Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000402.1 Hibiscus syriacus cultivar Beakdansim tig00000738_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: 1701760
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1234085 original size:36 final size:34
Alignment explanation
Indices: 1233921--1234085 Score: 99
Period size: 36 Copynumber: 4.6 Consensus size: 34
1233911 ACTAAAAGAG
* * * *
1233921 AAAAAGAAAAAAATGAAAAAAA-TAATAA-TAATA
1 AAAAAGAGAAAAATGAAAAAAACGAA-AAGAAAAA
* *
1233954 AAAATGAGAAGAA-GAAAAAGAA-GAAAAGAAAAA
1 AAAAAGAGAAAAATGAAAAA-AACGAAAAGAAAAA
*
1233987 TGAGAAAAAAGAAAAATGATGGAAAAAACGAAAAGAAAAA
1 --A-AAAAGAGAAAAATGA---AAAAAACGAAAAGAAAAA
*
1234027 AAAAATG-G-AAAATGGAAGAAAAATGAAAGAGAAAAA
1 AAAAA-GAGAAAAAT-GAA-AAAAACGAAA-AGAAAAA
1234063 CAAAAAGAGAAAAATGAAAAAAA
1 -AAAAAGAGAAAAATGAAAAAAA
1234086 GAGAAATAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 31
0.71 0.08 0.21
Matches are distributed among these distances:
32 8 0.08
33 17 0.16
34 1 0.01
35 10 0.10
36 27 0.26
37 18 0.17
38 6 0.06
39 2 0.02
40 15 0.14
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.08
Consensus pattern (34 bp):
AAAAAGAGAAAAATGAAAAAAACGAAAAGAAAAA
Found at i:1235425 original size:37 final size:36
Alignment explanation
Indices: 1235371--1235442 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
1235361 AAACAGGTCA
1235371 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
*
1235407 ATCTGTAAGCCTTCACGGAAGATTAGTGAAGCAAAC
1 ATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAAC
1235443 TCATTTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
Found at i:1235526 original size:55 final size:55
Alignment explanation
Indices: 1235457--1235765 Score: 348
Period size: 55 Copynumber: 5.7 Consensus size: 55
1235447 TTTATGAAGA
* * *
1235457 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACCTGTTTATTGAAGATTTT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCTGTTTATTGAAGATTGT
* *
1235512 TCGAGTTCTATACTCTCTGAAAGAATAGAGAGCAGACCCGTTTTATTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCTG-TTTATTGAAGATTGT
* * *
1235568 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGA-TTCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCT-GTTTATTGAAGATTGT
*
1235623 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCAT-TTTA-TGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGA-CC-TGTTTATTGAAGATTGT
* * * ** *
1235678 TCGAGTTC----CTCCCTG-AGCGGATAGGGAGTGGACCTGTTTATTGAAGATTGA
1 TCGAGTTCTATACTCTCTGAAG-GAATAGAGAGCAGACCTGTTTATTGAAGATTGT
* *
1235729 TCGAG-TCTTATACTCCCTGAAGGAATAGGGAGCAGAC
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCAGAC
1235766 TTATCATTTG
Statistics
Matches: 220, Mismatches: 20, Indels: 28
0.82 0.07 0.10
Matches are distributed among these distances:
49 1 0.00
50 10 0.05
51 31 0.14
55 123 0.56
56 54 0.25
58 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCTGTTTATTGAAGATTGT
Found at i:1235594 original size:111 final size:110
Alignment explanation
Indices: 1235457--1235765 Score: 398
Period size: 111 Copynumber: 2.8 Consensus size: 110
1235447 TTTATGAAGA
* * *
1235457 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACCTGTTTATTGAAGATTTTTCGAGTTCTA
1 TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTCTA
* *
1235522 TACTCTCTGAAAGAATAGAGAGCAGACCCGTTTTATTGAAGATTGT
66 TACTCTCTGAAGGAATAGAGAGCAGACCCATTTTA-TGAAGATTGT
* * *
1235568 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGA-TTCGTTTGTTGAAGATTGTTCGAGTTCT
1 TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCT-GTTTATTGAAGATTGTTCGAGTTCT
*
1235632 ATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGT
65 ATACTCTCTGAAGGAATAGAGAGCAGACCCATTTTATGAAGATTGT
* * * *
1235678 TCGAGTTC----CTCCCTG-AGCGGATAGGGAGTGGACCTGTTTATTGAAGATTGATCGAG-TCT
1 TCGAGTTCTATACTCTCTGAAG-GAATAGGGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTC-
* *
1235737 TATACTCCCTGAAGGAATAGGGAGCAGAC
64 TATACTCTCTGAAGGAATAGAGAGCAGAC
1235766 TTATCATTTG
Statistics
Matches: 175, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
105 4 0.02
106 62 0.35
107 1 0.01
110 19 0.11
111 89 0.51
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (110 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTCTA
TACTCTCTGAAGGAATAGAGAGCAGACCCATTTTATGAAGATTGT
Found at i:1235778 original size:106 final size:106
Alignment explanation
Indices: 1235468--1235790 Score: 332
Period size: 106 Copynumber: 3.0 Consensus size: 106
1235458 CGAGTCCTAT
* * *
1235468 ACTCTCTGAAGGAATAGGGAGCAGACCTGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAA
1 ACTCCCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTCTATACTCTCTGAA
* *
1235533 AGAATAGAGAGCAGACCCGTTTTA-TTGAAGATTGTTCGAGTTC
66 GGAATAGAGAGCAGA--C-TTATATTTGAAGATTGTTCGAGTTC
* * * *
1235576 TATACTCTCTGAAGGAATAGAGAGCGGA-TTCGTTTGTTGAAGATTGTTCGAGTTCTATACTCTC
1 ---ACTCCCTGAAGGAATAGGGAGCGGACCT-GTTTATTGAAGATTGTTCGAGTTCTATACTCTC
* ** *
1235640 TGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTC
62 TGAAGGAATAGAGAGCAGACTTATATT-TGAAGATTGTTCGAGTTC
* * * *
1235686 -CTCCCTG-AGCGGATAGGGAGTGGACCTGTTTATTGAAGATTGATCGAG-TCTTATACTCCCTG
1 ACTCCCTGAAG-GAATAGGGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTC-TATACTCTCTG
* * *
1235748 AAGGAATAGGGAGCAGACTTATCATTTGAAGATTTTTCAAGTT
64 AAGGAATAGAGAGCAGACTTAT-ATTTGAAGATTGTTCGAGTT
1235791 TCATTTATCC
Statistics
Matches: 179, Mismatches: 26, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
105 4 0.02
106 79 0.44
107 3 0.02
108 1 0.01
109 2 0.01
110 19 0.11
111 71 0.40
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (106 bp):
ACTCCCTGAAGGAATAGGGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTCTATACTCTCTGAA
GGAATAGAGAGCAGACTTATATTTGAAGATTGTTCGAGTTC
Found at i:1245537 original size:3 final size:3
Alignment explanation
Indices: 1245529--1245587 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
1245519 GGCATGTTTG
**
1245529 TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA TAAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
1245574 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
1245588 TCAATAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1245561 original size:24 final size:24
Alignment explanation
Indices: 1245529--1245596 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
1245519 GGCATGTTTG
* **
1245529 TAATAATAATAATTTTAATAATAA
1 TAATAATAATAAATAAAATAATAA
1245553 TAATAATAATAAATAAAATAATAA
1 TAATAATAATAAATAAAATAATAA
1245577 TAATAATAATATCAATAAAA
1 TAATAATAATA--AATAAAA
1245597 AAATGGGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
24 32 0.82
26 7 0.18
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (24 bp):
TAATAATAATAAATAAAATAATAA
Found at i:1245584 original size:21 final size:22
Alignment explanation
Indices: 1245529--1245594 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 22
1245519 GGCATGTTTG
**
1245529 TAATAATAATAAT-TTTAATAA
1 TAATAATAATAATAAATAATAA
1245550 TAATAATAATAATAAATAA-AA
1 TAATAATAATAATAAATAATAA
1245571 TAATAATAATAATAATATCAATAA
1 TAATAATAATAATAA-AT-AATAA
1245595 AAAAATGGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 30 0.77
22 5 0.13
23 2 0.05
24 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TAATAATAATAATAAATAATAA
Found at i:1246354 original size:14 final size:14
Alignment explanation
Indices: 1246335--1246362 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1246325 AATATAAATC
1246335 TATTGACTGACCTT
1 TATTGACTGACCTT
1246349 TATTGACTGACCTT
1 TATTGACTGACCTT
1246363 AGTAGTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (14 bp):
TATTGACTGACCTT
Found at i:1248776 original size:35 final size:34
Alignment explanation
Indices: 1248684--1248783 Score: 155
Period size: 35 Copynumber: 2.9 Consensus size: 34
1248674 AAAAGATGAA
* *
1248684 CACTTGAATCGAAAGTGCGACGCCTCCTTCCGTT
1 CACTTGAATCGAAAGTGCGATGCTTCCTTCCGTT
1248718 CGACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTT
1 C-ACTTGAATCGAAAGTG-CGATGCTTCCTTCCGTT
1248754 CACTTGAATCGAAAGTGTCGATGCTTCCTT
1 CACTTGAATCGAAAGTG-CGATGCTTCCTT
1248784 TCATTCTTCT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
34 1 0.02
35 44 0.72
36 16 0.26
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (34 bp):
CACTTGAATCGAAAGTGCGATGCTTCCTTCCGTT
Found at i:1248810 original size:20 final size:20
Alignment explanation
Indices: 1248783--1248843 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
1248773 GATGCTTCCT
1248783 TTCA-TTCTTCTTATTCACC
1 TTCATTTCTTCTTATTCACC
*
1248802 TTCATTTCTTTTTATTCACC
1 TTCATTTCTTCTTATTCACC
*
1248822 TTCATTTCTTTCTTCTTCACC
1 TTCATTTC-TTCTTATTCACC
1248843 T
