAGCATAGCTCA
1 TCAA-CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCA
* *
45248 AGGCGAGAAGGGCTACCTG
65 AGGCGAGAAGGGTTATCTG
* * * *
45267 -C--CAAAGACGTTCGAGTTCGATTACAGTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
* * *
45329 GGCGAGAAGTGCTACCTG
66 GGCGAGAAGGGTTATCTG
45347 -C--CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAGCATAACTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-C-ATTTACAGCATAACTC
* *
45409 AAGGCGAGAAGAGTTATCTA
64 AAGGCGAGAAGGGTTATCTG
* * * * *
45429 TCAACCAAGACCGTCGAGTTCGATTACATTAAGCTCAAAGGCACATCATTTGCAGCATAACTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
*
45494 GGCGAAAAGGGTTATCTG
66 GGCGAGAAGGGTTATCTG
* * * * * * * *
45512 CCAATAAAAGACCTTCAAGTTTGATCACACTCAGCTTAAAGGCACATCAAATTTACAACATAGCT
1 TCAA-CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTACAGCATAACT
*
45577 CAAGGCGAAAAGGGTTATCTG
63 CAAGGCGAGAAGGGTTATCTG
* * * * * * * * *
45598 TCAACCAAGACCTTTGAGTTTGATTACCCTCAACTTAAAGGCACATCATTTGCGGCATAGCTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
* * *
45663 GGCAAGAAGGGCTATATG
66 GGCGAGAAGGGTTATCTG
* * * *
45681 CCAACAAAAGACCTTCGAGTTCGATTACACTAAGCTCAAAGGCACATCCA-GTACAACATAACTC
1 TCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CATTTACAGCATAACTC
*
45745 AAGGTGAGAAGGGTTATCTG
64 AAGGCGAGAAGGGTTATCTG
45765 TCAA
1 TCAA
45769 ATTTACAGCA
Statistics
Matches: 780, Mismatches: 129, Indels: 29
0.83 0.14 0.03
Matches are distributed among these distances:
80 112 0.14
81 1 0.00
82 30 0.04
83 138 0.18
84 201 0.26
85 229 0.29
86 69 0.09
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (83 bp):
TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
GGCGAGAAGGGTTATCTG
Found at i:45052 original size:169 final size:169
Alignment explanation
Indices: 44761--45768 Score: 1266
Period size: 169 Copynumber: 6.0 Consensus size: 169
44751 AAAAGCACCT
* * * * * * *
44761 TCAACAAAGACCTTCGAGTTTGATTCCATTCAGCTCAAAGGCATATCCAATTTACAGCATAACTC
1 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-C-ATTTGCAGCATAGCTC
* ** * * **
44826 AAGGCAAGAATAGTTATTTGTCAA-CCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAC
64 AAGGCGAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAC
*
44890 ATCCAATTTACAACATAACTTAAGGCGAGAAGGGTTATCTG
129 ATCCAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTG
* *** *
44931 TCAACCAAGACCTTCGAGTTCAATTACACTCAGCTCAAATATACATCATTTGCAGTATAGCTCAA
1 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* *
44996 GGCGAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGATCGATTACACTTAGCTCAAAGGCACAT
66 GGCGAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
* *
45061 CCAATTTAAAACATAACTCAAGGTGAGAAGGGTTATCTG
131 CCAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTG
* * *
45100 TCAACCAAGACCTTCAAATTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAA
1 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * * * *
45165 GGTGAGAAGGGTTATCTACCAATAAAAGATCTTCGAGTTCGATTACACTCAGCTTAAAGACACAT
66 GGCGAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
** * * * *
45230 -C-ATTTGTAGCATAGCTCAAGGCGAGAAGGGCTACCTG
131 CCAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTG
* * *
45267 -C--CAAAGACGTTCGAGTTCGATTACAGTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
