Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 51 of 172
Found at i:16654344 original size:46 final size:44
Alignment explanation
Indices: 16654201--16654344 Score: 123
Period size: 46 Copynumber: 3.1 Consensus size: 44
16654191 CCCGCCCCTA
*
16654201 AGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * * *
16654248 CA-CGAACTCGGACTCAACTTAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
16654294 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
16654340 AGTGA
1 AGTGA
16654345 CATGTCACTT
Statistics
Matches: 77, Mismatches: 12, Indels: 16
0.73 0.11 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 32 0.42
47 29 0.38
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:16661765 original size:46 final size:46
Alignment explanation
Indices: 16661698--16661870 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
16661688 AACCCGCCCC
* *
16661698 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
16661744 TAAGTGAAGTCGGACTCAACTCAACGAGTTCAGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-G--GAC-A-TTCGCATCCA
* * *
16661792 TCA-CGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
16661837 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
16661871 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 2 0.02
46 58 0.55
47 25 0.24
48 2 0.02
49 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:16661811 original size:93 final size:93
Alignment explanation
Indices: 16661703--16661873 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
16661693 GCCCCTAAGT
* *
16661703 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAAGTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
16661768 CGAGTTCAGATGCCTAGTTACATCTCAC
66 CGAGTTCAGATGCCTAGTTACATCTCAC
* *
16661796 GAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
16661861 CGAGTTCGGATGC
66 CGAGTTCAGATGC
16661874 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATCTCAC
Found at i:16664119 original size:43 final size:43
Alignment explanation
Indices: 16664057--16664204 Score: 124
Period size: 43 Copynumber: 3.5 Consensus size: 43
16664047 CAATACCGAC
** * *
16664057 GTCCCAGATGTGGTCTTACATGTAATTCAATATCGATGCCTCT
1 GTCCCAGACATGGTCTTACACGTAATTCAATATCGATGCCTAT
* * * *
16664100 ATCCCAGACATGGTCTTACACG-AAATCAGATA-CGATGTCAAT
1 GTCCCAGACATGGTCTTACACGTAATTCA-ATATCGATGCCTAT
* * * *
16664142 GTCCCAGACATGGTCCTATACGTAAATCTC-A-ATCGAGGCCTGT
1 GTCCCAGACATGGTCTTACACGT-AAT-TCAATATCGATGCCTAT
*
16664185 GTCCCAGACACGGTCTTACA
1 GTCCCAGACATGGTCTTACA
16664205 TGATATCTTA
Statistics
Matches: 81, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
42 32 0.40
43 45 0.56
44 2 0.02
45 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAATTCAATATCGATGCCTAT
Found at i:16666326 original size:22 final size:22
Alignment explanation
Indices: 16666301--16666346 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
16666291 TCATGTTTCC
16666301 TTGTTTGAGCTCTAGAAATTCT
1 TTGTTTGAGCTCTAGAAATTCT
16666323 TTGTTTGAGCTCTAGAAATTCT
1 TTGTTTGAGCTCTAGAAATTCT
16666345 TT
1 TT
16666347 CTTTTTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (22 bp):
TTGTTTGAGCTCTAGAAATTCT
Found at i:16671748 original size:93 final size:93
Alignment explanation
Indices: 16671584--16671755 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
16671574 CGCCCATAAG
* *
16671584 CGAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAGGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
16671649 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
*
16671677 CGAACTCGGACTCAACTCAACGAGTTCG-GACATTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTCGAG-CATTCGCATCCATAAGTGAACTCGGACTCAACTC
*
16671741 AATGAGTTCGGATGC
65 AACGAGTTCGGATGC
16671756 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 1 0.01
93 73 0.99
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGAGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:16671751 original size:46 final size:47
Alignment explanation
Indices: 16671577--16671752 Score: 193
Period size: 46 Copynumber: 3.8 Consensus size: 47
16671567 TGTAACCCGC
* *
16671577 CCATAAGCGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
* * *
16671623 CCATAGGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-A-TTCGCAT
* *
16671673 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
* *
16671716 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
16671753 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 59 0.55
47 31 0.29
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (47 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
Found at i:16675639 original size:51 final size:51
Alignment explanation
Indices: 16675562--16675694 Score: 146
Period size: 51 Copynumber: 2.6 Consensus size: 51
16675552 CGGATACCCG
* * *
16675562 GTGG-CTTGCACATAGTACCACCCTTGT-AGTCAAAGCTACCTTCTT-CACAAA
1 GTGGCCTT-CACATAGTACCACACTTGTGA-TCAAAACCACC-TCTTACACAAA
* *
16675613 GTGGCCTTCACATAGTACCACACTTGTGATCAAAACCATCTCTTACACATA
1 GTGGCCTTCACATAGTACCACACTTGTGATCAAAACCACCTCTTACACAAA
* * *
16675664 GTGGCCTACACTTAGTACCACACATGTGATC
1 GTGGCCTTCACATAGTACCACACTTGTGATC
16675695 GAAGCTATTG
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
50 4 0.06
51 63 0.89
52 4 0.06
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGATCAAAACCACCTCTTACACAAA
Found at i:16675711 original size:51 final size:51
Alignment explanation
Indices: 16675607--16675740 Score: 144
Period size: 51 Copynumber: 2.6 Consensus size: 51
16675597 CTACCTTCTT
* * * * *
16675607 CACAAAGTGGCCTTCACATAGTACCACACTTGTGATCAAAACCATCTCTTA
1 CACATAGTGGCCTACACTTAGTACCACACATGTGATCAAAACCATCTCATA
* * * *
16675658 CACATAGTGGCCTACACTTAGTACCACACATGTGATCGAAGCTAT-TGGATA
1 CACATAGTGGCCTACACTTAGTACCACACATGTGATCAAAACCATCT-CATA
* * *
16675709 CACATAGTAGCCTGCACTTAGTACTACACATG
1 CACATAGTGGCCTACACTTAGTACCACACATG
16675741 CGACCTAACC
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
50 1 0.01
51 69 0.99
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (51 bp):
CACATAGTGGCCTACACTTAGTACCACACATGTGATCAAAACCATCTCATA
Found at i:16681472 original size:30 final size:30
Alignment explanation
Indices: 16681446--16681504 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
16681436 CATTTTCTTT
16681446 ATTCGATAG-CCAAGGCTATCCCTTTTCATA
1 ATTCGATAGTCCAA-GCTATCCCTTTTCATA
*
16681476 ATTCGATAGTCGAAGCTATCCCTTTTCAT
1 ATTCGATAGTCCAAGCTATCCCTTTTCAT
16681505 GATTTGATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (30 bp):
ATTCGATAGTCCAAGCTATCCCTTTTCATA
Found at i:16681529 original size:30 final size:30
Alignment explanation
Indices: 16681463--16681593 Score: 133
Period size: 30 Copynumber: 4.4 Consensus size: 30
16681453 AGCCAAGGCT
* * * *
16681463 ATCCCTTTTCATAATTCGATAGTCG-AAGCT
1 ATCCCTTTTCATGATTTGATGGTCGTAA-CC
16681493 ATCCCTTTTCATGATTTGATGGTCGTAACC
1 ATCCCTTTTCATGATTTGATGGTCGTAACC
* * *
16681523 ACCCCTTTTCATTG-TTTGGTGGTCGTTACC
1 ATCCCTTTTCA-TGATTTGATGGTCGTAACC
* * *
16681553 ATCCCTTTTCATTA-TTGATGGTTGTCACC
1 ATCCCTTTTCATGATTTGATGGTCGTAACC
16681582 ATCCCTTTTCAT
1 ATCCCTTTTCAT
16681594 AACCAATAGT
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
29 25 0.29
30 57 0.66
31 4 0.05
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (30 bp):
ATCCCTTTTCATGATTTGATGGTCGTAACC
Found at i:16681533 original size:60 final size:59
Alignment explanation
Indices: 16681465--16681627 Score: 170
Period size: 60 Copynumber: 2.8 Consensus size: 59
16681455 CCAAGGCTAT
*
16681465 CCCTTTTCATAATTCGATAGTCGAAGCTATCCCTTTTCATGATTTGATGGTCGTAACCAC
1 CCCTTTTCATAATTCGATAGTCGAAGCCATCCCTTTTCAT-ATTTGATGGTCGTAACCAC
** * * * * * * *
16681525 CCCTTTTCATTGTTTGGTGGTCGTTA-CCATCCCTTTTCAT-TATTGATGGTTGTCACCAT
1 CCCTTTTCATAATTCGATAGTCG-AAGCCATCCCTTTTCATAT-TTGATGGTCGTAACCAC
* *
16681584 CCCTTTTCATAA-CCAATAGTCGAAGCCATCCCTTTTCATATTTG
1 CCCTTTTCATAATTCGATAGTCGAAGCCATCCCTTTTCATATTTG
16681628 TCGATGACCG
Statistics
Matches: 81, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
57 1 0.01
58 23 0.28
59 25 0.31
60 31 0.38
61 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (59 bp):
CCCTTTTCATAATTCGATAGTCGAAGCCATCCCTTTTCATATTTGATGGTCGTAACCAC
Found at i:16683803 original size:17 final size:17
Alignment explanation
Indices: 16683769--16683823 Score: 92
Period size: 17 Copynumber: 3.2 Consensus size: 17
16683759 GATGGTCCGA
*
16683769 AATGGGCCATATGGGCCC
1 AATGGGCC-TACGGGCCC
16683787 AATGGGCCTACGGGCCC
1 AATGGGCCTACGGGCCC
16683804 AATGGGCCTACGGGCCC
1 AATGGGCCTACGGGCCC
16683821 AAT
1 AAT
16683824 TGGATAAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
17 28 0.78
18 8 0.22
ACGTcount: A:0.22, C:0.31, G:0.33, T:0.15
Consensus pattern (17 bp):
AATGGGCCTACGGGCCC
Found at i:16684052 original size:27 final size:28
Alignment explanation
Indices: 16684033--16684285 Score: 251
Period size: 27 Copynumber: 9.4 Consensus size: 28
16684023 ATTACCAAAG
16684033 TACTCC-CGATTTACAGAATTACCATTT
1 TACTCCTCGATTTACAGAATTACCATTT
*
16684060 TA-TCCTCGATTTACAGAATTACCGTTT
1 TACTCCTCGATTTACAGAATTACCATTT
16684087 TAC-CCTCGATTTACAGAATTACCATTT
1 TACTCCTCGATTTACAGAATTACCATTT
**
16684114 TAC-CCTC-AGTTTACAGAATTACTGTTT
1 TACTCCTCGA-TTTACAGAATTACCATTT
* *
16684141 TAC-CCTCGATTTATAGAATTACCGTTT
1 TACTCCTCGATTTACAGAATTACCATTT
* * *
16684168 TAC-CCTCGATTTATAAAATTACCGTTT
1 TACTCCTCGATTTACAGAATTACCATTT
* ***
16684195 TAC-CCTTGATTTACAGAATTACTGGTT
1 TACTCCTCGATTTACAGAATTACCATTT
* *
16684222 TAC-CCTC-AGTTTACAAAATTATCATTT
1 TACTCCTCGA-TTTACAGAATTACCATTT
* * *
16684249 TAC-CCTCGATTTACAAAACTACCGTTT
1 TACTCCTCGATTTACAGAATTACCATTT
16684276 TAC-CCTCGAT
1 TACTCCTCGAT
16684286 AGTGAAATTA
Statistics
Matches: 199, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
26 5 0.03
27 192 0.96
28 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (28 bp):
TACTCCTCGATTTACAGAATTACCATTT
Found at i:16684080 original size:54 final size:54
Alignment explanation
Indices: 16684039--16684285 Score: 318
Period size: 54 Copynumber: 4.6 Consensus size: 54
16684029 AAAGTACTCC
*
16684039 CGATTTACAGAATTACCATTTTATCCTCGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
*
16684093 CGATTTACAGAATTACCATTTTACCCTC-AGTTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCTCGA-TTTACAGAATTACCGTTTTACCCT
* * * *
16684147 CGATTTATAGAATTACCGTTTTACCCTCGATTTATAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* *** * * *
16684201 TGATTTACAGAATTACTGGTTTACCCTC-AGTTTACAAAATTATCATTTTACCCT
1 CGATTTACAGAATTACCATTTTACCCTCGA-TTTACAGAATTACCGTTTTACCCT
* * *
16684255 CGATTTACAAAACTACCGTTTTACCCTCGAT
1 CGATTTACAGAATTACCATTTTACCCTCGAT
16684286 AGTGAAATTA
Statistics
Matches: 170, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
