Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008820.1 Hibiscus syriacus cultivar Beakdansim tig00111988_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: 121124
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1497 original size:17 final size:17
Alignment explanation
Indices: 1472--1514 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1462 TCCACTTCGG
* *
1472 GAGCCATCACCCGCCCA
1 GAGCTATCACCCACCCA
* *
1489 GAGCTATCACTCACCTA
1 GAGCTATCACCCACCCA
1506 GAGCTATCA
1 GAGCTATCA
1515 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.40, G:0.16, T:0.16
Consensus pattern (17 bp):
GAGCTATCACCCACCCA
Found at i:2031 original size:19 final size:20
Alignment explanation
Indices: 1977--2043 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1967 AATAGTTACT
* *
1977 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1997 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2017 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2036 TCGCAACG
1 TCGCAACG
2044 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2051 original size:14 final size:14
Alignment explanation
Indices: 2032--2089 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2022 ATGCGAAATG
2032 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2046 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2062 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2078 AAAATCGCAACG
1 AAAATCGCAACG
2090 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2074 original size:32 final size:33
Alignment explanation
Indices: 2016--2106 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
2006 GGAAATGGCT
*
2016 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2049 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2081 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
2107 TGTGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2141 original size:14 final size:14
Alignment explanation
Indices: 2122--2210 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
2112 TTTGTGTTCG
2122 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
2136 CGTTGCGATTCATT-T
1 CGTTGCGATT--TTGT
2151 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
2167 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2183 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2199 CGTTGCGATTTT
1 CGTTGCGATTTT
2211 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
14 33 0.52
15 3 0.05
16 7 0.11
17 10 0.16
18 11 0.17
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2185 original size:32 final size:32
Alignment explanation
Indices: 2118--2226 Score: 193
Period size: 32 Copynumber: 3.4 Consensus size: 32
2108 GTGATTTGTG
2118 TTCGCGTTGCGATTTTGTCGTTGCGA-TTCAT
1 TTCGCGTTGCGATTTTGTCGTTGCGATTTCAT
2149 TTCGCGTTGCGATTTTGTCGTTGCGATTTCAT
1 TTCGCGTTGCGATTTTGTCGTTGCGATTTCAT
2181 TTCGCGTTGCGATTTTGTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTGTCGTTGCGA-TTTCAT
*
2214 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
2227 AGCCATTTCC
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
31 26 0.35
32 31 0.41
33 18 0.24
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (32 bp):
TTCGCGTTGCGATTTTGTCGTTGCGATTTCAT
Found at i:2225 original size:19 final size:19
Alignment explanation
Indices: 2169--2268 Score: 77
Period size: 19 Copynumber: 5.5 Consensus size: 19
2159 GATTTTGTCG
*
2169 TTGCGA-TTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
*
2187 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
2201 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*** *
2220 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
**
2240 TTGCGATAGTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2259 TTGCGATTTT
1 TTGCGATTTT
2269 AAGTTTCGTG
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
14 6 0.09
15 3 0.05
16 4 0.06
17 4 0.06
18 9 0.14
19 23 0.35
20 17 0.26
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2245 original size:20 final size:19
Alignment explanation
Indices: 2211--2265 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
2201 TTGCGATTTT
2211 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* *
2230 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
2250 CATTTCGCATTGCGAT
1 CATTTCGCATTGCGAT
2266 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:4118 original size:14 final size:14
Alignment explanation
Indices: 4099--4134 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4089 ATTGTTTAAT
4099 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
4113 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
4127 TGATTTGT
1 TGATTTGT
4135 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:4274 original size:19 final size:19
Alignment explanation
Indices: 4252--4317 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
4242 TCGCAACGAG
4252 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
4271 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
4290 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
4304 AAATCGCAATGCGA
1 AAATCGCAATGCGA
4318 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
19 28 0.64
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AAATCGCAATGCGAAATGA
Found at i:4361 original size:20 final size:20
