Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003375.1 Hibiscus syriacus cultivar Beakdansim tig00007095_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: 90863
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:5919 original size:30 final size:30
Alignment explanation
Indices: 5883--5940 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
5873 TCCTATTTTG
5883 TATTCAATTTAGCCACTAACCTTAGTTTAA
1 TATTCAATTTAGCCACTAACCTTAGTTTAA
*
5913 TATTCAATTTAGCCATTAACCTTAGTTT
1 TATTCAATTTAGCCACTAACCTTAGTTT
5941 TAGTATTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (30 bp):
TATTCAATTTAGCCACTAACCTTAGTTTAA
Found at i:6034 original size:6 final size:6
Alignment explanation
Indices: 6023--6058 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
6013 GATTCCTTAG
* *
6023 AATTAT AATTAT AATTGT AATTGT AATTAT AATTAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT
6059 TATGTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (6 bp):
AATTAT
Found at i:7203 original size:40 final size:40
Alignment explanation
Indices: 7138--7327 Score: 183
Period size: 40 Copynumber: 4.8 Consensus size: 40
7128 AGTTTCCAAT
*
7138 TTCGCAACGCGAATATGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAATGCG-ATA-GTCAAATTCGCAACACAGAAGTCAAA
*
7178 TTCGCAATGCGATAGTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAATGCGATAGTCAAATTCGCAACACAGAAGTCAAA
* * *
7218 TTCGCAACGCGATAGTCAAATTCGCAACGC-GATAATCAAA
1 TTCGCAATGCGATAGTCAAATTCGCAACACAGA-AGTCAAA
* * * * * *
7258 TTCGCAATACAAAAGTCAAATTCGCAACGCGGAATTTCAAA
1 TTCGCAATGCGATAGTCAAATTCGCAACACAGAA-GTCAAA
* *
7299 TTCGCAACTG-AAT-TTCAAATTCGCAACAC
1 TTCGCAA-TGCGATAGTCAAATTCGCAACAC
7328 GAATTTAATT
Statistics
Matches: 129, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
38 2 0.02
39 7 0.05
40 103 0.80
41 16 0.12
42 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (40 bp):
TTCGCAATGCGATAGTCAAATTCGCAACACAGAAGTCAAA
Found at i:7235 original size:60 final size:60
Alignment explanation
Indices: 7159--7327 Score: 218
Period size: 60 Copynumber: 2.8 Consensus size: 60
7149 AATATGTAAA
* * *
7159 TCGCAACACAGAAGTCAAATTCGCAATGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGGAAGTCAAATTCGCAATGCGATAATCAAATTCGCAACACAAAAGTCAAAT
* *
7219 TCGCAACGC-GATAGTCAAATTCGCAACGCGATAATCAAATTCGCAATACAAAAGTCAAAT
1 TCGCAACGCGGA-AGTCAAATTCGCAATGCGATAATCAAATTCGCAACACAAAAGTCAAAT
* * *
7279 TCGCAACGCGGAATTTCAAATTCGCAACTG-AAT-TTCAAATTCGCAACAC
1 TCGCAACGCGGAA-GTCAAATTCGCAA-TGCGATAATCAAATTCGCAACAC
7328 GAATTTAATT
Statistics
Matches: 96, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
59 2 0.02
60 77 0.80
61 16 0.17
62 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (60 bp):
TCGCAACGCGGAAGTCAAATTCGCAATGCGATAATCAAATTCGCAACACAAAAGTCAAAT
Found at i:7313 original size:19 final size:19
Alignment explanation
Indices: 7273--7325 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
7263 AATACAAAAG
7273 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CGGAATT
*
7294 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACGGAATT
7313 TCAAATTCGCAAC
1 TCAAATTCGCAAC
7326 ACGAATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 19 0.61
21 12 0.39
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (19 bp):
TCAAATTCGCAACGGAATT
Found at i:7333 original size:20 final size:20
Alignment explanation
Indices: 7138--7331 Score: 150
Period size: 20 Copynumber: 9.7 Consensus size: 20
7128 AGTTTCCAAT
7138 TTCGCAACGCGAATATGT-AAA
1 TTCGCAACGCG-A-ATGTCAAA
*
7159 -TCGCAACACAGAA-GTCAAA
1 TTCGCAACGC-GAATGTCAAA
*
7178 TTCGCAATGCG-ATAGTCAAA
1 TTCGCAACGCGAAT-GTCAAA
* * *
7198 TTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGAATGTCAAA
7218 TTCGCAACGCG-ATAGTCAAA
1 TTCGCAACGCGAAT-GTCAAA
*
7238 TTCGCAACGCG-ATAATCAAA
1 TTCGCAACGCGAAT-GTCAAA
** * *
7258 TTCGCAATACAAAAGTCAAA
1 TTCGCAACGCGAATGTCAAA
*
7278 TTCGCAACGCGGAATTTCAAA
1 TTCGCAACGC-GAATGTCAAA
* *
7299 TTCGCAAC-TGAATTTCAAA
1 TTCGCAACGCGAATGTCAAA
*
7318 TTCGCAACACGAAT
1 TTCGCAACGCGAAT
7332 TTAATTTCAC
Statistics
Matches: 140, Mismatches: 23, Indels: 21
0.76 0.12 0.11
Matches are distributed among these distances:
18 3 0.02
19 24 0.17
20 95 0.68
21 18 0.13
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.21
Consensus pattern (20 bp):
TTCGCAACGCGAATGTCAAA
Found at i:7344 original size:19 final size:20
Alignment explanation
Indices: 7273--7345 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 20
7263 AATACAAAAG
* *
7273 TCAAATTCGCAACGCGGAATT
1 TCAAATTCACAACAC-GAATT
* *
7294 TCAAATTCGCAAC-TGAATT
1 TCAAATTCACAACACGAATT
*
7313 TCAAATTCGCAACACGAATT
1 TCAAATTCACAACACGAATT
*
7333 T-AATTTCACAACA
1 TCAAATTCACAACA
7346 GGTTTTAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 28 0.60
20 6 0.13
21 13 0.28
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.27
Consensus pattern (20 bp):
TCAAATTCACAACACGAATT
Found at i:8321 original size:24 final size:24
Alignment explanation
Indices: 8262--8332 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
8252 GAAATTTTTA
* * *
8262 TTGGTCAATACCCAGACTTTGATC
1 TTGGTCAATACTCGGATTTTGATC
*
8286 TTGGTTAATACTCGGATTTTGATC
1 TTGGTCAATACTCGGATTTTGATC
8310 TTGGTCAATACTCGGATTTTGAT
1 TTGGTCAATACTCGGATTTTGAT
8333 GATGTGATGG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTGGTCAATACTCGGATTTTGATC
Found at i:10583 original size:18 final size:18
Alignment explanation
Indices: 10560--10595 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10550 AAGCAAAAGG
*
10560 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
10578 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
10596 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:10957 original size:20 final size:20
Alignment explanation
Indices: 10934--10987 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
10924 TCGCAACTCG