1 T
1248844 CTTATACAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 4 0.11
20 22 0.59
21 11 0.30
ACGTcount: A:0.13, C:0.30, G:0.00, T:0.57
Consensus pattern (20 bp):
TTCATTTCTTCTTATTCACC
Found at i:1250254 original size:16 final size:14
Alignment explanation
Indices: 1250222--1250248 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1250212 GCATGCTTAT
1250222 GCATGGCATTACAA
1 GCATGGCATTACAA
1250236 GCATGGCATTACA
1 GCATGGCATTACA
1250249 CAAGCACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (14 bp):
GCATGGCATTACAA
Found at i:1251509 original size:34 final size:34
Alignment explanation
Indices: 1251471--1251535 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
1251461 ATTGAAGTTT
1251471 TTTTTATTAATCTGTCAGTTAATTTTATGTTAAC
1 TTTTTATTAATCTGTCAGTTAATTTTATGTTAAC
1251505 TTTTTATTAATCTGTCAGTTAATTTTATGTT
1 TTTTTATTAATCTGTCAGTTAATTTTATGTT
1251536 CAGGCAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.25, C:0.08, G:0.09, T:0.58
Consensus pattern (34 bp):
TTTTTATTAATCTGTCAGTTAATTTTATGTTAAC
Found at i:1253594 original size:23 final size:23
Alignment explanation
Indices: 1253530--1253594 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1253520 CTTATATGGA
1253530 ACTTCGGTGCATTTCTACGCGGC
1 ACTTCGGTGCATTTCTACGCGGC
* * *
1253553 ACTACGGTGCAATTCTACGTGGC
1 ACTTCGGTGCATTTCTACGCGGC
*
1253576 ACTTCGGTGCATTTATACG
1 ACTTCGGTGCATTTCTACG
1253595 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGGC
Found at i:1255443 original size:23 final size:22
Alignment explanation
Indices: 1255384--1255449 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 22
1255374 TAATTAAATA
1255384 ATTTATATATATT-TATAAAAGTT
1 ATTTATA-ATATTATA-AAAAGTT
*
1255407 ATATGA-AATCATTATAAAAAGTAT
1 AT-TTATAAT-ATTATAAAAAGT-T
1255431 ATTTATAATATTATAAAAA
1 ATTTATAATATTATAAAAA
1255450 TATTTACTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
22 2 0.06
23 24 0.67
24 10 0.28
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (22 bp):
ATTTATAATATTATAAAAAGTT
Found at i:1255621 original size:23 final size:23
Alignment explanation
Indices: 1255586--1255648 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1255576 ATATATATTT
1255586 TAAA-AATT-ATATTATTTCAAA
1 TAAATAATTAATATTATTTCAAA
1255607 TAAATAATTAATATTATTTCAAA
1 TAAATAATTAATATTATTTCAAA
* * * *
1255630 TGAGTAAATAATATGATTT
1 TAAATAATTAATATTATTT
1255649 TAAAATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.11
22 4 0.11
23 28 0.78
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (23 bp):
TAAATAATTAATATTATTTCAAA
Found at i:1255681 original size:21 final size:21
Alignment explanation
Indices: 1255634--1255682 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
1255624 TTCAAATGAG
1255634 TAAATAATATGATTTTAAAAT
1 TAAATAATATGATTTTAAAAT
1255655 TAAATAA-AT-ATTTTAAAAT
1 TAAATAATATGATTTTAAAAT
*
1255674 T-TATAATAT
1 TAAATAATAT
1255683 TATAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.15
19 13 0.50
20 2 0.08
21 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TAAATAATATGATTTTAAAAT
Found at i:1274423 original size:21 final size:21
Alignment explanation
Indices: 1274393--1274436 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1274383 TCCAATCAAA
1274393 GAACAACACGTTCA-TCCCATT
1 GAACAACACGTTCACT-CCATT
*
1274414 GAACACCACGTTCACTCCATT
1 GAACAACACGTTCACTCCATT
1274435 GA
1 GA
1274437 TGAGCATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.32, C:0.34, G:0.11, T:0.23
Consensus pattern (21 bp):
GAACAACACGTTCACTCCATT
Found at i:1289688 original size:170 final size:173
Alignment explanation
Indices: 1289377--1289732 Score: 429
Period size: 170 Copynumber: 2.1 Consensus size: 173
1289367 TACATGTATC
* *
1289377 CATGCAACCATGATATTCAACGAGTTCAAAGTTCGAATCTTGACATTCATTCTTTCTACACACAA
1 CATGCAACCATGATATTCAACGAGTCCAAAGTTCGAATCTTGACATTCA-TCTTTATACACACAA
* * *
1289442 AAATAATAAGAACAAAATCGAGTATGACCCGAAGTTGAGAATACCATTGTTAACATTATACAATC
65 AAAGAATAAGAACAAAATCGAGTACGACCCGAAGTTGAGAATACCATTGTTAACATTATACAAAC
* *
1289507 AAGAATTTTCATTTAA-TAATAAACAGTCATTGTTAACATTACTA
130 AAGAATTTTCA-TCAAGTAACAAACAGTCATTGTTAACATTACTA
* * *
1289551 CATGCAACCATGATATTCAGCGAGTCCAAAGTTCGAAT-TTTAC--TC-TCTTTTATACACATAA
1 CATGCAACCATGATATTCAACGAGTCCAAAGTTCGAATCTTGACATTCATC-TTTATACACACAA
* * * * *
1289612 AAAGAATAAGAACGAAATTGAGTACGACTCGAAGTTGAGATTACCATTGTTAACATTGTGA-AAA
65 AAAGAATAAGAACAAAATCGAGTACGACCCGAAGTTGAGAATACCATTGTTAACATTAT-ACAAA
* * * * *
1289676 GAA-AATTTTTCATCAAGTAGCAGACATTTATTGTTAACATTACTA
129 CAAGAA-TTTTCATCAAGTAACAAACAGTCATTGTTAACATTACTA
*
1289721 CATGCATCCATG
1 CATGCAACCATG
1289733 CAAGTGCAAC
Statistics
Matches: 157, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
169 7 0.04
170 107 0.68
171 3 0.02
173 4 0.03
174 36 0.23
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (173 bp):
CATGCAACCATGATATTCAACGAGTCCAAAGTTCGAATCTTGACATTCATCTTTATACACACAAA
AAGAATAAGAACAAAATCGAGTACGACCCGAAGTTGAGAATACCATTGTTAACATTATACAAACA
AGAATTTTCATCAAGTAACAAACAGTCATTGTTAACATTACTA
Found at i:1289750 original size:21 final size:21
Alignment explanation
Indices: 1289721--1289769 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1289711 AACATTACTA
1289721 CATGCATCCATGCAAGTGCAAC
1 CATG-ATCCATGCAAGTGCAAC
1289743 CATGATCCATGCAAGTGCAAC
1 CATGATCCATGCAAGTGCAAC
1289764 CATGAT
1 CATGAT
1289770 ATTTAATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (21 bp):
CATGATCCATGCAAGTGCAAC
Found at i:1297531 original size:21 final size:21
Alignment explanation
Indices: 1297504--1297602 Score: 85
Period size: 21 Copynumber: 4.8 Consensus size: 21
1297494 AATCAGTTTC
*
1297504 CAAAATCGCAACGCGATTTTT
1 CAAAATCGCAACGCGATATTT
* * * *
1297525 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGATATTT
* **
1297546 CAAATTCGCATTGCGAT-TTT
1 CAAAATCGCAACGCGATATTT
*
1297566 CCAAAATCGCAACGCGA-ATAT
1 -CAAAATCGCAACGCGATATTT
*
1297587 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1297603 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (21 bp):
CAAAATCGCAACGCGATATTT
Found at i:1297593 original size:20 final size:20
Alignment explanation
Indices: 1297569--1297818 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
1297559 CGATTTTCCA
** *
1297569 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
1297589 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
1297609 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
*
1297629 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
1297649 AAATCGCAACGC-ATATGGGT
1 AAATCGCAACGCGA-ATCCGT
* *
1297669 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1297689 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1297709 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1297729 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1297749 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1297769 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1297789 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
1297809 AAATCACAAC
1 AAATCGCAAC
1297819 ACTGAAATTT
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:1297926 original size:22 final size:22
Alignment explanation
Indices: 1297901--1297970 Score: 99
Period size: 22 Copynumber: 3.3 Consensus size: 22
1297891 TATCACTCTC
1297901 TCCGGCGACATCCGTTCCTATA
1 TCCGGCGACATCCGTTCCTATA
1297923 TCCGGCGACATCCGTTCCTATA
1 TCCGGCGACATCCGTTCCTATA
** *
1297945 TCCAACGACATCC-TTCCCA-A
1 TCCGGCGACATCCGTTCCTATA
1297965 TCCGGC
1 TCCGGC
1297971 AACAGGTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 5 0.12
21 5 0.12
22 33 0.77
ACGTcount: A:0.20, C:0.40, G:0.16, T:0.24
Consensus pattern (22 bp):
TCCGGCGACATCCGTTCCTATA
Found at i:1298562 original size:24 final size:24
Alignment explanation
Indices: 1298523--1298569 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1298513 AAATTTGGTC
1298523 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1298547 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1298570 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1298761 original size:12 final size:12
Alignment explanation
Indices: 1298744--1298768 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1298734 ATATAATCCT
1298744 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1298756 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1298768 G
1 G
1298769 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1301145 original size:19 final size:19
Alignment explanation
Indices: 1301105--1301221 Score: 181
Period size: 19 Copynumber: 6.4 Consensus size: 19
1301095 GATTCTCTCG