Alignment explanation
Indices: 4336--4392 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
4326 TCGCATTGCG
*
4336 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
4356 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
4376 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
4393 GTCAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:4790 original size:13 final size:14
Alignment explanation
Indices: 4758--4792 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4748 ATTGTTTAAT
4758 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
4772 TGATTTGTAAATG-
1 TGATTTGTAAAAGA
4785 TGATTTGT
1 TGATTTGT
4793 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:6090 original size:24 final size:24
Alignment explanation
Indices: 6034--6092 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
6024 AGTCAGTATT
* *
6034 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
6058 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
6082 CGAATTTTGAT
1 CGAAATTTGAT
6093 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:8500 original size:32 final size:33
Alignment explanation
Indices: 8459--8551 Score: 170
Period size: 32 Copynumber: 2.8 Consensus size: 33
8449 GGAAATTACT
8459 ATCGCAATGCGAAATGAAAATCGCAACGAGAG-
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
8491 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
8524 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
8552 CGAATTTAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 31 0.53
33 28 0.47
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:8573 original size:19 final size:20
Alignment explanation
Indices: 8551--8593 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
8541 AAATCGCAAC
8551 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
8570 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
8590 GCGA
1 GCGA
8594 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:8578 original size:14 final size:14
Alignment explanation
Indices: 8579--8612 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
8569 TGCGATTTTC
8579 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
8593 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
8607 ATTTTC
1 ATTTTC
8613 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:8752 original size:14 final size:14
Alignment explanation
Indices: 8733--8769 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
8723 CATCAATTAA
8733 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
8747 ACAAATCACCTTTT
1 ACAAATCAACTTTT
8761 ACAAATCAA
1 ACAAATCAA
8770 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:10189 original size:21 final size:21
Alignment explanation
Indices: 10123--10189 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
10113 GTGAATCGGG
*
10123 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
10143 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
10165 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
10186 CTCT
1 CTCT
10190 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:10208 original size:42 final size:41
Alignment explanation
Indices: 10123--10245 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
10113 GTGAATCGGG
* * * * *
10123 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
10165 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
10207 CTCTTCAACGATAGGAGTGGACTCTTGATGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
10246 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:11933 original size:20 final size:19
Alignment explanation
Indices: 11888--11948 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
11878 TCTTTTGGTT
11888 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
11907 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
11928 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
11947 GA
1 GA
11949 GAATCGCAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.12
20 26 0.81
21 2 0.06
ACGTcount: A:0.44, C:0.15, G:0.25, T:0.16
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:11970 original size:33 final size:33
Alignment explanation
Indices: 11913--12000 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
11903 ACGAGATAAT
* *
11913 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
11947 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
11980 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
12001 AAATCACAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 38 0.75
34 13 0.25
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:12032 original size:19 final size:19
Alignment explanation
Indices: 12010--12075 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
12000 AAAATCACAA
*
12010 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
12029 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
* * *
12048 TGCGATAGTT-ATTCCGCTT
1 TGCGAT-TTTGATTTCGCGT
12067 TGCGATTTT
1 TGCGATTTT
12076 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 2 0.05
19 36 0.90
20 2 0.05
ACGTcount: A:0.11, C:0.17, G:0.24, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:12688 original size:20 final size:20
Alignment explanation
Indices: 12595--12688 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
