Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002271.1 Hibiscus syriacus cultivar Beakdansim tig00004617_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: 140144
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1301 original size:22 final size:23
Alignment explanation
Indices: 1276--1327 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1266 TCTCAAAAGA
* *
1276 CCACATA-GGTTGTATCGAAGTG
1 CCACATAGGGTTGTACCAAAGTG
1298 CCACATAGGGTTGTACCAAAGTG
1 CCACATAGGGTTGTACCAAAGTG
1321 CCACATA
1 CCACATA
1328 TTTATCCTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (23 bp):
CCACATAGGGTTGTACCAAAGTG
Found at i:1347 original size:21 final size:21
Alignment explanation
Indices: 1321--1369 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1311 TACCAAAGTG
* * *
1321 CCACATATTTATCCTGGAGGA
1 CCACATAATTATCCCGAAGGA
*
1342 CCACATAATTATCCCGAATGA
1 CCACATAATTATCCCGAAGGA
1363 CCACATA
1 CCACATA
1370 GACCCTCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (21 bp):
CCACATAATTATCCCGAAGGA
Found at i:1911 original size:55 final size:55
Alignment explanation
Indices: 1826--2002 Score: 248
Period size: 55 Copynumber: 3.2 Consensus size: 55
1816 ATACTTAGAA
* *
1826 GTATCGATACACT-CTACAGTGTACCGATACATAATTAGCACTCGATGTTTTGAGG
1 GTATCGATACACTCCT-CAGTGTACCGATACACAAATAGCACTCGATGTTTTGAGG
* * * * *
1881 GTATCGATACACTCCTCAGTGTACCAATACACAAATAGCACTCAATATTTTTAAG
1 GTATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGAGG
* * *
1936 GTATCGATACACTCCTCAGTGTACCGATACACAAATGGCATTTGATGTTTTGAGG
1 GTATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGAGG
1991 GTATCGATACAC
1 GTATCGATACAC
2003 AAATGACATT
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
55 104 0.98
56 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (55 bp):
GTATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGAGG
Found at i:2006 original size:35 final size:35
Alignment explanation
Indices: 1960--2037 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 35
1950 CTCAGTGTAC
* *
1960 CGATACACAAATGGCATTTGATGTTTTGAGGGTAT
1 CGATACACAAATGACATTCGATGTTTTGAGGGTAT
1995 CGATACACAAATGACATTCGATGTTTTGAGGGTAT
1 CGATACACAAATGACATTCGATGTTTTGAGGGTAT
2030 CGATACAC
1 CGATACAC
2038 TCCTCAGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (35 bp):
CGATACACAAATGACATTCGATGTTTTGAGGGTAT
Found at i:2287 original size:26 final size:27
Alignment explanation
Indices: 2238--2291 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
2228 AACTTGTACA
2238 TTTAAAACTCTCAAACATCCCAAATTC
1 TTTAAAACTCTCAAACATCCCAAATTC
2265 TTTAAAACTCTC-AACATCCCAAATTC
1 TTTAAAACTCTCAAACATCCCAAATTC
2291 T
1 T
2292 CATTTAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.31
Consensus pattern (27 bp):
TTTAAAACTCTCAAACATCCCAAATTC
Found at i:4434 original size:39 final size:39
Alignment explanation
Indices: 4380--4530 Score: 284
Period size: 39 Copynumber: 3.9 Consensus size: 39
4370 TTTATTATCA
4380 TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTC
1 TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTC
4419 TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTC
1 TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTC
*
4458 TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTT
1 TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTC
*
4497 TATGCAAATATAGAAAGAAAGAAACCTATAAGGG
1 TATGCAAATATAGAAAGAAAGAAACCAATAAGGG
4531 TTTTTTTAAA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 110 1.00
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.19
Consensus pattern (39 bp):
TATGCAAATATAGAAAGAAAGAAACCAATAAGGGGGTTC
Found at i:5298 original size:25 final size:25
Alignment explanation
Indices: 5264--5317 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
5254 TTAATTACAG
5264 GATCACTTGCATGCATACGTACCTA
1 GATCACTTGCATGCATACGTACCTA
*
5289 GATCACTTGCTTGCATACGTACCTA
1 GATCACTTGCATGCATACGTACCTA
5314 GATC
1 GATC
5318 CAACAATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (25 bp):
GATCACTTGCATGCATACGTACCTA
Found at i:17551 original size:119 final size:114
Alignment explanation
Indices: 17345--17570 Score: 380
Period size: 119 Copynumber: 1.9 Consensus size: 114
17335 AATCCGACAG
17345 ATCCGATCCATTTTTCAATTTTATAGTTCGGATCGGGTATCCGATTTTTTTCGGATTTTCGGATC
1 ATCCGATCCATTTTTCAATTTTATAGTTCGGATCGGGTATCCGATTTTTTTCGGATTTTCGGATC
17410 GGATACGGATCGATCAAAATCCAATTTCGAATTATCCGAAAATTTGGAT
66 GGATACGGATCGATCAAAATCCAATTTCGAATTATCCGAAAATTTGGAT
*
17459 ATCCGATCCGTTTTTCAATTTTCGGATAGTTCGGATCGGGTATCCGAATTTTTTTTCGGATTTTC
1 ATCCGATCCATTTTTCAATTTT---ATAGTTCGGATCGGGTATCCG-A-TTTTTTTCGGATTTTC
* *
17524 GGATCGGATACGGATTGATCAAAATCCAATTTCGGATTATCCGAAAA
61 GGATCGGATACGGATCGATCAAAATCCAATTTCGAATTATCCGAAAA
17571 CCCGAAAAAA
Statistics
Matches: 104, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
114 21 0.20
117 21 0.20
118 1 0.01
119 61 0.59
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (114 bp):
ATCCGATCCATTTTTCAATTTTATAGTTCGGATCGGGTATCCGATTTTTTTCGGATTTTCGGATC
GGATACGGATCGATCAAAATCCAATTTCGAATTATCCGAAAATTTGGAT
Found at i:21240 original size:21 final size:21
Alignment explanation
Indices: 21214--21287 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
21204 ATTCTGACTA
21214 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
21235 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
21256 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
21277 TCGCAATGCGA
1 TCGCATTGCGA
21288 AAACGTAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:21246 original size:41 final size:42
