Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000880.1 Hibiscus syriacus cultivar Beakdansim tig00001713_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: 1459553
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1319190 original size:24 final size:25
Alignment explanation
Indices: 1319120--1319195 Score: 68
Period size: 28 Copynumber: 2.9 Consensus size: 25
1319110 AATAATATCG
1319120 TAATAGTTATGTTTAAAATTAATTACT
1 TAAT-GTTAT-TTTAAAATTAATTACT
1319147 TAAAT-TTGAATTAATT-AAATTAATTA-T
1 T-AATGTT--ATT--TTAAAATTAATTACT
1319174 TAATGTTATTTTAAAATTAATT
1 TAATGTTATTTTAAAATTAATT
1319196 TAATTTAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 17
0.71 0.00 0.29
Matches are distributed among these distances:
23 2 0.05
24 9 0.21
25 3 0.07
26 5 0.12
27 6 0.14
28 15 0.36
29 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.50
Consensus pattern (25 bp):
TAATGTTATTTTAAAATTAATTACT
Found at i:1319204 original size:16 final size:16
Alignment explanation
Indices: 1319172--1319214 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1319162 TAAATTAATT
*
1319172 ATTAATGTTATTTTAAA
1 ATTAAT-TTAATTTAAA
1319189 ATTAATTTAATTTAAA
1 ATTAATTTAATTTAAA
* *
1319205 TTTAAATTAA
1 ATTAATTTAA
1319215 ATTTTTCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTAATTTAATTTAAA
Found at i:1319823 original size:19 final size:20
Alignment explanation
Indices: 1319779--1319823 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1319769 ATTTGTTTTT
*
1319779 AATAAATTTTTATATATGAA
1 AATAAATTTTTATATATCAA
* *
1319799 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATATATCAA
1319818 AATAAA
1 AATAAA
1319824 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATATATCAA
Found at i:1326788 original size:16 final size:16
Alignment explanation
Indices: 1326767--1326798 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1326757 TCGCCGACAA
*
1326767 AATTTTATTATTCACG
1 AATTTTACTATTCACG
1326783 AATTTTACTATTCACG
1 AATTTTACTATTCACG
1326799 TAAATAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (16 bp):
AATTTTACTATTCACG
Found at i:1335402 original size:47 final size:45
Alignment explanation
Indices: 1335335--1335444 Score: 150
Period size: 47 Copynumber: 2.4 Consensus size: 45
1335325 TATAAAATCT
*
1335335 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
* *
1335380 CTTACCATTTAAATCCCATAAGCTCATAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
* *
1335427 CTTGCCA-TTATTCCATAA
1 CTTACCATTTATCCCATAA
1335445 CCATATACCA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
44 8 0.14
45 10 0.17
46 2 0.03
47 38 0.66
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
Found at i:1335466 original size:20 final size:20
Alignment explanation
Indices: 1335441--1335483 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1335431 CCATTATTCC
* *
1335441 ATAACCATATACCATAGAAA
1 ATAACCATAAACAATAGAAA
*
1335461 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGAAA
1335481 ATA
1 ATA
1335484 GCCCAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.58, C:0.19, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGAAA
Found at i:1342154 original size:21 final size:20
Alignment explanation
Indices: 1342118--1342159 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
1342108 AGTTAATTTT
*
1342118 TTATAAAATAGTAAATGATA
1 TTATAAAATAGTAAATCATA
1342138 TTATAAAAATA-TCAAATCATA
1 TTAT-AAAATAGT-AAATCATA
1342159 T
1 T
1342160 AAATTATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
TTATAAAATAGTAAATCATA
Found at i:1342810 original size:47 final size:47
Alignment explanation
Indices: 1342753--1342843 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
1342743 CTTATCATTT
* *
1342753 ATCCTATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAA
1 ATCCCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTTAA
* * *
1342800 ATCCCATAAGCTCATAAGCTTATTTTATCAATATACTTGCCATT
1 ATCCCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATT
1342844 ATTCCATAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (47 bp):
ATCCCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTTAA
Found at i:1342877 original size:20 final size:20
Alignment explanation
Indices: 1342849--1342891 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1342839 CCATTATTCC
* *
1342849 ATAACCATATACCATAGAAA
1 ATAACCATAAACAATAGAAA
* *
1342869 ATAATCATAAACAATAGACA
1 ATAACCATAAACAATAGAAA
1342889 ATA
1 ATA
1342892 GCCCAATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.58, C:0.16, G:0.05, T:0.21
Consensus pattern (20 bp):
ATAACCATAAACAATAGAAA
Found at i:1347832 original size:15 final size:15
Alignment explanation
Indices: 1347808--1347851 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
1347798 TTATCTTTTT
*
1347808 CTTTATCCCTTTCAA
1 CTTTACCCCTTTCAA
1347823 CTTTACCCCTTTCAA
1 CTTTACCCCTTTCAA
1347838 CTTTACCCCTTTCA
1 CTTTACCCCTTTCA
1347852 GCATTATCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.18, C:0.39, G:0.00, T:0.43
Consensus pattern (15 bp):
CTTTACCCCTTTCAA
Found at i:1347880 original size:15 final size:15
Alignment explanation
Indices: 1347862--1347912 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
1347852 GCATTATCTA
*
1347862 TTTCTACACCACCAC
1 TTTCAACACCACCAC
* *
1347877 TTTCAACAACATCAC
1 TTTCAACACCACCAC
* *
1347892 TTTCAACACTACCAT
1 TTTCAACACCACCAC
1347907 TTTCAA
1 TTTCAA
1347913 TAATACCCTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.31
Consensus pattern (15 bp):
TTTCAACACCACCAC
Found at i:1348983 original size:38 final size:38
Alignment explanation
Indices: 1348932--1349007 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
1348922 ATCAATAACA
* * *
1348932 TATTGAAGACAACATACATTAGTGACCATACGTAAAGT
1 TATTGAAGACAACATACATCAATGACCATACCTAAAGT
*
1348970 TATTGAAGACAACATACATCAATGACTATACCTAAAGT
1 TATTGAAGACAACATACATCAATGACCATACCTAAAGT
1349008 ATACATAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (38 bp):
TATTGAAGACAACATACATCAATGACCATACCTAAAGT
Found at i:1350326 original size:18 final size:19
Alignment explanation
Indices: 1350305--1350347 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1350295 GTTTTATTGA
*
1350305 TATTTAATATTTTTTA-TT
1 TATTTAATATTTTTAATTT
**
1350323 TATTTTTTATTTTTAATTT
1 TATTTAATATTTTTAATTT
1350342 TATTTA
1 TATTTA
1350348 TTCTATATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTAATATTTTTAATTT
Found at i:1350328 original size:11 final size:11
Alignment explanation
Indices: 1350312--1350349 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1350302 TGATATTTAA
1350312 TATTTTTTATT
1 TATTTTTTATT
1350323 TATTTTTTATT
1 TATTTTTTATT
1350334 T-TTAATTTTATT
1 TATT--TTTTATT
1350346 TATT
1 TATT
1350350 CTATATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.08
11 12 0.50
12 8 0.33
13 2 0.08
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TATTTTTTATT
Found at i:1350362 original size:27 final size:27
Alignment explanation
Indices: 1350307--1350364 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1350297 TTTATTGATA
* *
1350307 TTTAATATTTTTTATTTATTTTTTATT
1 TTTAATATTTTTTATTTATATATTATT
*
1350334 TTTAAT-TTTATTTATTCTATATATTTTT
1 TTTAATATTT-TTTATT-TATATATTATT
1350362 TTT
1 TTT
1350365 GTTGTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 3 0.12
27 12 0.46
28 11 0.42
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTAATATTTTTTATTTATATATTATT
Found at i:1350396 original size:33 final size:34
Alignment explanation
Indices: 1350313--1350396 Score: 84
Period size: 33 Copynumber: 2.5 Consensus size: 34
1350303 GATATTTAAT
* * * *
1350313 ATTTT-TTATTTATTTTTTATTTTTAATTTTATTT
1 ATTTTATTA-TTATTTTTTAGTTGTAATTTTAGTA
*
1350347 ATTCTATATATT-TTTTTT-GTTGTAATTTTAGTA
1 ATTTTAT-TATTATTTTTTAGTTGTAATTTTAGTA
1350380 ATTTTATTATTATTTTT
1 ATTTTATTATTATTTTT
1350397 AATAAAGTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
32 4 0.10
33 22 0.54
34 10 0.24
35 3 0.07
36 2 0.05
ACGTcount: A:0.23, C:0.01, G:0.04, T:0.73
Consensus pattern (34 bp):
ATTTTATTATTATTTTTTAGTTGTAATTTTAGTA
Found at i:1355864 original size:22 final size:22
Alignment explanation
Indices: 1355799--1355878 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 22
1355789 AGAACCCCAT
*
1355799 GGGGGTATCGGTTCCCC-T--A
1 GGGGGAATCGGTTCCCCTTCAA
* *
1355818 GGGGGAAGCGGTTCCCATTCAAA
1 GGGGGAATCGGTTCCCCTTC-AA
1355841 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGGTTCCCCTTCAA
* *
1355863 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
1355879 TCTGCCCTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.28
20 1 0.02
22 16 0.32
23 19 0.38
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCTTCAA
Found at i:1361603 original size:24 final size:24
Alignment explanation
Indices: 1361593--1361707 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
1361583 CATAATTCAC
* * *
1361593 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
1361617 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
1361641 GTCAAGTATCAGATCATAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
1361665 GTC-AGATATCAGATCAGAATTCAT
1 GTCAAG-TATCAGATCAGAATCCAT
1361689 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
1361708 ATCAAATCGA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.02
24 78 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:1361724 original size:48 final size:47
Alignment explanation
Indices: 1361573--1361724 Score: 153
Period size: 48 Copynumber: 3.2 Consensus size: 47
1361563 GGATATATCA
* * * * *
1361573 AAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGTC
1 AAAATCAGATCAGAATTCAAGTCAAGTATCAGATCAAAATCCAAGTC
* * * *
1361620 AAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCATAATCCATGTC
1 AA-AATCAGATCAGAATTCAAGTCAAGTATCAGATCAAAATCCAAGTC
* * *
1361668 AGATATCAGATCAGAATTCATGTCAAGTATCAGATCAGAAAT-CAAATC
1 A-AAATCAGATCAGAATTCAAGTCAAGTATCAGATCA-AAATCCAAGTC
1361716 GAAAATCAG
1 -AAAATCAG
1361725 GTAAAATATT
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
47 2 0.02
48 80 0.92
49 5 0.06
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (47 bp):
AAAATCAGATCAGAATTCAAGTCAAGTATCAGATCAAAATCCAAGTC
Found at i:1361724 original size:72 final size:71
Alignment explanation
Indices: 1361573--1361724 Score: 173
Period size: 72 Copynumber: 2.1 Consensus size: 71
1361563 GGATATATCA
* * *
1361573 AAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATC
1 AAAATCAGATCATAATCCACGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATC
*
1361638 CAAGTC
66 CAAATC
* * * * *
1361644 AAGTATCAGATCATAATCCATGTC-AGATATCAGATCAGAATTCATGTCAAGTATCAGATCAGAA
1 AA-AATCAGATCATAATCCACGTCAAG-TATCAGATCAAAATCCAGGTCAAGTATCAGATCAG-A
1361708 AT-CAAATC
63 ATCCAAATC
1361716 GAAAATCAG
1 -AAAATCAG
1361725 GTAAAATATT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
71 4 0.06
72 58 0.87
73 5 0.07
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (71 bp):
AAAATCAGATCATAATCCACGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATC
CAAATC
Found at i:1368343 original size:15 final size:15
Alignment explanation
Indices: 1368325--1368356 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1368315 TTTTCATTTG
1368325 TTTCTTTTCTTCATC
1 TTTCTTTTCTTCATC
*
1368340 TTTCTTTTCTTGATC
1 TTTCTTTTCTTCATC
1368355 TT
1 TT
1368357 CTTCTTCCTT
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:0.06, C:0.22, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTCTTTTCTTCATC
Found at i:1369890 original size:21 final size:24
Alignment explanation
Indices: 1369859--1369918 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 24
1369849 AGCCAAAAGG
*
1369859 AGTATTATCGGTACCA-TA-ACTA
1 AGTAGTATCGGTACCACTACACTA
*
1369881 AG-AGTATCGGTACTACTACACTA
1 AGTAGTATCGGTACCACTACACTA
*
1369904 AGTAGTATCGATACC
1 AGTAGTATCGGTACC
1369919 GTATATGGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 11 0.35
22 4 0.13
23 6 0.19
24 10 0.32
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (24 bp):
AGTAGTATCGGTACCACTACACTA
Found at i:1370009 original size:20 final size:21
Alignment explanation
Indices: 1369977--1370024 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
1369967 ACTGCCTCGA
*
1369977 CAGTATC-AGCACTGCATAAG
1 CAGTATCGAGCACTACATAAG
*
1369997 CAGTATCGA-CACTACCTAAG
1 CAGTATCGAGCACTACATAAG
*
1370017 CAATATCG
1 CAGTATCG
1370025 GTACTTCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (21 bp):
CAGTATCGAGCACTACATAAG
Found at i:1374236 original size:17 final size:18
Alignment explanation
Indices: 1374218--1374250 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1374208 TAATTAAATA
1374218 AAATA-TTAAA-AAATTT
1 AAATACTTAAATAAATTT
1374234 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
1374251 ACAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATACTTAAATAAATTT
Found at i:1375717 original size:25 final size:24