12585 CGCTAAGTAA
*
12595 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
12615 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
12635 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
12656 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
12676 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
12689 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:12707 original size:41 final size:41
Alignment explanation
Indices: 12616--12750 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
12606 AAAGTCAGTA
* * * ** *
12616 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
12656 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
12698 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
12739 TCGCGTTGCGAT
1 TCGCGTTGCGAT
12751 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:12721 original size:20 final size:20
Alignment explanation
Indices: 12677--12769 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
12667 ATAGTCAGTA
* **
12677 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
12698 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
12718 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
12739 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
12759 TCGCATTGCGA
1 TCGCATTGCGA
12770 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:12751 original size:41 final size:41
Alignment explanation
Indices: 12677--12772 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
12667 ATAGTCAGTA
*
12677 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
12718 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
12759 TCGCATTGCGAATT
1 TCGCATTGCGAATT
12773 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:14786 original size:22 final size:22
Alignment explanation
Indices: 14753--14797 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
14743 GATATAAAAA
14753 ATTATTTTTTATTAAATATTTTT
1 ATTATTTTTTATTAAAT-TTTTT
*
14776 ATTA-TTTTTATTTAATTTTTT
1 ATTATTTTTTATTAAATTTTTT
14797 A
1 A
14798 AATAATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 11 0.52
23 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTATTTTTTATTAAATTTTTT
Found at i:21704 original size:87 final size:88
Alignment explanation
Indices: 21570--21729 Score: 243
Period size: 87 Copynumber: 1.8 Consensus size: 88
21560 CAATTCCGTC
*
21570 TCACTAGGATCACCCACAAACTTAGACTATGAATTCATTAAGAGTATAAAATTAAACCTTACAGA
1 TCACTAGGATCACCCACAAACTTAGACTATGAATTCATTAAGAGTATAAAACTAAACCTTACAGA
21635 TCGGTGTATCCATCAAGGCTGTT
66 TCGGTGTATCCATCAAGGCTGTT
* * * *
21658 TCACTAGGA-CTACCCA-AATCTTAGGCTATGAATTCATTAAGAGTATAACACTCAACCTTACAG
1 TCACTAGGATC-ACCCACAAACTTAGACTATGAATTCATTAAGAGTATAAAACTAAACCTTACAG
*
21721 ATTGGTGTA
65 ATCGGTGTA
21730 CACGATATGT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
87 51 0.78
88 14 0.22
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (88 bp):
TCACTAGGATCACCCACAAACTTAGACTATGAATTCATTAAGAGTATAAAACTAAACCTTACAGA
TCGGTGTATCCATCAAGGCTGTT
Found at i:22207 original size:25 final size:25
Alignment explanation
Indices: 22178--22253 Score: 152
Period size: 25 Copynumber: 3.0 Consensus size: 25
22168 CCACCTAAAG
22178 TTAAAATATACCCACTAGTGGAACT
1 TTAAAATATACCCACTAGTGGAACT
22203 TTAAAATATACCCACTAGTGGAACT
1 TTAAAATATACCCACTAGTGGAACT
22228 TTAAAATATACCCACTAGTGGAACT
1 TTAAAATATACCCACTAGTGGAACT
22253 T
1 T
22254 ACTTCATCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (25 bp):
TTAAAATATACCCACTAGTGGAACT
Found at i:23627 original size:66 final size:66
Alignment explanation
Indices: 23521--23656 Score: 272
Period size: 66 Copynumber: 2.1 Consensus size: 66
23511 GATCATCTCT
23521 AGGAGTTTTCATAGAATAAGAAATATTCTCATCTAATTTCAAGTCATGATTGCTATGCTTTTTAA
1 AGGAGTTTTCATAGAATAAGAAATATTCTCATCTAATTTCAAGTCATGATTGCTATGCTTTTTAA
23586 G
66 G
23587 AGGAGTTTTCATAGAATAAGAAATATTCTCATCTAATTTCAAGTCATGATTGCTATGCTTTTTAA
1 AGGAGTTTTCATAGAATAAGAAATATTCTCATCTAATTTCAAGTCATGATTGCTATGCTTTTTAA
23652 G
66 G
23653 AGGA
1 AGGA
23657 AAAACATTTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (66 bp):
AGGAGTTTTCATAGAATAAGAAATATTCTCATCTAATTTCAAGTCATGATTGCTATGCTTTTTAA
G
Found at i:24435 original size:20 final size:20
Alignment explanation
Indices: 24410--24448 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24400 TTTGAAGTTG
*
24410 GTTGTTTTCCTTGTTTGGGA
1 GTTGTTTTCCTTCTTTGGGA
*
24430 GTTGTTTTTCTTCTTTGGG
1 GTTGTTTTCCTTCTTTGGG
24449 TTGGGAGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.10, G:0.28, T:0.59
Consensus pattern (20 bp):
GTTGTTTTCCTTCTTTGGGA
Found at i:29495 original size:42 final size:41
Alignment explanation
Indices: 29455--29558 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 41
29445 AAGTTTAATT
* *
29455 TTAATAATTTATTAATATTATCATTTTAATAAGTAATTAATATA
1 TTAATAATATATT-AT-TT-TCATTTTAATAAATAATTAATATA
* *
29499 CTTAATAATATATTATTTTTATTTTAATAAATATTTAATATA
1 -TTAATAATATATTATTTTCATTTTAATAAATAATTAATATA
*
29541 TT-ATAATATTTCTATTTT
1 TTAATAATATAT-TATTTT
29559 AATAAGATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
40 8 0.15
41 8 0.15
42 21 0.40
43 2 0.04
44 2 0.04
45 12 0.23
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (41 bp):
TTAATAATATATTATTTTCATTTTAATAAATAATTAATATA
Found at i:29551 original size:35 final size:34