1301105 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1301125 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1301144 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1301158 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1301177 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1301196 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1301215 TTGCGAT
1 TTGCGAT
1301222 AGTCAATTTT
Statistics
Matches: 90, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
14 6 0.07
16 7 0.08
17 7 0.08
19 55 0.61
20 15 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1301167 original size:33 final size:35
Alignment explanation
Indices: 1301124--1301221 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 35
1301114 TCATTTCCGC
1301124 ATTGCGATTTTCATTTCGCATTGCGATTC-TCTCG
1 ATTGCGATTTTCATTTCGCATTGCGATTCATCTCG
*
1301158 -TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 ATTGCGATTTTCATTTCGCATTGCGA--TTCATCTCG
1301194 CATTGCGATTTTCATTTCGCATTGCGAT
1 -ATTGCGATTTTCATTTCGCATTGCGAT
1301222 AGTCAATTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
33 25 0.43
35 3 0.05
36 5 0.09
38 25 0.43
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (35 bp):
ATTGCGATTTTCATTTCGCATTGCGATTCATCTCG
Found at i:1301199 original size:52 final size:53
Alignment explanation
Indices: 1301088--1301203 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
1301078 AATGAAAATT
1301088 GCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTC
1 GCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTC
1301141 GCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTTC
1 GCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTC
1301193 GCATTGCGATT
1 GCATTGCGATT
1301204 TTCATTTCGC
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 31 0.49
53 32 0.51
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (53 bp):
GCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTC
Found at i:1303313 original size:20 final size:20
Alignment explanation
Indices: 1303288--1303353 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
1303278 TAGTTTACTT
* *
1303288 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
1303308 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
1303327 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
1303346 TCGCAACG
1 TCGCAACG
1303354 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:1303373 original size:33 final size:33
Alignment explanation
Indices: 1303325--1303417 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1303315 GCGAAACCAA
*
1303325 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
1303358 AATCGCAATGTGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1303391 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1303418 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1303382 original size:19 final size:19
Alignment explanation
Indices: 1303358--1303422 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
1303348 GCAACGACAG
* *
1303358 AATCGCAATGTGAAATGAA
1 AATCGCAACGCGAAATGAA
1303377 AATCGCAA--CGAAA-G--
1 AATCGCAACGCGAAATGAA
1303391 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1303410 AATCGCAATGCGA
1 AATCGCAACGCGA
1303423 TTTTGGTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 8 0.21
16 6 0.15
17 5 0.13
19 20 0.51
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1303396 original size:14 final size:14
Alignment explanation
Indices: 1303344--1303400 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1303334 GCGAAATGAA
*
1303344 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
1303358 AATCGCAATGTGAAATG
1 AATCGCAA--CGAAA-G
1303375 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1303391 AATCGCAACG
1 AATCGCAACG
1303401 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1303440 original size:19 final size:19
Alignment explanation
Indices: 1303418--1303546 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1303408 AAAATCGCAA
1303418 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1303437 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1303451 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1303470 TACGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1303484 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1303503 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1303522 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1303542 TGCGA
1 TGCGA
1303547 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1303460 original size:33 final size:33
Alignment explanation
Indices: 1303418--1303509 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
1303408 AAAATCGCAA
1303418 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
*
1303451 TGCGATTTTGGTTTCGCGTTACGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1303484 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1303510 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 52 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1303749 original size:93 final size:93
Alignment explanation
Indices: 1303590--1304062 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
1303580 TTGAATGGAT
*
1303590 AAATTTACTTTTAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1303655 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1303683 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1303748 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1303776 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1303841 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1303869 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1303933 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1303961 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1304026 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1304054 AAATTTACT
1 AAATTTACT
1304063 AAGCAATCTA
Statistics
Matches: 375, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 92 0.25
93 283 0.75
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1303999 original size:185 final size:186
Alignment explanation
Indices: 1303590--1304062 Score: 912
Period size: 185 Copynumber: 2.5 Consensus size: 186
1303580 TTGAATGGAT
*
1303590 AAATTTACTTTTAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1303655 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
1303720 TACTATTTCACAGTGTTATAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1303776 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1303841 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1303905 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1303961 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1304026 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1304063 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 169 0.60
186 115 0.40
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1305785 original size:14 final size:14
Alignment explanation
Indices: 1305766--1305855 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1305756 TTGAAATGAA
1305766 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1305780 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1305797 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1305813 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
1305832 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1305846 AATCGCAACG
1 AATCGCAACG
1305856 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1305803 original size:33 final size:33
Alignment explanation
Indices: 1305758--1305872 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
1305748 TCTTTTGGTT
1305758 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1305791 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1305824 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1305857 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1305873 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1305804 original size:19 final size:18
Alignment explanation
Indices: 1305765--1305877 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1305755 GTTGAAATGA
1305765 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1305780 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1305797 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1305813 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1305830 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1305846 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1305863 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1305878 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1305908 original size:14 final size:14
Alignment explanation