53 2 0.01
54 166 0.98
55 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.39
Consensus pattern (54 bp):
CGATTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
Found at i:16684130 original size:81 final size:82
Alignment explanation
Indices: 16684040--16684282 Score: 339
Period size: 81 Copynumber: 3.0 Consensus size: 82
16684030 AAGTACTCCC
** * *
16684040 GATTTACAGAATTACCATTTTATCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAA
1 GATTTACAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAA
*
16684105 TTACCATTTTACCCTCA
66 TTACCGTTTTACCCTCA
* *
16684122 G-TTTACAGAATTACTGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTATAAAA
1 GATTTACAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAA
*
16684186 TTACCGTTTTACCCT-T
66 TTACCGTTTTACCCTCA
* * * *
16684202 GATTTACAGAATTACTGGTTTACCCTC-AGTTTACAAAATTATCATTTTACCCTCGATTTACAAA
1 GATTTACAGAATTACTGTTTTACCCTCGA-TTTACAGAATTACCGTTTTACCCTCGATTTACAAA
*
16684266 ACTACCGTTTTACCCTC
65 ATTACCGTTTTACCCTC
16684283 GATAGTGAAA
Statistics
Matches: 143, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
80 2 0.01
81 140 0.98
82 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.39
Consensus pattern (82 bp):
GATTTACAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAA
TTACCGTTTTACCCTCA
Found at i:16684321 original size:27 final size:27
Alignment explanation
Indices: 16684291--16684431 Score: 156
Period size: 27 Copynumber: 5.2 Consensus size: 27
16684281 TCGATAGTGA
16684291 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
** *
16684318 AATTTTTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* ** *
16684345 AATTATTGAAATACCGTTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
16684372 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * * *
16684399 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
16684426 AATTAC
1 AATTAC
16684432 CATTTTGCCC
Statistics
Matches: 97, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 97 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:16684669 original size:27 final size:26
Alignment explanation
Indices: 16684631--16684713 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 26
16684621 CGGAGGAAGC
16684631 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCAC-AATATCT
*
16684658 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTATGCCACAATATCT
* * * * *
16684684 ATATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTATGCCACAATATCT
16684711 GTT
1 GTT
16684714 GACCGATCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
26 9 0.18
27 40 0.82
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTATGCCACAATATCT
Found at i:16684833 original size:22 final size:22
Alignment explanation
Indices: 16684801--16684859 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
16684791 CCCGTTATTA
*
16684801 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
16684823 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
16684845 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
16684860 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:16685249 original size:6 final size:6
Alignment explanation
Indices: 16685238--16685381 Score: 154
Period size: 6 Copynumber: 23.8 Consensus size: 6
16685228 CTGTCACCTA
* *
16685238 ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATACTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG
* * *
16685286 ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG -TTACTA
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATT-CTG
16685335 ATAT-TG ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG ATTCT
1 AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
16685382 CAGTTTGATT
Statistics
Matches: 117, Mismatches: 10, Indels: 22
0.79 0.07 0.15
Matches are distributed among these distances:
5 8 0.07
6 101 0.86
7 6 0.05
8 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:16685321 original size:67 final size:67
Alignment explanation
Indices: 16685244--16685370 Score: 229
Period size: 67 Copynumber: 1.9 Consensus size: 67
16685234 CCTAATTCTG
16685244 ATTCTGATTCTGATTCTGTTACTAATACTGATTCTGATTCTGATTCTGATT-CTGATTCTGTCAC
1 ATTCTGATTCTGATTCTGTTACTAATACTGATTCTGATTCTGATTCTG-TTACTGATTCTGTCAC
16685308 CTA
65 CTA
*
16685311 ATTCTGATTCTGATTCTGTTACTAATATTGATTCTGATTCTGATTCTGTTACTGATTCTG
1 ATTCTGATTCTGATTCTGTTACTAATACTGATTCTGATTCTGATTCTGTTACTGATTCTG
16685371 ATTCTGATTC
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
66 2 0.03
67 56 0.97
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.48
Consensus pattern (67 bp):
ATTCTGATTCTGATTCTGTTACTAATACTGATTCTGATTCTGATTCTGTTACTGATTCTGTCACC
TA
Found at i:16685326 original size:73 final size:73
Alignment explanation
Indices: 16685213--16685376 Score: 242
Period size: 73 Copynumber: 2.2 Consensus size: 73
16685203 TTGCATTCAT
* **
16685213 ATTCTGATTTTGATTCTGTCACCTAATTCTGATTCTGATTCTGATT-CTGTTACTAATACTGATT
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTG-TTACTAATACTAATACTGATT
16685277 CTGATTCTG
65 CTGATTCTG
* * *
16685286 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGTTACTAATATTGATTCTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGTTACTAATACTAATACTGATTC
16685351 TGATTCTG
66 TGATTCTG
16685359 -TTACTGATTCTGATTCTG
1 ATT-CTGATTCTGATTCTG
16685377 ATTCTCAGTT
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
72 4 0.05
73 79 0.95
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (73 bp):
ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGTTACTAATACTAATACTGATTC
TGATTCTG
Found at i:16685390 original size:24 final size:24
Alignment explanation
Indices: 16685239--16685402 Score: 144
Period size: 24 Copynumber: 6.8 Consensus size: 24
16685229 TGTCACCTAA
16685239 TTCTGATTCTGATTCTGATTCT-G
1 TTCTGATTCTGATTCTGATTCTAG
* *
16685262 TTACTAATACTGATTCTGATTCT-G
1 TT-CTGATTCTGATTCTGATTCTAG
* *
16685286 ATTCTGATTCTGATTCTG-TCACCTAA
1 -TTCTGATTCTGATTCTGAT--TCTAG
*
16685312 TTCTGATTCTGATTCTG-TTACTAA
1 TTCTGATTCTGATTCTGATT-CTAG
16685336 TAT-TGATTCTGATTCTGATTCT-G
1 T-TCTGATTCTGATTCTGATTCTAG
16685359 TTACTGATTCTGATTCTGATTCTCAG
1 TT-CTGATTCTGATTCTGATTCT-AG
**
16685385 TT-TGATTCCAATTCTGAT
1 TTCTGATTCTGATTCTGAT
16685403 AATGTTTCTT
Statistics
Matches: 119, Mismatches: 10, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
22 1 0.01
23 4 0.03
24 86 0.72
25 25 0.21
26 3 0.03
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (24 bp):
TTCTGATTCTGATTCTGATTCTAG
Found at i:16687412 original size:27 final size:27
Alignment explanation
Indices: 16687397--16687646 Score: 315
Period size: 27 Copynumber: 9.3 Consensus size: 27
16687387 CCAAAGTACT
*
16687397 CTCGATTTACTGAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
16687424 CTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
16687451 CTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
* *
16687478 CTC-AGTTTACAGAATTACTGTTTTATC
1 CTCGA-TTTACAGAATTACCGTTTTACC
* *
16687505 CTCGATTTATAGAATTACCATTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
* ** * *
16687532 CTTGATTTGTAAAATTACCATTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
* * *
16687559 CTTGATTTACAGAATTACTGGTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
* * *
16687586 CTC-AGTTTACAAAATTATCATTTTACC
1 CTCGA-TTTACAGAATTACCGTTTTACC
*
16687613 CTCGATTTACAGAATTACCATTTTACC
1 CTCGATTTACAGAATTACCGTTTTACC
16687640 CTCGATT
1 CTCGATT
16687647 GTGAAATTAC
Statistics
Matches: 195, Mismatches: 24, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
26 2 0.01
27 191 0.98
28 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (27 bp):
CTCGATTTACAGAATTACCGTTTTACC
Found at i:16687681 original size:27 final size:27
Alignment explanation
Indices: 16687651--16687791 Score: 174
Period size: 27 Copynumber: 5.2 Consensus size: 27
16687641 TCGATTGTGA
*
16687651 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
16687678 AATTTCCGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
16687705 AATTACTGAAATACCCTTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
16687732 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
16687759 AATTACTGAGATACCCTTGTGGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
16687786 AATTAC
1 AATTAC
16687792 CATTTTGCCC
Statistics
Matches: 97, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 97 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:16687719 original size:54 final size:54
Alignment explanation
Indices: 16687651--16687792 Score: 203
Period size: 54 Copynumber: 2.6 Consensus size: 54
16687641 TCGATTGTGA
* * *
16687651 AATTACTAAAATACCCCTGTAGGGTAGAATTTCCGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAG
* * *
16687705 AATTACTGAAATACCCTTATAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAG
* * *
16687759 AATTACTGAGATACCCTTGTGGGGTAAAATTACC
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACC
16687793 ATTTTGCCCC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (54 bp):
AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAG
Found at i:16688029 original size:27 final size:26
Alignment explanation
Indices: 16687991--16688073 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
16687981 CGGAGGAAGC
*
16687991 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
16688018 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
16688044 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
16688071 GTT
1 GTT
16688074 GACTGATCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:16688406 original size:27 final size:27
Alignment explanation
Indices: 16688392--16688457 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
16688382 TTTGCCTCAT
16688392 TATCTG-ATTCTGGTGGCTCTGCCACAA
1 TATCTGTA-TCTGGTGGCTCTGCCACAA
* * *
16688419 TATCTGTATCTGGTGACTCTGTCACGA
1 TATCTGTATCTGGTGGCTCTGCCACAA
16688446 TATCTGT-TCTGG
1 TATCTGTATCTGG
16688458 CAGCCATGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.14
27 29 0.83
28 1 0.03
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (27 bp):
TATCTGTATCTGGTGGCTCTGCCACAA
Found at i:16688611 original size:6 final size:6
Alignment explanation
Indices: 16688600--16688834 Score: 200
Period size: 6 Copynumber: 38.8 Consensus size: 6
16688590 CTGTCACCTA
* * *
16688600 ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATACTG ATTCTG ATTCTA
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG
* * *
16688648 ATTCTG -TTAGTG ATTCTG ATTCTG ATTCT- ATCACCTA ATTCTG ATTCTG
1 ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
* *
16688697 ATTCTG -TTACTA ATACTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG
1 ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
* * * *