Alignment explanation
Indices: 29500--29568 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
29490 ATTAATATAC
* *
29500 TTAATAATATATTATTTTTATTTTAATAA-ATAT
1 TTAATAATATAATATTTCTATTTTAATAAGATAT
29533 TTAATATATTATAATATTTCTATTTTAATAAGATAT
1 TTAATA-A-TATAATATTTCTATTTTAATAAGATAT
29569 AATAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 6 0.19
34 1 0.03
35 20 0.65
36 4 0.13
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (34 bp):
TTAATAATATAATATTTCTATTTTAATAAGATAT
Found at i:29563 original size:17 final size:17
Alignment explanation
Indices: 29512--29563 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
29502 AATAATATAT
*
29512 TATTTTTATTTTAATAAA
1 TATTTATATTTTAAT-AA
*
29530 TATTTAATATATT-ATAA
1 TATTT-ATATTTTAATAA
*
29547 TATTTCTATTTTAATAA
1 TATTTATATTTTAATAA
29564 GATATAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 5 0.18
17 11 0.39
18 7 0.25
19 5 0.18
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTATATTTTAATAA
Found at i:29568 original size:27 final size:26
Alignment explanation
Indices: 29533--29603 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 26
29523 TAATAAATAT
*
29533 TTAATATATTATAATATTTCTATTTTAA
1 TTAAGATATTATAATATTT-T-TTTTAA
*
29561 -TAAGATATAATAAT-TTTTTTTTAA
1 TTAAGATATTATAATATTTTTTTTAA
* *
29585 TTTAGAGA-TATAATATTTT
1 TTAAGATATTATAATATTTT
29604 AATAATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
24 11 0.31
25 10 0.28
26 3 0.08
27 12 0.33
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (26 bp):
TTAAGATATTATAATATTTTTTTTAA
Found at i:29569 original size:24 final size:25
Alignment explanation
Indices: 29542--29604 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 25
29532 TTTAATATAT
29542 TATAATATTTCTATTTTAA-TA-AGA
1 TATAATATTT-TATTTTAATTAGAGA
*
29566 TATAATAATTTTTTTTTAATTTAGAGA
1 TATAAT-ATTTTATTTTAA-TTAGAGA
29593 TATAATATTTTA
1 TATAATATTTTA
29605 ATAATAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 13 0.39
25 4 0.12
26 7 0.21
27 9 0.27
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (25 bp):
TATAATATTTTATTTTAATTAGAGA
Found at i:35507 original size:2 final size:2
Alignment explanation
Indices: 35495--35539 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
35485 AGTAAAATAG
* *
35495 AT AT CT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35537 AT A
1 AT A
35540 ACAACACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:35807 original size:28 final size:28
Alignment explanation
Indices: 35756--35838 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 28
35746 GCAAAAACAA
* *
35756 GACGGGATCAAGTCTCATAAAGAATCAG
1 GACGGGATCAAATCTCATGAAGAATCAG
* * *
35784 GACGGGATCAAATCCCATGTAGAATTAG
1 GACGGGATCAAATCTCATGAAGAATCAG
* *
35812 GACTGAATCAAATCTCATGCAA-AATCA
1 GACGGGATCAAATCTCATG-AAGAATCA
35839 AGATGAAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
28 43 0.98
29 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (28 bp):
GACGGGATCAAATCTCATGAAGAATCAG
Found at i:38307 original size:2 final size:2
Alignment explanation
Indices: 38296--38452 Score: 109
Period size: 2 Copynumber: 82.5 Consensus size: 2
38286 TGCCTAAAAC
*
38296 TA TA -A TA TA TA TA TA CTA TT TA -A TA T- 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
* * * * * *
38336 TA TA TA TA TT TC TA -A AA AA TA TA T- TA AA AA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
38375 TA TA TA CTA TG TA TA -A TA TA TA T- TT 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
* * * *
38416 TA TA T- TT TA AA TA TA -A TA TA CA CA 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
38453 TTTTGAAAAC
Statistics
Matches: 127, Mismatches: 16, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
1 10 0.08
2 113 0.89
3 4 0.03
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:38364 original size:70 final size:75
Alignment explanation
Indices: 38290--38507 Score: 200
Period size: 76 Copynumber: 2.9 Consensus size: 75
38280 TACATTTGCC
*
38290 TAAAACTATA-ATATATATATACTAT-T-TAATAT-TA-TATATATATATATATATATATTTCTA
1 TAAAAATATATAT-TATATATACTATGTATAATATATATTATATATATATATATATATATTT-TA
38350 AA-A-AATATAT
64 AATATAATATAT
38360 TAAAAATATATATTATATATACTATGTATAATATATATTTTATATATATATATATATATATTTTA
1 TAAAAATATATATTATATATACTATGTATAATATATA--TTATATATATATATATATATATTTTA
38425 AATATAATATA-
64 AATATAATATAT
* * * * * ** * *
38436 CACATATATATATATATTTTTGAAAACTGTATAATATATACTATAATATATACACTATATATATT
1 TAAAAATATATAT-TATATAT-ACTA-TGTATAATATATATTAT-ATATATATA-TATATATATT
*
38501 TTCAATA
61 TTAAATA
38508 ACTATTAAAG
Statistics
Matches: 123, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
70 21 0.17
71 3 0.02
72 6 0.05
73 2 0.02
75 4 0.03
76 34 0.28
77 14 0.11
78 10 0.08
79 29 0.24
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (75 bp):
TAAAAATATATATTATATATACTATGTATAATATATATTATATATATATATATATATATTTTAAA
TATAATATAT
Found at i:38377 original size:9 final size:9
Alignment explanation
Indices: 38365--38418 Score: 63
Period size: 9 Copynumber: 5.9 Consensus size: 9
38355 TATATTAAAA
38365 ATATATATT
1 ATATATATT
*
38374 ATATATACT
1 ATATATATT
* *
38383 ATGTATAAT
1 ATATATATT
*
38392 ATATATTTT
1 ATATATATT
38401 ATATATATAT
1 ATATATAT-T
38411 ATATATAT
1 ATATATAT