Alignment explanation
Indices: 21185--21287 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
21175 CGCAAATCAG
* * *
21185 TTTCCAGATTCGCAACGCGATTCTGAC-TA-TCGCATTGCGAT
1 TTTCCAAATTCGCAATGCGATT-TGACAAATTCGCATTGCGAT
* ** *
21226 TTTCCAAATTCGCATTGCGATTTTCCAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCAATGCGATTTGACAAATTCGCATTGCGAT
*
21268 TTTCCTAATTCGCAATGCGA
1 TTTCCAAATTCGCAATGCGA
21288 AAACGTAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
40 2 0.04
41 20 0.39
42 29 0.57
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (42 bp):
TTTCCAAATTCGCAATGCGATTTGACAAATTCGCATTGCGAT
Found at i:21319 original size:20 final size:20
Alignment explanation
Indices: 21309--21382 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
21299 GCAATGCGAA
*
21309 TCTGACTATCGCAACAAGAT
1 TCTGACTATCGCAACGAGAT
*
21329 TTTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
*
21349 TCTGACTATCGCAACGCGAT
1 TCTGACTATCGCAACGAGAT
21369 TCTGACTATCGCAA
1 TCTGACTATCGCAA
21383 TACTGAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (20 bp):
TCTGACTATCGCAACGAGAT
Found at i:21340 original size:40 final size:40
Alignment explanation
Indices: 21296--21383 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
21286 GAAAACGTAA
* *
21296 ATCGCAATGCGAATCTGACTATCGCAACAAGATTTTGACT
1 ATCGCAATGAGAATCTGACTATCGCAACAAGATTCTGACT
* * **
21336 ATCGCAACGAGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAATGAGAATCTGACTATCGCAACAAGATTCTGACT
21376 ATCGCAAT
1 ATCGCAAT
21384 ACTGAATTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (40 bp):
ATCGCAATGAGAATCTGACTATCGCAACAAGATTCTGACT
Found at i:22251 original size:24 final size:24
Alignment explanation
Indices: 22224--22277 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
22214 GTATTCGAAA
22224 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
22248 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
22272 TTTGAT
1 TTTGAT
22278 GATTTTTCAG
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:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:24797 original size:20 final size:20
Alignment explanation
Indices: 24709--24797 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
24699 CAACGCGGAA
*
24709 ATCGCAACAC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
* *
24729 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
24749 ATCGCAACGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
24769 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
24789 ATCACAACG
1 ATCGCAACG
24798 AGAGAATCGC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 60 0.97
21 2 0.03
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:24857 original size:34 final size:33
Alignment explanation
Indices: 24769--24864 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
24759 GGAATTGACT
* ** *
24769 ATCGCAACGCGGAAATGACTATCACAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
24803 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
24836 ATCGTAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
24865 CGAATTTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:24923 original size:34 final size:34
Alignment explanation
Indices: 24880--24975 Score: 140
Period size: 34 Copynumber: 2.8 Consensus size: 34
24870 TTAGTTTCGT
24880 GTTGCGATTTTCATTTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTTCGCATTGCGATTCTCTC
*
24914 GTTGCGATTTTCA-TTTCGCATTGCGATTTTTCTC
1 GTTGCGATTTTCATTTTCGCATTGCGA-TTCTCTC
** *
24948 GTTGCGATAGTCATTTCCGCATTGCGAT
1 GTTGCGATTTTCATTTTCGCATTGCGAT
24976 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
33 13 0.23
34 31 0.55
35 12 0.21
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (34 bp):
GTTGCGATTTTCATTTTCGCATTGCGATTCTCTC
Found at i:25100 original size:14 final size:15
Alignment explanation
Indices: 25081--25118 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
25071 CATCAATTAA
25081 ACAAATCAA-CATTT
1 ACAAATCAATCATTT
*
25095 ACAAAT-AATCTTTT
1 ACAAATCAATCATTT
25109 ACAAATCAAT
1 ACAAATCAAT
25119 TAAACAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 16 0.76
15 3 0.14
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (15 bp):
ACAAATCAATCATTT
Found at i:27118 original size:20 final size:20
Alignment explanation
Indices: 27093--27181 Score: 142
Period size: 20 Copynumber: 4.5 Consensus size: 20
27083 AAACTTAAAA
*
27093 ATCGCAACGCGAAAATGACC
1 ATCGCAACGCGAAAATGACT
27113 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
27133 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
27153 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
27173 ATCGCAACG
1 ATCGCAACG
27182 AGAGAATCGC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:27266 original size:20 final size:20
Alignment explanation
Indices: 27224--27382 Score: 121
Period size: 20 Copynumber: 8.6 Consensus size: 20
27214 GCGATTCTTT
**
27224 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
*
27244 CATTGCGATAGTCATTTTTG
1 CATTGCGATAGTCATTTTCG
* * *
27264 CATTGCAATAGCCATTTTCA
1 CATTGCGATAGTCATTTTCG
27284 CATTGCGAT--T--TTGTT-G
1 CATTGCGATAGTCATT-TTCG
**
27300 --TTGCGATTTTCA-TTTCG
1 CATTGCGATAGTCATTTTCG
*
27317 CATTGCGAT--TC--TCTCG
1 CATTGCGATAGTCATTTTCG
27333 --TTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
27351 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
27371 CATTGCGATAGT
1 CATTGCGATAGT
27383 AAACTATTCT
Statistics
Matches: 112, Mismatches: 13, Indels: 28
0.73 0.08 0.18