10934 AATTTGACTTTCGCGTTACA
1 AATTTGACTTTCGCGTTACA
* * *
10954 AATTTGAGTTTCGCGTTGCG
1 AATTTGACTTTCGCGTTACA
*
10974 AATTTGACTATCGC
1 AATTTGACTTTCGC
10988 AACGCTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTACA
Found at i:11137 original size:25 final size:25
Alignment explanation
Indices: 11099--11148 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
11089 AAATCAATTA
*
11099 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
11124 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
11149 GAAAATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:11555 original size:18 final size:18
Alignment explanation
Indices: 11534--11570 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11524 GTAATTGGAG
11534 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
11552 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
11570 T
1 T
11571 AAATTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:12437 original size:13 final size:13
Alignment explanation
Indices: 12419--12451 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
12409 CAAGTGTCAT
12419 TAGCTTGTATTTA
1 TAGCTTGTATTTA
12432 TAGCTTGTATTTA
1 TAGCTTGTATTTA
12445 TAGCTTG
1 TAGCTTG
12452 GAATGTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.52
Consensus pattern (13 bp):
TAGCTTGTATTTA
Found at i:12770 original size:50 final size:51
Alignment explanation
Indices: 12675--12784 Score: 179
Period size: 50 Copynumber: 2.2 Consensus size: 51
12665 ATCAACTTTT
12675 ACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATTAA
1 ACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATTAA
* *
12727 AC-AATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTAA
1 ACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAA
12776 ACAAATCAA
1 ACAAATCAA
12785 CTTTCAATGT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
49 8 0.15
50 29 0.53
51 16 0.29
52 2 0.04
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (51 bp):
ACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAA
Found at i:14169 original size:21 final size:21
Alignment explanation
Indices: 14145--14243 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
14135 GCGGGTGGGA
*
14145 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
14166 CCTCTTGAACGGTGGGATGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
14187 CTTCTTCG-ATGATGAAAGGGG
1 CCTCTT-GAACGATGAGAGGGG
*
14208 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
*
14229 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
14244 TAGGTGCATC
Statistics
Matches: 59, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
20 2 0.03
21 55 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:14201 original size:42 final size:42
Alignment explanation
Indices: 14125--14218 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
14115 ATGAATCAGG
*
14125 CTCTTGAACGGCGGGTGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGCGGGTGGGACCTCTTGAACGATGAAAGGGGC
* * *
14167 CTCTTGAACGGTGGGATGGG-CTTCTTCG-ATGATGAAAGGGGC
1 CTCTTGAACGGCGGG-TGGGACCTCTT-GAACGATGAAAGGGGC
14209 CTCTTGAACG
1 CTCTTGAACG
14219 ATAGGAGGCG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 41 0.89
43 5 0.11
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGCGGGTGGGACCTCTTGAACGATGAAAGGGGC
Found at i:14241 original size:42 final size:42
Alignment explanation
Indices: 14140--14243 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
14130 GAACGGCGGG
* * * *
14140 TGGGACCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGA
1 TGGG-CCTCTTGAATGATGAAAGGGGCCTCTTGAACGATAGGA
*
14183 TGGGCTTCTTCG-ATGATGAAAGGGGCCTCTTGAACGATAGGA
1 TGGGCCTCTT-GAATGATGAAAGGGGCCTCTTGAACGATAGGA
14225 -GGCGCCTCTTGAATGATGA
1 TGG-GCCTCTTGAATGATGA
14244 TAGGTGCATC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
41 3 0.06
42 44 0.85
43 5 0.10
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (42 bp):
TGGGCCTCTTGAATGATGAAAGGGGCCTCTTGAACGATAGGA
Found at i:16502 original size:20 final size:20
Alignment explanation
Indices: 16463--16502 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16453 TGCAATTTTG
* * *
16463 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
16483 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
16503 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:17016 original size:40 final size:40
Alignment explanation
Indices: 16972--17143 Score: 185
Period size: 40 Copynumber: 4.3 Consensus size: 40
16962 ATATTGTGTT
16972 TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTA
*
17012 TCGCGTTGCGGATTTGACTATCGCGTTGCGAATTTGACT-
1 TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTA
** * *
17051 TCTATGTTGCG-ATTT-ACAAATTAGCGTTGCGAATTTGACTA
1 TC-GCGTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGACTA
* *
17092 TCGCGTTGCGAATTTGACT-TCTGTGTTGCG-ATTT-ACAAA
1 TCGCGTTGCGAATTTGACTATC-GCGTTGCGAATTTGAC-TA
17131 TTCGCGTTGCGAA
1 -TCGCGTTGCGAA
17144 ATTGGAAACT
Statistics
Matches: 112, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
38 4 0.04
39 13 0.12
40 87 0.78
41 6 0.05
42 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTA
Found at i:17040 original size:60 final size:60
Alignment explanation
Indices: 16972--17143 Score: 224
Period size: 60 Copynumber: 2.9 Consensus size: 60
16962 ATATTGTGTT
* * * *
16972 TCGCGTTGCGAATTTGACTATC-GCGTTGCGAATTTGAC-TA-TCGCGTTGCGGATTTGACTA
1 TCGCGTTGCGAATTTGACT-TCTACGTTGCG-ATTT-ACAAATTAGCGTTGCGAATTTGACTA
*
17032 TCGCGTTGCGAATTTGACTTCTATGTTGCGATTTACAAATTAGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTCTACGTTGCGATTTACAAATTAGCGTTGCGAATTTGACTA
** *
17092 TCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGAA
1 TCGCGTTGCGAATTTGACTTCTACGTTGCGATTTACAAATTAGCGTTGCGAA
17144 ATTGGAAACT
Statistics
Matches: 102, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
58 2 0.02
59 7 0.07