38419 ATTTTAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
9 28 0.76
10 9 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (9 bp):
ATATATATT
Found at i:40419 original size:24 final size:24
Alignment explanation
Indices: 40392--40440 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
40382 AATAACTTAG
*
40392 AAGCTCAAAATGTTATGAATATCT
1 AAGCTCAAAATGTTATCAATATCT
40416 AAGCTCAAAATGTTATCAATATCT
1 AAGCTCAAAATGTTATCAATATCT
40440 A
1 A
40441 TAAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (24 bp):
AAGCTCAAAATGTTATCAATATCT
Found at i:40507 original size:19 final size:19
Alignment explanation
Indices: 40483--40523 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
40473 TGTTCACTAA
40483 GAAAGTAGGTTGCAATATG
1 GAAAGTAGGTTGCAATATG
40502 GAAAGTAGGTTGCAATATG
1 GAAAGTAGGTTGCAATATG
40521 GAA
1 GAA
40524 TGTTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.32, T:0.24
Consensus pattern (19 bp):
GAAAGTAGGTTGCAATATG
Found at i:41090 original size:74 final size:73
Alignment explanation
Indices: 40934--41142 Score: 206
Period size: 74 Copynumber: 2.8 Consensus size: 73
40924 AATATTTGGC
* * *
40934 GATCGATACTTTTAAATATCGGAAAAAA-TTGAA-GATAAGATCGAAATTTAAAATATAGATACT
1 GATCGATACTTTTAAATAT--TAAAAAAGTT-AATGAAAAGATCGAAATTTAAAATATAGATAAT
*
40997 TATACGGTAAT
63 TATACGATAAT
* * * *
41008 AATTGATACTTTTAAATATTAAAAAAGTTTATGAAAAGATCGAAATTTAAAAATATTGATAATTA
1 GATCGATACTTTTAAATATTAAAAAAGTTAATGAAAAGATCGAAATTT-AAAATATAGATAATTA
** *
41073 TGTGATGAT
65 TACGATAAT
* * * * * *
41082 GATCGATACTTTTATATATTGAAAAAGTTAATGAAGATGATCGATAGTTAAAATATCGATA
1 GATCGATACTTTTAAATATTAAAAAAGTTAATGAA-AAGATCGAAATTTAAAATATAGATA
41143 CCTATATTAT
Statistics
Matches: 111, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
72 7 0.06
73 17 0.15
74 77 0.69
75 10 0.09
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.34
Consensus pattern (73 bp):
GATCGATACTTTTAAATATTAAAAAAGTTAATGAAAAGATCGAAATTTAAAATATAGATAATTAT
ACGATAAT
Found at i:41155 original size:74 final size:74
Alignment explanation
Indices: 40934--41168 Score: 192
Period size: 74 Copynumber: 3.2 Consensus size: 74
40924 AATATTTGGC
* * * *
40934 GATCGATACTTTTAAATATCGGAAAAAA-TTGAA-GATAAGATCGAAA-TTTAAAATATAGAT-A
1 GATCGATACTTTTAAATAT--TAAAAAAGTT-AATGAAAAGATCGAAAGTTAAAAATATCGATAA
* * *
40995 CTTATACGGTAAT
63 C-TATATGATGAT
* * * * * *
41008 AATTGATACTTTTAAATATTAAAAAAGTTTATGAAAAGATCGAAATTTAAAAATATTGATAATTA
1 GATCGATACTTTTAAATATTAAAAAAGTTAATGAAAAGATCGAAAGTTAAAAATATCGATAACTA
*
41073 TGTGATGAT
66 TATGATGAT
* * * * *
41082 GATCGATACTTTTATATATTGAAAAAGTTAATGAAGATGATCGATAGTT-AAAATATCGATACCT
1 GATCGATACTTTTAAATATTAAAAAAGTTAATGAA-AAGATCGAAAGTTAAAAATATCGATAACT
*
41146 ATATTATGAT
65 ATATGATGAT
* *
41156 GTTCGATAATTTT
1 GATCGATACTTTT
41169 TCATTTATAT
Statistics
Matches: 129, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
72 7 0.05
73 14 0.11
74 97 0.75
75 11 0.09
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.36
Consensus pattern (74 bp):
GATCGATACTTTTAAATATTAAAAAAGTTAATGAAAAGATCGAAAGTTAAAAATATCGATAACTA
TATGATGAT
Found at i:41337 original size:69 final size:69
Alignment explanation
Indices: 41253--41434 Score: 213
Period size: 71 Copynumber: 2.6 Consensus size: 69
41243 TTTTAATTCG
*
41253 AAAGTATTGATACTTTTCCACAAATATCGATACTTTTAAATTGAAAAAAAATGAAAATGAGAAGA
1 AAAGTATTGATACTTTTCCACAAATATCAATACTTTTAAATTGAAAAAAAATGAAAATGAGAAGA
41318 CTAC
66 CTAC
* * * * * *
41322 AAAGTATTGATACTTTTCCCCAAATATTAATACTTTCGAATTTTTAAAAAATATGAAAATGAGAA
1 AAAGTATTGATACTTTTCCACAAATATCAATACTTT-TAA-ATTGAAAAAAAATGAAAATGAGAA
** *
41387 GGTTGC
64 GACTAC
* * *
41393 AAAGTACTGATA-TTTGTCCATAAATATCAATACTTTTTAATT
1 AAAGTATTGATACTTT-TCCACAAATATCAATACTTTTAAATT
41435 TTTATAGATA
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
69 35 0.38
70 6 0.06
71 52 0.56
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.35
Consensus pattern (69 bp):
AAAGTATTGATACTTTTCCACAAATATCAATACTTTTAAATTGAAAAAAAATGAAAATGAGAAGA
CTAC
Found at i:43507 original size:32 final size:32
Alignment explanation
Indices: 43471--43534 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
43461 TAACAATATT
43471 TTACTATTGCTACATGTTGTTAATAAAATCAA
1 TTACTATTGCTACATGTTGTTAATAAAATCAA
*
43503 TTACTATTGTTACATGTTGTTAATAAAATCAA
1 TTACTATTGCTACATGTTGTTAATAAAATCAA
43535 AAATGTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (32 bp):
TTACTATTGCTACATGTTGTTAATAAAATCAA
Found at i:44178 original size:32 final size:32
Alignment explanation
Indices: 44137--44197 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
44127 GTTGTGCACA
* *
44137 TCATCTTCAATATCTTACATAACACACTCCAT
1 TCATCTTCAATATCTTACACAACAAACTCCAT
*
44169 TCATCTTCAATCTCTTACACAACAAACTC
1 TCATCTTCAATATCTTACACAACAAACTC
44198 ATTTTATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.34, C:0.33, G:0.00, T:0.33
Consensus pattern (32 bp):
TCATCTTCAATATCTTACACAACAAACTCCAT
Found at i:44521 original size:34 final size:33
Alignment explanation
Indices: 44468--44554 Score: 138
Period size: 34 Copynumber: 2.5 Consensus size: 33
44458 ACCCGAACCC
*
44468 AAAAATATTATATATATATAATTAATATAAAATAT
1 AAAAATA-T-TATATATATAATTAATATAAAAAAT
44503 ATAAAATATTATATATATAATTAATATAAAAAAT
1 A-AAAATATTATATATATAATTAATATAAAAAAT
44537 AAAAATATTATATATATA
1 AAAAATATTATATATATA
44555 TATATAATCG