Matches are distributed among these distances:
14 14 0.12
16 11 0.10
17 6 0.05
18 4 0.04
19 7 0.06
20 70 0.62
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.41
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:29323 original size:20 final size:20
Alignment explanation
Indices: 29252--29322 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
29242 TCTGAAACTT
29252 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
29272 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
29292 ACTATCGCAACGCGGAAATG
1 AAAATCGCAACACGAAAATG
29312 AAAATCGCAAC
1 AAAATCGCAAC
29323 GACAGAATCG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:29691 original size:22 final size:22
Alignment explanation
Indices: 29666--29721 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
29656 TGATTTCGCA
29666 GGAGATGGAGG-CTGATATCGTC
1 GGAGATGG-GGACTGATATCGTC
* *
29688 GGAGATGGGGACTGATTTCTTC
1 GGAGATGGGGACTGATATCGTC
*
29710 GGAGATAGGGAC
1 GGAGATGGGGAC
29722 GGATGTCGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.23, C:0.12, G:0.41, T:0.23
Consensus pattern (22 bp):
GGAGATGGGGACTGATATCGTC
Found at i:29942 original size:20 final size:20
Alignment explanation
Indices: 29926--30071 Score: 256
Period size: 20 Copynumber: 7.3 Consensus size: 20
29916 CAGATTCGTG
*
29926 TTGCGATTTACGTATTCGTA
1 TTGCGATTTACGTATTCGCA
*
29946 TTGCGATTTACGTATTTGCA
1 TTGCGATTTACGTATTCGCA
*
29966 TTGCGATTTACGTATTCGTA
1 TTGCGATTTACGTATTCGCA
29986 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
30006 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
30026 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
30046 TTGCGATTTACGTATTCACA
1 TTGCGATTTACGTATTCGCA
30066 TTGCGA
1 TTGCGA
30072 ATTAGGAAAG
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 120 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:30107 original size:21 final size:21
Alignment explanation
Indices: 30068--30113 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
30058 TATTCACATT
**
30068 GCGAATTAGGAAAGTCGCAAC
1 GCGAATTAGGAAAAACGCAAC
* *
30089 GCGAATTTGGAAAAACGCAAT
1 GCGAATTAGGAAAAACGCAAC
30110 GCGA
1 GCGA
30114 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.15
Consensus pattern (21 bp):
GCGAATTAGGAAAAACGCAAC
Found at i:33350 original size:6 final size:6
Alignment explanation
Indices: 33340--33388 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
33330 ACACACACAA
* * * *
33340 AGAGAG GGAGAG GGAGAG GGAGAG AGAGAG AGAGAG AGAGAA AGAGAG
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
33388 A
1 A
33389 TAATTAGGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (6 bp):
AGAGAG
Found at i:33385 original size:8 final size:8
Alignment explanation
Indices: 33340--33388 Score: 62
Period size: 8 Copynumber: 6.1 Consensus size: 8
33330 ACACACACAA
*
33340 AGAGAGGG
1 AGAGAGAG
*
33348 AGAGGGAG
1 AGAGAGAG
*
33356 AGGGAGAG
1 AGAGAGAG
33364 AGAGAGAG
1 AGAGAGAG
33372 AGAGAGAG
1 AGAGAGAG
*
33380 AAAGAGAG
1 AGAGAGAG
33388 A
1 A
33389 TAATTAGGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (8 bp):
AGAGAGAG
Found at i:34952 original size:18 final size:17
Alignment explanation
Indices: 34913--34955 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
34903 ATTATATGGA
34913 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
34929 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
34947 TATTATTAT
1 TATTATTAT
34956 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:35208 original size:2 final size:2
Alignment explanation
Indices: 35201--35225 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35191 TCTTATAATT
35201 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 T
35226 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35445 original size:36 final size:38
Alignment explanation
Indices: 35396--35471 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
35386 AGTGAGAGGG
*
35396 TAGCTTTTCTATTTT-TAAATA-TTTGGTGTATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATA
*
35432 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATA
35470 TA
1 TA
35472 TATTTTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 12 0.34
37 7 0.20
38 16 0.46
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.55
Consensus pattern (38 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATA
Found at i:36663 original size:5 final size:5
Alignment explanation
Indices: 36653--36681 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
36643 TTCATCTTTC
36653 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
36682 CATCACTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:38080 original size:8 final size:8
Alignment explanation
Indices: 38067--38105 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
38057 GAACATTTCA
*
38067 TGCATTCT
1 TGCATTTT
38075 TGCA-TTT
1 TGCATTTT
38082 TGCATTTT
1 TGCATTTT
*
38090 TGCCTTTT
1 TGCATTTT
38098 TGCATTTT
1 TGCATTTT
38106 CATCTACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:39306 original size:9 final size:9
Alignment explanation
Indices: 39294--39333 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
39284 TAAAAAGGGC
39294 AAAAAGAAAA
1 AAAAAG-AAA
*
39304 AAAAAGCAA
1 AAAAAGAAA
*
39313 AAAAAGAAC
1 AAAAAGAAA
39322 AAAAAGAAA
1 AAAAAGAAA
39331 AAA
1 AAA
39334 GAAAAAGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 20 0.77
10 6 0.23
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:39967 original size:22 final size:22
Alignment explanation