Alignment explanation
Indices: 1375683--1375729 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1375673 ATACTTTTAA
* *
1375683 TAAATTAAAATAAATTATATATTAT
1 TAAATGAAAATAAA-AATATATTAT
1375708 TAAATGAAAATAAAAATATATT
1 TAAATGAAAATAAAAATATATT
1375730 CAATTAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAATGAAAATAAAAATATATTAT
Found at i:1376673 original size:31 final size:31
Alignment explanation
Indices: 1376626--1376697 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
1376616 GTTAACTTAG
* *
1376626 GTGACCACATCCTAATTAAATAAAAACGAAA
1 GTGACCATATCCTAATTAAATAAAAACAAAA
* *
1376657 GTGACCATATCTTAATTAAATAAAAATAAAA
1 GTGACCATATCCTAATTAAATAAAAACAAAA
1376688 GTGACCATAT
1 GTGACCATAT
1376698 ATTATGCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (31 bp):
GTGACCATATCCTAATTAAATAAAAACAAAA
Found at i:1385004 original size:21 final size:21
Alignment explanation
Indices: 1384980--1385023 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1384970 GTCACTGTTG
*
1384980 ACCACCGTCGCGCCACCAATC
1 ACCACCGTCGCACCACCAATC
* * *
1385001 ACCATCGTCTCACCGCCAATC
1 ACCACCGTCGCACCACCAATC
1385022 AC
1 AC
1385024 TCTTCAAGGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.50, G:0.11, T:0.14
Consensus pattern (21 bp):
ACCACCGTCGCACCACCAATC
Found at i:1387202 original size:43 final size:43
Alignment explanation
Indices: 1387096--1387217 Score: 136
Period size: 43 Copynumber: 2.8 Consensus size: 43
1387086 GATTTCTTAC
*
1387096 ATTTCGCAGCGTTTGTCTCTAAAACGCCGCTAAAGAACCTGAA
1 ATTTCGCAGCGTTTGTGTCTAAAACGCCGCTAAAGAACCTGAA
* * * * * * *
1387139 ATTTCACGGTGTTAGCGTCTAAAATGCCGCTAAAGAACTTGAA
1 ATTTCGCAGCGTTTGTGTCTAAAACGCCGCTAAAGAACCTGAA
* * **
1387182 CTTTCGCAGCATTTGTGTCTAAAACATCGCTAAAGA
1 ATTTCGCAGCGTTTGTGTCTAAAACGCCGCTAAAGA
1387218 GCAAGACTTT
Statistics
Matches: 61, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (43 bp):
ATTTCGCAGCGTTTGTGTCTAAAACGCCGCTAAAGAACCTGAA
Found at i:1389371 original size:256 final size:255
Alignment explanation
Indices: 1388808--1389392 Score: 768
Period size: 256 Copynumber: 2.2 Consensus size: 255
1388798 ATTTTTATTC
* *
1388808 AATATATGAATTAGAAACCCGACCCGACATGACACAAAATAATAAAAAATTATTTTTATTCAATA
1 AATATATGAATTAGAAACCCGACCCGACCTG-----AAATAATAAAAAAATATTTTTATTCAATA
* *
1388873 AAAACATTGACTTAATTGAAAAAAATTATATATAGGGGTATTATTGTAATTATTCCTAAATATAT
61 AAAACAGTGACTTAATTGAAAAAAATTATATAGAGGGGTATTATTGTAATTATTCCTAAATATAT
* * * *
1388938 AAGGTAAAATTATATATTTTTTTGGGTCGGTCCCGTTTTTTTCATCCTAAACTTGAACCCGACCA
126 AAGGTAAAATTATATATATTTTCGGGTCGG---CGTATTTTTCATCC---ACTTAAACCCG---A
* * *
1389003 GACTCGACCCAAATATCACACTTAAAAAACCCGACCTGACCCGAACAAAATAAAGTTTCACCCGA
182 GACCCGACCCAAATATCACACTTAAAAAACCCAACCCGACCCGAACAAAATAAAGTTTCACCCGA
*
1389068 CCCAACCTG
247 CCCAACCCG
* *
1389077 AATATATGAATTAGAAATCCAACCCGACCTGAAATAATAAAAAAATATTTTTATTCAATAAAAAC
1 AATATATGAATTAGAAACCCGACCCGACCTGAAATAATAAAAAAATATTTTTATTCAATAAAAAC
1389142 AGTGACTTAATTGAAAAACAATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAG
66 AGTGACTTAATTGAAAAA-AAT-TATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAG
**
1389207 GTAAAATTATATATATTTTCGGGTCGG-GTATTTTTCA-CC-C-TAAACCCG-G-CCCGACCTGA
129 GTAAAATTATATATATTTTCGGGTCGGCGTATTTTTCATCCACTTAAACCCGAGACCCGACCCAA
* *
1389266 ATATCACACTTAAAAAAACCAACCCAACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACC
194 ATATCACACTT---AAAA--AACCCAACCCGACCCGAACAAAATAAAGTTTCACCCGACCCAACC
1389331 CG
254 CG
*
1389333 AATATATGAATTAGAAACCCGATCCGACCTGAAATAATAAAAAAATATTTTTATTCAATA
1 AATATATGAATTAGAAACCCGACCCGACCTGAAATAATAAAAAAATATTTTTATTCAATA
1389393 TATGAATAAG
Statistics
Matches: 288, Mismatches: 21, Indels: 27
0.86 0.06 0.08
Matches are distributed among these distances:
251 18 0.06
252 1 0.00
254 4 0.01
256 106 0.37
257 1 0.00
261 2 0.01
262 9 0.03
264 50 0.17
265 3 0.01
266 66 0.23
269 28 0.10
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.28
Consensus pattern (255 bp):
AATATATGAATTAGAAACCCGACCCGACCTGAAATAATAAAAAAATATTTTTATTCAATAAAAAC
AGTGACTTAATTGAAAAAAATTATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGT
AAAATTATATATATTTTCGGGTCGGCGTATTTTTCATCCACTTAAACCCGAGACCCGACCCAAAT
ATCACACTTAAAAAACCCAACCCGACCCGAACAAAATAAAGTTTCACCCGACCCAACCCG
Found at i:1392138 original size:22 final size:22
Alignment explanation
Indices: 1392090--1392138 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1392080 TGACCACTAT
*
1392090 ATCCCGAAGGACCACTGGACAC
1 ATCCCGAAGGACCACTGAACAC
* *
1392112 GTCCCGAAGGACCACTGAATAC
1 ATCCCGAAGGACCACTGAACAC
1392134 ATCCC
1 ATCCC
1392139 AAAAGACCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.37, G:0.20, T:0.12
Consensus pattern (22 bp):
ATCCCGAAGGACCACTGAACAC
Found at i:1392773 original size:63 final size:64
Alignment explanation
Indices: 1392699--1392856 Score: 180
Period size: 63 Copynumber: 2.5 Consensus size: 64
1392689 ATTCCTTAAC
* *
1392699 GGGTGCATCGATGCACT-ACTTATGCATCGGTGCA-TGAATCATATTCGATGTTTGTATTTAAT-
1 GGGTGCATCGATGCACTCA-TTATGCATCGATGCACT-AATCACATTCGATGTTTGTATTTAATC
*
1392761 G
64 A
* * * *
1392762 GGGTGCATCGATGCACTCATTATGCATCGATGCACTAATGACATTCGATGTTTTTGTTTTATCA
1 GGGTGCATCGATGCACTCATTATGCATCGATGCACTAATCACATTCGATGTTTGTATTTAATCA
* *
1392826 GAGTGCATCGATGCACTTCA-TGTGCATCGAT
1 GGGTGCATCGATGCAC-TCATTATGCATCGAT
1392857 ACACCTTGAA
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 52 0.63
64 27 0.33
65 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (64 bp):
GGGTGCATCGATGCACTCATTATGCATCGATGCACTAATCACATTCGATGTTTGTATTTAATCA
Found at i:1397724 original size:17 final size:18
Alignment explanation
Indices: 1397696--1397729 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1397686 ATGGGAGACA
1397696 AAATATTCAAATCTAATT
1 AAATATTCAAATCTAATT
*
1397714 AAATA-TCAAATTTAAT
1 AAATATTCAAATCTAAT
1397730 GAAAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTCAAATCTAATT
Found at i:1399160 original size:17 final size:18
Alignment explanation
Indices: 1399134--1399173 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1399124 ACGCTTACAG
1399134 AAAAAAGAAAT-AA-GAA
1 AAAAAAGAAATGAATGAA
1399150 AAAAGAAGAAATGAATGAA
1 AAAA-AAGAAATGAATGAA
1399169 AAAAA
1 AAAAA
1399174 GATAAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.19
17 7 0.33
18 3 0.14
19 7 0.33
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (18 bp):
AAAAAAGAAATGAATGAA
Found at i:1400003 original size:114 final size:114