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
33 17 0.34
34 25 0.50
35 2 0.04
36 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
AAAAATATTATATATATAATTAATATAAAAAAT
Found at i:55107 original size:21 final size:22
Alignment explanation
Indices: 55083--55123 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55073 CTTATGATCG
55083 TGTA-AATACATATCTTTAAAA
1 TGTATAATACATATCTTTAAAA
* *
55104 TGTATTATACATATTTTTAA
1 TGTATAATACATATCTTTAA
55124 TTTTTTGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (22 bp):
TGTATAATACATATCTTTAAAA
Found at i:60346 original size:2 final size:2
Alignment explanation
Indices: 60339--60401 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
60329 CGCTGTATAC
60339 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
60381 AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
60402 AATGAAATTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:65557 original size:15 final size:15
Alignment explanation
Indices: 65537--65568 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
65527 ACAAATAGAA
65537 TTTTTATATAAATAT
1 TTTTTATATAAATAT
*
65552 TTTTTATTTAAATAT
1 TTTTTATATAAATAT
65567 TT
1 TT
65569 AGAATTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTATATAAATAT
Found at i:74908 original size:7 final size:7
Alignment explanation
Indices: 74891--74926 Score: 63
Period size: 7 Copynumber: 5.0 Consensus size: 7
74881 ACCATTTATT
74891 AACCAATA
1 AACC-ATA
74899 AACCATA
1 AACCATA
74906 AACCATA
1 AACCATA
74913 AACCATA
1 AACCATA
74920 AACCATA
1 AACCATA
74927 GACAATAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 24 0.86
8 4 0.14
ACGTcount: A:0.58, C:0.28, G:0.00, T:0.14
Consensus pattern (7 bp):
AACCATA
Found at i:76136 original size:30 final size:30
Alignment explanation
Indices: 76079--76142 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
76069 TCTTCATCAA
* * *
76079 TTTTCCAAAATTTACGAATTTATCCCAAAC
1 TTTTCCAAAACTTACGAAATGATCCCAAAC
* *
76109 TTTT-CAAAACTTACGAAATGATCCCCAAT
1 TTTTCCAAAACTTACGAAATGATCCCAAAC
76138 TTTTC
1 TTTTC
76143 TAAGGCTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (30 bp):
TTTTCCAAAACTTACGAAATGATCCCAAAC
Found at i:78082 original size:18 final size:18
Alignment explanation
Indices: 78061--78096 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
78051 GGTAAGTTGG
78061 ACTAG-TTGGATGAGCTGA
1 ACTAGTTTGG-TGAGCTGA
78079 ACTAGTTTGGTGAGCTGA
1 ACTAGTTTGGTGAGCTGA
78097 GCCAGAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.25, C:0.11, G:0.33, T:0.31
Consensus pattern (18 bp):
ACTAGTTTGGTGAGCTGA
Found at i:83129 original size:34 final size:34
Alignment explanation
Indices: 83091--83159 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
83081 TGTCTTAAAA
83091 CAAGTTTTGGAGCTCCATTTTATAATAATTTTAC
1 CAAGTTTTGGAGCTCCATTTTATAATAATTTTAC
83125 CAAGTTTTGGAGCTCCATTTTATAATAATTTTAC
1 CAAGTTTTGGAGCTCCATTTTATAATAATTTTAC
83159 C
1 C
83160 TGTGTTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (34 bp):
CAAGTTTTGGAGCTCCATTTTATAATAATTTTAC
Found at i:85609 original size:53 final size:54
Alignment explanation
Indices: 85452--85651 Score: 242
Period size: 54 Copynumber: 3.7 Consensus size: 54
85442 GTGTACTATA
* * *
85452 TATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTTTTGGCAC
1 TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTTTCGACAC
* * *
85506 TATGTGTGCAGCCCACAAAATTCATCATATGTTGATGAAC-ACTCGTTTCGACGC
1 TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAAC-CGTTTCGACAC
* * * **
85560 TAGGTGTGCAAACCATGAAATTCATCAT-TGTTGATGAACAACAATTTCGACAC
1 TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTTTCGACAC
* * * *
85613 TATGTGTGCAACCCACGGAATTCATAATAAGTTTATGAA
1 TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAA
85652 TTTCTGTATG
Statistics
Matches: 122, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
53 44 0.36
54 78 0.64
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (54 bp):
TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTTTCGACAC
Found at i:85614 original size:107 final size:108
Alignment explanation
Indices: 85455--85651 Score: 270
Period size: 107 Copynumber: 1.8 Consensus size: 108
85445 TACTATATAT
* * ** * * *
85455 GTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCGTTTTGGCACTATGTGTGCAGCCC
1 GTGTGCAAACCACGAAATTCATCATATGTTGATGAACAACAATTTCGACACTATGTGTGCAACCC
* *
85520 ACAAAATTCATCATATGTTGATGAACACTCGTTTCGACGCTAG
66 ACAAAATTCATAATAAGTTGATGAACACTCGTTTCGACGCTAG
*
85563 GTGTGCAAACCATGAAATTCATCAT-TGTTGATGAACAACAATTTCGACACTATGTGTGCAACCC
1 GTGTGCAAACCACGAAATTCATCATATGTTGATGAACAACAATTTCGACACTATGTGTGCAACCC
** *
85627 ACGGAATTCATAATAAGTTTATGAA
66 ACAAAATTCATAATAAGTTGATGAA
85652 TTTCTGTATG
Statistics
Matches: 76, Mismatches: 13, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
107 54 0.71
108 22 0.29
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (108 bp):
GTGTGCAAACCACGAAATTCATCATATGTTGATGAACAACAATTTCGACACTATGTGTGCAACCC
ACAAAATTCATAATAAGTTGATGAACACTCGTTTCGACGCTAG
Found at i:85677 original size:107 final size:108
Alignment explanation
Indices: 85470--85679 Score: 235
Period size: 107 Copynumber: 2.0 Consensus size: 108
85460 CAACCCACGG
** * * * *
85470 AATTCATCATATGTTGATGAACAACCGTTTTGGCACTATGTGTGCAGCCCACAAAATTCATCATA