Indices: 1305889--1305945 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1305879 TTTGGTTTCG
1305889 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1305903 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1305922 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1305936 CGTTGCGATT
1 CGTTGCGATT
1305946 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1305921 original size:33 final size:33
Alignment explanation
Indices: 1305873--1305953 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1305863 AAAATCGCAA
**
1305873 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1305906 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
1305939 TGCGATTGTCATTTC
1 TGCGATTTTCATTTC
1305954 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1305956 original size:21 final size:21
Alignment explanation
Indices: 1305930--1306005 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1305920 CGCGTTGCGA
1305930 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
1305951 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
1305971 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
1305992 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1306006 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:1305986 original size:41 final size:41
Alignment explanation
Indices: 1305929--1306006 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1305919 TCGCGTTGCG
*
1305929 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
*
1305970 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
1306007 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:1306132 original size:33 final size:33
Alignment explanation
Indices: 1306085--1306155 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1306075 AATACTAACT
* *
1306085 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1306118 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1306151 TGAAA
1 TGAAA
1306156 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1306389 original size:22 final size:22
Alignment explanation
Indices: 1306337--1306391 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1306327 TGGTTGTGAG
**
1306337 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1306359 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1306381 GGATTTCTTCG
1 GGATTTCTTCG
1306392 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1306557 original size:39 final size:40
Alignment explanation
Indices: 1306514--1306595 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
1306504 TACGCGTAGC
*
1306514 GATTATAATGGCGCTTTA-A-ATATCGCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGAT-TCGCGTTGCGATTTACG
** * *
1306553 GATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
1306593 GAT
1 GAT
1306596 ACGCGTTGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.39
40 20 0.56
41 2 0.06
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (40 bp):
GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
Found at i:1306730 original size:20 final size:20
Alignment explanation
Indices: 1306537--1306729 Score: 219
Period size: 20 Copynumber: 9.7 Consensus size: 20
1306527 CTTTAAATAT
1306537 CGCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
* * *
1306558 -TCGTTGCGATTTACAGATT
1 CGCGTTGCGATTTACGGATA
*
1306577 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1306597 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1306617 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1306637 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1306657 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1306677 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1306697 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1306717 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1306730 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 145 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1306746 original size:21 final size:21
Alignment explanation
Indices: 1306716--1306798 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1306706 ATTTTCATAT
*
1306716 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1306737 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1306758 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1306779 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1306799 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1306789 original size:42 final size:43
Alignment explanation
Indices: 1306696--1306794 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1306686 ATTTATGTGT
* *
1306696 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1306737 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1306779 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1306795 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1309058 original size:19 final size:20
Alignment explanation
Indices: 1309009--1309089 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 20
1308999 GTTACTGATA
1309009 AAAATAATATAAATATAATT
1 AAAATAATATAAATATAATT
* *
1309029 CAGAT-ATATAAATAT-ATT
1 AAAATAATATAAATATAATT
* *
1309047 AAAATAAAATAAAT-TTA-T
1 AAAATAATATAAATATAATT
* *
1309065 AATAT-ATATATATATAATT
1 AAAATAATATAAATATAATT
1309084 ATAAAT
1 A-AAAT
1309090 TTAATAGCAG
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
17 6 0.13
18 14 0.30
19 20 0.43
20 6 0.13
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (20 bp):
AAAATAATATAAATATAATT
Found at i:1310388 original size:29 final size:29
Alignment explanation
Indices: 1310312--1310396 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 29
1310302 AAATTAAAAA
*
1310312 AAATAAACACAAATATAATATTAAA-AATTT
1 AAATAAAAACAAATA-AATA-TAAACAATTT
*
1310342 AAATAAAAATAAATTAAATATAAACAATTT
1 AAATAAAAACAAA-TAAATATAAACAATTT
* *
1310372 -TATAATAAACAAATAAATAAAAACA
1 AAATAA-AAACAAATAAATATAAACA
1310397 CATCAATCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
29 19 0.40
30 26 0.55
31 2 0.04
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (29 bp):
AAATAAAAACAAATAAATATAAACAATTT
Found at i:1312563 original size:59 final size:60
Alignment explanation
Indices: 1312455--1312567 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 60
1312445 ATTTTACAAC
* * * * *
1312455 TTTTAATAGTCGGAGGGCTCAACAAAGCAACATCATATAGTCGGAAGACCATTTTGTAAA
1 TTTTAATAATCGGAGGACTCAACAAAACAACACCATATACTCGGAAGACCATTTTGTAAA
* *
1312515 TTTTAATAATCGG-GGACTCAACAAAACAACACCCTATAACT-GGGAGACCATTT
1 TTTTAATAATCGGAGGACTCAACAAAACAACACCATAT-ACTCGGAAGACCATTT
1312568 GTGTGCTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 31 0.69
60 14 0.31
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (60 bp):
TTTTAATAATCGGAGGACTCAACAAAACAACACCATATACTCGGAAGACCATTTTGTAAA
Found at i:1312850 original size:4 final size:4
Alignment explanation
Indices: 1312841--1312869 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1312831 TAATATTGTA
1312841 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1312870 ATACCTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:1314568 original size:89 final size:89
Alignment explanation
Indices: 1314462--1314639 Score: 218
Period size: 89 Copynumber: 2.0 Consensus size: 89
1314452 TATCATTTAT
*
1314462 ATTTAATCCACTAATAGGGA-AAGAATAATATTATTACATAATTG-TATATG-ATAGAAGAGTAA
1 ATTTAATCCACTAATA-GGACAAGAATAATATTATAACATAA-TGATATATGAAT-GAAGAGTAA
*
1314524 AGAATATAAATAATCCTTAAATTATAC
63 AGAATATAAACAATCCTTAAATTATAC
* * * * * *
1314551 ATTTAATTCACTAATAGGACAAGATTAATATTATAATATAATGATATATGAATGAAGGGTAAGGT
1 ATTTAATCCACTAATAGGACAAGAATAATATTATAACATAATGATATATGAATGAAGAGTAAAGA
* *
1314616 ATATAAACAGTTCTTAAATTATAC
66 ATATAAACAATCCTTAAATTATAC
1314640 TACAATCATA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
88 5 0.07
89 69 0.91
90 2 0.03
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (89 bp):
ATTTAATCCACTAATAGGACAAGAATAATATTATAACATAATGATATATGAATGAAGAGTAAAGA
ATATAAACAATCCTTAAATTATAC
Found at i:1321999 original size:19 final size:20
Alignment explanation
Indices: 1321967--1322004 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1321957 CAGGTTATTT
*
1321967 TTTTTGTAATTTAAAAATAG
1 TTTTTGTAAATTAAAAATAG
*
1321987 TTTTT-TAAATTAATAATA
1 TTTTTGTAAATTAAAAATA
1322005 TTGTTAAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTTGTAAATTAAAAATAG
Found at i:1328100 original size:14 final size:14
Alignment explanation
Indices: 1328081--1328126 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1328071 AGTGAAAGGA
1328081 TTTCATGTGCATGT
1 TTTCATGTGCATGT
* *
1328095 TTTCATGGGAACTTGT
1 TTTCATGTG--CATGT
1328111 TTTCATGTGCATGT
1 TTTCATGTGCATGT
1328125 TT
1 TT