Alignment explanation
Indices: 1399633--1400038 Score: 360
Period size: 116 Copynumber: 3.5 Consensus size: 114
1399623 AGAAGATGAA
* * * * * ** * ** *
1399633 TCAACATTTCTAATGG-AGGGGTTCATAATAAGAAGAACTCATTCAATAAGGGATAAGAAATTCA
1 TCAACATTTATAATGGCA-GGGTTCATAATGAGAAGAACTCATCCGATGAGATAGAAGAAGGTCC
* *
1399697 TAATGAGAAGAACTTGTTCAACCTAGATTCATCCTTCATATAAAGAGTTGGA
65 TAAT-AGAAGAACTTGTTCAACCTAGGTTCATCCTTCA-ATAAAGAGTTGGG
* * * * *
1399749 TCAACATTTATAATGG-AGGGGTTCATAATGAGAAGAACTCGTCTGATGAGAGAGAACAAGGTCG
1 TCAACATTTATAATGGCA-GGGTTCATAATGAGAAGAACTCATCCGATGAGATAGAAGAAGGTCC
* * ** *
1399813 TAATAAGAAGAACTTATTCAACCCTA-GCTC-GGCTATCAA-AGAAGATGGTGGG
65 TAAT-AGAAGAACTTGTTCAA-CCTAGGTTCATCCT-TCAATA-AAGA-GTTGGG
* * * *
1399865 CCGAACATTT-TCATTGACAGGGTTCATAATGAGAAGAACTCATCCGATGAGATAGAAGAAGTTC
1 TC-AACATTTAT-AATGGCAGGGTTCATAATGAGAAGAACTCATCCGATGAGATAGAAGAAGGTC
*
1399929 CTAGT-G-AGAACTTGTTCAACCTAGGTTCATCCTTCACATAAAGGAGTTGGG
64 CTAATAGAAGAACTTGTTCAACCTAGGTTCATCCTTCA-ATAAA-GAGTTGGG
* * *
1399980 TCAACATTTATGATGGCAGGGTTCATAATGAGAAGAACTAATCCGATGAAATAGAAGAA
1 TCAACATTTATAATGGCAGGGTTCATAATGAGAAGAACTCATCCGATGAGATAGAAGAA
1400039 ATTCATAATA
Statistics
Matches: 235, Mismatches: 42, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
113 4 0.02
114 69 0.29
115 20 0.09
116 84 0.36
117 57 0.24
118 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (114 bp):
TCAACATTTATAATGGCAGGGTTCATAATGAGAAGAACTCATCCGATGAGATAGAAGAAGGTCCT
AATAGAAGAACTTGTTCAACCTAGGTTCATCCTTCAATAAAGAGTTGGG
Found at i:1400394 original size:2 final size:2
Alignment explanation
Indices: 1400387--1400421 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1400377 TTTAGTTTTA
1400387 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1400422 GAAAACCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1400532 original size:38 final size:37
Alignment explanation
Indices: 1400444--1400741 Score: 199
Period size: 38 Copynumber: 8.2 Consensus size: 37
1400434 AAATTGTTCT
* *
1400444 AAAAATATTATATATTATATAGTTTTGAAAAC-CTTCT-
1 AAAAATA-T-TATATTATATAGTTTTGAAAACTATTTTG
1400481 -AAAATA--ATA-TATATAGTTTTGAAAAACTATTTTG
1 AAAAATATTATATTATATAGTTTTG-AAAACTATTTTG
*
1400515 AAAAATATTATATTATATAGTTTTGAAAAC-CTTTTG
1 AAAAATATTATATTATATAGTTTTGAAAACTATTTTG
1400551 -AAAATA--ATA-TATATAGTTTTGGAAAACTATTTTG
1 AAAAATATTATATTATATAGTTTT-GAAAACTATTTTG
*
1400585 AAAACTTTTTGAATATATATATATATAGTTTTCGAAAACTATTTTG
1 AAAA----AT--AT-TATAT-TATATAGTTTT-GAAAACTATTTTG
* *
1400631 ---AA-A--ATATTATGTAG-TTTG-AAA-TTTTTTG
1 AAAAATATTATATTATATAGTTTTGAAAACTATTTTG
* *
1400659 AAAATAT-TAAAATATATATAGTTTTAGAAAACTATTTTG
1 AAAA-ATATTATAT-TATATAGTTTT-GAAAACTATTTTG
*
1400698 AAAAATATTATATTATATAAGTTTTGAAAAC-ATTATG
1 AAAAATATTATATTATAT-AGTTTTGAAAACTATTTTG
*
1400735 GAAAATA
1 AAAAATA
1400742 ATATGTAATT
Statistics
Matches: 210, Mismatches: 16, Indels: 70
0.71 0.05 0.24
Matches are distributed among these distances:
28 6 0.03
29 3 0.01
30 1 0.00
31 16 0.08
32 26 0.12
33 16 0.08
34 8 0.04
35 21 0.10
36 15 0.07
37 20 0.10
38 28 0.13
39 21 0.10
41 1 0.00
43 1 0.00
44 3 0.01
46 24 0.11
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (37 bp):
AAAAATATTATATTATATAGTTTTGAAAACTATTTTG
Found at i:1400537 original size:69 final size:72
Alignment explanation
Indices: 1400444--1400588 Score: 251
Period size: 70 Copynumber: 2.1 Consensus size: 72
1400434 AAATTGTTCT
1400444 AAAAATATTATATATTATATAGTTTTGAAAACCTTCT-AAAATAATATATATAGTTTTGAAAAAC
1 AAAAATATTATATATTATATAGTTTTGAAAACCTTCTGAAAATAATATATATAGTTTTGAAAAAC
1400508 TATTTTG
66 TATTTTG
* *
1400515 AAAAATA-T-TATATTATATAGTTTTGAAAACCTTTTGAAAATAATATATATAGTTTTGGAAAAC
1 AAAAATATTATATATTATATAGTTTTGAAAACCTTCTGAAAATAATATATATAGTTTTGAAAAAC
1400578 TATTTTG
66 TATTTTG
1400585 AAAA
1 AAAA
1400589 CTTTTTGAAT
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
69 26 0.37
70 38 0.54
71 7 0.10
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (72 bp):
AAAAATATTATATATTATATAGTTTTGAAAACCTTCTGAAAATAATATATATAGTTTTGAAAAAC
TATTTTG
Found at i:1400588 original size:45 final size:46
Alignment explanation
Indices: 1400535--1400634 Score: 166
Period size: 46 Copynumber: 2.2 Consensus size: 46
1400525 TATTATATAG
*
1400535 TTTTGAAAACCTTTTGAAAATA-ATATATATAGTTTTGGAAAACTA
1 TTTTGAAAACCTTTTGAAAATATATATATATAGTTTTCGAAAACTA
* *
1400580 TTTTGAAAACTTTTTGAATATATATATATATAGTTTTCGAAAACTA
1 TTTTGAAAACCTTTTGAAAATATATATATATAGTTTTCGAAAACTA
1400626 TTTTGAAAA
1 TTTTGAAAA
1400635 TATTATGTAG
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 20 0.39
46 31 0.61
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (46 bp):
TTTTGAAAACCTTTTGAAAATATATATATATAGTTTTCGAAAACTA
Found at i:1400745 original size:40 final size:40
Alignment explanation
Indices: 1400659--1400739 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
1400649 AAATTTTTTG
*
1400659 AAAATATTAAAATATATATAGTTTTAGAAAACTATTTTGA
1 AAAATATTAAAATATATATAGTTTTAGAAAACTATTTGGA
* *
1400699 AAAATATTATATTATATA-AGTTTT-GAAAAC-ATTATGGA
1 AAAATATTAAAATATATATAGTTTTAGAAAACTATT-TGGA
1400737 AAA
1 AAA
1400740 TAATATGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 3 0.08
38 12 0.32
39 6 0.16
40 16 0.43
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (40 bp):
AAAATATTAAAATATATATAGTTTTAGAAAACTATTTGGA
Found at i:1403770 original size:37 final size:35
Alignment explanation
Indices: 1403718--1403941 Score: 197
Period size: 37 Copynumber: 6.1 Consensus size: 35
1403708 TATAATGTAA
1403718 TTTT-GAAAATATTTTTGAAAACATATCATATATAG
1 TTTTAGAAAATATTTTTGAAAACATAT-ATATATAG
* *
1403753 TCTTTAGAAAATGTTTTTGAAAGCATATAATATATAG
1 T-TTTAGAAAATATTTTTGAAAACATAT-ATATATAG
* **
1403790 TTTTTA-AAAATCATTTTTTGAAAATATATA-ATACGG
1 -TTTTAGAAAAT-A-TTTTTGAAAACATATATATATAG
*
1403826 TTTT-GAAAATACGTTGTTGAAAACATATATTATATAG
1 TTTTAGAAAATA--TTTTTGAAAACATATA-TATATAG
* * *
1403863 TTTTAAAAACACATTTTTGAAAACGTATAATATACATAG
1 TTTTAGAAA-ATATTTTTGAAAAC--AT-ATATATATAG
1403902 TTTTA-AAAAGTATTTTTGAAAACATATATAATATAG
1 TTTTAGAAAA-TATTTTTGAAAACATATAT-ATATAG
1403938 TTTT
1 TTTT
1403942 TTAAAACGCT
Statistics
Matches: 154, Mismatches: 19, Indels: 31
0.75 0.09 0.15
Matches are distributed among these distances:
34 1 0.01
35 28 0.18
36 23 0.15
37 52 0.34
38 32 0.21
39 15 0.10
40 3 0.02
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (35 bp):
TTTTAGAAAATATTTTTGAAAACATATATATATAG
Found at i:1403819 original size:38 final size:37
Alignment explanation