Indices: 39939--39982 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39929 AGCTACCCCA
39939 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
39961 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
39983 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:41054 original size:36 final size:36
Alignment explanation
Indices: 40947--41067 Score: 161
Period size: 36 Copynumber: 3.3 Consensus size: 36
40937 ATTGAAAACA
* *
40947 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
* * *
40983 TTTCCCTTGGAACTAAGTTTTGTCTCTCTTAAGACAG
1 TTTCCCTT-GAAATAAATTTTGTCTCTCTTGAGACAG
* * *
41020 TTTCTCTTGAAATAATTTTTGTCTATCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
41056 TTTCCCTTGAAA
1 TTTCCCTTGAAA
41068 CAAAACCTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
36 43 0.59
37 30 0.41
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
Found at i:41155 original size:67 final size:68
Alignment explanation
Indices: 41046--41202 Score: 205
Period size: 68 Copynumber: 2.4 Consensus size: 68
41036 TTTTGTCTAT
* **
41046 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTT-TT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
41107 CTCC
66 -TCC
* * *
41111 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
41176 TCC
66 TCC
* *
41179 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
41203 ACAGATATCT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.35
68 30 0.38
69 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
TCC
Found at i:42030 original size:105 final size:105
Alignment explanation
Indices: 41846--42565 Score: 1150
Period size: 105 Copynumber: 6.9 Consensus size: 105
41836 GCACTCGAGG
* * ** *
41846 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
41911 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
41952 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
42017 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
42057 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT---CAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * * *
42119 ACCAATTTCAACTTCACAATGAATGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
42159 CAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
42224 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* **
42264 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
42329 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
42369 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
42434 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
42474 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
42534 TTCAATTTCAACTTCACGACGGAGGATATTGG
66 GCCAATTTCAACTTCACAACGAAGGATATTGG
42566 GCTCTGAACA
Statistics
Matches: 582, Mismatches: 29, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
100 33 0.06
101 1 0.00
102 99 0.17
103 2 0.00
104 2 0.00
105 406 0.70
106 39 0.07
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:42210 original size:207 final size:208
Alignment explanation
Indices: 41846--42565 Score: 1126
Period size: 207 Copynumber: 3.5 Consensus size: 208
41836 GCACTCGAGG
* * ** *
41846 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT--AC-AACAACTTCTCAATTTCAG
41911 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
63 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
41976 AAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAG
128 AAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
42041 GATATTGGACTTCAGA
193 GATATTGGACTTCAGA
* *
42057 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT-CAACAACTTCTCAATTTCAGAAC
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTACAACAACTTCTCAATTTCAGAGC
* * * *
42121 CAATTTCAACTTCACAATGAATGATATTGGACTTCAGACAACGCAAGTTTAACTTCACGACGAAG
66 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
42186 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
131 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
42251 ATTGGACTTCAGA
196 ATTGGACTTCAGA
* **
42264 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT--ACAACAACTTCTCAATTTCAGA
*
42329 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGA
64 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
42394 AGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
129 AGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
*
42459 ATATTGGACTCCAGA
194 ATATTGGACTTCAGA
* *
42474 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT-CAACAAAATT-TC-A-TTCAGAT
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTACAAC-AACTTCTCAATTTCAGAG
* * *
42535 TCAATTTCAACTTCACGACGGAGGATATTGG
65 CCAATTTCAACTTCACAACGAAGGATATTGG
42566 GCTCTGAACA
Statistics
Matches: 471, Mismatches: 34, Indels: 14
0.91 0.07 0.03
Matches are distributed among these distances:
205 32 0.07
206 1 0.00
207 203 0.43
208 5 0.01
210 195 0.41
211 35 0.07
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (208 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTACAACAACTTCTCAATTTCAGAGC
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
ATTGGACTTCAGA
Found at i:43764 original size:18 final size:16
Alignment explanation
Indices: 43722--43764 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
43712 ATTATATGGA
43722 TATTTTATTCATTTAT
1 TATTTTATTCATTTAT
*
43738 TTTTATTATTCATGTTAT
1 TATT-TTATTCAT-TTAT
43756 TATTGTTAT
1 TATT-TTAT
43765 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 11 0.50
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (16 bp):
TATTTTATTCATTTAT
Found at i:44018 original size:2 final size:2
Alignment explanation