1 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * *
45329 GGCGAGAAGTGCTACCTGCC----AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
66 GGCGAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
* * *
45390 CCAATTTACAGCATAACTCAAGGCGAGAAGAGTTATCTA
131 CCAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTG
* * * *
45429 TCAACCAAGACCGTCGAGTTCGATTACATTAAGCTCAAAGGCACATCATTTGCAGCATAACTCAA
1 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * * * *
45494 GGCGAAAAGGGTTATCTGCCAATAAAAGACCTTCAAGTTTGATCACACTCAGCTTAAAGGCACAT
66 GGCGAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
* * *
45559 CAAATTTACAACATAGCTCAAGGCGAAAAGGGTTATCTG
131 CCAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTG
* * * * * *
45598 TCAACCAAGACCTTTGAGTTTGATTACCCTCAACTTAAAGGCACATCATTTGCGGCATAGCTCAA
1 TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * * * *
45663 GGCAAGAAGGGCTATATGCCAACAAAAGACCTTCGAGTTCGATTACACTAAGCTCAAAGGCACAT
66 GGCGAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
* *
45728 CC-A-GTACAACATAACTCAAGGTGAGAAGGGTTATCTG
131 CCAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTG
45765 TCAA
1 TCAA
45769 ATTTACAGCA
Statistics
Matches: 716, Mismatches: 112, Indels: 23
0.84 0.13 0.03
Matches are distributed among these distances:
160 38 0.05
161 1 0.00
162 29 0.04
163 1 0.00
164 70 0.10
165 71 0.10
166 1 0.00
167 63 0.09
168 34 0.05
169 371 0.52
170 37 0.05
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (169 bp):
TCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
GGCGAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT
CCAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTG
Found at i:45410 original size:329 final size:333
Alignment explanation
Indices: 44852--45768 Score: 1234
Period size: 329 Copynumber: 2.7 Consensus size: 333
44842 TTTGTCAACC
* * *
44852 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCCAATTTACAACATAACTTAAGGCG
1 AAGACCTTCGAGTTCGATTACACTCAGCTTAAAGGCACAT-CAATTTACAACATAGCTCAAGGCG
* ***
44917 AGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCAATTACACTCAGCTCAAATATACATCATTT
65 AGAAGGGTTATCTGTC-ACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
* * * *
44982 GCAGTATAGCTCAAGGCGAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGATCGATTACACTTA
129 GCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCC---AAAAGACCTTCGAGTTCGATTACACTAA
*
45047 GCTCAAAGGCACATCCAATTTAAAACATAACTCAAGGTGAGAAGGGTTATCTGTCAACCAAGACC
191 GCTCAAAGGCACATCCAATTTACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAACCAAGACC
* * * * * *
45112 TTCAAATTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAAGGTGAGAAGGGT
256 GTCAAATTCGATTACACTAAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAAAAGGGT
45177 TATCTACCAATAA
321 TATCTACCAATAA
* * ** *
45190 AAGATCTTCGAGTTCGATTACACTCAGCTTAAAGACACATC-ATTTGTAGCATAGCTCAAGGCGA
1 AAGACCTTCGAGTTCGATTACACTCAGCTTAAAGGCACATCAATTTACAACATAGCTCAAGGCGA
* * * * *
45254 GAAGGGCTACCTG-C-CAAAGACGTTCGAGTTCGATTACAGTCAGCTCAAAGGCACATCATTTGC
66 GAAGGGTTATCTGTCACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGC
* * *
45317 AGCATAGCTCAAGGCGAGAAGTGCTACCTGCC-AAAGACCTTCGAGTTCGATTACACTCAGCTCA
131 AGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTCGATTACACTAAGCTCA
* * * * *
45381 AAGGCACATCCAATTTACAGCATAACTCAAGGCGAGAAGAGTTATCTATCAACCAAGACCGTCGA
196 AAGGCACATCCAATTTACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAACCAAGACCGTCAA
* *
45446 GTTCGATTACATTAAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAAAAGGGTTATCT
261 ATTCGATTACACTAAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAAAAGGGTTATCT
*
45511 GCCAATAA
326 ACCAATAA
* * *
45519 AAGACCTTCAAGTTTGATCACACTCAGCTTAAAGGCACATCAAATTTACAACATAGCTCAAGGCG
1 AAGACCTTCGAGTTCGATTACACTCAGCTTAAAGGCACATC-AATTTACAACATAGCTCAAGGCG
* * * * * *
45584 AAAAGGGTTATCTGTCAACCAAGACCTTTGAGTTTGATTACCCTCAACTTAAAGGCACATCATTT
65 AGAAGGGTTATCTGTC-ACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
* * *
45649 GCGGCATAGCTCAAGGCAAGAAGGGCTATATGCCAACAAAAGACCTTCGAGTTCGATTACACTAA
129 GCAGCATAGCTCAAGGCGAGAAGGGCTATCTG-C--CAAAAGACCTTCGAGTTCGATTACACTAA
*
45714 GCTCAAAGGCACATCC-A-GTACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAA
191 GCTCAAAGGCACATCCAATTTACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAA
45769 ATTTACAGCA
Statistics
Matches: 502, Mismatches: 68, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
329 189 0.38
331 30 0.06
332 1 0.00
333 70 0.14
334 66 0.13
335 2 0.00
336 62 0.12
337 3 0.01
338 79 0.16
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (333 bp):
AAGACCTTCGAGTTCGATTACACTCAGCTTAAAGGCACATCAATTTACAACATAGCTCAAGGCGA
GAAGGGTTATCTGTCACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGC
AGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTCGATTACACTAAGCTCA
AAGGCACATCCAATTTACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAACCAAGACCGTCAA
ATTCGATTACACTAAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCGAAAAGGGTTATCT
ACCAATAA
Found at i:45792 original size:40 final size:40
Alignment explanation
Indices: 45732--45808 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
45722 GCACATCCAG
45732 TACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAAATT
1 TACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAAATT
*
45772 TACAGCATAACTCAAGGTGAGAAGGGTTATCTGTCAA
1 TACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAA
45809 CAAAAACTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (40 bp):
TACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAAATT
Found at i:46462 original size:38 final size:38
Alignment explanation
Indices: 46418--46709 Score: 155
Period size: 38 Copynumber: 7.6 Consensus size: 38
46408 GTAATATAAC
**
46418 ATAATTTTTGAAAATGTTTTTGAAAAAAAATATAATAT
1 ATAATTTTTGAAAAAATTTTTGAAAAAAAATATAATAT
* * *
46456 ATAATTTTCAGAAAACAATTTTCGAAAAAAATATATATTAT
1 ATAATTTT-TGAAAA-AATTTTTGAAAAAAA-ATATAATAT
* * * * *
46497 ATAGTTTTTGAAAACATTTTTTAAAATAGATATAATAT
1 ATAATTTTTGAAAAAATTTTTGAAAAAAAATATAATAT
* * * ** *
46535 AT-AGTTTTGGAAACA-TTTTGAAAACACTTATATATTAT
1 ATAATTTTTGAAAAAATTTTTGAAAA-A-AAATATAATAT
** * * * * *
46573 ATAGCTTTTAAAAAAACATTTTGAAAATATATATATTAT
1 ATAATTTTTGAAAAAA-TTTTTGAAAAAAAATATAATAT
* * *
46612 A-AAGTTTTTTAAAAACA-TTTTGAAAATATATATAATAT
1 ATAA-TTTTTGAAAAA-ATTTTTGAAAAAAAATATAATAT
* * * *
46650 ATAGTTTTT-AAAACATTTTTTGAAAACTTATATATAATAT
1 ATAATTTTTGAAAA-AATTTTTGAAAA--AAAATATAATAT
* *
46690 ATAGTTTTT-AAAACATTTTT
1 ATAATTTTTGAAAAAATTTTT
46710 TAAATATATA
Statistics