Indices: 1403718--1403982 Score: 192
Period size: 37 Copynumber: 7.1 Consensus size: 37
1403708 TATAATGTAA
* *
1403718 TTTTGAAAATA-TTTTTGAAAACATATCATATATAGT
1 TTTTAAAAATAGTTTTTGAAAACATATAATATATAGT
* *
1403754 CTTTAGAAAAT-GTTTTTGAAAGCATATAATATATAGT
1 TTTTA-AAAATAGTTTTTGAAAACATATAATATATAGT
* *
1403791 TTTTAAAAATCATTTTTTG-AAA-ATAT-ATA-ATACGG
1 TTTTAAAAAT-AGTTTTTGAAAACATATAATATATA-GT
* * *
1403826 TTTTGAAAATACGTTGTTGAAAACATATATTATATAG-
1 TTTTAAAAATA-GTTTTTGAAAACATATAATATATAGT
* * *
1403863 TTTTAAAAACACATTTTTGAAAACGTATAATATACATAG-
1 TTTTAAAAATA-GTTTTTGAAAACATATAATAT--ATAGT
1403902 TTTTAAAAAGTA-TTTTTGAAAACATAT-ATAATATAGT
1 TTTTAAAAA-TAGTTTTTGAAAACATATAAT-ATATAGT
* * * *
1403939 TTTTTAAAA-CGCTTTTTTGGAAACATATATAATATATAAT
1 TTTTAAAAATAG--TTTTT-GAAA-ACATATAATATATAGT
1403979 TTTT
1 TTTT
1403983 GTAAACATAT
Statistics
Matches: 184, Mismatches: 24, Indels: 38
0.75 0.10 0.15
Matches are distributed among these distances:
34 4 0.02
35 18 0.10
36 19 0.10
37 75 0.41
38 30 0.16
39 20 0.11
40 16 0.09
41 2 0.01
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (37 bp):
TTTTAAAAATAGTTTTTGAAAACATATAATATATAGT
Found at i:1403918 original size:110 final size:110
Alignment explanation
Indices: 1403718--1403934 Score: 268
Period size: 110 Copynumber: 2.0 Consensus size: 110
1403708 TATAATGTAA
* * ** *
1403718 TTTTGAAAATATTTTTGAAAACATATCATATATAGTCTTTAGAAAATGTTTTTGAAAGCATATAA
1 TTTTGAAAATATTGTTGAAAACATATCATATATAGTCTTTAAAAAACATTTTTGAAAACATATAA
1403783 TATATAGTTTTTAAAAATCATTTTTTG-AAA-ATATATAATACGG
66 TATATAGTTTTTAAAAATCATTTTTTGAAAACATATATAATACGG
*
1403826 TTTTGAAAATACGTTGTTGAAAACATAT-ATTATATAGT-TTTAAAAACACATTTTTGAAAACGT
1 TTTTGAAAATA--TTGTTGAAAACATATCA-TATATAGTCTTTAAAAA-ACATTTTTGAAAACAT
1403889 ATAATATACATAG-TTTTAAAAAGT-A-TTTTTGAAAACATATATAATA
62 ATAATAT--ATAGTTTTTAAAAA-TCATTTTTTGAAAACATATATAATA
1403935 TAGTTTTTTA
Statistics
Matches: 94, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
108 11 0.12
109 8 0.09
110 47 0.50
111 13 0.14
112 15 0.16
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (110 bp):
TTTTGAAAATATTGTTGAAAACATATCATATATAGTCTTTAAAAAACATTTTTGAAAACATATAA
TATATAGTTTTTAAAAATCATTTTTTGAAAACATATATAATACGG
Found at i:1403955 original size:75 final size:72
Alignment explanation
Indices: 1403729--1403969 Score: 217
Period size: 75 Copynumber: 3.3 Consensus size: 72
1403719 TTTGAAAATA
* * *
1403729 TTTTTGAAAAC-ATATCATATATAGTCTTTAGAAAATGTTTTTGAAAGCATATA-ATATATAGTT
1 TTTTTGAAAACTATAT-ATACATAGT-TTTA-AAAATATTTTTGAAAACATATATA-ATATAGTT
*
1403792 TTTAAAAATCAT
62 TTTAAAAA-CAC
* * * *
1403804 TTTTTGAAAA-TATATAATAC--GGTTTTGAAAATACGTTGTTGAAAACATATATTATATAG-TT
1 TTTTTGAAAACTATAT-ATACATAGTTTTAAAAATA--TTTTTGAAAACATATATAATATAGTTT
1403865 TTAAAAACAC
63 TTAAAAACAC
1403875 ATTTTTGAAAACGTATAATATACATAGTTTTAAAAAGTATTTTTGAAAACATATATAATATAGTT
1 -TTTTTGAAAAC-TAT-ATATACATAGTTTTAAAAA-TATTTTTGAAAACATATATAATATAGTT
* *
1403940 TTTTAAAACGC
62 TTTAAAAACAC
*
1403951 TTTTTTGGAAAC-ATATATA
1 -TTTTTGAAAACTATATATA
1403970 ATATATAATT
Statistics
Matches: 137, Mismatches: 17, Indels: 26
0.76 0.09 0.14
Matches are distributed among these distances:
71 7 0.05
72 22 0.16
73 27 0.20
74 9 0.07
75 41 0.30
76 29 0.21
77 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (72 bp):
TTTTTGAAAACTATATATACATAGTTTTAAAAATATTTTTGAAAACATATATAATATAGTTTTTA
AAAACAC
Found at i:1403969 original size:40 final size:40
Alignment explanation
Indices: 1403850--1403982 Score: 111
Period size: 38 Copynumber: 3.5 Consensus size: 40
1403840 TGTTGAAAAC
* * * * *
1403850 ATATAT-TATATAGTTTTAAAAACACATTTTTGAAAACGT
1 ATATATATATATAGTTTTTAAAACGCTTTTTTGGAAACAT
* * *
1403889 ATA-ATATACATAG-TTTTAAAAAG-TATTTTT-GAAA-AC
1 ATATATATATATAGTTTTTAAAACGCT-TTTTTGGAAACAT
1403925 ATATATA-ATATAGTTTTTTAAAACGCTTTTTTGGAAACAT
1 ATATATATATATAG-TTTTTAAAACGCTTTTTTGGAAACAT
*
1403965 ATATA-ATATATAATTTTT
1 ATATATATATATAGTTTTT
1403983 GTAAACATAT
Statistics
Matches: 73, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
36 8 0.11
37 6 0.08
38 28 0.38
39 20 0.27
40 11 0.15
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.44
Consensus pattern (40 bp):
ATATATATATATAGTTTTTAAAACGCTTTTTTGGAAACAT
Found at i:1404048 original size:12 final size:12
Alignment explanation
Indices: 1404026--1404076 Score: 79
Period size: 12 Copynumber: 4.3 Consensus size: 12
1404016 ATAGTTTTTA
1404026 TTATA-TATTAT
1 TTATATTATTAT
1404037 TTATATTATTAT
1 TTATATTATTAT
1404049 TTATTATT-TTAT
1 TTA-TATTATTAT
1404061 TTATATTATTAT
1 TTATATTATTAT
1404073 TTAT
1 TTAT
1404077 TTAATTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.24
12 24 0.65
13 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATATTATTAT
Found at i:1404077 original size:24 final size:26
Alignment explanation
Indices: 1404022--1404077 Score: 98
Period size: 24 Copynumber: 2.2 Consensus size: 26
1404012 TTAAATAGTT
1404022 TTTATTATATATTATTTATATTATTA
1 TTTATTATATATTATTTATATTATTA
1404048 TTTATTAT-T-TTATTTATATTATTA
1 TTTATTATATATTATTTATATTATTA
1404072 TTTATT
1 TTTATT
1404078 TAATTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 21 0.70
25 1 0.03
26 8 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTATTATATATTATTTATATTATTA
Found at i:1404091 original size:24 final size:24
Alignment explanation
Indices: 1404022--1404091 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 24
1404012 TTAAATAGTT
1404022 TTTATTATATATTATTTATATTATTA
1 TTTATT-TA-ATTATTTATATTATTA
*
1404048 TTTA-TTATTTTATTTATATTATTA
1 TTTATTTA-ATTATTTATATTATTA
1404072 TTTATTTAATTAATTT-TATT
1 TTTATTTAATT-ATTTATATT
1404092 TTTCTACAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
24 28 0.70
25 8 0.20
26 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTATTTAATTATTTATATTATTA
Found at i:1405323 original size:4 final size:4
Alignment explanation
Indices: 1405314--1405344 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1405304 CCTTTATATT
1405314 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1405345 TCTTTTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1406616 original size:19 final size:18
Alignment explanation
Indices: 1406594--1406630 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1406584 TTTTACTAAC
1406594 TTGTTTCCTTTTCATTTTT
1 TTGTTTCCTTTT-ATTTTT
*
1406613 TTGTTTTCTTTTATTTTT
1 TTGTTTCCTTTTATTTTT
1406631 ATGATACGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.05, C:0.11, G:0.05, T:0.78