60 93 0.91
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (60 bp):
TCGCGTTGCGAATTTGACTTCTACGTTGCGATTTACAAATTAGCGTTGCGAATTTGACTA
Found at i:17122 original size:20 final size:20
Alignment explanation
Indices: 16972--17110 Score: 185
Period size: 20 Copynumber: 7.0 Consensus size: 20
16962 ATATTGTGTT
16972 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
16992 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
17012 TCGCGTTGCGGATTTGACTA
1 TCGCGTTGCGAATTTGACTA
17032 TCGCGTTGCGAATTTGACT-
1 TCGCGTTGCGAATTTGACTA
** *
17051 TCTATGTTGCG-ATTT-ACAAA
1 TC-GCGTTGCGAATTTGAC-TA
*
17071 TTAGCGTTGCGAATTTGACTA
1 -TCGCGTTGCGAATTTGACTA
17092 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
17111 TCTGTGTTGC
Statistics
Matches: 103, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
18 2 0.02
19 6 0.06
20 87 0.84
21 6 0.06
22 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:17139 original size:20 final size:20
Alignment explanation
Indices: 16971--17142 Score: 112
Period size: 20 Copynumber: 8.6 Consensus size: 20
16961 AATATTGTGT
*
16971 TTCGCGTTGCGAATTTGACTA
1 TTCGCGTTGCG-ATTTGACAA
*
16992 -TCGCGTTGCGAATTTGACTA
1 TTCGCGTTGCG-ATTTGACAA
*
17012 -TCGCGTTGCGGATTTGACTA
1 TTCGCGTTGC-GATTTGACAA
17032 -TCGCGTTGCGAATTTGAC--
1 TTCGCGTTGCG-ATTTGACAA
**
17050 TTCTATGTTGCGATTT-ACAAA
1 TTC-GCGTTGCGATTTGAC-AA
* *
17071 TTAGCGTTGCGAATTTGACTA
1 TTCGCGTTGCG-ATTTGACAA
17092 -TCGCGTTGCGAATTTGAC--
1 TTCGCGTTGCG-ATTTGACAA
*
17110 TTCTGTGTTGCGATTT-ACAAA
1 TTC-GCGTTGCGATTTGAC-AA
17131 TTCGCGTTGCGA
1 TTCGCGTTGCGA
17143 AATTGGAAAC
Statistics
Matches: 128, Mismatches: 9, Indels: 29
0.77 0.05 0.17
Matches are distributed among these distances:
18 4 0.03
19 13 0.10
20 98 0.77
21 11 0.09
22 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
TTCGCGTTGCGATTTGACAA
Found at i:21813 original size:20 final size:19
Alignment explanation
Indices: 21765--21813 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
21755 AAAATTTATC
21765 TTTTATATTTAAACTTTTTT
1 TTTTA-ATTTAAACTTTTTT
* *
21785 TTGTCAATTTAATCTTTATTT
1 TT-TTAATTTAAACTTT-TTT
21806 TTTTAATT
1 TTTTAATT
21814 ACTTTGTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTAATTTAAACTTTTTT
Found at i:22203 original size:20 final size:20
Alignment explanation
Indices: 22178--22251 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
22168 GCGAAATAAA
22178 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATCTCCAG
** *
22198 AATCGCAAATCAGTTC-CCAG
1 AATCGCAACGC-GATCTCCAG
* **
22218 AATCGCAACGCGATTATTAAG
1 AATCGCAACGCGA-TCTCCAG
22239 AATCGCAACGCGA
1 AATCGCAACGCGA
22252 ATATGAAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 23 0.55
21 18 0.43
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGATCTCCAG
Found at i:22264 original size:20 final size:20
Alignment explanation
Indices: 22218--22473 Score: 180
Period size: 20 Copynumber: 12.7 Consensus size: 20
22208 CAGTTCCCAG
* **
22218 AATCGCAACGCGATTATTAA
1 AATCGCAACGCGAATACGAA
*
22238 GAATCGCAACGCGAATATGAA
1 -AATCGCAACGCGAATACGAA
* *
22259 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
22279 AATCGCAACGCGTAT-CCATA
1 AATCGCAACGCGAATACGA-A
22299 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
22320 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
22340 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
22360 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
22380 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
22400 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
22420 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
22441 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
22461 AATCGCAGCGCGA
1 AATCGCAACGCGA
22474 TTTTTAAAGC
Statistics
Matches: 192, Mismatches: 32, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.01
20 137 0.71
21 52 0.27
22 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:22302 original size:40 final size:40
Alignment explanation
Indices: 22239--22473 Score: 240
Period size: 40 Copynumber: 5.8 Consensus size: 40
22229 GATTATTAAG
* ** *
22239 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATA
* * *
22279 AATCGCAACGCGTATCCATAAATCGCAACGACAATACGTA-A
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGA-ACATATA
* * **
22320 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATA
* * * **
22360 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATA
* * *
22400 AATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTA-A
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGA-ACATATA
*
22441 AATCGCAACGCGTATCCGTAAATCGCAGCGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
22474 TTTTTAAAGC
Statistics
Matches: 164, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.01
40 96 0.59
41 62 0.38
42 5 0.03
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATA
Found at i:22303 original size:81 final size:81
Alignment explanation
Indices: 22218--22473 Score: 295
Period size: 81 Copynumber: 3.2 Consensus size: 81
22208 CAGTTCCCAG
* * * ** *
22218 AATCGCAACGCGATTA-TTAAGAATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAAT
1 AATCGCAACGCGAATACGTAA-AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAAT
*
22282 CGCAACGCGTATCCATA
65 CGCAACGCGTATCCGTA
* * **
22299 AATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAAT
1 AATCGCAACG-CGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAAT
*
22363 CGCAACGCGTATCTGTA
65 CGCAACGCGTATCCGTA
* * * *
22380 AATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTA-AAA
1 AATCGCAACGCGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACG-CGA-ACATATAAA
22443 TCGCAACGCGTATCCGTA
64 TCGCAACGCGTATCCGTA
*
22461 AATCGCAGCGCGA
1 AATCGCAACGCGA
22474 TTTTTAAAGC
Statistics
Matches: 147, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
80 30 0.20
81 112 0.76