Matches: 203, Mismatches: 36, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
36 8 0.04
37 14 0.07
38 65 0.32
39 49 0.24
40 43 0.21
41 24 0.12
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (38 bp):
ATAATTTTTGAAAAAATTTTTGAAAAAAAATATAATAT
Found at i:46510 original size:40 final size:41
Alignment explanation
Indices: 46434--46752 Score: 212
Period size: 40 Copynumber: 8.1 Consensus size: 41
46424 TTTGAAAATG
* * *
46434 TTTTTGAAAA-AAA-ATATAATATATAATTTTCAGAAAACAA
1 TTTTTGAAAACAAATATATATTATATAGTTTT-TGAAAACAA
*
46474 TTTTCGAAAA-AAATATATATTATATAGTTTTTGAAAAC-A
1 TTTTTGAAAACAAATATATATTATATAGTTTTTGAAAACAA
* * * *
46513 TTTTTTAAAATAGATATA-A-TATATAG-TTTTGGAAAC-A
1 TTTTTGAAAACAAATATATATTATATAGTTTTTGAAAACAA
** * *
46550 -TTTTGAAAACACTTATATATTATATAGCTTTT-AAAAAAA
1 TTTTTGAAAACAAATATATATTATATAGTTTTTGAAAACAA
* * * *
46589 CATTTTG-AAA-ATATATATATTATAAAGTTTTTTAAAA-ACA
1 -TTTTTGAAAACAAATATATATTATATAGTTTTTGAAAACA-A
* * *
46629 -TTTTG-AAA-ATATATATAATATATAGTTTTT-AAAACAT
1 TTTTTGAAAACAAATATATATTATATAGTTTTTGAAAACAA
** *
46666 TTTTTGAAAACTTATATATAATATATAGTTTTT-AAAAC-A
1 TTTTTGAAAACAAATATATATTATATAGTTTTTGAAAACAA
* *
46705 TTTTTTAAATATATATATATATATTATATAGTTTTT-AAAA-ATA
1 TTTTTGAAA-ACA-A-ATATATATTATATAGTTTTTGAAAACA-A
46748 TTTTT
1 TTTTT
46753 TATTTTTTTA
Statistics
Matches: 232, Mismatches: 28, Indels: 35
0.79 0.09 0.12
Matches are distributed among these distances:
36 13 0.06
37 15 0.06
38 51 0.22
39 45 0.19
40 59 0.25
41 20 0.09
42 23 0.10
43 6 0.03
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (41 bp):
TTTTTGAAAACAAATATATATTATATAGTTTTTGAAAACAA
Found at i:46720 original size:38 final size:37
Alignment explanation
Indices: 46481--46754 Score: 248
Period size: 38 Copynumber: 7.0 Consensus size: 37
46471 CAATTTTCGA
* *
46481 AAAAAATATATATTATATAGTTTTTGAAAACATTTTTT
1 AAAATATATATAATATATAGTTTTT-AAAACATTTTTT
* ** *
46519 AAAATAGATATAATATATAGTTTTGGAAACA-TTTTG
1 AAAATATATATAATATATAGTTTTTAAAACATTTTTT
* * * *
46555 AAAACACTTATATATTATATAGCTTTTAAAAAAACA-TTTTG
1 AAAATA--TATATAATATATAG-TTTT--TAAAACATTTTTT
* * *
46596 AAAATATATATATTATAAAGTTTTTTAAAAACA-TTTTG
1 AAAATATATATAATATATAG-TTTTT-AAAACATTTTTT
46634 AAAATATATATAATATATAGTTTTTAAAACATTTTTT
1 AAAATATATATAATATATAGTTTTTAAAACATTTTTT
46671 GAAAACTTATATATAATATATAGTTTTTAAAACATTTTTT
1 -AAAA--TATATATAATATATAGTTTTTAAAACATTTTTT
*
46711 AAATATATATATATATATTATATAGTTTTTAAAAATATTTTTT
1 -AA-A-ATATATATA-A-TATATAGTTTTT-AAAACATTTTTT
46754 A
1 A
46755 TTTTTTTATT
Statistics
Matches: 201, Mismatches: 20, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
36 15 0.07
37 14 0.07
38 66 0.33
39 21 0.10
40 43 0.21
41 17 0.08
42 14 0.07
43 11 0.05
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (37 bp):
AAAATATATATAATATATAGTTTTTAAAACATTTTTT
Found at i:46772 original size:14 final size:14
Alignment explanation
Indices: 46755--46788 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
46745 ATATTTTTTA
*
46755 TTTTT-TTATTTAT
1 TTTTTATTACTTAT
46768 TTTTTATTACTTAT
1 TTTTTATTACTTAT
46782 TTTTTAT
1 TTTTTAT
46789 ATTTGTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTACTTAT
Found at i:48044 original size:2 final size:2
Alignment explanation
Indices: 48039--48077 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
48029 CACATTTCAT