16688745 ATTCTG ATTCT- ATCACCTA ATTCTG ATTCTG ATTCTG ATTTTG -TTACTA
1 ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG
16688794 ATAT-TG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG ATTCT
1 AT-TCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
16688835 CATTTTGGTT
Statistics
Matches: 187, Mismatches: 22, Indels: 40
0.75 0.09 0.16
Matches are distributed among these distances:
5 17 0.09
6 152 0.81
7 13 0.07
8 5 0.03
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:16688710 original size:79 final size:78
Alignment explanation
Indices: 16688606--16688834 Score: 329
Period size: 79 Copynumber: 2.9 Consensus size: 78
16688596 CCTAATTCTG
*
16688606 ATTCTGATTCTGATTCTGTTACTAATACTGATTCTGATTCTAATTCTGTTAGTGATTCTGATTCT
1 ATTCTGATTCTGATTCTGTTACTAATACTGATTCTGATTCT-ATTCTGTTACTGATTCTGATTCT
16688671 GATTCTATCACCTA
65 GATTCTATCACCTA
*
16688685 ATTCTGATTCTGATTCTGTTACTAATACTGATTCTGATTCTGTTACTGATT-CTGATTCTGATTC
1 ATTCTGATTCTGATTCTGTTACTAATACTGATTCTGATTCTATT-CTG-TTACTGATTCTGATTC
16688749 TGATTCTATCACCTA
64 TGATTCTATCACCTA
* ** *
16688764 ATTCTGATTCTGATTCTGATT-TTGTTACTAATAT-TGATTCTGATTCTGTTACTGATTCTGATT
1 ATTCTGATTCTGATTCTG-TTACTAATACTGAT-TCTGATTCT-ATTCTGTTACTGATTCTGATT
16688827 CTGATTCT
63 CTGATTCT
16688835 CATTTTGGTT
Statistics
Matches: 137, Mismatches: 7, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
78 4 0.03
79 126 0.92
80 7 0.05
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.48
Consensus pattern (78 bp):
ATTCTGATTCTGATTCTGTTACTAATACTGATTCTGATTCTATTCTGTTACTGATTCTGATTCTG
ATTCTATCACCTA
Found at i:16688722 original size:85 final size:79
Alignment explanation
Indices: 16688575--16688834 Score: 303
Period size: 79 Copynumber: 3.2 Consensus size: 79
16688565 TTGCATTCAT
* * **
16688575 ATTCTGATTTTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
1 ATTCTGATTCTGATTCTATCACCTAATTCTGATTCTGATTCTGATTCTAATACTAATACTGATTC
*
16688640 TGATTCTAATTCTG-TTAGTG
66 TG--T-T-A--CTGATT-CTG
* *
16688660 ATTCTGATTCTGATTCTATCACCTAATTCTGATTCTGATTCTG-TTACTAATACTGATTCTGATT
1 ATTCTGATTCTGATTCTATCACCTAATTCTGATTCTGATTCTGATT-CTAATACTAATACTGATT
16688724 CTGTTACTGATTCTG
65 CTGTTACTGATTCTG
* ** *
16688739 ATTCTGATTCTGATTCTATCACCTAATTCTGATTCTGATTCTGATTTTGTTACTAATATTGATTC
1 ATTCTGATTCTGATTCTATCACCTAATTCTGATTCTGATTCTGATTCTAATACTAATACTGATTC
16688804 TGATT-CTG-TTACTG
66 TG-TTACTGATT-CTG
16688818 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
16688835 CATTTTGGTT
Statistics
Matches: 157, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
78 2 0.01
79 86 0.55
80 6 0.04
81 1 0.01
82 1 0.01
83 1 0.01
84 2 0.01
85 58 0.37
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.48
Consensus pattern (79 bp):
ATTCTGATTCTGATTCTATCACCTAATTCTGATTCTGATTCTGATTCTAATACTAATACTGATTC
TGTTACTGATTCTG
Found at i:16693623 original size:47 final size:48
Alignment explanation
Indices: 16693548--16693682 Score: 184
Period size: 49 Copynumber: 2.8 Consensus size: 48
16693538 GGTAAGACGC
16693548 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCACACATCAAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCACACATCAAAGT
* * * *
16693596 CGATGCCATGTCCC-GACATGGTCTTACACTGACTCTCATATATCGAGGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGA--CTCACACATCAAAGT
* *
16693645 CGATGCCATATCCCAGATATGGTCTTACACT-ACTCACA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCACA
16693683 TCTGTCGGTG
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
47 23 0.30
48 14 0.18
49 25 0.32
50 15 0.19
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTCACACATCAAAGT
Found at i:16693696 original size:49 final size:49
Alignment explanation
Indices: 16693548--16693710 Score: 183
Period size: 49 Copynumber: 3.3 Consensus size: 49
16693538 GGTAAGACGC
* **
16693548 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCACA-C-ATCAAAGT
1 CGATGCCATATCCCAGACATGGTCTTACACTGACTCACATCTATC-GGGT
* * *
16693596 CGATGCCATGTCCC-GACATGGTCTTACACTGACTCTCATATATCGAGGT
1 CGATGCCATATCCCAGACATGGTCTTACACTGACTCACATCTATCG-GGT
* *
16693645 CGATGCCATATCCCAGATATGGTCTTACACT-ACTCACATCTGTCGGTGT
1 CGATGCCATATCCCAGACATGGTCTTACACTGACTCACATCTATCGG-GT
16693694 CGATGCCA-AGTCCCAGA
1 CGATGCCATA-TCCCAGA
16693711 AAGTTATATG
Statistics
Matches: 100, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
47 23 0.23
48 16 0.16
49 46 0.46
50 15 0.15
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (49 bp):
CGATGCCATATCCCAGACATGGTCTTACACTGACTCACATCTATCGGGT
Found at i:16700651 original size:17 final size:17
Alignment explanation
Indices: 16700614--16700653 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
16700604 TGGTATGAAT
*
16700614 GAACTATTATTTCATAT
1 GAACTATTATTTCATAC
* *
16700631 GAACTATTATTTTATGC
1 GAACTATTATTTCATAC
16700648 GAACTA
1 GAACTA
16700654 CCTATTCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (17 bp):
GAACTATTATTTCATAC
Found at i:16705606 original size:33 final size:33
Alignment explanation
Indices: 16705569--16705662 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 33
16705559 AACACAGTGT
*
16705569 CAGTACAATCTGGGCCAAAGCCCTATTCAGTAA
1 CAGTACAATCTGGGCCTAAGCCCTATTCAGTAA
* * *
16705602 CAGTACAGTCTAGGCCTTAGCCC--TTC---AA
1 CAGTACAATCTGGGCCTAAGCCCTATTCAGTAA
*
16705630 CAGTAGCAATATGGGCCTAAGCCCTAATTCAGT
1 CAGTA-CAATCTGGGCCTAAGCCCT-ATTCAGT
16705663 CTCGACATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
28 7 0.15
29 14 0.30
31 3 0.07
32 3 0.07
33 19 0.41
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (33 bp):
CAGTACAATCTGGGCCTAAGCCCTATTCAGTAA
Found at i:16705744 original size:30 final size:31
Alignment explanation
Indices: 16705668--16705750 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
16705658 TCAGTCTCGA
16705668 CATAT-ACTAGGCCGAAGCCTTTTCATAAAT
1 CATATCACTAGGCCGAAGCCTTTTCATAAAT
*
16705698 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTAGGCCGAAGCCTTTTCATAAAT
16705729 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTAGGCCGAAGCCTTT
16705751 ACTGTAAGTG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 18 0.35
31 33 0.65
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (31 bp):
CATATCACTAGGCCGAAGCCTTTTCATAAAT
Found at i:16705997 original size:25 final size:25
Alignment explanation
Indices: 16705969--16706038 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
16705959 CTCTTTTAAT
* *
16705969 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTAGGGCAAAGCCCTTTTCGATA
*
16705994 AACTAGGGCAAAGCCCTTTTCGGTA
1 AACTAGGGCAAAGCCCTTTTCGATA
*
16706019 AACTAGGGCATAGCCCTTTT
1 AACTAGGGCAAAGCCCTTTT
16706039 AACACTTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (25 bp):
AACTAGGGCAAAGCCCTTTTCGATA
Found at i:16706910 original size:27 final size:27
Alignment explanation
Indices: 16706851--16706912 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
16706841 CATATTTTCC
16706851 ATTTTACCATACAGGGGTATTACGGTT
1 ATTTTACCATACAGGGGTATTACGGTT
* *
16706878 ACTTTACCCTACAGGGGCT-TTACGGTCT
1 ATTTTACCATACAGGGG-TATTACGGT-T
16706906 -TTTTACC
1 ATTTTACC
16706913 TATTAGGGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 28 0.93
28 2 0.07
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (27 bp):
ATTTTACCATACAGGGGTATTACGGTT
Found at i:16706996 original size:27 final size:27
Alignment explanation
Indices: 16706966--16707063 Score: 83
Period size: 27 Copynumber: 3.6 Consensus size: 27
16706956 GTCAATCTAC
16706966 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
16706993 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
** **
16707019 AGAAAGTTAAGGGTATTTTTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
* *
16707049 AAATCAGGGGTATTT
1 AAACCAAGGGTATTT
16707064 TGGTAAATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
26 1 0.02
27 32 0.56
28 7 0.12
29 16 0.28
30 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:16707069 original size:27 final size:27
Alignment explanation
Indices: 16707029--16707179 Score: 146
Period size: 27 Copynumber: 5.6 Consensus size: 27
16707019 AGAAAGTTAA
* **
16707029 GGGTATTTTTGTAATTTTGTAAATCAG
1 GGGTATTTTGGTAATTTTACAAATCAG
* *
16707056 GGGTATTTTGGTAAATTTACAAATTAG
1 GGGTATTTTGGTAATTTTACAAATCAG
* *
16707083 GGGTATTTCGGT-ATTTTCACAAACCAG
1 GGGTATTTTGGTAATTTT-ACAAATCAG
*
16707110 TGGTATTTTGGTAATTTTACAAA-CTAG
1 GGGTATTTTGGTAATTTTACAAATC-AG
* **
16707137 GGGTATTTTGGTAATTCTACCCTAT-AG
1 GGGTATTTTGGTAATTTTA-CAAATCAG
*
16707164 GGGTATTTTAGTAATT
1 GGGTATTTTGGTAATT
16707180 CCATAATTGA
Statistics
Matches: 103, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
26 5 0.05
27 91 0.88
28 7 0.07
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAG
Found at i:16707214 original size:27 final size:26
Alignment explanation
Indices: 16707188--16707275 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 26
16707178 TTCCATAATT
*
16707188 GAGGGTAAAACTGTAACTTTGTAAATT
1 GAGGGTAAAACTGTAA-TTTGTAAATC
16707215 GAGGGTAAAA-TAGTAATTTTGTAAATC
1 GAGGGTAAAACT-GTAA-TTTGTAAATC
* * *
16707242 AAGGGTAAAACAGTAATTCTATAAATC
1 GAGGGTAAAACTGTAATT-TGTAAATC
16707269 GAGGGTA
1 GAGGGTA
16707276 CTTTGGTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
26 3 0.06
27 49 0.94
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.30
Consensus pattern (26 bp):
GAGGGTAAAACTGTAATTTGTAAATC
Found at i:16709111 original size:46 final size:46
Alignment explanation
Indices: 16709057--16709221 Score: 185
Period size: 46 Copynumber: 3.6 Consensus size: 46
16709047 GTTGAGCATC
*
16709057 CGAACTCGTTGAGTTGAGTCTGAGTTCACTTACGGATGCGAATGTT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTT
* * * *
16709103 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAA-T--G--TT
*
16709150 CGAACTCGTTAAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTT
* *
16709196 CAAACTCGTTGAGTTGAGTCTGAGTT
1 CGAACTCGTTGAGTTGAGTCCGAGTT
16709222 TGTGAGATCT
Statistics
Matches: 97, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 50 0.52
47 27 0.28
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTT
Found at i:16709168 original size:47 final size:47
Alignment explanation
Indices: 16709103--16709269 Score: 164
Period size: 47 Copynumber: 3.6 Consensus size: 47
16709093 TGCGAATGTT
16709103 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
* * * * *
16709150 CGAACTCGTTAAGTTGAGTCCGAGTTCACTTACGGATGCGAA-T--G--TT
1 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATC
* * * *
16709196 CAAACTCGTTGAGTTGAGTCTGAGTTTGTGAGATCTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
* *
16709243 CGAACTCATTTAGTTGAGTCCGAGTTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTC
16709270 ACTTATGGAT
Statistics