Indices: 44013--44037 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44003 ATCTTATAAT
44013 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 T
44038 TTATTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44247 original size:36 final size:38
Alignment explanation
Indices: 44198--44273 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
44188 AGTGAGAGGG
*
44198 TAGCTTTTCTATTTT-TAAATA-TTTGGTGTATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATA
*
44234 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATA
44272 TA
1 TA
44274 TATTTTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 12 0.34
37 7 0.20
38 16 0.46
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.55
Consensus pattern (38 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATA
Found at i:44354 original size:14 final size:14
Alignment explanation
Indices: 44331--44366 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
44321 ATTTTTTTTC
*
44331 TTTATCTTATTTAT
1 TTTATTTTATTTAT
*
44345 TTTATTTTATTTTT
1 TTTATTTTATTTAT
44359 TTTATTTT
1 TTTATTTT
44367 TCCCTTTTAT
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:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:44367 original size:9 final size:9
Alignment explanation
Indices: 44325--44367 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
44315 TTTACTATTT
44325 TTTTTCTTTA
1 TTTTT-TTTA
* *
44335 TCTTATTTA
1 TTTTTTTTA
44344 TTTTATTTTA
1 TTTT-TTTTA
44354 TTTTTTTTA
1 TTTTTTTTA
44363 TTTTT
1 TTTTT
44368 CCCTTTTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 17 0.61
10 11 0.39
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:46734 original size:50 final size:50
Alignment explanation
Indices: 46666--46765 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
46656 TCATTAAAAA
46666 CAAAATTATGATCTTTTGAAGTGATAGTGTGATACTTACAATCAAACAGC
1 CAAAATTATGATCTTTTGAAGTGATAGTGTGATACTTACAATCAAACAGC
46716 CAAAATTATGATCTTTTGAAGTGATAGTGTGATACTTACAATCAAACAGC
1 CAAAATTATGATCTTTTGAAGTGATAGTGTGATACTTACAATCAAACAGC
46766 TAAGACAGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (50 bp):
CAAAATTATGATCTTTTGAAGTGATAGTGTGATACTTACAATCAAACAGC
Found at i:56295 original size:51 final size:50
Alignment explanation
Indices: 56173--56301 Score: 161
Period size: 51 Copynumber: 2.5 Consensus size: 50
56163 CCCTACGTGG
* * * * *
56173 CGTATAGCGCGCTGCAGGGGCCGCGCTATATCCACGTGTATGCCAGATCAC
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGCA-GCCAAATCAC
*
56224 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCA-CCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATA-CCCACGT-GCAGCCAAATCAC
*
56275 CGTATAGCGCGGTGCAGGGGGAGCGCT
1 CGTATAGCGCGGTGCAGGGGGCGCGCT
56302 TTACTGCTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
51 61 0.88
52 6 0.09
53 2 0.03
ACGTcount: A:0.19, C:0.29, G:0.34, T:0.17
Consensus pattern (50 bp):
CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGCAGCCAAATCAC
Found at i:56654 original size:31 final size:31
Alignment explanation
Indices: 56640--56710 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
56630 TGTTAATATG
56640 ACCATTAAATTTTAGATAAAATATCAAATTA
1 ACCATTAAATTTTAGATAAAATATCAAATTA
* *
56671 ACCCTTAAATTTTAGATAAAATATCAAAATA
1 ACCATTAAATTTTAGATAAAATATCAAATTA
*
56702 ACCCTTAAA
1 ACCATTAAA
56711 CATAAAATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (31 bp):
ACCATTAAATTTTAGATAAAATATCAAATTA
Found at i:56724 original size:31 final size:31
Alignment explanation
Indices: 56655--56724 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
56645 TAAATTTTAG
* ** * *
56655 ATAAAATATCAAATTAACCCTTAAATTTTAG
1 ATAAAATATCAAAATAACCCTTAAACATAAA
56686 ATAAAATATCAAAATAACCCTTAAACATAAA
1 ATAAAATATCAAAATAACCCTTAAACATAAA
*
56717 ATGAAATA
1 ATAAAATA
56725 GTATTAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.56, C:0.13, G:0.03, T:0.29
Consensus pattern (31 bp):
ATAAAATATCAAAATAACCCTTAAACATAAA
Found at i:64825 original size:30 final size:31
Alignment explanation
Indices: 64766--64826 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
64756 AAGAAGTTAA
* **
64766 CATTTTGTTATAAATCGATAATGTTAATAAC
1 CATTTTGTTACAAATCGATAACATTAATAAC
*
64797 CATTTTGTTACAAATCG-TCACATTAATAAC
1 CATTTTGTTACAAATCGATAACATTAATAAC
64827 GTTAGTGACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (31 bp):
CATTTTGTTACAAATCGATAACATTAATAAC
Found at i:80946 original size:15 final size:15
Alignment explanation
Indices: 80908--80946 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
80898 TGGGTTCGTG
80908 TTCTCAAAATTGAAA
1 TTCTCAAAATTGAAA
*
80923 TTCCCAAAATTGAAA
1 TTCTCAAAATTGAAA
*
80938 TTCTTAAAA
1 TTCTCAAAA
80947 ACGTTCATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (15 bp):
TTCTCAAAATTGAAA
Found at i:82986 original size:13 final size:13
Alignment explanation
Indices: 82964--83002 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
82954 TTTATCTTTT
82964 AAATTT-TATAAA
1 AAATTTATATAAA
82976 AAATTTATATAAA
1 AAATTTATATAAA
82989 AAATTTAT-TAAA
1 AAATTTATATAAA
83001 AA
1 AA
83003 GTATATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTTATATAAA
Found at i:87234 original size:171 final size:172
Alignment explanation
Indices: 86948--87286 Score: 608
Period size: 171 Copynumber: 2.0 Consensus size: 172
86938 CTTAGTATCT
* *
86948 TTTTATAGGGATATATAGTTGATCACAAAGAAAACTAAATAAAGTAAAAAATTACTTTAATAAAG
1 TTTTATAGGGATAGATACTTGATCACAAAGAAAACTAAATAAAGTAAAAAATTACTTTAATAAAG
*
87013 TTCTCTACTTTTAATCAAAATAGGTTTATTACTTTCCCAATTAAATTATGTCACTTTGAATTCGA