48039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48078 TATTCTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48107 original size:21 final size:20
Alignment explanation
Indices: 48077--48146 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 20
48067 TATATATATA
48077 TTATTCTTATTCTTTTTTATT
1 TTATT-TTATTCTTTTTTATT
*
48098 TTCATTTTATTTTTTTTTATT
1 TT-ATTTTATTCTTTTTTATT
*
48119 TTATTTTGTT-TTATGTTTA-T
1 TTATTTTATTCTT-T-TTTATT
48139 TTATTTTA
1 TTATTTTA
48147 CCATTTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.05
20 16 0.37
21 22 0.51
22 3 0.07
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.77
Consensus pattern (20 bp):
TTATTTTATTCTTTTTTATT
Found at i:48109 original size:5 final size:5
Alignment explanation
Indices: 48077--48187 Score: 79
Period size: 5 Copynumber: 21.4 Consensus size: 5
48067 TATATATATA
*
48077 TTATT CTTATT CTT-TT TTATT TTCATT TTATT TTTTT TTATT TTATT
1 TTATT -TTATT -TTATT TTATT TT-ATT TTATT TTATT TTATT TTATT
* *
48124 TTGTT TTATGT TTA-T TTATT TTACCATT TTA-T TT-TT TTATT CCTTATA
1 TTATT TTAT-T TTATT TTATT TT---ATT TTATT TTATT TTATT --TTATT
48172 TTA-T TTATT TTATT TT
1 TTATT TTATT TTATT TT
48188 TCCCCTTCTT
Statistics
Matches: 87, Mismatches: 6, Indels: 25
0.74 0.05 0.21
Matches are distributed among these distances:
4 15 0.17
5 46 0.53
6 17 0.20
7 4 0.05
8 5 0.06
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:48345 original size:20 final size:20
Alignment explanation
Indices: 48316--48355 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
48306 AAAGGTAAGT
48316 AATTTGAA-TTGAATATTTTA
1 AATTTGAATTTGAAT-TTTTA
*
48336 AATTTTAATTTGAATTTTTA
1 AATTTGAATTTGAATTTTTA
48356 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
AATTTGAATTTGAATTTTTA
Found at i:49216 original size:44 final size:43
Alignment explanation
Indices: 49123--49282 Score: 132
Period size: 43 Copynumber: 3.7 Consensus size: 43
49113 TTACTCATGG
* *
49123 TCTTATTTTTTTTATCTTTTATAATT-AGGATTTCTAATTTTT-TATA
1 TCTTA-TTCTTTTATC-TTTATAATTGAGG--GTCTAATTTTTCTA-A
*
49169 TCTTATTCTTTTATCTTTATAACTGAGGGTCTAATTTTTCTCAA
1 TCTTATTCTTTTATCTTTATAATTGAGGGTCTAATTTTTCT-AA
* * * *
49213 TCTTACT-TTTTATCTTTATTATTGA-AGTCTTTAACTTTTCTAA
1 TCTTATTCTTTTATCTTTATAATTGAGGGTC--TAATTTTTCTAA
* *
49256 TCTCATTC-TTTACCTTTATAATTGAGG
1 TCTTATTCTTTTATCTTTATAATTGAGG
49283 CTTCTAAATT
Statistics
Matches: 94, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
42 3 0.03
43 48 0.51
44 25 0.27
45 13 0.14
46 5 0.05
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (43 bp):
TCTTATTCTTTTATCTTTATAATTGAGGGTCTAATTTTTCTAA
Found at i:53611 original size:19 final size:18
Alignment explanation
Indices: 53587--53623 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
53577 TTTAATTTAC
53587 ACCTAATAAAAAATTAATT
1 ACCTAAT-AAAAATTAATT
*
53606 ACCTAATTAAAATTAATT
1 ACCTAATAAAAATTAATT
53624 TCTAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (18 bp):
ACCTAATAAAAATTAATT
Found at i:54255 original size:42 final size:45
Alignment explanation
Indices: 54174--54273 Score: 152
Period size: 43 Copynumber: 2.3 Consensus size: 45
54164 ATGGTAACAA
54174 ATTTTATTTAATAACAATTTTATTATCATTATTTAAA-TTTTTTAT
1 ATTTTATTTAATAACAA-TTTATTATCATTATTTAAATTTTTTTAT
*