Matches: 92, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 24 0.26
47 49 0.53
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (47 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
Found at i:16709211 original size:93 final size:93
Alignment explanation
Indices: 16709052--16709315 Score: 393
Period size: 93 Copynumber: 2.8 Consensus size: 93
16709042 GGATGGTTGA
* *
16709052 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
*
16709117 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATCTAACTAG
*
16709145 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTCAAACTCGTTGAGT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
* *
16709210 TGAGTCTGAGTTTGTGAGATCTAACTAG
66 TGAGTCCGAGTTCGTGAGATCTAACTAG
* * * * * ** * *
16709238 GCATCCGAACTCATTTAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
16709303 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
16709316 ACTTAGGGGC
Statistics
Matches: 153, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 153 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATCTAACTAG
Found at i:16711660 original size:16 final size:16
Alignment explanation
Indices: 16711639--16711670 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16711629 CGGAAAGTCA
16711639 AGAAATATGAATCCTC
1 AGAAATATGAATCCTC
16711655 AGAAATATGAATCCTC
1 AGAAATATGAATCCTC
16711671 GTCCCCAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (16 bp):
AGAAATATGAATCCTC
Found at i:16725007 original size:42 final size:42
Alignment explanation
Indices: 16724890--16725036 Score: 118
Period size: 43 Copynumber: 3.4 Consensus size: 42
16724880 GGAAAGCTCG
* * *
16724890 TACAATGCCAACGTCCAAGATGTGGTCTTACATGTAATCAAA
1 TACAATGCCAACGTCCCAGATGTGGTCTTACACGAAATCAAA
* * ** * * * *
16724932 TATCGATACCAGTGTCACAAACAG-AGTCTTACACGAAATCAAA
1 TA-CAATGCCAACGTCCCAGA-TGTGGTCTTACACGAAATCAAA
16724975 TACAATGCCAACGTCCCAGATGTGGTCTTACACGTAAATACCAAA
1 TACAATGCCAACGTCCCAGATGTGGTCTTACACG-AAAT--CAAA
* *
16725020 T-CGATGCCAACATCCCA
1 TACAATGCCAACGTCCCA
16725037 AACATGGTTT
Statistics
Matches: 78, Mismatches: 21, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
41 1 0.01
42 24 0.31
43 33 0.42
44 15 0.19
45 5 0.06
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (42 bp):
TACAATGCCAACGTCCCAGATGTGGTCTTACACGAAATCAAA
Found at i:16732141 original size:22 final size:19
Alignment explanation
Indices: 16732102--16732143 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
16732092 TGTAAAGTTG
16732102 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
16732121 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
16732143 A
1 A
16732144 ATAACTATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:16732257 original size:29 final size:30
Alignment explanation
Indices: 16732198--16732258 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
16732188 GCCTTTTAAA
* * *
16732198 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCAACCAAATTTT
*
16732228 AATATTTGCAAAAAGA-GCAACCAAATTTT
1 AATATTTACAAAAAGAGGCAACCAAATTTT
16732257 AA
1 AA
16732259 AAATAGTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.31
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCAACCAAATTTT
Found at i:16735496 original size:40 final size:41
Alignment explanation
Indices: 16735420--16735687 Score: 298
Period size: 40 Copynumber: 6.6 Consensus size: 41
16735410 AACCCAAGTA
* * *
16735420 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
* *
16735459 CCTTCGAGTCTTAGCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
*
16735499 CCTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTA---GCACAAATG
* * *
16735542 CCTTCAGGACTTCGCCAGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
* *
16735582 CCTTCGGGACTTAGCCCGTATATAG-GAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTA---GCACAAATG
* * *
16735625 CCTCCGGGACTTCGCCCAGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
*
16735665 CCTTCGGGACTTAGCCCGAATAT
1 CCTTCGGGACTTAGCCCGGATAT
16735688 CATCCGAATA
Statistics
Matches: 191, Mismatches: 26, Indels: 23
0.80 0.11 0.10
Matches are distributed among these distances:
39 12 0.06
40 109 0.57
41 1 0.01
43 68 0.36
44 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
Found at i:16735540 original size:83 final size:83
Alignment explanation
Indices: 16735420--16735687 Score: 384
Period size: 83 Copynumber: 3.3 Consensus size: 83
16735410 AACCCAAGTA
* * * *
16735420 CCTTCGGGATTTAG-CCGGATATAGC-A--ACTCGTACAAATGCCTTCGAGTCTTAGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAGCAACTACTCGCACAAATGCCTTCGAGACTTCGCCCGGATA
16735481 TAGTCACTAGCACAAATG
66 TAGTCACTAGCACAAATG
* *
16735499 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGCCTTC-AGGACTTCGCCAGGAT
1 CCTTCGGGACTTAGCCCGGATATAGCAACTACTCGCACAAATGCCTTCGA-GACTTCGCCCGGAT
16735563 ATAGTCACTAGCACAAATG
65 ATAGTCACTAGCACAAATG
* * * * *
16735582 CCTTCGGGACTTAGCCCGTATATAGGAACTACTCGCACAAATGCCTCCGGGACTTCGCCCAGATA
1 CCTTCGGGACTTAGCCCGGATATAGCAACTACTCGCACAAATGCCTTCGAGACTTCGCCCGGATA
16735647 TAGTCACTAGCACAAATG
66 TAGTCACTAGCACAAATG
*
16735665 CCTTCGGGACTTAGCCCGAATAT
1 CCTTCGGGACTTAGCCCGGATAT
16735688 CATCCGAATA
Statistics
Matches: 169, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
79 13 0.08
80 10 0.06
81 1 0.01
82 1 0.01
83 144 0.85
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (83 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTACTCGCACAAATGCCTTCGAGACTTCGCCCGGATA
TAGTCACTAGCACAAATG
Found at i:16743675 original size:83 final size:83
Alignment explanation
Indices: 16743552--16743779 Score: 356
Period size: 83 Copynumber: 2.8 Consensus size: 83
16743542 AACCCAAGTA
* * *
16743552 CCTTCGGGATTTAG-CCGGATATAGC-A--ACTCACACAAATGCCTTCGGGTCTTAGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAGCAACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
16743613 TAGTCACTAGCACAAATG
66 TAGTCACTAGCACAAATG
* *
16743631 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGCCTTCGGGACTTCGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAGCAACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
16743696 TAGTCACTAGCACAAATG
66 TAGTCACTAGCACAAATG
** *
16743714 CCTTTAGGACTTAGCCCGGATATAGGAACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAGCAACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
16743779 T
66 T
16743780 CATCCGAATA
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
79 13 0.10
80 10 0.07
81 1 0.01
83 111 0.82
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (83 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
TAGTCACTAGCACAAATG
Found at i:16743679 original size:43 final size:42
Alignment explanation
Indices: 16743552--16743779 Score: 285
Period size: 40 Copynumber: 5.5 Consensus size: 42
16743542 AACCCAAGTA
* *
16743552 CCTTCGGGATTTAG-CCGGATATAGCA--ACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCACTACTCGCACAAATG
*
16743591 CCTTCGGGTCTTAGCCCGGATATAGTCACTA---GCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CACTACTCGCACAAATG
*
16743631 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGC-ACTACTCGCACAAATG
*
16743674 CCTTCGGGACTTCGCCCGGATATAGTCACTA---GCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CACTACTCGCACAAATG
** *
16743714 CCTTTAGGACTTAGCCCGGATATAGGAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATA-GCACTACTCGCACAAATG
16743757 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
16743780 CATCCGAATA
Statistics
Matches: 163, Mismatches: 13, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
39 13 0.08
40 79 0.48
41 3 0.02
43 67 0.41
44 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (42 bp):
CCTTCGGGACTTAGCCCGGATATAGCACTACTCGCACAAATG
Found at i:16748575 original size:29 final size:29
Alignment explanation
Indices: 16748532--16748605 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
16748522 TAATCAACCA
* *
16748532 CGCACACTTATTGCCATGTCCTTT-AAACT
1 CGCACACTTAGTGCCATG-CATTTCAAACT
**
16748561 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
16748590 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
16748606 ATCTCACAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.10
29 35 0.90
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:16763306 original size:57 final size:58
Alignment explanation
Indices: 16763230--16763352 Score: 142
Period size: 57 Copynumber: 2.1 Consensus size: 58
16763220 TACCAATCTA
* * * * *
16763230 GGCTAAATCCTATCCATAGCATATGCTCTAGAGAGCTTA-ATATAG-ATTACTCGTCTG
1 GGCTAAATCCAATCCATAGCATAAGCTCAAGAGAGCTTACAT-TAGAATTACCCGTCCG
** * *
16763287 GGCTAAATCCAATTTATAGCCTAAGCTCAAGAGGGCTTACATTAGAATTACCCGTCCG
1 GGCTAAATCCAATCCATAGCATAAGCTCAAGAGAGCTTACATTAGAATTACCCGTCCG
16763345 GGCTAAAT
1 GGCTAAAT
16763353 TCTATCTGCA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
57 35 0.64
58 20 0.36
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (58 bp):
GGCTAAATCCAATCCATAGCATAAGCTCAAGAGAGCTTACATTAGAATTACCCGTCCG
Found at i:16772834 original size:47 final size:46
Alignment explanation
Indices: 16772780--16772897 Score: 119
Period size: 47 Copynumber: 2.5 Consensus size: 46
16772770 GATTTTATGA
**
16772780 GATGAATGTGAATGTGTATATATGAGATAAGGCCTAATGGCCAATGT
1 GATGAATGTGAA-GTGTATATATGAGATAAGGCAGAATGGCCAATGT
* * * * * *
16772827 GATGAATGTGAACATGCATATGTGTGATAAGGTAGAATGGCTAATGT
1 GATGAATGTGAA-GTGTATATATGAGATAAGGCAGAATGGCCAATGT
* *
16772874 GATAAACGTGGAAGTGTATATATG
1 GATGAATGT-GAAGTGTATATATG
16772898 TGGCGAAGCC
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
47 53 0.95
48 3 0.05
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.30
Consensus pattern (46 bp):
GATGAATGTGAAGTGTATATATGAGATAAGGCAGAATGGCCAATGT
Found at i:16774873 original size:17 final size:15
Alignment explanation
Indices: 16774840--16774882 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
16774830 TAGTTTATGC
16774840 TATTTTCTTAATATTT
1 TATTTT-TTAATATTT
16774856 TATTTTTTCAATATTTT
1 TATTTTTT-AATA-TTT
*
16774873 TAATTTTTAA
1 TATTTTTTAA
16774883 ATTATTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 12 0.50
17 10 0.42
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTTAATATTT
Found at i:16788040 original size:42 final size:42
Alignment explanation
Indices: 16787992--16788101 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 42
16787982 ACTGAGATTA
*
16787992 CGTGTAAGACCATATCTGGGATATGACATCGATATGAAA-CTT
1 CGTGTAAGACCATATCTGGGATATGACATCGATATGAAATC-C
* * * * *
16788034 CGTGTAAGACCATACCTAGGCTATTGGCATCGATATGAGATCC
1 CGTGTAAGACCATATCTGGGATA-TGACATCGATATGAAATCC
* *
16788077 CATGTAAGACTATATCTGGGATATG
1 CGTGTAAGACCATATCTGGGATATG
16788102 GCATTGGTGT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
42 22 0.40