82 5 0.03
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.18
Consensus pattern (81 bp):
AATCGCAACGCGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAATC
GCAACGCGTATCCGTA
Found at i:22371 original size:121 final size:121
Alignment explanation
Indices: 22239--22467 Score: 377
Period size: 121 Copynumber: 1.9 Consensus size: 121
22229 GATTATTAAG
* *
22239 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCATAAATCG
1 AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCATAAATCG
22304 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
66 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * * * * *
22360 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCATAAATCG
22425 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCA
66 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCA
22468 GCGCGATTTT
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 99 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (121 bp):
AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCATAAATCG
CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:23065 original size:20 final size:19
Alignment explanation
Indices: 23034--23111 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 19
23024 TTCTAAACTT
*
23034 AAAATCGAAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
*
23054 AAAACCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
23074 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
23095 AAAATCGCAACGAGAAA
1 AAAATCGCAAC-AGAAA
23112 CCAAAATCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 29 0.60
21 19 0.40
ACGTcount: A:0.54, C:0.18, G:0.18, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:23095 original size:21 final size:21
Alignment explanation
Indices: 23049--23109 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
23039 CGAAACATGA
*
23049 AAATGAAAACCGCAAC-ACGA-
1 AAATGAAAATCGCAACGA-GAG
**
23069 AAATGACTATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
23090 AAATGAAAATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
23110 AACCAAAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.10
Consensus pattern (21 bp):
AAATGAAAATCGCAACGAGAG
Found at i:23165 original size:33 final size:33
Alignment explanation
Indices: 23123--23244 Score: 127
Period size: 33 Copynumber: 3.5 Consensus size: 33
23113 CAAAATCGCA
23123 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* * * *
23156 TTGCGATTTTAATTTTGCATTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
23189 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCG
23229 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
23245 AACCAAAAGA
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
33 41 0.59
34 7 0.10
39 1 0.01
40 21 0.30
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:23221 original size:20 final size:21
Alignment explanation
Indices: 23189--23244 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
23179 GATTCTCTCA
**
23189 TTGCGATAGTCATTTC-CGCG
1 TTGCGATTTTCATTTCTCGCG
*
23209 TTGCGATTTTCA-TTCTCTCG
1 TTGCGATTTTCATTTCTCGCG
23229 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
23245 AACCAAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.10
20 25 0.81
21 3 0.10
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.46
Consensus pattern (21 bp):
TTGCGATTTTCATTTCTCGCG
Found at i:25289 original size:21 final size:21
Alignment explanation
Indices: 25265--25331 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
25255 TCATTCCTCG
25265 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
25286 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
25307 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
25328 AGAG
1 AGAG
25332 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:25289 original size:42 final size:42
Alignment explanation
Indices: 25213--25331 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
25203 GACTCGCCTG
* * * * * * *
25213 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
25255 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
25297 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
25332 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:26723 original size:13 final size:13
Alignment explanation
Indices: 26676--26728 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
26666 TTGATTGTTT
26676 AATTGATTTGTAA
1 AATTGATTTGTAA
*
26689 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
**
26703 ATATTGATTTGTTT
1 A-ATTGATTTGTAA
*
26717 AATTGATGTGTA
1 AATTGATTTGTA
26729 CATAATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.34
14 20 0.62
15 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:26851 original size:19 final size:20
Alignment explanation
Indices: 26816--26860 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
26806 AAAACAGACT
26816 ATCGCAACGCGGAAATGAAA
1 ATCGCAACGCGGAAATGAAA
*
26836 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGAAA
26855 ATCGCA
1 ATCGCA
26861 TTTAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGAAA
Found at i:29177 original size:24 final size:24
Alignment explanation
Indices: 29143--29196 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
29133 CTGAAAAATC
29143 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
29167 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
29191 ATCAAA
1 ATCAAA
29197 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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:29210 original size:24 final size:24
Alignment explanation
Indices: 29143--29210 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
29133 CTGAAAAATC
* * *
29143 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
29167 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
29191 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