Consensus pattern (18 bp):
TTGTTTCCTTTTATTTTT
Found at i:1408791 original size:97 final size:96
Alignment explanation
Indices: 1408603--1408800 Score: 292
Period size: 97 Copynumber: 2.1 Consensus size: 96
1408593 TCACGCGTAT
*
1408603 ATGAGTGAATGAAAGTTGTCACTGGATGACTTTACTTAACTAGCTTGGGGTGGAAGGTATGCTCA
1 ATGAGTGAATGAAAGTTGTCACTGGATGACTCTACTTAACTAGCTTGGGGTGGAAGGTATGCTCA
* * *
1408668 TTTTCACCTAGAGTGTGGGAAAGTAGGTGTG
66 CTTTCACCTAGAGTATGGGAAAGTAGGAGTG
*
1408699 ATGAGTGAATGAAAGTAT-TTA-TGGGATGACTCTACTTAACTAGCTTGGGGGTGGAAGGTATGC
1 ATGAGTGAATGAAAGT-TGTCACT-GGATGACTCTACTTAACTAGCTT-GGGGTGGAAGGTATGC
* *
1408762 TCCCTTTCACGTAGAGTATGGGAAAGTAGGAGTG
63 TCACTTTCACCTAGAGTATGGGAAAGTAGGAGTG
1408796 ATGAG
1 ATGAG
1408801 CTGACTCCTT
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
95 1 0.01
96 40 0.43
97 51 0.55
ACGTcount: A:0.27, C:0.11, G:0.32, T:0.30
Consensus pattern (96 bp):
ATGAGTGAATGAAAGTTGTCACTGGATGACTCTACTTAACTAGCTTGGGGTGGAAGGTATGCTCA
CTTTCACCTAGAGTATGGGAAAGTAGGAGTG
Found at i:1420653 original size:10 final size:9
Alignment explanation
Indices: 1420624--1420653 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1420614 TTATCATTTA
*
1420624 TTTAATGTT
1 TTTACTGTT
1420633 TTTACTGTT
1 TTTACTGTT
1420642 TTTACTGTT
1 TTTACTGTT
1420651 TTT
1 TTT
1420654 CATTGCCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.13, C:0.07, G:0.10, T:0.70
Consensus pattern (9 bp):
TTTACTGTT
Found at i:1429625 original size:37 final size:37
Alignment explanation
Indices: 1429573--1429894 Score: 219
Period size: 38 Copynumber: 8.5 Consensus size: 37
1429563 TATAATAATA
*
1429573 ATATAATATA-A-TTTTTTAAAATATTTTTTGAAAAC
1 ATATAATATATAGTTTTTAAAAATATTTTTTGAAAAC
* * *
1429608 ATATAATATATAGTTTTTAGAAAAAACGTTTTTGAAAGC
1 ATATAATATATAGTTTTTA-AAAATA-TTTTTTGAAAAC
* *
1429647 ATATAATATATAGTTTTTAAAAATCTGTTTTTGAAAAT
1 ATATAATATATAGTTTTTAAAAATAT-TTTTTGAAAAC
* * *
1429685 ATATAAT-T-T-GGTTTTGAAAATAAGTTTTTGAAAAC
1 ATATAATATATAGTTTTTAAAAAT-ATTTTTTGAAAAC
* * * * * *
1429720 ATTTATTATACAGTTTTGAAAACACA-TTTTTGAAAAT
1 ATATAATATATAGTTTTTAAAA-ATATTTTTTGAAAAC
* * *
1429757 GTATAATATACATAG-TTTTAAAAACAATTTTTGAAAAC
1 ATATAATAT--ATAGTTTTTAAAAATATTTTTTGAAAAC
* ** *
1429795 GTAT-ATAATATAGTTTTTAAAACGATTTTTTGGAAAC
1 ATATAAT-ATATAGTTTTTAAAAATATTTTTTGAAAAC
* *
1429832 GTATATAATATATAATTTTTGAAAACATATTATTTTTGAAAAT
1 --ATATAATATATAGTTTTT-AAAA-ATA-T-TTTTTGAAAAC
* *
1429875 ATAATATTTTATAGTTTTTA
1 AT-ATAATATATAGTTTTTA
1429895 TTATTTATTA
Statistics
Matches: 223, Mismatches: 41, Indels: 40
0.73 0.13 0.13
Matches are distributed among these distances:
35 35 0.16
36 7 0.03
37 46 0.21
38 56 0.25
39 46 0.21
40 6 0.03
41 4 0.02
42 14 0.06
43 9 0.04
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.44
Consensus pattern (37 bp):
ATATAATATATAGTTTTTAAAAATATTTTTTGAAAAC
Found at i:1429811 original size:112 final size:111
Alignment explanation
Indices: 1429573--1429894 Score: 276
Period size: 112 Copynumber: 2.8 Consensus size: 111
1429563 TATAATAATA
* * * *
1429573 ATATAATATAATTTTTTAAAATATTTTTTGAAAACATATAATATATAGTTTTTAGAAAAAACGTT
1 ATATAATAT-AGTTTTTAAAATAGTTTTTGAAAACATATAATATACAGTTTTTAGAAAAAACATT
* **
1429638 TTTGAAAGCATATAATATATAGTTTTTAAAAATCTGTTTTTGAAAAT
65 TTTGAAAACATATAATATATAGTTTTTAAAAATCAATTTTTGAAAAT
* * * * * *
1429685 ATATAATTTGGTTTTGAAAATAAGTTTTTGAAAACATTTATTATACAG-TTTT-GAAAACACATT
1 ATATAATATAGTTTTTAAAAT-AGTTTTTGAAAACATATAATATACAGTTTTTAGAAAAAACATT
**
1429748 TTTGAAAATGTATAATATACATAG-TTTTAAAAA-CAATTTTTGAAAACGT
65 TTTGAAAACATATAATAT--ATAGTTTTTAAAAATCAATTTTTGAAAA--T
* * * * *
1429797 ATATAATATAGTTTTTAAAACGATTTTTTGGAAACGTATATAATATATAATTTTT-GAAAACATA
1 ATATAATATAGTTTTTAAAA-TAGTTTTTGAAAAC--ATATAATATACAGTTTTTAGAAAA-A-A
* * * *
1429861 TTATTTTTGAAAATATAATATTTTATAGTTTTTA
61 -CATTTTTGAAAACAT-ATAATATATAGTTTTTA
1429895 TTATTTATTA
Statistics
Matches: 166, Mismatches: 30, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
110 35 0.21
111 22 0.13
112 63 0.38
114 9 0.05
115 9 0.05
117 5 0.03
118 18 0.11
119 5 0.03
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.44
Consensus pattern (111 bp):
ATATAATATAGTTTTTAAAATAGTTTTTGAAAACATATAATATACAGTTTTTAGAAAAAACATTT
TTGAAAACATATAATATATAGTTTTTAAAAATCAATTTTTGAAAAT
Found at i:1429866 original size:17 final size:17
Alignment explanation
Indices: 1429841--1429884 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
1429831 CGTATATAAT
*
1429841 ATATAATTTTTGAAAAC
1 ATATTATTTTTGAAAAC
*
1429858 ATATTATTTTTGAAAAT
1 ATATTATTTTTGAAAAC
*
1429875 ATAATATTTT
1 ATATTATTTT
1429885 ATAGTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (17 bp):
ATATTATTTTTGAAAAC
Found at i:1429899 original size:17 final size:18
Alignment explanation
Indices: 1429879--1429935 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 18
1429869 GAAAATATAA
1429879 TATTTTA-TAGTT-TTTAT
1 TATTTTATTA-TTATTTAT
1429896 TA-TTTATTATTATTTAT
1 TATTTTATTATTATTTAT
1429913 TATTTTTATT-TATATTT-T
1 TA-TTTTATTAT-TATTTAT
1429931 TATTT
1 TATTT
1429936 AATTTCATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
16 6 0.17
17 14 0.40
18 4 0.11
19 11 0.31
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
TATTTTATTATTATTTAT
Found at i:1429905 original size:10 final size:10
Alignment explanation
Indices: 1429892--1429934 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
1429882 TTTATAGTTT
1429892 TTATTATTTA
1 TTATTATTTA
1429902 TTATTATTTA
1 TTATTATTTA
1429912 TTATT-TTTA
1 TTATTATTTA
1429921 TT-TATATTT-
1 TTAT-TATTTA
1429930 TTATT
1 TTATT
1429935 TAATTTCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.03
9 10 0.33
10 19 0.63
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTATTATTTA
Found at i:1429915 original size:13 final size:13
Alignment explanation
Indices: 1429889--1429936 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
1429879 TATTTTATAG
1429889 TTTTTA-TTATTTA
1 TTTTTATTTA-TTA
*
1429902 TTATTATTTATTA
1 TTTTTATTTATTA
1429915 TTTTTATTTA-TA
1 TTTTTATTTATTA
1429927 TTTTTATTTA
1 TTTTTATTTA
1429937 ATTTCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
12 12 0.38
13 17 0.53
14 3 0.09
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTATTTATTA
Found at i:1439887 original size:129 final size:129
Alignment explanation
Indices: 1439556--1439853 Score: 506
Period size: 129 Copynumber: 2.3 Consensus size: 129
1439546 TAAGATTAGA
* *