1328127 ATTTTGAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 14 0.54
16 12 0.46
ACGTcount: A:0.15, C:0.13, G:0.22, T:0.50
Consensus pattern (14 bp):
TTTCATGTGCATGT
Found at i:1340236 original size:4 final size:4
Alignment explanation
Indices: 1340157--1340246 Score: 72
Period size: 4 Copynumber: 22.5 Consensus size: 4
1340147 TTCAATGCAC
* * * * * * *
1340157 ACAT GCAT ACAT GCAT ACGT ACGT ACGT ACGT ACGT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* ** * *
1340205 ACAT ACAT ACGT ACAT ATGT ATAT ACAT ACAT ATAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
1340247 GTGTCTGTAT
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 72 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (4 bp):
ACAT
Found at i:1348174 original size:13 final size:13
Alignment explanation
Indices: 1348156--1348181 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1348146 ATTTTTTCTA
1348156 AAAAATATTTTTT
1 AAAAATATTTTTT
1348169 AAAAATATTTTTT
1 AAAAATATTTTTT
1348182 GGAGTTTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:1349309 original size:21 final size:21
Alignment explanation
Indices: 1349280--1349322 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1349270 TTCTAATTTT
*
1349280 TTAGTATTA-GTATGAACAAAA
1 TTAGAATTATGTAT-AACAAAA
*
1349301 TTAGAATTATTTATAACAAAA
1 TTAGAATTATGTATAACAAAA
1349322 T
1 T
1349323 GAGGAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (21 bp):
TTAGAATTATGTATAACAAAA
Found at i:1349479 original size:3 final size:3
Alignment explanation
Indices: 1349471--1349525 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
1349461 ACTTAATAAA
* * *
1349471 ATT ATT ATT GTT ATT ATT ATT -TT ATT AAT -TT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1349517 ATT -TT ATT A
1 ATT ATT ATT A
1349526 ATTTAAGACG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 5 0.12
3 38 0.88
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1349503 original size:28 final size:28
Alignment explanation
Indices: 1349472--1349530 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
1349462 CTTAATAAAA
1349472 TTATTATTGTTATTATTATTTTATTAAT
1 TTATTATTGTTATTATTATTTTATTAAT
1349500 TTATTATTGTTATTATTATTTTATTAAT
1 TTATTATTGTTATTATTATTTTATTAAT
1349528 TTA
1 TTA
1349531 AGACGACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (28 bp):
TTATTATTGTTATTATTATTTTATTAAT
Found at i:1362691 original size:19 final size:18
Alignment explanation
Indices: 1362648--1362692 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1362638 AATATAGTCC
1362648 AACCAAATTGGCAAATTT
1 AACCAAATTGGCAAATTT
* *
1362666 ATTCCAATTTGGCAAATTCT
1 A-ACCAAATTGGCAAATT-T
1362686 AACCAAA
1 AACCAAA
1362693 ATCGAGACGA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.05
19 18 0.86
20 2 0.10
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (18 bp):
AACCAAATTGGCAAATTT
Found at i:1365609 original size:23 final size:21
Alignment explanation
Indices: 1365583--1365629 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
1365573 TGAATTCAAA
* *
1365583 TTAGGATTTATTTTATTTATATT
1 TTAGGAATTATCTT-TTTA-ATT
1365606 TTAGGAATTATCTTTTTAATT
1 TTAGGAATTATCTTTTTAATT
1365627 TTA
1 TTA
1365630 AATGTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 4 0.18
23 12 0.55
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.62
Consensus pattern (21 bp):
TTAGGAATTATCTTTTTAATT
Found at i:1368573 original size:23 final size:23
Alignment explanation
Indices: 1368543--1368599 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
1368533 ACGAACGGAT
* * *
1368543 GTAAACGAACAGAATAAATTAAC
1 GTAAACGAAAACAATAAATGAAC
1368566 GTAAACGAAAACAATAAATGAAC
1 GTAAACGAAAACAATAAATGAAC
* *
1368589 ATAAATGAAAA
1 GTAAACGAAAA
1368600 TAGATTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.61, C:0.11, G:0.12, T:0.16
Consensus pattern (23 bp):
GTAAACGAAAACAATAAATGAAC
Found at i:1368791 original size:14 final size:14
Alignment explanation
Indices: 1368768--1368874 Score: 124
Period size: 14 Copynumber: 7.6 Consensus size: 14
1368758 TTGACTAAAT
*
1368768 ATAAATGAACGAAC
1 ATAAACGAACGAAC
1368782 ATAAACGAACGAAC
1 ATAAACGAACGAAC
* * *
1368796 ATAAATGAACAAAT
1 ATAAACGAACGAAC
1368810 ATAAACGAACGAAC
1 ATAAACGAACGAAC
* *
1368824 ATAAATGAATGAAC
1 ATAAACGAACGAAC
*
1368838 ATAAACGATCGAAC
1 ATAAACGAACGAAC
* *
1368852 ATAAATGGACGAAC
1 ATAAACGAACGAAC
*
1368866 ATATACGAA
1 ATAAACGAA
1368875 TATATATATA
Statistics
Matches: 75, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 75 1.00
ACGTcount: A:0.56, C:0.15, G:0.14, T:0.15
Consensus pattern (14 bp):
ATAAACGAACGAAC
Found at i:1368802 original size:28 final size:28
Alignment explanation
Indices: 1368768--1368874 Score: 160
Period size: 28 Copynumber: 3.8 Consensus size: 28
1368758 TTGACTAAAT
1368768 ATAAATGAACGAACATAAACGAACGAAC
1 ATAAATGAACGAACATAAACGAACGAAC
* *
1368796 ATAAATGAACAAATATAAACGAACGAAC
1 ATAAATGAACGAACATAAACGAACGAAC
* *
1368824 ATAAATGAATGAACATAAACGATCGAAC
1 ATAAATGAACGAACATAAACGAACGAAC
* *
1368852 ATAAATGGACGAACATATACGAA
1 ATAAATGAACGAACATAAACGAA
1368875 TATATATATA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.56, C:0.15, G:0.14, T:0.15
Consensus pattern (28 bp):
ATAAATGAACGAACATAAACGAACGAAC
Found at i:1368823 original size:42 final size:42
Alignment explanation
Indices: 1368764--1368874 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
1368754 AAATTTGACT
*
1368764 AAATATAAATGAACGAACATAAACGAACGAACATAAATGAAC
1 AAATATAAATGAACGAACATAAACGAACGAACATAAACGAAC
* * * *
1368806 AAATATAAACGAACGAACATAAATGAATGAACATAAACGATC
1 AAATATAAATGAACGAACATAAACGAACGAACATAAACGAAC
* * * *
1368848 GAACATAAATGGACGAACATATACGAA
1 AAATATAAATGAACGAACATAAACGAA
1368875 TATATATATA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.15
Consensus pattern (42 bp):
AAATATAAATGAACGAACATAAACGAACGAACATAAACGAAC
Found at i:1372002 original size:10 final size:10
Alignment explanation
Indices: 1371987--1372011 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1371977 TTTACCTTTC
1371987 TGTCTTGAGA
1 TGTCTTGAGA
1371997 TGTCTTGAGA
1 TGTCTTGAGA
1372007 TGTCT
1 TGTCT
1372012 GTGTTGTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.44
Consensus pattern (10 bp):
TGTCTTGAGA
Found at i:1382631 original size:25 final size:25
Alignment explanation
Indices: 1382603--1382653 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1382593 GACTTGGACA
1382603 AAATCGAGTCTTGACAGTAACAACG
1 AAATCGAGTCTTGACAGTAACAACG
1382628 AAATCGAGTCTTGACAGTAACAACG
1 AAATCGAGTCTTGACAGTAACAACG
1382653 A
1 A
1382654 TTCACTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (25 bp):
AAATCGAGTCTTGACAGTAACAACG
Found at i:1398488 original size:36 final size:36
Alignment explanation
Indices: 1398422--1398490 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
1398412 TTAAATCTAT
* ***
1398422 ATATAATTTATTTATTTTTTATGTTCTTTATAAATA
1 ATATAATTTATATATTTTTTAAAATCTTTATAAATA
1398458 ATATAATTTCATATATTTTTTAAAAT-TTTATAA
1 ATATAATTT-ATATATTTTTTAAAATCTTTATAA
1398491 CGGATCATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 16 0.57
37 12 0.43
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (36 bp):
ATATAATTTATATATTTTTTAAAATCTTTATAAATA
Found at i:1399800 original size:19 final size:21
Alignment explanation
Indices: 1399778--1399822 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
1399768 TTATTGTCAC
*
1399778 TTTTATTATTTAA-T-TTATT
1 TTTTATCATTTAATTATTATT
1399797 TTTTATCATTTAATTATTATT
1 TTTTATCATTTAATTATTATT
1399818 TTTTA
1 TTTTA
1399823 ACAATTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 1 0.04
21 10 0.43
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTATCATTTAATTATTATT
Found at i:1404660 original size:19 final size:19
Alignment explanation
Indices: 1404638--1404698 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
1404628 TTTAAAAGTA
1404638 TATAAATTTAATTAATATT
1 TATAAATTTAATTAATATT
**** * *
1404657 TATATGCATAATTTAAAAGTA
1 TATAAATTTAA-TTAATA-TT
1404678 TATAAATTTAATTAATATT
1 TATAAATTTAATTAATATT
1404697 TA
1 TA
1404699 AAAACATAAT
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
19 10 0.36
20 10 0.36
21 8 0.29
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (19 bp):
TATAAATTTAATTAATATT
Found at i:1404689 original size:21 final size:21
Alignment explanation
Indices: 1404628--1404690 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
1404618 AATAAAATAT
1404628 TTTAAAAGTATATAAATTTAA
1 TTTAAAAGTATATAAATTTAA
** **
1404649 -TTAATATTTATATGCA--TAA
1 TTTAA-AAGTATATAAATTTAA
1404668 TTTAAAAGTATATAAATTTAA
1 TTTAAAAGTATATAAATTTAA
1404689 TT
1 TT
1404691 AATATTTAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