66 TTCTCTACTTTTAATCAAAATAGGTTTATTACTTTCCCAATTAAATTATGTCACTTTGAATTCAA
* *
87078 GTCAAACTTTATTAAATCTCCACTTTAACATGAATTCTAAAA
131 GTCAAACTTTAATAAATCTCCACTTTAACACGAATTCTAAAA
* *
87120 TTTTATATGGATAGATACTTGATTACAAAGAAAACTAAATAAA-TAAAAAATTACTTTAATAAAG
1 TTTTATAGGGATAGATACTTGATCACAAAGAAAACTAAATAAAGTAAAAAATTACTTTAATAAAG
87184 TTCTCTACTTTTAATCAAAATAGGTTTATTACTTTCCCAATTAAATTATGTCACTTTGAATTCAA
66 TTCTCTACTTTTAATCAAAATAGGTTTATTACTTTCCCAATTAAATTATGTCACTTTGAATTCAA
87249 GTCAAACTTTAATAAATCTCCACTTTAACACGAATTCT
131 GTCAAACTTTAATAAATCTCCACTTTAACACGAATTCT
87287 GAAAGTGCAA
Statistics
Matches: 160, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
171 121 0.76
172 39 0.24
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (172 bp):
TTTTATAGGGATAGATACTTGATCACAAAGAAAACTAAATAAAGTAAAAAATTACTTTAATAAAG
TTCTCTACTTTTAATCAAAATAGGTTTATTACTTTCCCAATTAAATTATGTCACTTTGAATTCAA
GTCAAACTTTAATAAATCTCCACTTTAACACGAATTCTAAAA
Found at i:90033 original size:44 final size:44
Alignment explanation
Indices: 89983--90066 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
89973 CTAAATTTTA
89983 TTCTTCTCAAATATGTTATGCCCACATAACTAAACTCTCTCTTT
1 TTCTTCTCAAATATGTTATGCCCACATAACTAAACTCTCTCTTT
90027 TTCTTCTCAAATATGTTATGCCCACATAACTAAACTCTCT
1 TTCTTCTCAAATATGTTATGCCCACATAACTAAACTCTCT
90067 TTTCCTTATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.39
Consensus pattern (44 bp):
TTCTTCTCAAATATGTTATGCCCACATAACTAAACTCTCTCTTT
Found at i:90079 original size:42 final size:43
Alignment explanation
Indices: 89989--90081 Score: 152
Period size: 44 Copynumber: 2.2 Consensus size: 43
89979 TTTATTCTTC
* *
89989 TCAAATATGTTATGCCCACATAACTAAACTCTCTCTTTTTCTTC
1 TCAAATATGTTATGCCCACATAACTAAAC-CTCTCTTTTCCTTA
90033 TCAAATATGTTATGCCCACATAACTAAA-CTCTCTTTTCCTTA
1 TCAAATATGTTATGCCCACATAACTAAACCTCTCTTTTCCTTA
90075 TCAAATA
1 TCAAATA
90082 CATTATTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 19 0.40
44 28 0.60
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (43 bp):
TCAAATATGTTATGCCCACATAACTAAACCTCTCTTTTCCTTA
Found at i:90698 original size:14 final size:15
Alignment explanation
Indices: 90666--90698 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
90656 CTGCTCGTGT
90666 TTTTTCACGAAAAAG
1 TTTTTCACGAAAAAG
*
90681 TTTTTCACGTAAAA-
1 TTTTTCACGAAAAAG
90695 TTTT
1 TTTT
90699 GGTGTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (15 bp):
TTTTTCACGAAAAAG
Found at i:92271 original size:18 final size:17
Alignment explanation
Indices: 92250--92287 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
92240 AATTATAAAG
*
92250 TTATCCTAATATATATAA
1 TTATACTAATAT-TATAA
92268 TTATACTAATATTATAA
1 TTATACTAATATTATAA
92285 TTA
1 TTA
92288 GTCTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATACTAATATTATAA
Found at i:93633 original size:8 final size:8
Alignment explanation
Indices: 93617--93668 Score: 52
Period size: 8 Copynumber: 6.1 Consensus size: 8
93607 TAAAATTGTA
93617 ATAATTAAT
1 ATAA-TAAT
93626 ATAATAAT
1 ATAATAAT
93634 ATAA-AAT
1 ATAATAAT
93641 AATAATATATT
1 -ATAATA-A-T
93652 ATAATAAT
1 ATAATAAT
*
93660 ATTATAAT
1 ATAATAAT
93668 A
1 A
93669 CTTATAACGA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
7 3 0.08
8 21 0.55
9 6 0.16
10 7 0.18
11 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:93644 original size:13 final size:13
Alignment explanation
Indices: 93615--93661 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
93605 TGTAAAATTG
93615 TAATAAT-TAATA
1 TAATAATATAATA
*
93627 TAATAATATAAAA
1 TAATAATATAATA
*
93640 TAATAATATATTA
1 TAATAATATAATA
93653 TAATAATAT
1 TAATAATAT
93662 TATAATACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
12 7 0.23
13 24 0.77
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:93900 original size:36 final size:36
Alignment explanation
Indices: 93852--93975 Score: 169
Period size: 36 Copynumber: 3.4 Consensus size: 36
93842 GATTTGTTCA
**
93852 TGCTTCACTACTCTTTTGTGAAGGCTGAAGGTGCAT
1 TGCTTCACTACTCTTTTGTGAAGGCTGAATTTGCAT
* * *
93888 CGCTTCACTACTCTTTTGTGAAGGCTTAATTTGTAT
1 TGCTTCACTACTCTTTTGTGAAGGCTGAATTTGCAT
*
93924 TGCTTCATTACTCTTTTGTGAAGGCTTG-ATTTGCAT
1 TGCTTCACTACTCTTTTGTGAAGGC-TGAATTTGCAT
93960 TGCTTCCACTACTCTT
1 TGCTT-CACTACTCTT
93976 CCGTGGAGAT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
36 66 0.87
37 10 0.13
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.43
Consensus pattern (36 bp):
TGCTTCACTACTCTTTTGTGAAGGCTGAATTTGCAT
Found at i:104523 original size:18 final size:17
Alignment explanation
Indices: 104502--104539 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
104492 AATTATAAAG
*
104502 TTATCCTAATATATATAA
1 TTATACTAATAT-TATAA
104520 TTATACTAATATTATAA
1 TTATACTAATATTATAA
104537 TTA
1 TTA
104540 GTCTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATACTAATATTATAA
Found at i:105549 original size:19 final size:19
Alignment explanation
Indices: 105525--105572 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
105515 CGGGCGGAAT
105525 AACCCTAGGGTGTAATGAA
1 AACCCTAGGGTGTAATGAA
105544 AACCCTAGGGTGTAATGAA
1 AACCCTAGGGTGTAATGAA
105563 AACCCTAGGG
1 AACCCTAGGG
105573 ATCCTGCTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (19 bp):
AACCCTAGGGTGTAATGAA
Found at i:107270 original size:22 final size:22
Alignment explanation
Indices: 107245--107293 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
107235 ATATCATATC
107245 AATGTCCATTTGTTTATTTTCT
1 AATGTCCATTTGTTTATTTTCT
107267 AATGTCCATTTGTTTATTTTCT
1 AATGTCCATTTGTTTATTTTCT
107289 AATGT