1439556 GGCGTAGTATTAGTACTTATGTTTCAATTGAGGCTAGTATTGGCACAGACAAGATATTCTAGACG
1 GGCGTAGTATTGGTACTTATGTTTCAATTGAGGCTAGTATTGGCACAAACAAGATATTCTAGACG
*
1439621 GTGTAAAAATCGCGTTCAAAATGGTTTGAAAACTTTATTTTGTGCATGAAGAAGAGGCTAACAT
66 GTGTAAAAATCGCGTTCAAAATGGTTTGAAAACTTGATTTTGTGCATGAAGAAGAGGCTAACAT
* *
1439685 GGCGTATTATTGGTACTTATGTTTCAATTGAGGATAGTATTGGCACAAACAAGATATTCTAGACG
1 GGCGTAGTATTGGTACTTATGTTTCAATTGAGGCTAGTATTGGCACAAACAAGATATTCTAGACG
* * *
1439750 GTGTAAAAATCGCGATCAAAATGGTTTGAAAGCTTGCTTTTGTGCATGAAGAAGAGGCTAACAT
66 GTGTAAAAATCGCGTTCAAAATGGTTTGAAAACTTGATTTTGTGCATGAAGAAGAGGCTAACAT
* *
1439814 GGTGTAGTATTGGTACTTATGTTTCAATTGAAGCTAGTAT
1 GGCGTAGTATTGGTACTTATGTTTCAATTGAGGCTAGTAT
1439854 CGATACATAC
Statistics
Matches: 157, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 157 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (129 bp):
GGCGTAGTATTGGTACTTATGTTTCAATTGAGGCTAGTATTGGCACAAACAAGATATTCTAGACG
GTGTAAAAATCGCGTTCAAAATGGTTTGAAAACTTGATTTTGTGCATGAAGAAGAGGCTAACAT
Found at i:1441411 original size:20 final size:20
Alignment explanation
Indices: 1441383--1441422 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1441373 TTTTCCGTCA
1441383 TGTCACGTTTACCACAATTG
1 TGTCACGTTTACCACAATTG
* *
1441403 TGTCGCGTTTACTACAATTG
1 TGTCACGTTTACCACAATTG
1441423 CGGGTATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (20 bp):
TGTCACGTTTACCACAATTG
Found at i:1443022 original size:38 final size:37
Alignment explanation
Indices: 1442978--1443061 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 37
1442968 CTAAACCCAA
1442978 ACCCGACCCAACCCGAATATCACACTTAAAAAAACCCG
1 ACCCGACCCAACCCGAATATCACACTT-AAAAAACCCG
* *
1443016 ACCCGACTCGACCCGAATATCACACTTAAAAAACCCG
1 ACCCGACCCAACCCGAATATCACACTTAAAAAACCCG
*
1443053 ACCTGACCC
1 ACCCGACCC
1443062 GAACAAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 17 0.40
38 25 0.60
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (37 bp):
ACCCGACCCAACCCGAATATCACACTTAAAAAACCCG
Found at i:1445236 original size:47 final size:47
Alignment explanation
Indices: 1445165--1445265 Score: 175
Period size: 47 Copynumber: 2.1 Consensus size: 47
1445155 TGAAGATCTC
* *
1445165 GCAGCAACGTGGAAGATAACTCCAATGGTGGCTCTAAGAAAATAGTA
1 GCAGCAACGTGGAAGATAACTCCAATCGTGACTCTAAGAAAATAGTA
*
1445212 GTAGCAACGTGGAAGATAACTCCAATCGTGACTCTAAGAAAATAGTA
1 GCAGCAACGTGGAAGATAACTCCAATCGTGACTCTAAGAAAATAGTA
1445259 GCAGCAA
1 GCAGCAA
1445266 TGGGGGCTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (47 bp):
GCAGCAACGTGGAAGATAACTCCAATCGTGACTCTAAGAAAATAGTA
Found at i:1446727 original size:45 final size:44
Alignment explanation
Indices: 1446678--1446764 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
1446668 ACTAATTTAT
* * *
1446678 TAATAGATAATAAAAAGATGATGAAATGACTAATTATTATTTTTC
1 TAATAAATAATAAAAAAAT-ATGAAATGAATAATTATTATTTTTC
* *
1446723 TAATAAATAATAAAAAAATATTAAATTAATAATTATTATTTT
1 TAATAAATAATAAAAAAATATGAAATGAATAATTATTATTTT
1446765 ACTACACCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 20 0.54
45 17 0.46
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (44 bp):
TAATAAATAATAAAAAAATATGAAATGAATAATTATTATTTTTC
Found at i:1448754 original size:20 final size:20
Alignment explanation
Indices: 1448729--1448821 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
1448719 TTTTCCCAAT
1448729 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1448749 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1448769 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
1448790 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1448811 TCGCAATGCGA
1 TCGCAATGCGA
1448822 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1448771 original size:41 final size:41
Alignment explanation
Indices: 1448726--1448821 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
1448716 CGATTTTCCC
1448726 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1448767 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1448808 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1448822 TACTGACTAT
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:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:1448775 original size:21 final size:20
Alignment explanation
Indices: 1448729--1448821 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1448719 TTTTCCCAAT
*
1448729 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1448749 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1448769 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
1448790 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1448811 TCGCAATGCGA
1 TCGCAATGCGA
1448822 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1448835 original size:20 final size:20
Alignment explanation
Indices: 1448810--1448923 Score: 111
Period size: 20 Copynumber: 5.7 Consensus size: 20
1448800 AATTGGGAAA
*
1448810 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1448830 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1448850 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1448871 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
1448891 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1448911 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1448924 TTACTTAGCG
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 64 0.82
21 14 0.18
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1448854 original size:61 final size:61
Alignment explanation
Indices: 1448807--1448923 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1448797 GCGAATTGGG
* * ** *
1448807 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATACTGACTATCGCAACGCGATAATAA
* * *
1448868 AAAATCGCAACGAGATACTTACTTTCGCAACACGATACTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATACTGACTATCGCAACGCGAT
1448924 TTACTTAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATACTGACTATCGCAACGCGATAATAA
Found at i:1449500 original size:19 final size:19
Alignment explanation
Indices: 1449476--1449520 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1449466 GCAACGAGAT
*
1449476 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
1449495 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
1449514 AATCGCA
1 AATCGCA
1449521 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:1449538 original size:19 final size:19
Alignment explanation
Indices: 1449516--1449700 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