19 10 0.33
20 8 0.27
21 12 0.40
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTAAAAGTATATAAATTTAA
Found at i:1404707 original size:40 final size:40
Alignment explanation
Indices: 1404628--1404709 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
1404618 AATAAAATAT
* **
1404628 TTTAAAAGTATATAAATTTAATTAATATTTATATGCATAA
1 TTTAAAAGTATATAAATTTAATTAATATTTAAAAACATAA
1404668 TTTAAAAGTATATAAATTTAATTAATATTTAAAAACATAA
1 TTTAAAAGTATATAAATTTAATTAATATTTAAAAACATAA
1404708 TT
1 TT
1404710 AGACATTGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (40 bp):
TTTAAAAGTATATAAATTTAATTAATATTTAAAAACATAA
Found at i:1404775 original size:2 final size:2
Alignment explanation
Indices: 1404768--1404795 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1404758 ATCAAATCAA
1404768 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1404796 TTAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1407284 original size:2 final size:2
Alignment explanation
Indices: 1407272--1407303 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1407262 ATTTTCCTCC
*
1407272 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1407304 ACAATCCTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1408334 original size:19 final size:19
Alignment explanation
Indices: 1408312--1408372 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
1408302 TTTAAAAGTA
1408312 TATAAATTTAATTAATATT
1 TATAAATTTAATTAATATT
**** * *
1408331 TATATGCATAATTTAAAAGTA
1 TATAAATTTAA-TTAATA-TT
1408352 TATAAATTTAATTAATATT
1 TATAAATTTAATTAATATT
1408371 TA
1 TA
1408373 AAAACATAAT
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
19 10 0.36
20 10 0.36
21 8 0.29
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (19 bp):
TATAAATTTAATTAATATT
Found at i:1408363 original size:21 final size:21
Alignment explanation
Indices: 1408302--1408364 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
1408292 AATAAAATAT
1408302 TTTAAAAGTATATAAATTTAA
1 TTTAAAAGTATATAAATTTAA
** **
1408323 -TTAATATTTATATGCA--TAA
1 TTTAA-AAGTATATAAATTTAA
1408342 TTTAAAAGTATATAAATTTAA
1 TTTAAAAGTATATAAATTTAA
1408363 TT
1 TT
1408365 AATATTTAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
19 10 0.33
20 8 0.27
21 12 0.40
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTAAAAGTATATAAATTTAA
Found at i:1408381 original size:40 final size:40
Alignment explanation
Indices: 1408302--1408383 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
1408292 AATAAAATAT
* **
1408302 TTTAAAAGTATATAAATTTAATTAATATTTATATGCATAA
1 TTTAAAAGTATATAAATTTAATTAATATTTAAAAACATAA
1408342 TTTAAAAGTATATAAATTTAATTAATATTTAAAAACATAA
1 TTTAAAAGTATATAAATTTAATTAATATTTAAAAACATAA
1408382 TT
1 TT
1408384 AGACATTGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (40 bp):
TTTAAAAGTATATAAATTTAATTAATATTTAAAAACATAA
Found at i:1421837 original size:18 final size:18
Alignment explanation
Indices: 1421814--1421859 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1421804 TTCACGGAAT
1421814 ATAAGATTACCAGCGGGA
1 ATAAGATTACCAGCGGGA
* * *
1421832 ATAAGATTATCGGTGGGA
1 ATAAGATTACCAGCGGGA
1421850 ATAAGATTAC
1 ATAAGATTAC
1421860 TAGGAATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (18 bp):
ATAAGATTACCAGCGGGA
Found at i:1424651 original size:2 final size:2
Alignment explanation
Indices: 1424639--1424676 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1424629 ATTTTCCTCC
*
1424639 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1424677 ACAATCCTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1425708 original size:19 final size:19
Alignment explanation
Indices: 1425686--1425746 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
1425676 TTTAAAAGTA
1425686 TATAAATTTAATTAATATT
1 TATAAATTTAATTAATATT
**** * *
1425705 TATATGCATAATTTAAAAGTA
1 TATAAATTTAA-TTAATA-TT
1425726 TATAAATTTAATTAATATT
1 TATAAATTTAATTAATATT
1425745 TA
1 TA
1425747 AAAACATAAT
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
19 10 0.36
20 10 0.36
21 8 0.29
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (19 bp):
TATAAATTTAATTAATATT
Found at i:1425737 original size:21 final size:21
Alignment explanation
Indices: 1425676--1425738 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
1425666 AATAAAATAT
1425676 TTTAAAAGTATATAAATTTAA
1 TTTAAAAGTATATAAATTTAA
** **
1425697 -TTAATATTTATATGCA--TAA
1 TTTAA-AAGTATATAAATTTAA
1425716 TTTAAAAGTATATAAATTTAA
1 TTTAAAAGTATATAAATTTAA
1425737 TT
1 TT
1425739 AATATTTAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
19 10 0.33
20 8 0.27
21 12 0.40
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTAAAAGTATATAAATTTAA
Found at i:1425755 original size:40 final size:40
Alignment explanation
Indices: 1425676--1425757 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
1425666 AATAAAATAT
* **
1425676 TTTAAAAGTATATAAATTTAATTAATATTTATATGCATAA
1 TTTAAAAGTATATAAATTTAATTAATATTTAAAAACATAA
1425716 TTTAAAAGTATATAAATTTAATTAATATTTAAAAACATAA
1 TTTAAAAGTATATAAATTTAATTAATATTTAAAAACATAA
1425756 TT
1 TT
1425758 AGACATTGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (40 bp):
TTTAAAAGTATATAAATTTAATTAATATTTAAAAACATAA
Found at i:1427787 original size:3 final size:3
Alignment explanation
Indices: 1427779--1427804 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1427769 GAATTGGGTT
1427779 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
1427805 ATTTATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:1428703 original size:2 final size:2
Alignment explanation
Indices: 1428696--1428732 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1428686 CTTATGATTC
1428696 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1428733 CAATTATACC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1439966 original size:18 final size:18
Alignment explanation
Indices: 1439943--1439988 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1439933 TTCACGGAAT
1439943 ATAAGATTACCAGCGGGA
1 ATAAGATTACCAGCGGGA
* * *
1439961 ATAAGATTATCGGTGGGA
1 ATAAGATTACCAGCGGGA
1439979 ATAAGATTAC
1 ATAAGATTAC
1439989 TAGGAATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (18 bp):
ATAAGATTACCAGCGGGA
Found at i:1441983 original size:9 final size:9
Alignment explanation
Indices: 1441969--1441994 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1441959 ACAAAGCTTG
1441969 AAGTAATCA
1 AAGTAATCA
1441978 AAGTAATCA
1 AAGTAATCA
1441987 AAGTAATC
1 AAGTAATC
1441995 GAAGAGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.23
Consensus pattern (9 bp):
AAGTAATCA
Found at i:1443585 original size:2 final size:2
Alignment explanation
Indices: 1443573--1443616 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1443563 ATTTTCCTCC
*
1443573 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1443615 TA
1 TA
1443617 ACAATCCTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1444605 original size:19 final size:21
Alignment explanation
Indices: 1444583--1444634 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1444573 TTATTGTCAC
*
1444583 TTTTATTATTTAA-T-TTATT
1 TTTTATCATTTAATTATTATT
1444602 TTTTATCATTTAATTATTATT
1 TTTTATCATTTAATTATTATT
*
1444623 TTTTAACATTTA
1 TTTTATCATTTA
1444635 TATATAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
20 1 0.03
21 16 0.55
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCATTTAATTATTATT
Found at i:1448870 original size:23 final size:24
Alignment explanation
Indices: 1448838--1448882 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1448828 TTTAAATTTT
*
1448838 TTATTTAATA-AGGTATTTTATAC
1 TTATTAAATATAGGTATTTTATAC
*
1448861 TTATTAAATATTGGTATTTTAT
1 TTATTAAATATAGGTATTTTAT
1448883 GCAATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (24 bp):
TTATTAAATATAGGTATTTTATAC
Found at i:1455102 original size:87 final size:86
Alignment explanation
Indices: 1454956--1455129 Score: 294
Period size: 87 Copynumber: 2.0 Consensus size: 86
1454946 TATCCTGATT
* * *
1454956 GATACAGCATGTTCATCAAAAACTAGTAACAAGGGAAATGGTAATCTTGATGACTGAACTTTTGT
1 GATACAGCATGTTCATCAAAAACTAGAAACAAGGGAAATGGTAATATTGATGAATGAACTTTTGT
1455021 GGTAATGAAAAAAAACCTGTTC
66 GGTAATG-AAAAAAACCTGTTC
* *
1455043 GATACAGCATGTTCATCAAAATCTAGAAACAAGGGGAATGGTAATATTGATGAATGAACTTTTGT
1 GATACAGCATGTTCATCAAAAACTAGAAACAAGGGAAATGGTAATATTGATGAATGAACTTTTGT
1455108 GGTAATGAAAAAAACCTGTTC
66 GGTAATGAAAAAAACCTGTTC
1455129 G
1 G
1455130 TAAACCGGTA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
86 15 0.18
87 67 0.82
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.28
Consensus pattern (86 bp):
GATACAGCATGTTCATCAAAAACTAGAAACAAGGGAAATGGTAATATTGATGAATGAACTTTTGT