1 AATTCATCATATGTTGATGAACAACAATTTCGACACTATGTGTGCAACCCACAAAATTCATAATA
* * * * *
85535 TGTTGATGAACACTCGTTTCGACGCTAGGTGTGCAAACCATGA
66 AGTTGATGAACACTCGTATCGACACTACGTCTGCAAACCATGA
**
85578 AATTCATCAT-TGTTGATGAACAACAATTTCGACACTATGTGTGCAACCCACGGAATTCATAATA
1 AATTCATCATATGTTGATGAACAACAATTTCGACACTATGTGTGCAACCCACAAAATTCATAATA
* ** * *
85642 AGTTTATGAA-TTTCTGTATGGGCACTACGTCTGCAAAC
66 AGTTGATGAACACTC-GTATCGACACTACGTCTGCAAAC
85680 TATAGAGTTT
Statistics
Matches: 83, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
106 2 0.02
107 71 0.86
108 10 0.12
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (108 bp):
AATTCATCATATGTTGATGAACAACAATTTCGACACTATGTGTGCAACCCACAAAATTCATAATA
AGTTGATGAACACTCGTATCGACACTACGTCTGCAAACCATGA
Found at i:85867 original size:45 final size:45
Alignment explanation
Indices: 85754--85939 Score: 275
Period size: 45 Copynumber: 4.2 Consensus size: 45
85744 GTTATAAAAT
* *
85754 AATGAAATGTATAACGATGCATTAAAGGCATAAAAGGAT-CCATA
1 AATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATA
* * *
85798 AATGAAATGCATAACGGTGTATTAAAGTCATGAAAGGATGCCATA
1 AATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATA
* *
85843 AATGAAATGCATAGCGATGCATTAAAGGCATGAAAGGATGCCATT
1 AATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATA
* * *
85888 AATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGCCCTA
1 AATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATA
85933 AATGAAA
1 AATGAAA
85940 ATAATGAATA
Statistics
Matches: 126, Mismatches: 15, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
44 34 0.27
45 92 0.73
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.23
Consensus pattern (45 bp):
AATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATA
Found at i:92026 original size:36 final size:36
Alignment explanation
Indices: 91935--92489 Score: 576
Period size: 36 Copynumber: 14.7 Consensus size: 36
91925 TTTGAAAACG
* * * *
91935 TATTTTGGAAAACATATAATATAT-GGTTTTGAAAA
1 TATTTTTGAAAACGTATAATATATAGTTTTTAAAAA
91970 TATTTTTTGGAAAACGTATAATATATAGTTTTTAAAAA
1 TA-TTTTT-GAAAACGTATAATATATAGTTTTTAAAAA
* * *
92008 TATCTTTGAAAACTTATAATATATAATTTTTAAAAAA
1 TATTTTTGAAAACGTATAATATATAGTTTTT-AAAAA
92045 TATTTTTGAAAACGTATAATATATAGTTTCTTTAAAAAA
1 TATTTTTGAAAACGTATAATATATAG-TT-TTT-AAAAA
* *
92084 TATTTTTGAAAACGTATAATATATAATTTTTTAAAA
1 TATTTTTGAAAACGTATAATATATAGTTTTTAAAAA
92120 TATTTTTGAAAACGTATAATATATAGTTTCTTTAAAAAAAA
1 TATTTTTGAAAACGTATAATATATAG-TT-TTT---AAAAA
* *
92161 TATTTTTGAAAACATATAATATATAGTTTTTTAAAA
1 TATTTTTGAAAACGTATAATATATAGTTTTTAAAAA
92197 TATTTTTGAAAACGTATAATATATAGTTTCTTTAAAAAAA
1 TATTTTTGAAAACGTATAATATATAG-TT-TTT--AAAAA
92237 TATTTTTGAAAACGTATAATATATAGTTTTTAAAAAA
1 TATTTTTGAAAACGTATAATATATAGTTTTT-AAAAA
*
92274 TACTTTTGAAAACGTATAATATATAGTTTTTAAAAA
1 TATTTTTGAAAACGTATAATATATAGTTTTTAAAAA
* * * * *
92310 TACTTTTGTAAACATATGACATATAGTTTTTTTAAAAA
1 TATTTTTGAAAACGTATAATATATAG--TTTTTAAAAA
* * *
92348 TACTTTTGAAAACGTATAATATATGGTTTTGAAAACA
1 TATTTTTGAAAACGTATAATATATAGTTTTTAAAA-A
* * *
92385 T-TTTTTGGAAAACATATATTATATAATTTTTAAAAAAATGTA
1 TATTTTT-GAAAACGTATAATATATAGTTTTT---AAAA---A
* *
92427 TATTTTTGAAAACTTATAATATATATAGTTTTTTAAAA
1 TATTTTTGAAAACGTAT-A-ATATATAGTTTTTAAAAA
* * *
92465 TGA-ATTTGAAAACATATAAAATATA
1 T-ATTTTTGAAAACGTATAATATATA
92490 ATGGTTTTGA
Statistics
Matches: 449, Mismatches: 43, Indels: 55
0.82 0.08 0.10
Matches are distributed among these distances:
35 2 0.00
36 129 0.29
37 113 0.25
38 69 0.15
39 40 0.09
40 36 0.08
41 32 0.07
42 11 0.02
43 6 0.01
44 11 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
TATTTTTGAAAACGTATAATATATAGTTTTTAAAAA
Found at i:92079 original size:75 final size:74
Alignment explanation
Indices: 91935--92491 Score: 619
Period size: 77 Copynumber: 7.4 Consensus size: 74
91925 TTTGAAAACG
* ** * *
91935 TATTTTGGAAAACATATAATATATGGTTTTGAAAATAT-TTTTTGGAAAACGTATAATATATAG-
1 TATTTTTGAAAACATATAATATATAATTTTTAAAAAATATTTTT-GAAAACGTATAATATATAGT
91998 TTTTTAAAAA
65 TTTTTAAAAA
* *
92008 TATCTTTGAAAACTTATAATATATAATTTTTAAAAAATATTTTTGAAAACGTATAATATATAGTT
1 TATTTTTGAAAACATATAATATATAATTTTTAAAAAATATTTTTGAAAACGTATAATATATAGTT
92073 TCTTTAAAAAA
66 T-TTT-AAAAA
* *
92084 TATTTTTGAAAACGTATAATATATAATTTTT-TAAAATATTTTTGAAAACGTATAATATATAGTT
1 TATTTTTGAAAACATATAATATATAATTTTTAAAAAATATTTTTGAAAACGTATAATATATAGTT
92148 TCTTTAAAAAAAA
66 T-TTT---AAAAA
* *
92161 TATTTTTGAAAACATATAATATATAGTTTTT-TAAAATATTTTTGAAAACGTATAATATATAGTT
1 TATTTTTGAAAACATATAATATATAATTTTTAAAAAATATTTTTGAAAACGTATAATATATAGTT
92225 TCTTTAAAAAAA
66 T-TTT--AAAAA
* * *
92237 TATTTTTGAAAACGTATAATATATAGTTTTTAAAAAATACTTTTGAAAACGTATAATATATAG-T
1 TATTTTTGAAAACATATAATATATAATTTTTAAAAAATATTTTTGAAAACGTATAATATATAGTT
92301 TTTTAAAAA
66 TTTTAAAAA
* * * * * * * *
92310 TACTTTTGTAAACATATGACATATAGTTTTTTTAAAAATACTTTTGAAAACGTATAATATAT-GG
1 TATTTTTGAAAACATATAATATATA-ATTTTTAAAAAATATTTTTGAAAACGTATAATATATAGT
*
92374 TTTTGAAAACA
65 TTTTTAAAA-A
* *
92385 T-TTTTTGGAAAACATATATTATATAATTTTTAAAAAAATGTATATTTTTGAAAACTTATAATAT
1 TATTTTT-GAAAACATATAATATATAATTTTT--AAAAA---ATATTTTTGAAAACGTAT-A-AT
92449 ATATAGTTTTTT-AAAA
58 ATATAGTTTTTTAAAAA
* *
92465 TGA-ATTTGAAAACATATAAAATATAAT
1 T-ATTTTTGAAAACATATAATATATAAT
92492 GGTTTTGAAA
Statistics