1449506 GAAACCAAAA
*
1449516 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1449535 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1449554 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
1449573 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1449593 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1449609 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1449626 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1449640 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1449659 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* * *
1449679 ATCTCATTGTGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1449699 TC
1 TC
1449701 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.44
20 47 0.35
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1449593 original size:39 final size:38
Alignment explanation
Indices: 1449516--1449605 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
1449506 GAAACCAAAA
* *
1449516 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
1449554 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
1449593 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1449606 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:1449625 original size:33 final size:33
Alignment explanation
Indices: 1449588--1449675 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
1449578 GTTGCGATTT
* *
1449588 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
1449621 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1449654 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1449676 ATTATCTCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1451756 original size:42 final size:42
Alignment explanation
Indices: 1451696--1451818 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1451686 GCTCGACTCG
* * *
1451696 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1451738 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1451780 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1451819 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1451776 original size:21 final size:21
Alignment explanation
Indices: 1451752--1451818 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1451742 TCATTCCTCG
1451752 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1451773 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1451794 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1451815 AGAG
1 AGAG
1451819 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1453209 original size:13 final size:13
Alignment explanation
Indices: 1453174--1453211 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
1453164 TTGATTGTTT
1453174 AATTGATTTGTAA
1 AATTGATTTGTAA
1453187 AATGTGATTTGTAA
1 AAT-TGATTTGTAA
*
1453201 AGTTGATTTGT
1 AATTGATTTGT
1453212 TTAATTGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:1453219 original size:13 final size:13
Alignment explanation
Indices: 1453164--1453220 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
1453154 TGCTTATTTT
*
1453164 TTGA-TTGTTTAA
1 TTGATTTGTTAAA
*
1453176 TTGATTTGTAAAA
1 TTGATTTGTTAAA
1453189 TGTGATTTG-TAAA
1 T-TGATTTGTTAAA
*
1453202 GTTGATTTGTTTAA
1 -TTGATTTGTTAAA
1453216 TTGAT
1 TTGAT
1453221 GTTAACATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
12 4 0.11
13 22 0.59
14 11 0.30
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (13 bp):
TTGATTTGTTAAA
Found at i:1453412 original size:19 final size:19
Alignment explanation
Indices: 1453390--1453507 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
1453380 CGAAATTAAA
1453390 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1453409 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1453424 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1453442 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1453457 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1453475 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1453494 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1453508 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1453436 original size:33 final size:33
Alignment explanation
Indices: 1453394--1453487 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
1453384 ATTAAATTCG
1453394 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1453427 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1453460 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1453488 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1455797 original size:12 final size:12
Alignment explanation
Indices: 1455780--1455804 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1455770 TCTTCAGGGA
1455780 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1455792 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1455804 C
1 C
1455805 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1457285 original size:14 final size:15
Alignment explanation
Indices: 1457266--1457303 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1457256 CATCAATTAA
1457266 ACAAATCAA-CATTT
1 ACAAATCAATCATTT
*
1457280 ACAAAT-AATCTTTT
1 ACAAATCAATCATTT
1457294 ACAAATCAAT
1 ACAAATCAAT
1457304 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:1457687 original size:20 final size:20
Alignment explanation
Indices: 1457662--1457712 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1457652 ATTCATTTGA
*
1457662 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
1457682 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1457702 TTATCGCAACG
1 CTATCGCAACG
1457713 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1457778 original size:18 final size:18
Alignment explanation
Indices: 1457757--1457802 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1457747 GATTTTCTCG
1457757 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
1457775 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
1457793 TTGCGATTTC
1 TTGCGATTTC
1457803 TCGTTGCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:1457938 original size:14 final size:14
Alignment explanation
Indices: 1457919--1457955 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1457909 CATCAATTAA
1457919 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1457933 ACAAATCATCTTTT
1 ACAAATCAACATTT
1457947 ACAAATCAA
1 ACAAATCAA
1457956 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Done.