1 AATGT
107294 ATTCATATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (22 bp):
AATGTCCATTTGTTTATTTTCT
Found at i:109853 original size:29 final size:29
Alignment explanation
Indices: 109819--109877 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
109809 CTTAAATTAA
*
109819 TTTGATGTCATTGTTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
109848 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
109877 T
1 T
109878 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:114495 original size:29 final size:29
Alignment explanation
Indices: 114461--114519 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
114451 CCTAAATTAA
114461 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
114490 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
114519 T
1 T
114520 AGGTAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:115688 original size:23 final size:23
Alignment explanation
Indices: 115660--115748 Score: 160
Period size: 23 Copynumber: 3.9 Consensus size: 23
115650 TTACCAAATT
*
115660 TTCTCCCTTCATTTTCTCTTTTC
1 TTCTCCCTTCATTTTCTCTCTTC
115683 TTCTCCCTTCATTTTCTCTCTTC
1 TTCTCCCTTCATTTTCTCTCTTC
*
115706 TTCTCCCTTTATTTTCTCTCTTC
1 TTCTCCCTTCATTTTCTCTCTTC
115729 TTCTCCCTTCATTTTCTCTC
1 TTCTCCCTTCATTTTCTCTC
115749 CAAGAGTCAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.04, C:0.37, G:0.00, T:0.58
Consensus pattern (23 bp):
TTCTCCCTTCATTTTCTCTCTTC
Found at i:115723 original size:36 final size:36
Alignment explanation
Indices: 115657--115741 Score: 88
Period size: 36 Copynumber: 2.4 Consensus size: 36
115647 GGCTTACCAA
* *
115657 ATTTTCTCCCTTCATTTTCTCTTTTCTTCTCCCTTC
1 ATTTTCTCCCTTCATTCTCCCTTTTCTTCTCCCTTC
* * *
115693 ATTTTCTCTCTTC-TTCTCCCTTTATTTTCTCTCTTC
1 ATTTTCTCCCTTCATTCTCCCTTT-TCTTCTCCCTTC
115729 ---TTCTCCCTTCATT
1 ATTTTCTCCCTTCATT
115742 TTCTCTCCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
33 9 0.22
34 2 0.05
35 8 0.20
36 22 0.54
ACGTcount: A:0.06, C:0.35, G:0.00, T:0.59
Consensus pattern (36 bp):
ATTTTCTCCCTTCATTCTCCCTTTTCTTCTCCCTTC
Found at i:116238 original size:21 final size:21
Alignment explanation
Indices: 116206--116248 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
116196 ATTGCATTTT
116206 TAAGAGTGAGTATCGATATTG
1 TAAGAGTGAGTATCGATATTG
116227 TAAGAAGT-AGTATCGATATTG
1 TAAG-AGTGAGTATCGATATTG
116248 T
1 T
116249 TCATATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (21 bp):
TAAGAGTGAGTATCGATATTG
Found at i:121179 original size:13 final size:13
Alignment explanation
Indices: 121161--121190 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
121151 GATTGCGAAG
121161 AATTAAAAATTTA
1 AATTAAAAATTTA
121174 AATT-AAAATTTA
1 AATTAAAAATTTA
121186 AATTA
1 AATTA
121191 CTCGATTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAAAAATTTA
Found at i:121767 original size:22 final size:22
Alignment explanation
Indices: 121737--121790 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
121727 CGGTGTAGCC
121737 CCGGCCGCCGCTCTCAGTCGCT
1 CCGGCCGCCGCTCTCAGTCGCT
*
121759 CTGGCCGCCGCTCTCAGTCGCT
1 CCGGCCGCCGCTCTCAGTCGCT
*
121781 CCGGCGGCCG
1 CCGGCCGCCG
121791 GGCCAACCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.04, C:0.48, G:0.31, T:0.17
Consensus pattern (22 bp):
CCGGCCGCCGCTCTCAGTCGCT
Found at i:122672 original size:25 final size:26
Alignment explanation
Indices: 122629--122677 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
122619 AATAATAATA
**
122629 ATATATATATATACGTTTTCAAAAAC
1 ATATATATATATAAATTTTCAAAAAC
*
122655 ATATA-ATATATAAATTTTTAAAA
1 ATATATATATATAAATTTTCAAAA
122678 TGTTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (26 bp):
ATATATATATATAAATTTTCAAAAAC
Found at i:122727 original size:41 final size:40
Alignment explanation
Indices: 122644--122797 Score: 140
Period size: 42 Copynumber: 3.9 Consensus size: 40
122634 TATATATACG
* * * * *
122644 TTTTCAAAAAC-ATATAATATATAAATTTTTAAAATGTTTTT
1 TTTTAAAAAACTATATATTATATATATTTTCAAAATG--GTT
122685 TTTTAAAAAACTATATATTATATATATTTTCAAAATGGTT
1 TTTTAAAAAACTATATATTATATATATTTTCAAAATGGTT
* * *
122725 TTTAAAAATTATAGTATATATTATATATATTTT-AAAA-CG--
1 TTTTAAAA--A-ACTATATATTATATATATTTTCAAAATGGTT
*
122764 TTTTCAAAAACTATATATTATATA-ATTTTCAAAA
1 TTTTAAAAAACTATATATTATATATATTTTCAAAA
122798 AATATATTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
35 5 0.05
36 18 0.19
37 1 0.01
39 6 0.06
40 9 0.09
41 11 0.11
42 27 0.28
43 20 0.21
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (40 bp):
TTTTAAAAAACTATATATTATATATATTTTCAAAATGGTT
Found at i:122743 original size:43 final size:43
Alignment explanation
Indices: 122696--122787 Score: 125
Period size: 43 Copynumber: 2.1 Consensus size: 43
122686 TTTAAAAAAC
* *
122696 TATATATTATATATATTTTCAAAATGGTTTTTAAAAA-T-TATAG
1 TATATATTATATATATTTT-AAAA-CGTTTTCAAAAACTATATAG
*
122739 TATATATTATATATATTTTAAAACGTTTTCAAAAACTATATAT
1 TATATATTATATATATTTTAAAACGTTTTCAAAAACTATATAG
122782 TATATA
1 TATATA
122788 ATTTTCAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
41 10 0.23
42 5 0.11
43 29 0.66
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (43 bp):
TATATATTATATATATTTTAAAACGTTTTCAAAAACTATATAG
Found at i:122792 original size:25 final size:25
Alignment explanation
Indices: 122764--122840 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
122754 TTTTAAAACG
*
122764 TTTTCAAAAACTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
* * **
122789 TTTTCAAAAAATATATTTTCAAAATGG
1 TTTTCAAAAAATATATATT--ATATAA
* *