29211 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:30081 original size:20 final size:19
Alignment explanation
Indices: 30056--30247 Score: 161
Period size: 20 Copynumber: 9.6 Consensus size: 19
30046 GTAAGAATCT
30056 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTAC-GATTCG
*
30076 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACG-ATTCG
* * * *
30096 CATTGCAATTTACGGATACA
1 CGTTGCGATTTAC-GATTCG
* *
30116 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACG-ATTCG
*
30136 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTAC-GATTCG
*
30156 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACG-ATTCG
*
30176 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTAC-GATTCG
* *
30196 CATTGTGATTTTACGTATT-G
1 CGTTGCGA-TTTACG-ATTCG
*
30216 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTAC-GATTCG
30237 CGTTGCGATTT
1 CGTTGCGATTT
30248 TACGGGTACT
Statistics
Matches: 141, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
19 3 0.02
20 120 0.85
21 18 0.13
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATTTACGATTCG
Found at i:30084 original size:40 final size:40
Alignment explanation
Indices: 30053--30266 Score: 284
Period size: 40 Copynumber: 5.3 Consensus size: 40
30043 ATAGTAAGAA
* *
30053 TCTCGTTGCGATTTACAGATTCGCATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
* * * *
30093 TCGCATTGCAATTTACGGATACACATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
* *
30133 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
*
30173 TCTCGTTGCGATTTACGGATACGCATTGTGATTTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGTAT
* * **
30214 TGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGGT
1 TCTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGTAT
*
30255 ACTCGTTGCGAT
1 TCTCGTTGCGAT
30267 AGTCAGAATC
Statistics
Matches: 151, Mismatches: 22, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
40 96 0.64
41 55 0.36
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
TCTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
Found at i:32116 original size:199 final size:198
Alignment explanation
Indices: 31689--32366 Score: 839
Period size: 200 Copynumber: 3.4 Consensus size: 198
31679 TACACCATGA
*
31689 ACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTTTGGGATTGATACAATTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATTGATAC-ATTT
* * ** *
31754 T--AAATGTATCGACACTTTATACGTGCACCTTGTGGGGCATTCATTCTGGA-AAAAAGTATCGA
65 TAAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGACATTCATTCTGGACAAAAA-TATCGA
* * * *
31816 CACAAACTTAAAAAGTGTCGATACATTATGTAGAACTATTTTCTCATAAAATCGGTATATTTCTA
129 CACAAATTTAAAAAGTGTCGATACATTATGTTG-ACTATTTTCTCATAAAACCGGTATATTTATA
** *
31881 TTGGGT
193 CCGGTT
* * *
31887 ACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATAGATAC-TTTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATTGATACATTTT
*
31951 AATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGACATTCATTCTGGACAAAATATATCGA
66 AA-AAATGTATCGACACTTTATGCGTGCACCTCGTTTGACATTCATTCTGGACAAAA-ATATCGA
*
32016 CACAAATTTAAAAAGTGTCGATACATTATGTTGACTTATTCTCTCATAAAACCGGTATATTTATA
129 CACAAATTTAAAAAGTGTCGATACATTATGTTGAC-TATTTTCTCATAAAACCGGTATATTTATA
32081 CCGGTT
193 CCGGTT
* * * * * * * * * *
32087 ATATTG-AAAATTACATATTACATTGTAATTATAGGTTTGGATGTTTTTGAGATCGATACTTTTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATTGATACATTTT
* * *
32151 AAAAATGTATCTACACTTTATGCGTGCACCTCGTTTTGACATTCATTTTGGACAATAAGTATCGA
66 AAAAATGTATCGACACTTTATGCGTGCACCTCG-TTTGACATTCATTCTGGACAA-AAATATCGA
** * * * * *
32216 CACAAATTCCACAAGTGTCGATACATTATGTTGAAATGTTTTCTAAT-TAACCGGTATATTTATA
129 CACAAATTTAAAAAGTGTCGATACATTATGTTG-ACTATTTTCTCATAAAACCGGTATATTTATA
32280 CCGGTT
193 CCGGTT
* * *
32286 ACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCGATATTTTTGGGGTTGATAC-TTTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATTGATACATTTT
*
32350 AGAAAATGTATCTACAC
66 A-AAAATGTATCGACAC
32367 ATATTTAGGT
Statistics
Matches: 420, Mismatches: 48, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
196 4 0.01
198 56 0.13
199 153 0.36
200 203 0.48
201 4 0.01
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (198 bp):
ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATTGATACATTTT
AAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGACATTCATTCTGGACAAAAATATCGACA
CAAATTTAAAAAGTGTCGATACATTATGTTGACTATTTTCTCATAAAACCGGTATATTTATACCG
GTT
Found at i:37045 original size:15 final size:15
Alignment explanation
Indices: 37025--37059 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
37015 GTTCGACCGG
**
37025 ATAAAATTTTAAAAA
1 ATAAAATTAAAAAAA
37040 ATAAAATTAAAAAAA
1 ATAAAATTAAAAAAA
37055 ATAAA
1 ATAAA
37060 TTTATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAAATTAAAAAAA
Found at i:37693 original size:25 final size:25
Alignment explanation
Indices: 37665--37719 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
37655 TATTATTAAC
* *
37665 AAAAAATAGTTAAATTAATCAAATT
1 AAAAAAGAGTTAAATAAATCAAATT
* * *
37690 AAAAAAGGGTTAAATAAATGAAGTT
1 AAAAAAGAGTTAAATAAATCAAATT
37715 AAAAA
1 AAAAA
37720 TTATCTTGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.25
Consensus pattern (25 bp):
AAAAAAGAGTTAAATAAATCAAATT
Found at i:40307 original size:48 final size:48
Alignment explanation
Indices: 40190--40315 Score: 155
Period size: 48 Copynumber: 2.6 Consensus size: 48
40180 CCGGAACTGA
*** * *
40190 TGCTGATCT-CTATATAAATCTCCCGGATTGTCCCATTGAAACTGCTGC
1 TGCTGATCTGC-ATATAAATCTTGAGGATTTTCCAATTGAAACTGCTGC
40238 TGCTGATCTGCATATAAATCTTGAGGATTTTCCAATTGAAACTGCTGC
1 TGCTGATCTGCATATAAATCTTGAGGATTTTCCAATTGAAACTGCTGC
* * * *
40286 TGCTGATTTGTATATGAATCTTGAAGATTT
1 TGCTGATCTGCATATAAATCTTGAGGATTT
40316 CCCCATCCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
48 67 0.99
49 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (48 bp):