GGTAATGAAAAAAACCTGTTC
Found at i:1458668 original size:3 final size:3
Alignment explanation
Indices: 1458660--1458724 Score: 94
Period size: 3 Copynumber: 20.7 Consensus size: 3
1458650 TTCTAAGTTA
1458660 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
1458706 ATAT AAAT GAT AAT AAT AA
1 A-AT -AAT AAT AAT AAT AA
1458725 AAAAAAGACC
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
3 49 0.86
4 7 0.12
5 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1459101 original size:40 final size:40
Alignment explanation
Indices: 1459005--1459251 Score: 173
Period size: 40 Copynumber: 5.8 Consensus size: 40
1458995 AAAGGTGATA
* * *
1459005 ACACGGTTCCTACATGATGAGGATGGCTGGTTATCTAAGGGTG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG-T-TC-GAGGGTG
1459048 ACACGGCTT-CTACGTGATGAGGA-GGTCTGG-TCGAGGGATG
1 ACACGG-TTCCTACGTGATGAGGACGG-CTGGTTCGAGGG-TG
*
1459088 ACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAGGAGTGGTG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG------TT-CGAG-GGTG
* * *
1459136 ATAACTTGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 A-CAC--GGTTCCTACGTGATGAGGACGGCTGG-T-TCGA-GGGTG
*
1459182 ACACGGCTCCTACGTGATGAGGA-GGTCTGG-TC-AGGGGATG
1 ACACGGTTCCTACGTGATGAGGACGG-CTGGTTCGA-GGG-TG
1459222 ACACGGTTCCTACGTGATGAGGACGGCTGG
1 ACACGGTTCCTACGTGATGAGGACGGCTGG
1459252 CCATCTTTAG
Statistics
Matches: 170, Mismatches: 12, Indels: 47
0.74 0.05 0.21
Matches are distributed among these distances:
39 9 0.05
40 58 0.34
41 4 0.02
42 4 0.02
43 45 0.26
44 2 0.01
45 2 0.01
46 7 0.04
47 3 0.02
48 6 0.04
49 4 0.02
51 26 0.15
ACGTcount: A:0.20, C:0.19, G:0.36, T:0.26
Consensus pattern (40 bp):
ACACGGTTCCTACGTGATGAGGACGGCTGGTTCGAGGGTG
Found at i:1459175 original size:134 final size:134
Alignment explanation
Indices: 1458998--1459262 Score: 451
Period size: 134 Copynumber: 2.0 Consensus size: 134
1458988 GCCATCTAAA
* *
1458998 GGTGATAACACGGTTCCTACATGATGAGGATGGCTGGTTATCTAAGGGTGACACGGCTTCTACGT
1 GGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGT
1459063 GATGAGGAGGTCTGGTC-GAGGGATGACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTA
66 GATGAGGAGGTCTGGTCAG-GGGATGACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTA
1459127 GGAGT
130 GGAGT
** * * *
1459132 GGTGATAACTTGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGT
1 GGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGT
1459197 GATGAGGAGGTCTGGTCAGGGGATGACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAG
66 GATGAGGAGGTCTGGTCAGGGGATGACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAG
1459262 G
131 G
1459263 GATTATGGTT
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
134 122 0.99
135 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.26
Consensus pattern (134 bp):
GGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGT
GATGAGGAGGTCTGGTCAGGGGATGACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAG
GAGT
Found at i:1459310 original size:28 final size:28
Alignment explanation
Indices: 1459270--1459366 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 28
1459260 AGGGATTATG
* * * *
1459270 GTTTCAAGAGAAACCGATTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATGT
1459298 GTTTCAAAAGAAACAGACTCAAAGATGT
1 GTTTCAAAAGAAACAGACTCAAAGATGT
1459326 GTTTCAAGAA-AAACA-AGCTCAAAGATAATGT
1 GTTTCAA-AAGAAACAGA-CTCAAAG---ATGT
1459357 GTTTCAAAAG
1 GTTTCAAAAG
1459367 CAACTGTCTC
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.02
28 43 0.73
29 2 0.03
30 2 0.03
31 11 0.19
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATGT
Found at i:1459544 original size:66 final size:64
Alignment explanation
Indices: 1459368--1459549 Score: 179
Period size: 66 Copynumber: 2.8 Consensus size: 64
1459358 TTTCAAAAGC
* * * *
1459368 AACTGTCTCGAAAGAGACAAAATTCGTTTCAAAGGAAAC-AACCCAAAGA-CGGCGTTTAAAGGG
1 AACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATCGGCGTTTAAAGGG
* * ** * * * * *
1459431 AATTGTCTCAACCGAGACAAAATTTGTTTTTTAAGGGAAACGTTCTCAAAGATCGGTGTTTCATG
1 AACTGTCTCAA-AGAGACAAAA-TT-CATTTCAAGGGAAACGATCTCAAAGATCGGCGTTTAAAG
1459496 GG
63 GG
1459498 AAACTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGAT
1 -AACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGAT
1459550 GTTTGTTTTG
Statistics
Matches: 94, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
62 2 0.02
63 17 0.18
64 2 0.02
65 11 0.12
66 30 0.32
67 13 0.14
68 19 0.20
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (64 bp):
AACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATCGGCGTTTAAAGGG
Found at i:1459934 original size:31 final size:31
Alignment explanation
Indices: 1459891--1459975 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
1459881 ACAAAATTCG
*
1459891 TTTCAAGGGAAAC-GACTCAAAGATGGTTT-TA
1 TTTCAAGAGAAACAGACTCAAAGAT--TTTGTA
*
1459922 TTTCAAGAGAAACAAACTCAAAGATTTTGTA
1 TTTCAAGAGAAACAGACTCAAAGATTTTGTA
* * *
1459953 TTTCTAGAGAAACTGCCTCAAAG
1 TTTCAAGAGAAACAGACTCAAAG
1459976 GAGTCAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 3 0.07
31 33 0.72
32 10 0.22
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (31 bp):
TTTCAAGAGAAACAGACTCAAAGATTTTGTA
Found at i:1460021 original size:97 final size:96
Alignment explanation
Indices: 1459825--1460030 Score: 204
Period size: 98 Copynumber: 2.1 Consensus size: 96
1459815 TAAAACCTTG
* **
1459825 TTTCCAGAGAAACAAACTCAAAGATGATCTTGTTTTAAGAGAAAATGTTTCAAGAGACAAAATTC
1 TTTCAAGAGAAACAAACTCAAAGAT-ATCTTGTTTTAAGAGAAAATGCCTCAAGAGACAAAATTC
* *
1459890 GTTTCAAGGGAAACGACTCAAAGATGGT-TTT
65 GTTTCAAGAGAAACGACTCAAAGATGGTGTAT
* * *
1459921 ATTTCAAGAGAAACAAACTCAAAGAT-T-TTGTATTTCTAGAGAAACTGCCTCAAAGGAGTCAAA
1 -TTTCAAGAGAAACAAACTCAAAGATATCTTGT-TTT-AAGAGAAAATGCCTC-AA-GAGACAAA
* * * *
1459984 ATTTGTTTTAATAGAAACGATCTCAAAGGTGG-GTAT
61 ATTCGTTTCAAGAGAAACGA-CTCAAAGATGGTGTAT
*
1460020 TTTCAAAAGAA
1 TTTCAAGAGAA
1460031 GTTGTCTCGA
Statistics
Matches: 90, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
94 4 0.04
95 4 0.04
96 11 0.12
97 26 0.29
98 33 0.37
99 12 0.13
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (96 bp):
TTTCAAGAGAAACAAACTCAAAGATATCTTGTTTTAAGAGAAAATGCCTCAAGAGACAAAATTCG
TTTCAAGAGAAACGACTCAAAGATGGTGTAT
Found at i:1460484 original size:30 final size:30
Alignment explanation
Indices: 1460421--1460483 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
1460411 AGAGACAAAA
*
1460421 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCCAAAAAAACAAACTCAAAGAT
*
1460451 TTTTGTTT-CAAAAAAACAATCTCAAAGAT
1 TTTTGTTTCCAAAAAAACAAACTCAAAGAT
1460480 TTTT
1 TTTT
1460484 TCACGAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (30 bp):
TTTTGTTTCCAAAAAAACAAACTCAAAGAT
Found at i:1460544 original size:52 final size:53
Alignment explanation
Indices: 1460471--1460575 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 53
1460461 AAAAAACAAT
*
1460471 CTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAACACTTTGTTTCAAA
1 CTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAA
1460524 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAA
1 CTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAA
1460576 ATAAATAGAC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 43 0.84
53 8 0.16
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.31
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAA
Found at i:1460603 original size:30 final size:29
Alignment explanation
Indices: 1460569--1460681 Score: 92
Period size: 27 Copynumber: 4.0 Consensus size: 29
1460559 CAAAACTTTG
* * *
1460569 TTTCAAAATAAATAGACTCAAAGTTTTTTT
1 TTTCAAAAGAAACA-ACTCAAAGATTTTTT
1460599 TTTCAAAAGAAACAACTCAAAGA--TTTT
1 TTTCAAAAGAAACAACTCAAAGATTTTTT
* * *
1460626 ATTCAAAAGGAACAAACTCCAAGA---TTT
1 TTTCAAAAGAAAC-AACTCAAAGATTTTTT
* *
1460653 TTTCAAGAGGAACAAACTCAAAGATTTTT
1 TTTCAAAAGAAAC-AACTCAAAGATTTTT
1460682 CCTCAAAAGA
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
27 39 0.56
28 9 0.13
29 8 0.11
30 14 0.20
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TTTCAAAAGAAACAACTCAAAGATTTTTT
Found at i:1460644 original size:28 final size:27
Alignment explanation
Indices: 1460596--1460690 Score: 129
Period size: 27 Copynumber: 3.4 Consensus size: 27
1460586 TCAAAGTTTT
*
1460596 TTTTTTCAAAAGAAAC-AACTCAAAGA
1 TTTTTTCAAAAGGAACAAACTCAAAGA
*
1460622 TTTTATTCAAAAGGAACAAACTCCAAGA
1 TTTT-TTCAAAAGGAACAAACTCAAAGA
*
1460650 TTTTTTCAAGAGGAACAAACTCAAAGA
1 TTTTTTCAAAAGGAACAAACTCAAAGA
1460677 TTTTTCCTCAAAAG
1 TTTTT--TCAAAAG
1460691 AAATTGTCTT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.07
27 37 0.62
28 13 0.22
29 6 0.10
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (27 bp):