122816 TTTTTAAAAATTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
122841 ATGTTTTCAT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
25 20 0.51
27 19 0.49
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (25 bp):
TTTTCAAAAAATATATATTATATAA
Found at i:122808 original size:15 final size:16
Alignment explanation
Indices: 122783--122812 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
122773 ACTATATATT
122783 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
122799 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
122813 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:122813 original size:93 final size:87
Alignment explanation
Indices: 122706--122885 Score: 254
Period size: 93 Copynumber: 2.0 Consensus size: 87
122696 TATATATTAT
*
122706 ATATATTTTCAAAATGGTTTTTAAAAATTATAGTATATATTATATATATTTT-AAAACGTTTTCA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATA-TAT-TA-TATAAATATTTTCAAAACGTTTTC-
122770 AAAACTATATATTATATAATTTTCAAAAA
62 AAAACTATATA-TATAT-ATTTT-AAAAA
* *
122799 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATATTTTCAAAACGTTTTCAAAA
*
122864 GTATATATATATATTTTAAAAA
66 CTATATATATATATTTTAAAAA
122886 CGTTTTCAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
87 5 0.06
88 5 0.06
89 5 0.06
90 20 0.24
91 12 0.15
92 3 0.04
93 32 0.39
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (87 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATATTTTCAAAACGTTTTCAAAA
CTATATATATATATTTTAAAAA
Found at i:122847 original size:27 final size:25
Alignment explanation
Indices: 122747--122847 Score: 80
Period size: 27 Copynumber: 3.8 Consensus size: 25
122737 AGTATATATT
* *
122747 ATATATATTTTAAAACGTTTTCAAAA
1 ATATATATTATAAAATGTTTT-AAAA
* *
122773 ACTATATATTATATAAT-TTTCAAAA
1 A-TATATATTATAAAATGTTTTAAAA
*
122798 A-ATATATTTTCAAAATGGTTTTTAAAA
1 ATATATATTAT-AAAAT-G-TTTTAAAA
122825 ATTATATATTATATAAATGTTTT
1 A-TATATATTATA-AAATGTTTT
122848 CATAACGTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
23 8 0.14
24 4 0.07
25 5 0.08
26 4 0.07
27 24 0.41
28 2 0.03
29 12 0.20
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (25 bp):
ATATATATTATAAAATGTTTTAAAA
Found at i:122908 original size:37 final size:36
Alignment explanation
Indices: 122799--122979 Score: 113
Period size: 37 Copynumber: 5.0 Consensus size: 36
122789 TTTTCAAAAA
**
122799 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATAT
1 ATATATTTT-AAAAACG-TTTTAAAAA-T-TATATTATAT
* * * * * *
122839 AAATGTTTTCATAACGTTTTCAAAA--GTA-TATAT
1 ATATATTTTAAAAACGTTTTAAAAATTATATTATAT
122872 ATATATTTTAAAAACGTTTTCAAAAATTATATTATAT
1 ATATATTTTAAAAACGTTTT-AAAAATTATATTATAT
* ** * *
122909 A-AT-TTTCAAAAATATTTTAAAAACTATATAATAT
1 ATATATTTTAAAAACGTTTTAAAAATTATATTATAT
* * *
122943 ACATATTTTCAAAAATGTTTT-AAACTATATATTATAT
1 ATATATTTT-AAAAACGTTTTAAAAAT-TATATTATAT
122980 GTATTTCAAA
Statistics
Matches: 109, Mismatches: 24, Indels: 19
0.72 0.16 0.12
Matches are distributed among these distances:
33 21 0.19
34 21 0.19
35 14 0.13
36 10 0.09
37 25 0.23
38 8 0.07
39 3 0.03
40 7 0.06
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
ATATATTTTAAAAACGTTTTAAAAATTATATTATAT
Found at i:122914 original size:34 final size:34
Alignment explanation
Indices: 122815--122943 Score: 102
Period size: 34 Copynumber: 3.7 Consensus size: 34
122805 TTTCAAAATG
* * *
122815 GTTTTTAAAAATTATATATTATATAAATGTTTTCATAAC
1 GTTTTCAAAAA-T-TATATTATAT-AA--TTTTAAAAAC
*
122854 GTTTTC-AAAAGTATA-TATATATATTTTAAAAAC
1 GTTTTCAAAAATTATATTATATA-ATTTTAAAAAC
*
122887 GTTTTCAAAAATTATATTATATAATTTTCAAAAAT
1 GTTTTCAAAAATTATATTATATAATTTT-AAAAAC
* * *
122922 ATTTT-AAAAACTATATAATATA
1 GTTTTCAAAAATTATATTATATA
122944 CATATTTTCA
Statistics
Matches: 77, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
33 14 0.18
34 29 0.38
35 21 0.27
36 4 0.05
38 4 0.05
39 5 0.06
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (34 bp):
GTTTTCAAAAATTATATTATATAATTTTAAAAAC
Found at i:122975 original size:71 final size:71
Alignment explanation
Indices: 122868--123014 Score: 165
Period size: 71 Copynumber: 2.1 Consensus size: 71
122858 TCAAAAGTAT
* * *
122868 ATATATATATTTTAAAAACGTTTTCAAAAATTATATTATATA-ATTTTCAAAAATATTTTAAAAA
1 ATATACATATTTTAAAAACGTTTTCAAAAATTATATTATATATA-TTTCAAAAACAATTTAAAAA
122932 CTATATA
65 CTATATA
* * * **
122939 ATATACATATTTTCAAAAATGTTTT--AAACTATATATTATATGTATTTCAAAAACAATTTGCAA
1 ATATACATATTTT-AAAAACGTTTTCAAAAAT-TATATTATATATATTTCAAAAACAATTTAAAA
*
123002 ACTGTATA
64 ACTATATA
123010 ATATA
1 ATATA
123015 TATGTGTATA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
70 4 0.06
71 49 0.77
72 11 0.17
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (71 bp):
ATATACATATTTTAAAAACGTTTTCAAAAATTATATTATATATATTTCAAAAACAATTTAAAAAC
TATATA
Found at i:127282 original size:2 final size:2
Alignment explanation
Indices: 127275--127316 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
127265 TTTATGCACA
* *
127275 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AA AT AT -T 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
127316 A
1 A
127317 GGTTCAGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:128091 original size:8 final size:8
Alignment explanation
Indices: 128078--128116 Score: 78
Period size: 8 Copynumber: 4.9 Consensus size: 8
128068 GCATAGGCCA
128078 TAATTCAC
1 TAATTCAC
128086 TAATTCAC
1 TAATTCAC
128094 TAATTCAC
1 TAATTCAC
128102 TAATTCAC
1 TAATTCAC
128110 TAATTCA
1 TAATTCA
128117 ATCATAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (8 bp):
TAATTCAC
Done.