54219 ATTTTATTTAATATCAA-TT-TTATCATTATTTAAATTTTTTTAT
1 ATTTTATTTAATAACAATTTATTATCATTATTTAAATTTTTTTAT
*
54262 GTTTTATTTAAT
1 ATTTTATTTAAT
54274 GATTTTTAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
42 15 0.29
43 21 0.40
45 16 0.31
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (45 bp):
ATTTTATTTAATAACAATTTATTATCATTATTTAAATTTTTTTAT
Found at i:57813 original size:113 final size:113
Alignment explanation
Indices: 57683--57919 Score: 341
Period size: 113 Copynumber: 2.1 Consensus size: 113
57673 TATTCATTTC
* * * * *
57683 AATAAAAAATATCAATTTAATTTATGACGGGACAATGATTCTGTCGAAAATTTTGTTCAATTTTA
1 AATAAAAAATATCAATTTAATTTATGACGAGACAATAATTCCGTCGAAAATTTTGCTCAACTTTA
** *
57748 ATTAAAATATATC-AATTTAATTTGTGATGGAATAGTCATTCCGTCGGA
66 ATTAAAATATA-CAAATTTAATTTGTGATGGAATAGTCAACCCGTCGAA
* * * * *
57796 AATAAAAAATATTAATTTAATTTATGGCGAGATAATAATTCCGTCGGAAGTTTTGCTCAACTTTA
1 AATAAAAAATATCAATTTAATTTATGACGAGACAATAATTCCGTCGAAAATTTTGCTCAACTTTA
57861 ATTAAAATATACAAATTTAATTTGTGATGGAATAGTCAACCCGTCGAA
66 ATTAAAATATACAAATTTAATTTGTGATGGAATAGTCAACCCGTCGAA
57909 AATAAAAAATA
1 AATAAAAAATA
57920 ACTACATTTA
Statistics
Matches: 110, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
112 1 0.01
113 109 0.99
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (113 bp):
AATAAAAAATATCAATTTAATTTATGACGAGACAATAATTCCGTCGAAAATTTTGCTCAACTTTA
ATTAAAATATACAAATTTAATTTGTGATGGAATAGTCAACCCGTCGAA
Found at i:61172 original size:16 final size:16
Alignment explanation
Indices: 61147--61179 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
61137 ATTCATACAG
61147 AGCATCTGAATCATTC
1 AGCATCTGAATCATTC
*
61163 AGCATTTGAATCATTC
1 AGCATCTGAATCATTC
61179 A
1 A
61180 ACGCTTAATC
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:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (16 bp):
AGCATCTGAATCATTC
Found at i:62948 original size:22 final size:22
Alignment explanation
Indices: 62918--62977 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
62908 TAATTTATAA
* *
62918 AATTTTAAAATATTTAATATGT
1 AATTATAAAATATTAAATATGT
* *
62940 AATTATAAATTAATTAAATATTT
1 AATTATAAAAT-ATTAAATATGT
*
62963 AA-AATAAAATATTAA
1 AATTATAAAATATTAA
62978 TTATATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 5 0.16
22 15 0.48
23 11 0.35
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTATAAAATATTAAATATGT
Found at i:63862 original size:12 final size:12
Alignment explanation
Indices: 63797--63862 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
63787 AGGTATATTT
* *
63797 TATTATATTTAG
1 TATTTTATTTAA
*
63809 TATTTTTTTTAA
1 TATTTTATTTAA
*
63821 TAATTTATTTAA
1 TATTTTATTTAA
63833 TTATTTTAATTGTTTAA
1 -TATTTT-A---TTTAA
63850 TATTTTATTTAA
1 TATTTTATTTAA
63862 T
1 T
63863 TAATTTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
12 25 0.58
13 5 0.12
14 1 0.02
15 1 0.02
16 6 0.14
17 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:65446 original size:13 final size:13
Alignment explanation
Indices: 65405--65448 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
65395 TATTTAGTAC
*
65405 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
65418 TGTTTATTGGACT
1 TTTTTATTGTAAT
65431 TTTTTATTGTAAT
1 TTTTTATTGTAAT
65444 TTTTT
1 TTTTT
65449 TATTATTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Done.