TTTTTTCAAAAGGAACAAACTCAAAGA
Found at i:1461046 original size:36 final size:34
Alignment explanation
Indices: 1460934--1461053 Score: 98
Period size: 37 Copynumber: 3.4 Consensus size: 34
1460924 AGAAAATGAT
* * *
1460934 GTCTCAAGCGAGACAAAGTTTG-CTTTAAGATATA
1 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGA-AAA
** * * *
1460968 GTCTCAAATGAGACAAAATTTATTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAGTTT-GTTTTT-GAGAAA-A
1461005 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAA
1 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAA
*
1461039 CGATCTCAAGTGAGA
1 -G-TCTCAAGCGAGA
1461054 TCAACTTTGT
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
34 18 0.27
35 7 0.11
36 20 0.30
37 21 0.32
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (34 bp):
GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAA
Found at i:1461388 original size:156 final size:156
Alignment explanation
Indices: 1461099--1461398 Score: 403
Period size: 156 Copynumber: 1.9 Consensus size: 156
1461089 GGATCTCAAA
* * *
1461099 GGGAAAAGGTCTCAAGCGAGATGAAATTTGTTTTAAAAGAAACAAGAATCTAAGGTGAGATTAAT
1 GGGAAAAGGTCTCAAGCGAGATGAAATTTGTTTTAAAAGAAAC-AGAATCTAAGATGAGATCAAC
* * * *
1461164 TTTGTTTTTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAAACACA
65 TTTGTTTATAGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAATGTCTCAAACGAAACACA
1461229 ATTTGTTTTAAAATTCTCAAAATTTTT
130 ATTTGTTTTAAAATTCTCAAAATTTTT
* *
1461256 GGGAAAATGTCTCAAGCGAGATGAAATTTGTTTTGAAATAGATAC-G-ATCTCAA-ATGAGATCA
1 GGGAAAAGGTCTCAAGCGAGATGAAATTTGTTTT-AAA-AGAAACAGAATCT-AAGATGAGATCA
* *
1461318 ACTTTGTTTA-ATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAATGTCTCAAATGAGAC
63 ACTTTGTTTATA-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAATGTCTCAAACGAAAC
*
1461382 GA-AATTTGTTTTGAAAT
127 -ACAATTTGTTTTAAAAT
1461399 AAATTGTCTC
Statistics
Matches: 126, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
155 1 0.01
156 80 0.63
157 37 0.29
158 3 0.02
159 5 0.04
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (156 bp):
GGGAAAAGGTCTCAAGCGAGATGAAATTTGTTTTAAAAGAAACAGAATCTAAGATGAGATCAACT
TTGTTTATAGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAATGTCTCAAACGAAACACAA
TTTGTTTTAAAATTCTCAAAATTTTT
Found at i:1462997 original size:13 final size:12
Alignment explanation
Indices: 1462963--1462998 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1462953 CACTTTCTCT
1462963 TTTTTTCTTTGA
1 TTTTTTCTTTGA
*
1462975 TTTTTGCTTTGA
1 TTTTTTCTTTGA
1462987 TTTTTCTCTTTG
1 TTTTT-TCTTTG
1462999 CTCTTTGCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:1463015 original size:25 final size:24
Alignment explanation
Indices: 1462960--1463020 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
1462950 GTCCACTTTC
* *
1462960 TCTTTTTTTCTTTGATTTTTGCTT
1 TCTTTTTCTCTTTGATCTTTGCTT
* *
1462984 TGATTTTTCTCTTTGCTCTTTGCTCT
1 T-CTTTTTCTCTTTGATCTTTGCT-T
1463010 TC-TTTTCTCTT
1 TCTTTTTCTCTT
1463021 CGCTTTAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 10 0.33
25 18 0.60
26 2 0.07
ACGTcount: A:0.03, C:0.20, G:0.08, T:0.69
Consensus pattern (24 bp):
TCTTTTTCTCTTTGATCTTTGCTT
Found at i:1469845 original size:8 final size:7
Alignment explanation
Indices: 1469798--1469865 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 7
1469788 TAAGTTAAAT
1469798 AATAAT-
1 AATAATA
1469804 AATAAT-
1 AATAATA
1469810 AATAAT-
1 AATAATA
1469816 AATAAT-
1 AATAATA
1469822 AATAAT-
1 AATAATA
1469828 AATAATA
1 AATAATA
1469835 AATATATA
1 AATA-ATA
*
1469843 AATGATTA
1 AAT-AATA
*
1469851 AATGAT-
1 AATAATA
1469857 AATAATA
1 AATAATA
1469864 AA
1 AA
1469866 AAAAAGACCC
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
6 35 0.65
7 7 0.13
8 11 0.20
9 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (7 bp):
AATAATA
Found at i:1469863 original size:3 final size:3
Alignment explanation
Indices: 1469795--1469835 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1469785 TTGTAAGTTA
1469795 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1469836 ATATATAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1474353 original size:3 final size:3
Alignment explanation
Indices: 1474345--1474369 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1474335 GTACAACCCT
1474345 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
1474370 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1479894 original size:24 final size:24
Alignment explanation
Indices: 1479848--1479894 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1479838 AGAAGGAACC
**
1479848 CTTTAAATTTTAAGGTAGGTTATG
1 CTTTAAATTTTAAGGTAAATTATG
*
1479872 CTTTAAATTTTATGGTAAATTAT
1 CTTTAAATTTTAAGGTAAATTAT
1479895 ACGTCTAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (24 bp):
CTTTAAATTTTAAGGTAAATTATG
Found at i:1484434 original size:2 final size:2
Alignment explanation
Indices: 1484421--1484451 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
1484411 TCTAATCTAA
1484421 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
1484452 CTTTCTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1498805 original size:16 final size:15
Alignment explanation
Indices: 1498784--1498813 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1498774 AATATTGAAA
1498784 CTTGAACTCGAAAAGG
1 CTTGAACTC-AAAAGG
1498800 CTTGAACTCAAAAG
1 CTTGAACTCAAAAG
1498814 AAAATTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (15 bp):
CTTGAACTCAAAAGG
Found at i:1500082 original size:15 final size:15
Alignment explanation
Indices: 1500062--1500092 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1500052 TCTAAAAAAT
*
1500062 GAGTCAACTCAGACC
1 GAGTCAACTCAAACC
1500077 GAGTCAACTCAAACC
1 GAGTCAACTCAAACC
1500092 G
1 G
1500093 TACTAAGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.32, G:0.19, T:0.13
Consensus pattern (15 bp):
GAGTCAACTCAAACC
Found at i:1502681 original size:29 final size:28
Alignment explanation
Indices: 1502628--1502694 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
1502618 ATGTATATGC
*
1502628 ATGTATGTATCTGTGTATATATGCATCAGT
1 ATGTATGTATATGTGTATATATGCAT--GT
* *
1502658 -TGTATGTATATGTGTATCTCTGCATGT
1 ATGTATGTATATGTGTATATATGCATGT
1502685 ATGTATGTAT
1 ATGTATGTAT
1502695 GTATGATGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 9 0.27
29 22 0.67
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.46
Consensus pattern (28 bp):
ATGTATGTATATGTGTATATATGCATGT
Found at i:1504708 original size:15 final size:15
Alignment explanation
Indices: 1504688--1504724 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1504678 TGAGACATTA
*
1504688 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
1504703 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
1504718 CCCGCCC
1 CCCGCCC
1504725 GCCCAGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:1507644 original size:21 final size:21
Alignment explanation
Indices: 1507628--1507669 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1507618 GCATTGCATT
1507628 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
1507649 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
1507670 CCACGACCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:1507720 original size:5 final size:6
Alignment explanation
Indices: 1507673--1507718 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
1507663 TTGAAAACCA
*
1507673 CGACCA CGACCC CGACCC CGACCC CGACCC CGA-CC CGA-CC CGACCC
1 CGACCC CGACCC CGACCC CGACCC CGACCC CGACCC CGACCC CGACCC
1507719 GAGACGAGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 10 0.26
6 28 0.74
ACGTcount: A:0.20, C:0.63, G:0.17, T:0.00
Consensus pattern (6 bp):
CGACCC
Found at i:1508246 original size:6 final size:6
Alignment explanation
Indices: 1508220--1508267 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
1508210 TCTCGTCTGG
1508220 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1508265 GGT
1 GGT
1508268 AATACGTGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.36
6 27 0.64
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:1508395 original size:21 final size:19
Alignment explanation
Indices: 1508340--1508395 Score: 51
Period size: 21 Copynumber: 2.9 Consensus size: 19
1508330 AAATCTTTTT
1508340 TTTA-ACTATCGCAACGAA
1 TTTAGACTATCGCAACGAA
* ** *
1508358 TTTGGAAAATCGTAACGACA
1 TTTAGACTATCGCAACGA-A
1508378 TTGTAGACTATCGCAACG
1 TT-TAGACTATCGCAACG
1508396 CGAAATGAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
18 3 0.11
19 10 0.37
20 3 0.11
21 11 0.41
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (19 bp):
TTTAGACTATCGCAACGAA
Done.