43 32 0.58
44 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGATATGACATCGATATGAAATCC
Found at i:16791428 original size:27 final size:27
Alignment explanation
Indices: 16791397--16791487 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 27
16791387 CCCCAATATT
*
16791397 GGTAAAATTATCGAAATACCCTTGTAG
1 GGTAAAATGATCGAAATACCCTTGTAG
* * * *
16791424 TGTAAAATGATCGTAATACCCCTATAG
1 GGTAAAATGATCGAAATACCCTTGTAG
* *
16791451 GGTAAAATGA-CCATAATACCCTTGTAA
1 GGTAAAATGATCGA-AATACCCTTGTAG
*
16791478 GGTAGAATGA
1 GGTAAAATGA
16791488 CGATTATGCC
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
26 1 0.02
27 50 0.98
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (27 bp):
GGTAAAATGATCGAAATACCCTTGTAG
Found at i:16791762 original size:22 final size:22
Alignment explanation
Indices: 16791734--16791829 Score: 120
Period size: 22 Copynumber: 4.4 Consensus size: 22
16791724 GGCCTTTAGT
* *
16791734 CGTCCTGTCTAAGGTGTTGAGC
1 CGTCCTGCCTACGGTGTTGAGC
**
16791756 CGTCCTGCCTACGGTGTTGAAT
1 CGTCCTGCCTACGGTGTTGAGC
*
16791778 CGTCCTGCCTATGGTGTTGAGC
1 CGTCCTGCCTACGGTGTTGAGC
* *
16791800 TGTCCTGCCTACGGCGTTGAGC
1 CGTCCTGCCTACGGTGTTGAGC
*
16791822 TGTCCTGC
1 CGTCCTGC
16791830 TGACTTAGTG
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.10, C:0.28, G:0.30, T:0.31
Consensus pattern (22 bp):
CGTCCTGCCTACGGTGTTGAGC
Found at i:16791829 original size:44 final size:44
Alignment explanation
Indices: 16791733--16791819 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
16791723 CGGCCTTTAG
* *
16791733 TCGTCCTGTCTAAGGTGTTGAGCCGTCCTGCCTACGGTGTTGAA
1 TCGTCCTGCCTAAGGTGTTGAGCCGTCCTGCCTACGGCGTTGAA
* *
16791777 TCGTCCTGCCTATGGTGTTGAGCTGTCCTGCCTACGGCGTTGA
1 TCGTCCTGCCTAAGGTGTTGAGCCGTCCTGCCTACGGCGTTGA
16791820 GCTGTCCTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.11, C:0.26, G:0.30, T:0.32
Consensus pattern (44 bp):
TCGTCCTGCCTAAGGTGTTGAGCCGTCCTGCCTACGGCGTTGAA
Found at i:16801163 original size:116 final size:116
Alignment explanation
Indices: 16800948--16801176 Score: 368
Period size: 116 Copynumber: 2.0 Consensus size: 116
16800938 ATGCATACTA
* * *
16800948 CTATTTATGAAATTGTGTTGATATATAAATTTTGATATTTTTATGAAACGTATGTTTTAATTACT
1 CTATATATGAAATTGGGTTGATATATAAATTATGATATTTTTATGAAACGTATGTTTTAATTACT
* *
16801013 GGTTGTTACCTAAGTTAAGACTATGTAGAATTAAACTGTATAAATTCTCTG
66 AGTTGTTACCTAAGTTAAGACCATGTAGAATTAAACTGTATAAATTCTCTG
* *
16801064 CTATATATGAAATTGGGTTGATATATAAATTATGATATTTTTATGAGATGTATGTTTTAATTACT
1 CTATATATGAAATTGGGTTGATATATAAATTATGATATTTTTATGAAACGTATGTTTTAATTACT
* * *
16801129 AGTTGTTATCTAAGTTAAGACCATGTGGAGTTAAACTGTATAAATTCT
66 AGTTGTTACCTAAGTTAAGACCATGTAGAATTAAACTGTATAAATTCT
16801177 TTATAATATT
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
116 103 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (116 bp):
CTATATATGAAATTGGGTTGATATATAAATTATGATATTTTTATGAAACGTATGTTTTAATTACT
AGTTGTTACCTAAGTTAAGACCATGTAGAATTAAACTGTATAAATTCTCTG
Found at i:16807396 original size:12 final size:13
Alignment explanation
Indices: 16807375--16807414 Score: 64
Period size: 12 Copynumber: 3.1 Consensus size: 13
16807365 GTTGAAGAAG
16807375 AAGAAGAAAAAGA
1 AAGAAGAAAAAGA
16807388 AAGAA-AAAAAGA
1 AAGAAGAAAAAGA
16807400 AAGAAGGAAAAAGA
1 AAGAA-GAAAAAGA
16807414 A
1 A
16807415 GATGGAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.48
13 5 0.20
14 8 0.32
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAAAGA
Found at i:16807402 original size:16 final size:17
Alignment explanation
Indices: 16807372--16807416 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
16807362 AAAGTTGAAG
*
16807372 AAGAAGAAGAA-AAAGA
1 AAGAAAAAGAAGAAAGA
16807388 AAGAAAAA-AAGAAAGA
1 AAGAAAAAGAAGAAAGA
*
16807404 AGGAAAAAGAAGA
1 AAGAAAAAGAAGA
16807417 TGGAGAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 19 0.76
17 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAGAAAGA
Found at i:16810435 original size:14 final size:13
Alignment explanation
Indices: 16810407--16810443 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
16810397 ATCTTGGAAT
16810407 ATTAA-AACAATA
1 ATTAAGAACAATA
16810419 ATTAAGAACACATA
1 ATTAAGAACA-ATA
16810433 ATTAAGAACAA
1 ATTAAGAACAA
16810444 ATCAAGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 13 0.57
ACGTcount: A:0.62, C:0.11, G:0.05, T:0.22
Consensus pattern (13 bp):
ATTAAGAACAATA
Found at i:16811311 original size:16 final size:17
Alignment explanation
Indices: 16811280--16811318 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
16811270 TATGTAACAC
16811280 CCCAAAAATCCCGAAA-
1 CCCAAAAATCCCGAAAT
**
16811296 CCCAAAAATCTTGAAAT
1 CCCAAAAATCCCGAAAT
16811313 CCCAAA
1 CCCAAA
16811319 CTTTCTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.49, C:0.33, G:0.05, T:0.13
Consensus pattern (17 bp):
CCCAAAAATCCCGAAAT
Found at i:16812872 original size:29 final size:29
Alignment explanation
Indices: 16812820--16812919 Score: 139
Period size: 29 Copynumber: 3.5 Consensus size: 29
16812810 GTGAGCATGA
* *
16812820 ATATGAATGTGA-CTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
16812848 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* *
16812877 ATATACAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* *
16812906 ATATGAATATGATT
1 ATATAAATGTGATT
16812920 AGGCTCAATG
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 11 0.17
29 52 0.83
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTAATGGGCC
Found at i:16816938 original size:85 final size:85
Alignment explanation
Indices: 16816795--16817040 Score: 327
Period size: 85 Copynumber: 3.0 Consensus size: 85
16816785 TAACCTCTAC
*
16816795 TCGGATTATCGGCAAGACCTTTAGCTCAGACGAAATCTCCACACGAAGTTATCGGGTCTTACCCG
1 TCGGATTATCGGCGAGACCTTTAGCTCAGACGAAATCTCCACACGAAGTTATCGGGTCTTACCCG
16816860 GACAAAATCTCCACAAGTAG
66 GACAAAATCTCCACAAGTAG
*
16816880 TCGGATTATCGGCGAGAGCTTTAGCTCAGACGAAATCTCCACACGAAGTTATCGGGTCTTACCCG
1 TCGGATTATCGGCGAGACCTTTAGCTCAGACGAAATCTCCACACGAAGTTATCGGGTCTTACCCG
16816945 GACAAAATCTCCACAAGTAG
66 GACAAAATCTCCACAAGTAG
* * * *
16816965 TC-----ATC-G-G-G-TC-TTACCT-GGAC-ATAATCTCCACACGTAGTTATCGGGTCTTACCC
1 TCGGATTATCGGCGAGACCTTTAGCTCAGACGA-AATCTCCACACGAAGTTATCGGGTCTTACCC
* *
16817018 GGACATAATCTCCACACGTAG
65 GGACAAAATCTCCACAAGTAG
16817039 TC
1 TC
16817041 ATTGGGTCTT
Statistics
Matches: 152, Mismatches: 8, Indels: 13
0.88 0.05 0.08
Matches are distributed among these distances:
73 1 0.01
74 54 0.36
75 5 0.03
76 1 0.01
77 1 0.01
78 1 0.01
79 1 0.01
80 3 0.02
85 85 0.56
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (85 bp):
TCGGATTATCGGCGAGACCTTTAGCTCAGACGAAATCTCCACACGAAGTTATCGGGTCTTACCCG
GACAAAATCTCCACAAGTAG
Found at i:16816971 original size:37 final size:37
Alignment explanation
Indices: 16816913--16817091 Score: 286
Period size: 37 Copynumber: 4.8 Consensus size: 37
16816903 GCTCAGACGA
* * *
16816913 AATCTCCACACGAAGTTATCGGGTCTTACCCGGACAA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
* *
16816950 AATCTCCACAAGTAGTCATCGGGTCTTACCTGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
16816987 AATCTCCACACGTAGTTATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
* *
16817024 AATCTCCACACGTAGTCATTGGGTCTTACCCGGATAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
16817061 AATCTCCACACGTAGTCATCGGGTCTTACCC
1 AATCTCCACACGTAGTCATCGGGTCTTACCC
16817092 AGAATATATT
Statistics
Matches: 130, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 130 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:16817364 original size:48 final size:48
Alignment explanation
Indices: 16817240--16817424 Score: 291
Period size: 48 Copynumber: 3.8 Consensus size: 48
16817230 GCACATCGCC
* **
16817240 TACATATTTTACACAAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* *
16817290 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
16817338 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
16817386 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
16817425 TGCATGTTCA
Statistics
Matches: 126, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
48 84 0.67
49 2 0.02
50 40 0.32
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:16817429 original size:98 final size:97
Alignment explanation
Indices: 16817240--16817423 Score: 300
Period size: 98 Copynumber: 1.9 Consensus size: 97
16817230 GCACATCGCC
* *
16817240 TACATATTTTACACAAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACACAAGCCATTCGGCTTTACCACATATACATATCTCA-ATACATATTTCACATT
16817305 GACCATTCGGCTTTACCACATATGCATATCTCA
65 GACCATTCGGCTTTACCACATATGCATATCTCA
**
16817338 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC-ATACATATTTCACATT-
1 TACATATTTCACACAAGCCATTCGGCTTTACCACATATACATATCTCAATACATATTTCACATTG
16817401 AGCCATTCGGCTTTACCACATAT
66 A-CCATTCGGCTTTACCACATAT
16817424 ATGCATGTTC
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
95 1 0.01
96 36 0.44
98 44 0.54
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (97 bp):
TACATATTTCACACAAGCCATTCGGCTTTACCACATATACATATCTCAATACATATTTCACATTG
ACCATTCGGCTTTACCACATATGCATATCTCA
Found at i:16817473 original size:47 final size:47
Alignment explanation
Indices: 16817394--16817587 Score: 280
Period size: 47 Copynumber: 4.1 Consensus size: 47
16817384 CATACATATT
* * * *
16817394 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * *
16817441 CCACATTGGTCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
16817488 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
16817535 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
16817582 TCACAT
1 TCACAT
16817588 AAAATCCTAA
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 131 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:16817514 original size:22 final size:22
Alignment explanation
Indices: 16817487--16817558 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
16817477 GCTCACATTC
16817487 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
16817509 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
16817533 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
16817556 ATC
1 ATC
16817559 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:16817515 original size:94 final size:94
Alignment explanation
Indices: 16817347--16817587 Score: 281
Period size: 94 Copynumber: 2.6 Consensus size: 94
16817337 ATACATATTT
* * * *
16817347 CACATTAGCCATTCGGCTTTA-C-CACATATACATATCTCATACATAT-TTCACATTAGCCATTC
1 CACATTGGCCATTCGGCCTTATCACACATATACACA-CTC--ACAT-TCATCACATTAGCCATTC
* *
16817409 GGCTTTACCACATATATGCATGTTCATATTCAC
62 GGCCTTACCACATATATGCATGTTCACATTCAC
* * ** *
16817442 CACATTGGTCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCC
1 CACATTGGCCATTCGGCCTTATCACACATATACACACTCACATTCATCACATTAGCCATTCGGCC
* *
16817507 TTATCACATATATGCATGTTCACATTCAT
66 TTACCACATATATGCATGTTCACATTCAC
* * *
16817536 CACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 CACATTGGCCATTCGGCCTTATCACACATATACACACTCACATTCATCACAT
16817588 AAAATCCTAA
Statistics
Matches: 125, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
93 1 0.01
94 92 0.74
95 18 0.14
96 4 0.03
97 10 0.08
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.34
Consensus pattern (94 bp):
CACATTGGCCATTCGGCCTTATCACACATATACACACTCACATTCATCACATTAGCCATTCGGCC
TTACCACATATATGCATGTTCACATTCAC
Found at i:16832555 original size:40 final size:40
Alignment explanation
Indices: 16832317--16832541 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
16832307 TTGAATGATG
* * * *
16832317 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
16832357 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
16832397 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
16832436 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
16832476 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
16832517 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
16832542 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:16832563 original size:119 final size:119
Alignment explanation
Indices: 16832317--16832574 Score: 292
Period size: 119 Copynumber: 2.2 Consensus size: 119
16832307 TTGAATGATG
* *
16832317 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
16832382 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * **
16832436 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
16832499 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
16832556 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
16832575 TATGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:16842802 original size:17 final size:19
Alignment explanation
Indices: 16842764--16842803 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
16842754 ACAATTTAAT
*
16842764 ATGATTAACTTTTTGCAAA
1 ATGATTAACATTTTGCAAA
16842783 ATGATTAA-ATTTTG-AAA
1 ATGATTAACATTTTGCAAA
16842800 ATGA
1 ATGA
16842804 ACGAGACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 5 0.25
19 8 0.40
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (19 bp):
ATGATTAACATTTTGCAAA
Found at i:16843774 original size:18 final size:19
Alignment explanation
Indices: 16843753--16843791 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
16843743 ATAAATTTAA
16843753 ATTTTTTAAAATATT-TTT
1 ATTTTTTAAAATATTATTT
*
16843771 ATTTTTTGAAATATTATTT
1 ATTTTTTAAAATATTATTT
16843790 AT
1 AT
16843792 CATTTTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
ATTTTTTAAAATATTATTT
Found at i:16848082 original size:24 final size:24
Alignment explanation
Indices: 16848050--16848122 Score: 137
Period size: 24 Copynumber: 3.0 Consensus size: 24
16848040 CTAAGATAAC
*
16848050 TCACAAATGAAATTATGTTCATGA
1 TCACAAATGAAAGTATGTTCATGA
16848074 TCACAAATGAAAGTATGTTCATGA
1 TCACAAATGAAAGTATGTTCATGA
16848098 TCACAAATGAAAGTATGTTCATGA
1 TCACAAATGAAAGTATGTTCATGA
16848122 T
1 T
16848123 GGGTGTTGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (24 bp):
TCACAAATGAAAGTATGTTCATGA
Found at i:16857662 original size:40 final size:40
Alignment explanation
Indices: 16857607--16857791 Score: 246
Period size: 40 Copynumber: 4.6 Consensus size: 40
16857597 ACAATTTGGT
16857607 TACGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGC
1 TACGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGC
* *
16857647 TACGTATGGCACTTAGTGTACGATTCGAGATAGCTTTGGC
1 TACGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGC
* * *
16857687 TATGTATGGCACTTACTGTGCGATTTGAGATAGCTTCGGC
1 TACGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGC
* * *
16857727 TATGTATGGCACTTAATGTGCGAGATT-GAAATAGCTTCGGC
1 TACGTATGGCACTTAGTGTGC--GATTCGAGATAGCTTCGGC
* *
16857768 TAAGTATTGGCACTCAGTGTGCGA
1 TACGTA-TGGCACTTAGTGTGCGA
16857792 GAATTCAAGT
Statistics
Matches: 130, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
40 95 0.73
41 18 0.14
42 17 0.13
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (40 bp):
TACGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGC
Found at i:16870459 original size:27 final size:27
Alignment explanation
Indices: 16870428--16870605 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
16870418 TAAATTGTAC
16870428 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
16870455 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
16870481 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
16870509 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
16870537 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
16870564 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
16870591 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
16870606 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:16870542 original size:82 final size:81
Alignment explanation
Indices: 16870429--16870584 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16870419 AAATTGTACA
* *
16870429 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
16870493 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
16870510 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
16870575 TGCGAGTTGA
65 TGCGAATTGA
16870585 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:16870596 original size:82 final size:81
Alignment explanation
Indices: 16870425--16870605 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
16870415 GATTAAATTG
* *
16870425 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
16870490 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
16870506 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
16870570 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
16870588 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
16870606 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:16878521 original size:27 final size:27
Alignment explanation
Indices: 16878490--16878667 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
16878480 TAAATTGTAC
16878490 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
16878517 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
16878543 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
16878571 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
16878599 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
16878626 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
16878653 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
16878668 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:16878604 original size:82 final size:81
Alignment explanation
Indices: 16878491--16878646 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16878481 AAATTGTACA
* *
16878491 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
16878555 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
16878572 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
16878637 TGCGAGTTGA
65 TGCGAATTGA
16878647 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:16878658 original size:82 final size:81
Alignment explanation
Indices: 16878487--16878667 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
16878477 GATTAAATTG
* *
16878487 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
16878552 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
16878568 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
16878632 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
16878650 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
16878668 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:16885933 original size:28 final size:29
Alignment explanation
Indices: 16885825--16885936 Score: 113
Period size: 28 Copynumber: 4.0 Consensus size: 29
16885815 ACCTATATAT
* *
16885825 ATATGGCCTACTAGGCCC-AATCTCTTTC
1 ATATGGCCTACTAGGCCCAAATCACATTC
* * * *
16885853 ATATGGCCTATTAGG-CCAATTGACATTT
1 ATATGGCCTACTAGGCCCAAATCACATTC
* * *
16885881 ATGTGGCCCATTAGGCCCAAATCACATTC
1 ATATGGCCTACTAGGCCCAAATCACATTC
*
16885910 ATATGGCC-ACTAGACCCAAATCACATT
1 ATATGGCCTACTAGGCCCAAATCACATT
16885937 TACAGTCATG
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
27 2 0.03
28 49 0.72
29 17 0.25
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (29 bp):
ATATGGCCTACTAGGCCCAAATCACATTC
Found at i:16888874 original size:64 final size:64
Alignment explanation
Indices: 16888794--16888977 Score: 176
Period size: 67 Copynumber: 2.8 Consensus size: 64
16888784 AGACATTATG
* *
16888794 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * * *
16888858 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTATGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
16888923 AA
63 AA
* * * * *
16888925 ACTG--GCTAGGTCACATGGGCGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
16888978 CGAACTATAT
Statistics
Matches: 96, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 21 0.22
65 8 0.08
66 15 0.16
67 30 0.31
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:16893617 original size:43 final size:43
Alignment explanation
Indices: 16893556--16893724 Score: 175
Period size: 43 Copynumber: 4.0 Consensus size: 43
16893546 TAGGATTTCT
* *
16893556 GATATGTGATTACATGTAAGACCACGTCTAGGATGTTGGCATC
1 GATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATC
* ** * * * *
16893599 GATATGTGATTACGTGTAAGACCATTTCTGAGACATCGACATC
1 GATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATC
* * * *
16893642 -ATATTTGATT-CGTGTAAGACC-CTATCTGGGAAAG-TGGCATC
1 GATATGTGATTACATGTAAGACCAC-GTCTGGG-ACGTTGGCATC
16893683 GATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 GATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
16893725 TGTACGATAT
Statistics
Matches: 99, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
41 21 0.21
42 21 0.21
43 56 0.57
44 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (43 bp):
GATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:16898376 original size:55 final size:53
Alignment explanation
Indices: 16898263--16898660 Score: 366
Period size: 55 Copynumber: 7.5 Consensus size: 53
16898253 AACTTACCAT
* * * *
16898263 TGCCATGTCTTGACGTGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAACTCATCAA
* * *
16898316 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTAATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AACTCATCAA
* * * *
16898371 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAACTCATCAA
* * ***
16898425 TGCCATGCCTTGGCATGGTCTTACATGATA---T-CCTTATCTTAC-CA--AA
1 TGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAACTCATCAA
** * * *
16898471 TGCCATGTTCC-AAACATGGTCTAACATGGTATCCTTGTCTTAT-GAACTCACCAA
1 TGCCATG--CCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAACTCATCAA
* * *
16898525 TGCCATGCCTTGGCATAGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AACTCATCAA
* * * *
16898580 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAACTCATCAA
* *
16898634 TGTCATGCCTTGGCATGGTCTTACATG
1 TGCCATGCCTTGACATGGTCTTACATG
16898661 ATATCCTTAT
Statistics
Matches: 278, Mismatches: 48, Indels: 37
0.77 0.13 0.10
Matches are distributed among these distances:
46 9 0.03
47 15 0.05
48 3 0.01
49 8 0.03
50 1 0.00
51 3 0.01
52 13 0.05
53 56 0.20
54 78 0.28
55 88 0.32
56 4 0.01
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (53 bp):
TGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAACTCATCAA
Found at i:16898445 original size:54 final size:54
Alignment explanation
Indices: 16898252--16898668 Score: 383
Period size: 54 Copynumber: 7.9 Consensus size: 54
16898242 TTTCCTTTTT
* * * * * *
16898252 GAACTTACCATTGCCATGTCTTGACGTGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* ** *
16898305 GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTAATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATA
* * *
16898359 GTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATA
1 G-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* * * **
16898414 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATC-T-T-
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
** * * *
16898465 --AC-CA--AATGCCATGTTCC-AAACATGGTCTAACATGGTATCCTTGTCTTAT-
1 GAACTCACCAATGCCATG--CCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* * **
16898514 GAACTCACCAATGCCATGCCTTGGCATAGTCTTACATGGGA-CCTTTGCCTTATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATA
* * *
16898568 GTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATA
1 G-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* * * *
16898623 GAACTTATCAATGTCATGCCTTGGCATGGTCTTACATGATATCCTT
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTT
16898669 ATCTTACCAA
Statistics
Matches: 299, Mismatches: 47, Indels: 35
0.78 0.12 0.09
Matches are distributed among these distances:
46 9 0.03
47 22 0.07
48 4 0.01
49 3 0.01
51 2 0.01
52 9 0.03
53 65 0.22
54 93 0.31
55 88 0.29
56 4 0.01
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.35
Consensus pattern (54 bp):
GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
Found at i:16898648 original size:209 final size:209
Alignment explanation
Indices: 16898278--16898721 Score: 816
Period size: 209 Copynumber: 2.1 Consensus size: 209
16898268 TGTCTTGACG
* * *
16898278 TGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTGGCATGGTCTTACATG
1 TGGTCTTACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTGGCATAGTCTTACATG
16898343 GGACCTTTGCCTAATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGC
66 GGACCTTTGCCTAATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGC
16898408 CTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAAATG
131 CTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAAATG
16898473 CCATGTTCCAAACA
196 CCATGTTCCAAACA
*
16898487 TGGTCTAACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTGGCATAGTCTTACATG
1 TGGTCTTACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTGGCATAGTCTTACATG
*
16898552 GGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGC
66 GGACCTTTGCCTAATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGC
* *
16898617 CTTATAGAACTTATCAATGTCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAAATT
131 CTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAAATG
16898682 CCATGTTCCAAACA
196 CCATGTTCCAAACA
*
16898696 TGGTCTTACATGGTATCATTGTCTTA
1 TGGTCTTACATGGTATCCTTGTCTTA
16898722 CCAAATGCCA
Statistics
Matches: 226, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
209 226 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (209 bp):
TGGTCTTACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTGGCATAGTCTTACATG
GGACCTTTGCCTAATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGC
CTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAAATG
CCATGTTCCAAACA
Found at i:16898700 original size:47 final size:47
Alignment explanation
Indices: 16898647--16898768 Score: 199
Period size: 47 Copynumber: 2.6 Consensus size: 47
16898637 CATGCCTTGG
* * * *
16898647 CATGGTCTTACATGATATCCTTATCTTACCAAATTCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATATTCCAAA
*
16898694 CATGGTCTTACATGGTATCATTGTCTTACCAAATGCCATATTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATATTCCAAA
16898741 CATGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
16898769 GTGCCAATGC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATATTCCAAA
Found at i:16898957 original size:44 final size:44
Alignment explanation
Indices: 16898908--16898991 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
16898898 TCCTTAACCG
* *
16898908 TCAATTCCTCCTTAAATGCCATGTTATGAA-CATGGACTTTTCCT
1 TCAATTCCTCCTTAAATGCCATGGTA-CAACCATGGACTTTTCCT
* *
16898952 TCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 TCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTT
16898992 GAGATATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 33 0.94
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (44 bp):
TCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTTTCCT
Found at i:16906306 original size:28 final size:29
Alignment explanation
Indices: 16906229--16906308 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
16906219 CTATGTATGT
* * **
16906229 GATTTGGGCCTAATAGGCCATACGAATGT
1 GATTTGGGCCTAATGGGCCATATGAATAA
* *
16906258 GATTTGGGCCCAATGGACCATATGAATAA
1 GATTTGGGCCTAATGGGCCATATGAATAA
*
16906287 GA-TTGGGCCTAGTGGGCCATAT
1 GATTTGGGCCTAATGGGCCATAT
16906309 ACATGTATGT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 17 0.40
29 25 0.60
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (29 bp):
GATTTGGGCCTAATGGGCCATATGAATAA
Found at i:16908654 original size:17 final size:18
Alignment explanation
Indices: 16908621--16908654 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16908611 TTTAAGGAAG
16908621 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
16908639 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
16908655 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:16910855 original size:56 final size:56
Alignment explanation
Indices: 16910768--16910874 Score: 196
Period size: 56 Copynumber: 1.9 Consensus size: 56
16910758 TTACATGTAA
*
16910768 TCACATATCGATGCCACTGTCCCAGACAGGGTCTTACTCGCACACATATATCAGAG
1 TCACATATCGATGCCACTGTCCCAAACAGGGTCTTACTCGCACACATATATCAGAG
*
16910824 TCACATATCGATGCCACTGTCCCAAATAGGGTCTTACTCGCACACATATAT
1 TCACATATCGATGCCACTGTCCCAAACAGGGTCTTACTCGCACACATATAT
16910875 TGATGCCATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (56 bp):
TCACATATCGATGCCACTGTCCCAAACAGGGTCTTACTCGCACACATATATCAGAG
Found at i:16912374 original size:21 final size:21
Alignment explanation
Indices: 16912348--16912389 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
16912338 AATAAGGTGT
16912348 ACAATGGGTTGTATTCTGTGC
1 ACAATGGGTTGTATTCTGTGC
*
16912369 ACAATGGGTTGTATTTTGTGC
1 ACAATGGGTTGTATTCTGTGC
16912390 TCATTTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.12, G:0.29, T:0.40
Consensus pattern (21 bp):
ACAATGGGTTGTATTCTGTGC
Found at i:16913855 original size:40 final size:40
Alignment explanation
Indices: 16913810--16913961 Score: 207
Period size: 40 Copynumber: 3.8 Consensus size: 40
16913800 ATAACCACAA
* * *
16913810 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
16913850 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
16913890 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
16913930 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
16913962 CATTCAAATG
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.01
40 97 0.95
41 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:16928792 original size:12 final size:12
Alignment explanation
Indices: 16928760--16928794 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
16928750 TAGTTTCTTG
*
16928760 AAAAAAAAACTC
1 AAAAAAAAATTC
*
16928772 GAAAAAAAATTC
1 AAAAAAAAATTC
16928784 AAAAAAAAATT
1 AAAAAAAAATT
16928795 GGTTTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:16928850 original size:14 final size:15
Alignment explanation
Indices: 16928831--16928886 Score: 78
Period size: 16 Copynumber: 3.7 Consensus size: 15
16928821 GATATCAAGT
16928831 TGAAAAAAAAA-TCG
1 TGAAAAAAAAATTCG
*
16928845 TGAAAAAAAAATTCA
1 TGAAAAAAAAATTCG
16928860 TGAAAAAAAAAATTTCG
1 TG-AAAAAAAAA-TTCG
16928877 TGAAAAAAAA
1 TGAAAAAAAA
16928887 GAAGAAGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
14 11 0.30
15 4 0.11
16 17 0.46
17 5 0.14
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:16928853 original size:15 final size:15
Alignment explanation
Indices: 16928833--16928886 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
16928823 TATCAAGTTG
16928833 AAAAAAAAATCGTGA
1 AAAAAAAAATCGTGA
* *
16928848 AAAAAAAATTCATGA
1 AAAAAAAAATCGTGA
16928863 AAAAAAAAATTTCGTGA
1 AAAAAAAAA--TCGTGA
16928880 AAAAAAA
1 AAAAAAA
16928887 GAAGAAGAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 21 0.64
17 12 0.36
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (15 bp):
AAAAAAAAATCGTGA
Found at i:16928855 original size:17 final size:17
Alignment explanation
Indices: 16928833--16928886 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
16928823 TATCAAGTTG
16928833 AAAAAAAAA-TCGTG--
1 AAAAAAAAATTCGTGAA
*
16928847 AAAAAAAAATTCATGAA
1 AAAAAAAAATTCGTGAA
*
16928864 AAAAAAAATTTCGTGAA
1 AAAAAAAAATTCGTGAA
16928881 AAAAAA
1 AAAAAA
16928887 GAAGAAGAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.26
15 4 0.12
17 21 0.62
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (17 bp):
AAAAAAAAATTCGTGAA
Found at i:16937932 original size:43 final size:42
Alignment explanation
Indices: 16937897--16938051 Score: 195
Period size: 43 Copynumber: 3.7 Consensus size: 42
16937887 TGTGTTCTCG
*
16937897 TGTAAGACCATGTCTGGGACGTTGGCATCAATATGTGATTACG
1 TGTAAGACCATGTCTGGGACGTTGGCATC-ATATGTGATTACA
* * * * *
16937940 TGTAAGACCATGTCTGGGACATCGACATCGTATTTGATT-CA
1 TGTAAGACCATGTCTGGGACGTTGGCATCATATGTGATTACA
* * *
16937981 TGTAAGACCCTATCTGGGACGGTGGCATCGATATGTGATTACA
1 TGTAAGACCATGTCTGGGACGTTGGCATC-ATATGTGATTACA
*
16938024 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCATGTCTGGGACGTTGGCAT
16938052 TGTACGATAT
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
41 24 0.26
42 16 0.17
43 52 0.57
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCATATGTGATTACA
Found at i:16938409 original size:71 final size:71
Alignment explanation
Indices: 16938320--16938460 Score: 273
Period size: 71 Copynumber: 2.0 Consensus size: 71
16938310 AGATAGAAAT
16938320 AATTATTTTATGATTAATTTGAGGTCTATTATATGATTGCATGATTGTGTGAAAATTTCGTGAAG
1 AATTATTTTATGATTAATTTGAGGTCTATTATATGATTGCATGATTGTGTGAAAATTTCGTGAAG
16938385 AAATTC
66 AAATTC
*
16938391 AATTATTTTATGATTAATTTGAGGTCTATTATATGATTGCATGATTGTGTGAAAATTTTGTGAAG
1 AATTATTTTATGATTAATTTGAGGTCTATTATATGATTGCATGATTGTGTGAAAATTTCGTGAAG
16938456 AAATT
66 AAATT
16938461 TTATGCATAA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (71 bp):
AATTATTTTATGATTAATTTGAGGTCTATTATATGATTGCATGATTGTGTGAAAATTTCGTGAAG
AAATTC
Found at i:16944235 original size:10 final size:9
Alignment explanation
Indices: 16944216--16944298 Score: 53
Period size: 9 Copynumber: 8.7 Consensus size: 9
16944206 ATAAACTTAT
16944216 AAAAATATA
1 AAAAATATA
16944225 AAAAATCAT-
1 AAAAAT-ATA
16944234 AAAAATATA
1 AAAAATATA
**
16944243 AACACTTATA
1 AA-AAATATA
16944253 AAAAATAATA
1 AAAAAT-ATA
*
16944263 AATTAAAAATA
1 AA--AAATATA
*
16944274 AATAAT-TA
1 AAAAATATA
16944282 CAAAAATTATA
1 -AAAAA-TATA
16944293 AAAAAT
1 AAAAAT
16944299 TCATTTATTG
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
8 4 0.07
9 23 0.40
10 20 0.35
11 7 0.12
12 3 0.05
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (9 bp):
AAAAATATA
Found at i:16944237 original size:18 final size:17
Alignment explanation
Indices: 16944213--16944298 Score: 70
Period size: 18 Copynumber: 5.1 Consensus size: 17
16944203 AGTATAAACT
16944213 TATAAAAATATAAAAAA
1 TATAAAAATATAAAAAA
**
16944230 TCATAAAAATATAAACACT
1 T-ATAAAAATATAAA-AAA
*
16944249 TATAAAAA-ATAATAAA
1 TATAAAAATATAAAAAA
* *
16944265 T-TAAAAATA-AATAAT
1 TATAAAAATATAAAAAA
*
16944280 TACAAAAATTATAAAAAA
1 TATAAAAA-TATAAAAAA
16944298 T
1 T
16944299 TCATTTATTG
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
15 12 0.22
16 8 0.15
17 7 0.13
18 25 0.46
19 2 0.04
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
TATAAAAATATAAAAAA
Found at i:16944299 original size:10 final size:10
Alignment explanation
Indices: 16944212--16944299 Score: 53
Period size: 10 Copynumber: 9.2 Consensus size: 10
16944202 TAGTATAAAC
16944212 TTAT-AAAAA
1 TTATAAAAAA
16944221 -TATAAAAAA
1 TTATAAAAAA
*
16944230 TCAT-AAAAA
1 TTATAAAAAA
* *
16944239 -TATAAACAC
1 TTATAAAAAA
16944248 TTATAAAAAA
1 TTATAAAAAA
*
16944258 TAATAAATTAAA
1 TTATAAA--AAA
* *
16944270 -AATAAATAA
1 TTATAAAAAA
*
16944279 TTA-CAAAAA
1 TTATAAAAAA
16944288 TTATAAAAAA
1 TTATAAAAAA
16944298 TT
1 TT
16944300 CATTTATTGG
Statistics
Matches: 59, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
8 5 0.08
9 22 0.37
10 23 0.39
11 6 0.10
12 3 0.05
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:16947230 original size:15 final size:15
Alignment explanation
Indices: 16947207--16947244 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
16947197 TGTAAAACTA
16947207 ATGTATGGTATTTTT
1 ATGTATGGTATTTTT
*
16947222 ATGTTTGGTATTTTT
1 ATGTATGGTATTTTT
16947237 ATGCTATG
1 ATG-TATG
16947245 CTTTTATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.18, C:0.03, G:0.21, T:0.58
Consensus pattern (15 bp):
ATGTATGGTATTTTT
Found at i:16949237 original size:21 final size:21
Alignment explanation
Indices: 16949211--16949263 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
16949201 TGTTGTTTCT
* *
16949211 AATCTCACCGCTATAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
16949232 AATCTCACTGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
16949253 AATCTCACCGC
1 AATCTCACCGC
16949264 CACCGTTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:16949616 original size:9 final size:9
Alignment explanation
Indices: 16949572--16949704 Score: 52
Period size: 10 Copynumber: 13.6 Consensus size: 9
16949562 TTTTAAAATT
16949572 ATTTTTATCA
1 ATTTTTAT-A
*
16949582 GTTTTTATGAA
1 ATTTTTAT--A
*
16949593 ATTTCTATA
1 ATTTTTATA
*
16949602 AGTTTTATA
1 ATTTTTATA
16949611 ATTTTTATA
1 ATTTTTATA
** *
16949620 AGTATACATAAA
1 A-T-T-TTTATA
*
16949632 ATTTTAATA
1 ATTTTTATA
*
16949641 TTTTTTTATA
1 -ATTTTTATA
*
16949651 AATTTTATAA
1 ATTTTTAT-A
16949661 TATTTTTATTA
1 -ATTTTTA-TA
*
16949672 ATTTTAAATA
1 ATTTT-TATA
16949682 ATTTTTAT-
1 ATTTTTATA
*
16949690 ATTTTAATGA
1 ATTTTTAT-A
16949700 ATTTT
1 ATTTT
16949705 ATTGAAAAAT
Statistics
Matches: 90, Mismatches: 22, Indels: 22
0.67 0.16 0.16
Matches are distributed among these distances:
8 7 0.08
9 27 0.30
10 34 0.38
11 17 0.19
12 5 0.06
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (9 bp):
ATTTTTATA
Found at i:16949619 original size:18 final size:19
Alignment explanation
Indices: 16949572--16949622 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
16949562 TTTTAAAATT
*
16949572 ATTTTTATCAGTTTTTATGAA
1 ATTTTTATAAG-TTTTAT-AA
*
16949593 ATTTCTATAAGTTTTAT-A
1 ATTTTTATAAGTTTTATAA
16949611 ATTTTTATAAGT
1 ATTTTTATAAGT
16949623 ATACATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 12 0.44
20 6 0.22
21 9 0.33
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (19 bp):
ATTTTTATAAGTTTTATAA
Found at i:16949688 original size:20 final size:20
Alignment explanation
Indices: 16949583--16949690 Score: 73
Period size: 20 Copynumber: 5.4 Consensus size: 20
16949573 TTTTTATCAG
16949583 TTTTTATGAAATTTCTAT-A-A
1 TTTTTAT-AAATTT-TATAATA
* *
16949603 GTTTTATAATTTTTATAAGTA
1 TTTTTATAAATTTTATAA-TA
*** *
16949624 TACATA-AAATTTTA-ATATT
1 TTTTTATAAATTTTATA-ATA
16949643 TTTTTATAAATTTTATAATA
1 TTTTTATAAATTTTATAATA
*
16949663 TTTTTATTAATTTTA-AATAA
1 TTTTTATAAATTTTATAAT-A
16949683 TTTTTATA
1 TTTTTATA
16949691 TTTTAATGAA
Statistics
Matches: 67, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
18 3 0.04
19 14 0.21
20 46 0.69
21 4 0.06
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTTATAAATTTTATAATA
Found at i:16949692 original size:22 final size:20
Alignment explanation
Indices: 16949631--16949704 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
16949621 GTATACATAA
* *
16949631 AATTTTAATATTTTTTTATA
1 AATTTTAATAATTTTTTATT
16949651 AATTTT-ATAATATTTTTATT
1 AATTTTAATAAT-TTTTTATT
16949671 AATTTTAAATAA-TTTTTA-T
1 AATTTT-AATAATTTTTTATT
16949690 -ATTTTAATGAATTTT
1 AATTTTAAT-AATTTT
16949705 ATTGAAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
17 3 0.06
18 7 0.15
19 8 0.17
20 25 0.53
22 4 0.09
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (20 bp):
AATTTTAATAATTTTTTATT
Found at i:16958305 original size:27 final size:27
Alignment explanation
Indices: 16958248--16958306 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
16958238 ATACATCTCA
* *
16958248 TAGGGGCATATCAGTCATTTTACCATG
1 TAGGGGCATATCAATCATTTTACAATG
*
16958275 TAGGGGCATTTCAATCATTTTATCAAT-
1 TAGGGGCATATCAATCATTTTA-CAATG
16958302 TAGGG
1 TAGGG
16958307 AGTCTAGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (27 bp):
TAGGGGCATATCAATCATTTTACAATG
Found at i:16958550 original size:10 final size:10
Alignment explanation
Indices: 16958535--16958559 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16958525 CAGCTCAGTT
16958535 TGGCCCAAAA
1 TGGCCCAAAA
16958545 TGGCCCAAAA
1 TGGCCCAAAA
16958555 TGGCC
1 TGGCC
16958560 TCGGCCCATG
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:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (10 bp):
TGGCCCAAAA
Found at i:16961900 original size:23 final size:23
Alignment explanation
Indices: 16961871--16961933 Score: 90
Period size: 24 Copynumber: 2.7 Consensus size: 23
16961861 TATCAACTCA
16961871 TAAGAGCTTACTGTTTCAGCACG
1 TAAGAGCTTACTGTTTCAGCACG
*
16961894 TAAGAGCTTACTGTTTTCAGCTCG
1 TAAGAGCTTACTG-TTTCAGCACG
* *
16961918 TCAGAGCTTACCGTTT
1 TAAGAGCTTACTGTTT
16961934 TAGCTCAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 16 0.44
24 20 0.56
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (23 bp):
TAAGAGCTTACTGTTTCAGCACG
Found at i:16961923 original size:24 final size:23
Alignment explanation
Indices: 16961873--16961954 Score: 96
Period size: 23 Copynumber: 3.5 Consensus size: 23
16961863 TCAACTCATA
*
16961873 AGAGCTTACTG-TTTCAGCACGT
1 AGAGCTTACTGTTTTCAGCTCGT
16961895 AAGAGCTTACTGTTTTCAGCTCGT
1 -AGAGCTTACTGTTTTCAGCTCGT
* *
16961919 CAGAGCTTACCGTTTT-AGCTCAAT
1 -AGAGCTTACTGTTTTCAGCTC-GT
16961943 AGAGCTTACTGT
1 AGAGCTTACTGT
16961955 CCATTAGCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
23 27 0.52
24 25 0.48
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (23 bp):
AGAGCTTACTGTTTTCAGCTCGT
Found at i:16962100 original size:19 final size:19
Alignment explanation
Indices: 16962076--16962219 Score: 107
Period size: 19 Copynumber: 7.5 Consensus size: 19
16962066 AGAAGCTATG
16962076 TGTTATATGAATGAATTAC
1 TGTTATATGAATGAATTAC
* *
16962095 TGTTATATGGATGAAATAC
1 TGTTATATGAATGAATTAC
* *
16962114 TGTTTATACGAATGAGTTAC
1 TG-TTATATGAATGAATTAC
*
16962134 TGTTA-AAGAATGAATTAC
1 TGTTATATGAATGAATTAC
* * *
16962152 TATTATATGGAT-ACAGTAC
1 TGTTATATGAATGA-ATTAC
* **
16962171 TGTTTAGACAAAT-AAGTTAC
1 TG-TTATATGAATGAA-TTAC
*
16962191 TGTTAT-CGAATGAATTAC
1 TGTTATATGAATGAATTAC
16962209 TGTTTATATGA
1 TG-TTATATGA
16962220 TTGATAGTGA
Statistics
Matches: 96, Mismatches: 21, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
18 26 0.27
19 41 0.43
20 29 0.30
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (19 bp):
TGTTATATGAATGAATTAC
Found at i:16962172 original size:57 final size:57
Alignment explanation
Indices: 16962084--16962218 Score: 173
Period size: 57 Copynumber: 2.4 Consensus size: 57
16962074 TGTGTTATAT
* * * *
16962084 GAATGAATTACTGTTATATGGATGAAATACTGTTTATACGAATGAGTTACTGTTAAA
1 GAATGAATTACTATTATATGGATGAAATACTGTTTAGACAAATAAGTTACTGTTAAA
* **
16962141 GAATGAATTACTATTATATGGAT-ACAGTACTGTTTAGACAAATAAGTTACTGTTATC
1 GAATGAATTACTATTATATGGATGA-AATACTGTTTAGACAAATAAGTTACTGTTAAA
*
16962198 GAATGAATTACTGTTTATATG
1 GAATGAATTACT-ATTATATG
16962219 ATTGATAGTG
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
56 1 0.01
57 60 0.88
58 7 0.10
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (57 bp):
GAATGAATTACTATTATATGGATGAAATACTGTTTAGACAAATAAGTTACTGTTAAA
Found at i:16964542 original size:27 final size:28
Alignment explanation
Indices: 16964512--16964575 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 28
16964502 TATATTAATG
*
16964512 ACGAGATGAAAAAG-GTATAAATATGTT
1 ACGAGATGAAAAAGTATATAAATATGTT
* *
16964539 ACGAGATGGTACAAGTATATAAATATGTT
1 ACGAGAT-GAAAAAGTATATAAATATGTT
16964568 ACGAGATG
1 ACGAGATG
16964576 GTACAAGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 7 0.22
28 6 0.19
29 19 0.59
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (28 bp):
ACGAGATGAAAAAGTATATAAATATGTT
Done.