Matches: 426, Mismatches: 37, Indels: 35
0.86 0.07 0.07
Matches are distributed among these distances:
73 76 0.18
74 58 0.14
75 59 0.14
76 77 0.18
77 102 0.24
79 16 0.04
80 21 0.05
81 12 0.03
82 5 0.01
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (74 bp):
TATTTTTGAAAACATATAATATATAATTTTTAAAAAATATTTTTGAAAACGTATAATATATAGTT
TTTTAAAAA
Found at i:92550 original size:11 final size:12
Alignment explanation
Indices: 92534--92567 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
92524 ATAGTTTTTC
92534 ATTA-TTATTAT
1 ATTATTTATTAT
92545 ATTATTTATTAT
1 ATTATTTATTAT
92557 -TTATTTATTAT
1 ATTATTTATTAT
92568 GCATTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTATTTATTAT
Found at i:96068 original size:13 final size:14
Alignment explanation
Indices: 96050--96078 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
96040 ACAATGGTAA
96050 TGAAATTT-TCGAT
1 TGAAATTTGTCGAT
96063 TGAAATTTGTCGAT
1 TGAAATTTGTCGAT
96077 TG
1 TG
96079 TACTTTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TGAAATTTGTCGAT
Found at i:96246 original size:2 final size:2
Alignment explanation
Indices: 96239--96269 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
96229 TGAGAACTTT
96239 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 T
96270 TTGTACTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:99417 original size:24 final size:24
Alignment explanation
Indices: 99385--99458 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
99375 GTCCTAACTG
99385 TTTCATGAGTTTCAATTACAACAA
1 TTTCATGAGTTTCAATTACAACAA
99409 TTTCATGAGTTTCAATTACAACAA
1 TTTCATGAGTTTCAATTACAACAA
*
99433 TTTCATGAGTTT-AAGTTATAACAA
1 TTTCATGAGTTTCAA-TTACAACAA
99457 TT
1 TT
99459 CTAGAGTTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
23 2 0.04
24 46 0.96
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (24 bp):
TTTCATGAGTTTCAATTACAACAA
Found at i:104835 original size:17 final size:17
Alignment explanation
Indices: 104777--104837 Score: 68
Period size: 18 Copynumber: 3.5 Consensus size: 17
104767 TTTCATTCAG
*
104777 TAAACCTAGTTCACTAAT
1 TAAA-CTAGTTCATTAAT
* *
104795 TAAACTATTTCATTTAT
1 TAAACTAGTTCATTAAT
*
104812 ATAAACTGGTTCATTAAT
1 -TAAACTAGTTCATTAAT
104830 TAAACTAG
1 TAAACTAG
104838 CTCTTTAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
17 17 0.49
18 18 0.51
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (17 bp):
TAAACTAGTTCATTAAT
Found at i:107386 original size:27 final size:28
Alignment explanation
Indices: 107337--107396 Score: 104
Period size: 27 Copynumber: 2.1 Consensus size: 28
107327 TTATAACATC
107337 TTTTAAATCTTTCTCTTTATTAGCACAAT
1 TTTTAAATC-TTCTCTTTATTAGCACAAT
107366 TTTTAAATC-TCTCTTTATTAGCACAAT
1 TTTTAAATCTTCTCTTTATTAGCACAAT
107393 TTTT
1 TTTT
107397 GGCTTTTGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 22 0.71
29 9 0.29
ACGTcount: A:0.27, C:0.17, G:0.03, T:0.53
Consensus pattern (28 bp):
TTTTAAATCTTCTCTTTATTAGCACAAT
Found at i:107852 original size:10 final size:10
Alignment explanation
Indices: 107801--107870 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 10
107791 ATATATATAC
*
107801 TATTATTTAA
1 TATTATTTAT
*
107811 TATTATTTCCCT
1 TATTATTT--AT
*
107823 TATCA-TTAT
1 TATTATTTAT
107832 TAATATATTTAT
1 T-AT-TATTTAT
*
107844 TATTATTTAC
1 TATTATTTAT
*
107854 TACTATTTAT
1 TATTATTTAT
107864 TATTATT
1 TATTATT
107871 ATTGACCCGT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
9 2 0.04
10 30 0.65
11 5 0.11
12 9 0.20
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (10 bp):
TATTATTTAT
Found at i:111370 original size:17 final size:17
Alignment explanation
Indices: 111350--111384 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
111340 TAATATAAAA
* *
111350 TATATTTTATTTTATTT
1 TATATTATATTATATTT
111367 TATATTATATTATATTT
1 TATATTATATTATATTT
111384 T
1 T
111385 TCTTTTGTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATTATATTATATTT
Found at i:112867 original size:31 final size:31
Alignment explanation
Indices: 112832--112892 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
112822 TAAAACTAAA
112832 GTGACCATTTTATTACAAATCGATAATATTT
1 GTGACCATTTTATTACAAATCGATAATATTT
* * *
112863 GTGACTATTTTATTATAAATTGATAATATT
1 GTGACCATTTTATTACAAATCGATAATATT
112893 AATGATCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (31 bp):
GTGACCATTTTATTACAAATCGATAATATTT
Found at i:120637 original size:19 final size:19
Alignment explanation
Indices: 120613--120652 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
120603 ACAATGCAAA
*
120613 AAAATACTGTGCAGATTCG
1 AAAATACTATGCAGATTCG
120632 AAAATACTATGCAGATTCG
1 AAAATACTATGCAGATTCG
120651 AA
1 AA
120653 CAGTGCAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (19 bp):
AAAATACTATGCAGATTCG
Found at i:120666 original size:30 final size:31
Alignment explanation
Indices: 120632--120693 Score: 81
Period size: 34 Copynumber: 1.9 Consensus size: 31
120622 TGCAGATTCG
*
120632 AAAATACTATGCA-GATTCGAACAGTGCAGA
1 AAAATACAATGCATGATTCGAACAGTGCAGA
120662 AAAATACAATGCAGTTTGATTCGAACAGTGCA
1 AAAATACAATGCA---TGATTCGAACAGTGCA
120694 CAAAGCAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 12 0.44
34 15 0.56
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (31 bp):
AAAATACAATGCATGATTCGAACAGTGCAGA
Done.