TGCTGATCTGCATATAAATCTTGAGGATTTTCCAATTGAAACTGCTGC
Found at i:40328 original size:48 final size:48
Alignment explanation
Indices: 40228--40329 Score: 132
Period size: 48 Copynumber: 2.1 Consensus size: 48
40218 TGTCCCATTG
* * **
40228 AAACTGCTGCTGCTGATCTGCATATAAATCTTGAGGATTTTCCAATTG
1 AAACTGCTGCTGCTGATCTGCATATAAATCTTGAAGATTTCCCAATCC
* * * *
40276 AAACTGCTGCTGCTGATTTGTATATGAATCTTGAAGATTTCCCCATCC
1 AAACTGCTGCTGCTGATCTGCATATAAATCTTGAAGATTTCCCAATCC
40324 AAACTG
1 AAACTG
40330 AGCTGCAGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (48 bp):
AAACTGCTGCTGCTGATCTGCATATAAATCTTGAAGATTTCCCAATCC
Found at i:40481 original size:114 final size:114
Alignment explanation
Indices: 40270--40515 Score: 429
Period size: 114 Copynumber: 2.1 Consensus size: 114
40260 GAGGATTTTC
*
40270 CAATTGAAACTGCTGCTGCTGATTTGTATATGAATCTTGAAGATTTCCCCATCCAAACTGAGCTG
1 CAATT-AAACTGCTGCTGCTGATGTGTATATGAATCTTGAAGATTTCCCCATCCAAACTGAGCTG
*
40335 CAGGTGGTATCTCTAACATTGGTGGCACTGCTGTTGATCCAACGTTACCA
65 CAGGTGGTATCTCTAACATTGGTGGCACTGCTGTTGATCCAACGCTACCA
* *
40385 CAATTAAACTGCTGCTGTTGATGTGTATATGAATCTTGAGGATTTCCCCATCCAAACTGAGCTGC
1 CAATTAAACTGCTGCTGCTGATGTGTATATGAATCTTGAAGATTTCCCCATCCAAACTGAGCTGC
*
40450 AGGTGGTATCTCTAACATTGGTGGCATTGCTGTTGATCCAACGCTACCA
66 AGGTGGTATCTCTAACATTGGTGGCACTGCTGTTGATCCAACGCTACCA
*
40499 CAATTAAATTGCTGCTG
1 CAATTAAACTGCTGCTG
40516 ATTTACCCAT
Statistics
Matches: 125, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
114 120 0.96
115 5 0.04
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (114 bp):
CAATTAAACTGCTGCTGCTGATGTGTATATGAATCTTGAAGATTTCCCCATCCAAACTGAGCTGC
AGGTGGTATCTCTAACATTGGTGGCACTGCTGTTGATCCAACGCTACCA
Found at i:44629 original size:35 final size:35
Alignment explanation
Indices: 44583--44650 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
44573 TTGCAAGAAC
* *
44583 GGTACGGATACT-TCTACATTGGTATCGATACCCAT
1 GGTACCGATACTATC-ACATTAGTATCGATACCCAT
*
44618 GGTACCGATACTATCACTTTAGTATCGATACCC
1 GGTACCGATACTATCACATTAGTATCGATACCC
44651 CATGAAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 27 0.93
36 2 0.07
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (35 bp):
GGTACCGATACTATCACATTAGTATCGATACCCAT
Found at i:46031 original size:112 final size:112
Alignment explanation
Indices: 45833--46172 Score: 653
Period size: 112 Copynumber: 3.0 Consensus size: 112
45823 GGTTCGATTC
*
45833 ATTGTGGGTTAAGATCATTTCGAGTTTTGATCACTTCAAACTCGTATCATTTCATACTTCGATTG
1 ATTGTGGGTTAAGATCATTTCGA-ATTTGATCACTTCAAACTCGTATCATTTCATACTTCGATTG
45898 TTGTAAATCTGGGTCATTTCTGGTTCGGATTGGTTTGAATCCAAGTCA
65 TTGTAAATCTGGGTCATTTCTGGTTCGGATTGGTTTGAATCCAAGTCA
45946 ATTGTGGGTTAAGATCATTTCGAATTTGATCACTTCAAACTCGTATCATTTCATACTTCGATTGT
1 ATTGTGGGTTAAGATCATTTCGAATTTGATCACTTCAAACTCGTATCATTTCATACTTCGATTGT
46011 TGTAAATCTGGGTCATTTCTGGTTCGGATTGGTTTGAATCCAAGTCA
66 TGTAAATCTGGGTCATTTCTGGTTCGGATTGGTTTGAATCCAAGTCA
46058 ATTGTGGGTTAAGATCATTTCGAATTTGATCACTTCAAACTCGTATCATTTCATACTTCGATTGT
1 ATTGTGGGTTAAGATCATTTCGAATTTGATCACTTCAAACTCGTATCATTTCATACTTCGATTGT
*
46123 TGTAAATCTGGGTCATTTCTGGTTCGAATTGGTTTGAATCCAAGTCA
66 TGTAAATCTGGGTCATTTCTGGTTCGGATTGGTTTGAATCCAAGTCA
46170 ATT
1 ATT
46173 TATGTCCGAA
Statistics
Matches: 225, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
112 202 0.90
113 23 0.10
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (112 bp):
ATTGTGGGTTAAGATCATTTCGAATTTGATCACTTCAAACTCGTATCATTTCATACTTCGATTGT
TGTAAATCTGGGTCATTTCTGGTTCGGATTGGTTTGAATCCAAGTCA
Found at i:48765 original size:19 final size:18
Alignment explanation
Indices: 48743--48778 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48733 TTAAAGGCTA
*
48743 TTTGTACTATTTCTCTCTT
1 TTTGTAATATTTC-CTCTT
48762 TTTGTAATATTTCCTCT
1 TTTGTAATATTTCCTCT
48779 ATTAGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.14, C:0.19, G:0.06, T:0.61
Consensus pattern (18 bp):
TTTGTAATATTTCCTCTT
Found at i:49665 original size:43 final size:43
Alignment explanation
Indices: 49441--49664 Score: 351
Period size: 43 Copynumber: 5.2 Consensus size: 43
49431 CTAAAGTTAA
*
49441 CGGCGTTTTTGGGACAAACGCCACAAAAGGTCGAGATCTATAG
1 CGGCGTTTTTGGGACAAACGCCACAATAGGTCGAGATCTATAG
*
49484 CGGCGTTTTTGGGACAAACGCCTCAATAGGTCGAGATCTATAG
1 CGGCGTTTTTGGGACAAACGCCACAATAGGTCGAGATCTATAG
*
49527 CGGCGTTTTTGGGACAAACGCCGCAATAGGTCGAGATCTATAG
1 CGGCGTTTTTGGGACAAACGCCACAATAGGTCGAGATCTATAG
* * * *
49570 CGACGTTTTTGGAACAAACGCCGCAATAGGTCGAGATTTATAG
1 CGGCGTTTTTGGGACAAACGCCACAATAGGTCGAGATCTATAG
* * *
49613 CGGCGTTTTTGGAACAAACGCCACAAAAGGT-TAGATCTATAG
1 CGGCGTTTTTGGGACAAACGCCACAATAGGTCGAGATCTATAG
49655 CGGCGTTTTT
1 CGGCGTTTTT
49665 TATACAAACA
Statistics
Matches: 170, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
42 19 0.11
43 151 0.89
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (43 bp):
CGGCGTTTTTGGGACAAACGCCACAATAGGTCGAGATCTATAG
Found at i:54957 original size:42 final size:42
Alignment explanation
Indices: 54884--55369 Score: 357
Period size: 42 Copynumber: 11.9 Consensus size: 42
54874 AAGACGACCT
**
54884 TTAGCGGCGTTT-TTTA-AAAATGCCACTAAAGTACGTGTAA
1 TTAGCGGCGTTTGTGCATAAAATGCCACTAAAGTACGTGTAA
*
54924 TTAGCGGCGTTTGTGCATAAAATGCCACAAAAGTACGTGTAA
1 TTAGCGGCGTTTGTGCATAAAATGCCACTAAAGTACGTGTAA
* * ** * * ***
54966 TTAGTGGCGTTTGTGCTTGCAACGCCACTAAAGTAAG-ACCA
1 TTAGCGGCGTTTGTGCATAAAATGCCACTAAAGTACGTGTAA
* * *
55007 TTAGCGGCGTTT-T-TATAAAAATACCACTAAAGTA--TAGTAT
1 TTAGCGGCGTTTGTGCAT-AAAATGCCACTAAAGTACGT-GTAA
** * * * *
55047 TTCTCGGCATTTAT--ATAAAAATGCAACTAGAGTACGTGTAA
1 TTAGCGGCGTTTGTGCAT-AAAATGCCACTAAAGTACGTGTAA
* * * *
55088 TTAGCGGCGTTTGTGTATAAAACGCCACTAAAGAACATGTAA
1 TTAGCGGCGTTTGTGCATAAAATGCCACTAAAGTACGTGTAA
* * * **
55130 TTAGCGGCGTTTTTGCTTAAAACGCCACTAAAGTACGACCT--
1 TTAGCGGCGTTTGTGCATAAAATGCCACTAAAGTACG-TGTAA
* *
55171 TTAGCGGCGTTTGT--ATAAAATCGCCACTAAAGTAC-AGTAT
1 TTAGCGGCGTTTGTGCATAAAAT-GCCACTAAAGTACGTGTAA
* * * * * *
55211 TTATCAGCGTTTAT--ATAAAAACGCCACTATAGTGCGTGTAA
1 TTAGCGGCGTTTGTGCAT-AAAATGCCACTAAAGTACGTGTAA
* * *
55252 TTAGCGGCGTTTGTGCGTAAAATACCACTAAAATACGTGTAA
1 TTAGCGGCGTTTGTGCATAAAATGCCACTAAAGTACGTGTAA
* *
55294 TTAGCGGCGTTTGTGCTTAAAATGCCACTAAAGTA--TG-ACCT
1 TTAGCGGCGTTTGTGCATAAAATGCCACTAAAGTACGTGTA--A
55335 TTAGCGGCGTTTGT--ATAAAAATGCCACTAAAGTAC
1 TTAGCGGCGTTTGTGCAT-AAAATGCCACTAAAGTAC
55370 ATTATTTTCT
Statistics
Matches: 350, Mismatches: 74, Indels: 43
0.75 0.16 0.09
Matches are distributed among these distances:
38 1 0.00
39 8 0.02
40 108 0.31
41 73 0.21
42 156 0.45
43 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (42 bp):
TTAGCGGCGTTTGTGCATAAAATGCCACTAAAGTACGTGTAA
Found at i:55095 original size:164 final size:164
Alignment explanation
Indices: 54898--55376 Score: 683
Period size: 164 Copynumber: 2.9 Consensus size: 164
54888 CGGCGTTTTT
54898 TAAAAATGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCATAAAATGCCACAAAAGTACGTG
1 TAAAAATGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCATAAAATGCCACAAAAGTACGTG
* ** * *
54963 TAATTAGTGGCGTTTGTGCTTGCAACGCCACTAAAGTAAGACCATTAGCGGCGTTTTTATAAAAA
66 TAATTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTAAGACCTTTAGCGGCGTTTGTATAAAAA
* * * *
55028 TACCACTAAAGTATAGTATTTCTCGGCATTTATA
131 TGCCACTAAAGTACAGTATTTATCAGCATTTATA
* * * * * * *
55062 TAAAAATGCAACTAGAGTACGTGTAATTAGCGGCGTTTGTGTATAAAACGCCACTAAAGAACATG
1 TAAAAATGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCATAAAATGCCACAAAAGTACGTG
* *
55127 TAATTAGCGGCGTTTTTGCTTAAAACGCCACTAAAGTACGACCTTTAGCGGCGTTTGTAT-AAAA
66 TAATTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTAAGACCTTTAGCGGCGTTTGTATAAAAA
*
55191 TCGCCACTAAAGTACAGTATTTATCAGCGTTTATA
131 T-GCCACTAAAGTACAGTATTTATCAGCATTTATA
* * * * *
55226 TAAAAACGCCACTATAGTGCGTGTAATTAGCGGCGTTTGTGCGTAAAATACCACTAAAA-TACGT
1 TAAAAATGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCATAAAATGCCAC-AAAAGTACGT
* *
55290 GTAATTAGCGGCGTTTGTGCTTAAAATGCCACTAAAGTATGACCTTTAGCGGCGTTTGTATAAAA
65 GTAATTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTAAGACCTTTAGCGGCGTTTGTATAAAA
*
55355 ATGCCACTAAAGTACATTATTT
130 ATGCCACTAAAGTACAGTATTT
55377 TCTGGCGTTT
Statistics
Matches: 278, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
163 5 0.02
164 265 0.95
165 8 0.03
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (164 bp):
TAAAAATGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCATAAAATGCCACAAAAGTACGTG
TAATTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTAAGACCTTTAGCGGCGTTTGTATAAAAA
TGCCACTAAAGTACAGTATTTATCAGCATTTATA
Found at i:55102 original size:122 final size:121
Alignment explanation
Indices: 54879--55120 Score: 292
Period size: 122 Copynumber: 2.0 Consensus size: 121
54869 GGATCAAGAC
* * * *
54879 GACCTTTAGCGGCGTTTTTTAAAAATGCCACTAAAGTACGTGTAATTAGCGGCGTTTGTGCATAA
1 GACCATTAGCGGCGTTTTTTAAAAATACCACTAAAGTAC-TGTAATTAGCGGCATTTAT-CATAA
* * **
54944 AATGCCACAAAAGTACGTGTAATTAGTGGCGTTTGTGCT-TGCAACGCCACTAAAGTAA
64 AATGCAACAAAAGTACGTGTAATTAGCGGCGTTTGTG-TATAAAACGCCACTAAAGTAA
* **
55002 GACCATTAGCGGCGTTTTTATAAAAATACCACTAAAGTA-TAGTATTTCTCGGCATTTAT-ATAA
1 GACCATTAGCGGCGTTTTT-TAAAAATACCACTAAAGTACT-GTAATTAGCGGCATTTATCAT-A
* *
55065 AAATGCAACTAGAGTACGTGTAATTAGCGGCGTTTGTGTATAAAACGCCACTAAAG
63 AAATGCAACAAAAGTACGTGTAATTAGCGGCGTTTGTGTATAAAACGCCACTAAAG
55121 AACATGTAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
121 3 0.03
122 50 0.49
123 31 0.30
124 18 0.18
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (121 bp):
GACCATTAGCGGCGTTTTTTAAAAATACCACTAAAGTACTGTAATTAGCGGCATTTATCATAAAA
TGCAACAAAAGTACGTGTAATTAGCGGCGTTTGTGTATAAAACGCCACTAAAGTAA
Found at i:55260 original size:122 final size:122
Alignment explanation
Indices: 55106--55371 Score: 288
Period size: 122 Copynumber: 2.2 Consensus size: 122
55096 GTTTGTGTAT
* * * *
55106 AAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTTTGCTTAAAACGCCACTAAAGTACGACCT
1 AAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCGTAAAACACCACTAAAATACG-CCT
55171 -TTAGCGGCGTTTGT-ATAAAATCGCCACTAAAGTACAGTATTTATCAGCGTTTATATA
65 ATTAGCGGCGTTTGTCATAAAAT-GCCACTAAAGTACAGTATTTATCAGCGTTTATATA
* ** * * **
55228 AAAACGCCACTATAGTGCGTGTAATTAGCGGCGTTTGTGCGTAAAATACCACTAAAATACGTGTA
1 AAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCGTAAAACACCACTAAAATACGCCT-
* * * * *
55293 ATTAGCGGCGTTTGTGCTTAAAATGCCACTAAAGTA-TG-ACCTTTAGCGGCGTTTGTATA
65 ATTAGCGGCGTTTGT-CATAAAATGCCACTAAAGTACAGTA--TTTATCAGCGTTTATATA
* *
55352 AAAATGCCACTAAAGTACAT
1 AAAACGCCACTAAAGAACAT
55372 TATTTTCTGG
Statistics
Matches: 118, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
121 1 0.01
122 53 0.45
123 15 0.13
124 43 0.36
125 6 0.05
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (122 bp):
AAAACGCCACTAAAGAACATGTAATTAGCGGCGTTTGTGCGTAAAACACCACTAAAATACGCCTA
TTAGCGGCGTTTGTCATAAAATGCCACTAAAGTACAGTATTTATCAGCGTTTATATA
Found at i:58625 original size:12 final size:12
Alignment explanation
Indices: 58608--58638 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
58598 AAGAGGAGTA
58608 ATTTCAATTTTG
1 ATTTCAATTTTG
58620 ATTTCAATTTTG
1 ATTTCAATTTTG
58632 ATTTCAA
1 ATTTCAA
58639 AATGATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55
Consensus pattern (12 bp):
ATTTCAATTTTG
Found at i:60779 original size:20 final size:21
Alignment explanation
Indices: 60731--60781 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
60721 TAAAAATATT
*
60731 TAATAAAATAAAATAGATAAA
1 TAATAAAATAAAATAGAGAAA
*
60752 TAAT-AAATAAAA-AGGGAAA
1 TAATAAAATAAAATAGAGAAA
60771 TAATAAAATAA
1 TAATAAAATAA
60782 TAAATAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 9 0.33
20 14 0.52
21 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (21 bp):
TAATAAAATAAAATAGAGAAA
Found at i:60864 original size:17 final size:18
Alignment explanation
Indices: 60830--60871 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
60820 GTTGTTTTTA
60830 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
60848 AAATAAAAGA-AATAATT
1 AAATAAAAAATAAGAATT
60865 AAATAAA
1 AAATAAA
60872 TAATCTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:63632 original size:2 final size:2
Alignment explanation
Indices: 63627--63653 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
63617 ATCAATCTTT
63627 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 T
63654 TATTAAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63802 original size:2 final size:2
Alignment explanation
Indices: 63795--63835 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
63785 AGTTAGATTT
63795 TA 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 TA T
63836 TTCAATCATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65290 original size:2 final size:2
Alignment explanation
Indices: 65283--65314 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
65273 TAGCTCTATT
65283 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
65315 GAACTTCCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:71717 original size:31 final size:31
Alignment explanation
Indices: 71681--71773 Score: 79
Period size: 30 Copynumber: 3.1 Consensus size: 31
71671 AGAAATTAGA
71681 AGATTCAAAAGTTTGGGACTAATTTAGAATG
1 AGATTCAAAAGTTTGGGACTAATTTAGAATG
* * * *
71712 AGATTC-ATAGTTTGGG-GTGAAATTGGAAT-
1 AGATTCAAAAGTTTGGGACT-AATTTAGAATG
**
71741 -G-TTCAAAAGTATAAGGACTAATTTAGAATG
1 AGATTCAAAAGT-TTGGGACTAATTTAGAATG
71771 AGA
1 AGA
71774 GTTATAAGGA
Statistics
Matches: 45, Mismatches: 10, Indels: 13
0.66 0.15 0.19
Matches are distributed among these distances:
27 3 0.07
28 5 0.11
29 12 0.27
30 18 0.40
31 7 0.16
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (31 bp):
AGATTCAAAAGTTTGGGACTAATTTAGAATG
Found at i:78235 original size:13 final size:14
Alignment explanation
Indices: 78217--78249 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
78207 TAAATTTTAT
78217 TTTTTAA-AAAATA
1 TTTTTAAGAAAATA
78230 TTTTTAAGAAAATA
1 TTTTTAAGAAAATA
78244 TTTTTA
1 TTTTTA
78250 GTGTTAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (14 bp):
TTTTTAAGAAAATA
Found at i:78718 original size:18 final size:17
Alignment explanation
Indices: 78691--78736 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
78681 GTTTATGAGA
*
78691 GAATTTGAATCTGTGAAG
1 GAATTGGAATCTGT-AAG
* *
78709 GAATTGGAATCTGTCAT
1 GAATTGGAATCTGTAAG
78726 GAATTGGAATC
1 GAATTGGAATC
78737 CAATTCCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.33
Consensus pattern (17 bp):
GAATTGGAATCTGTAAG
Found at i:79319 original size:28 final size:28
Alignment explanation
Indices: 79287--79352 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
79277 ATCCAACCCG
79287 ACCCGACCCGAATATCACACTTAAAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
79315 ACCCGACCCGAATATCACACTTAAAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
*
79343 ACCCAACCCG
1 ACCCGACCCG
79353 CTCGACCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.44, C:0.36, G:0.08, T:0.12
Consensus pattern (28 bp):
ACCCGACCCGAATATCACACTTAAAAAA
Found at i:81727 original size:32 final size:32
Alignment explanation
Indices: 81691--81751 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
81681 GACTTGAATA
*
81691 CCTAAAA-GGATAACGTTTGTAGCGTTAGGGTG
1 CCTAAAAGGGA-AACGTTTGTAACGTTAGGGTG
81723 CCTAAAAGGGAAACGTTTGTAACGTTAGG
1 CCTAAAAGGGAAACGTTTGTAACGTTAGG
81752 CACCCTGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (32 bp):
CCTAAAAGGGAAACGTTTGTAACGTTAGGGTG
Found at i:82372 original size:17 final size:17
Alignment explanation
Indices: 82350--82383 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
82340 AATTTTCTAG
82350 GAATCCGACACTTTGGT
1 GAATCCGACACTTTGGT
82367 GAATCCGACACTTTGGT
1 GAATCCGACACTTTGGT
82384 TCAATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (17 bp):
GAATCCGACACTTTGGT
Found at i:84454 original size:16 final size:18
Alignment explanation
Indices: 84423--84456 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
84413 CAAATAATTA
84423 ATCACATACATTATATTT
1 ATCACATACATTATATTT
84441 ATCA-ATAC-TTATATTT
1 ATCACATACATTATATTT
84457 TGTAAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (18 bp):
ATCACATACATTATATTT
Found at i:87169 original size:78 final size:78
Alignment explanation
Indices: 87040--87197 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
87030 TCACGTTATA
87040 CACCAGAAATGAGAATGATATAGCAAGCAACATCTGTAGCTCTAGCAGCAGTAAAATTCACAATG
1 CACCAGAAATGAGAATGATATAGCAAGCAACATCTGTAGCTCTAGCAGCAGTAAAATTCACAATG
87105 AAAGACACATAAT
66 AAAGACACATAAT
87118 CACCAGAAATGAGAATGATATAGCAAGCAACATCTGTAGCTCTAGCAGCAGTAAAATTCACAATG
1 CACCAGAAATGAGAATGATATAGCAAGCAACATCTGTAGCTCTAGCAGCAGTAAAATTCACAATG
87183 AAAGACACATAAT
66 AAAGACACATAAT
87196 CA
1 CA
87198 GCAAAATTAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.19
Consensus pattern (78 bp):
CACCAGAAATGAGAATGATATAGCAAGCAACATCTGTAGCTCTAGCAGCAGTAAAATTCACAATG
AAAGACACATAAT
Found at i:89770 original size:20 final size:21
Alignment explanation
Indices: 89747--89796 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
89737 TATATTTTGG
**
89747 TAAATATTT-ATTATTTTTTT
1 TAAATATTTGATTAGATTTTT
* *
89767 TAAAAATTTGTTTAGATTTTT
1 TAAATATTTGATTAGATTTTT
89788 TAAATATTT
1 TAAATATTT
89797 TAATAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TAAATATTTGATTAGATTTTT
Found at i:90150 original size:17 final size:16
Alignment explanation
Indices: 90128--90160 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
90118 TGTAATTAAT
90128 TAAACTCAAATTCTTTA
1 TAAACTCAAATT-TTTA
90145 TAAACTCAAATTTTTA
1 TAAACTCAAATTTTTA
90161 AAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAACTCAAATTTTTA
Done.