Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 16 of 145
Found at i:5364984 original size:59 final size:56
Alignment explanation
Indices: 5364911--5365086 Score: 149
Period size: 64 Copynumber: 2.9 Consensus size: 56
5364901 ATTTTAATAA
*
5364911 GTGCCAATGTTGAAGTGGCTGACACC-AGTTCAAAACTATTAAAAAAATGAATTTTTTTT
1 GTGCCAATGTTGAAGTGGCCGACACCGA-TTCAAAACT-TT-AAAAAAT-AATTTTTTTT
* * *
5364970 GTGCCGATGTTGAAGTGGCCGACAGCGATTGAAAACTTTAAAAAATAATTTTTTATTTTTTTT
1 GTGCCAATGTTGAAGTGGCCGACACCGATTCAAAACTTTAAAAAAT-A------ATTTTTTTT
** * *
5365033 GGTGCCGGTGTTGAAGTGGTCGACATCGATTCAAAAC-TTAAAAAATGAATTTTT
1 -GTGCCAATGTTGAAGTGGCCGACACCGATTCAAAACTTTAAAAAAT-AATTTTT
5365087 ATTTTTGTTT
Statistics
Matches: 99, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
57 14 0.14
58 2 0.02
59 31 0.31
60 1 0.01
63 19 0.19
64 32 0.32
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.35
Consensus pattern (56 bp):
GTGCCAATGTTGAAGTGGCCGACACCGATTCAAAACTTTAAAAAATAATTTTTTTT
Found at i:5365116 original size:64 final size:64
Alignment explanation
Indices: 5364961--5365116 Score: 201
Period size: 64 Copynumber: 2.5 Consensus size: 64
5364951 AAAAAAATGA
* * *
5364961 ATTTTTTTTG-TGCCGATGTTGAAGTGGCCGACAGCGATTGAAAACTTTAAAAAATAATTTTTT
1 ATTTTTTTTGATGCCGGTGTTGAAGTGGTCGACAGCGATTCAAAACTTTAAAAAATAATTTTTT
* *
5365024 ATTTTTTTTGGTGCCGGTGTTGAAGTGGTCGACATCGATTCAAAAC-TTAAAAAATGAA-TTTTT
1 ATTTTTTTTGATGCCGGTGTTGAAGTGGTCGACAGCGATTCAAAACTTTAAAAAAT-AATTTTTT
* **
5365087 ATTTTTGTTTTATGTTGGTGTTGAAGTGGT
1 ATTTTT-TTTGATGCCGGTGTTGAAGTGGT
5365117 GGGCACCTAT
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
63 30 0.37
64 52 0.63
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (64 bp):
ATTTTTTTTGATGCCGGTGTTGAAGTGGTCGACAGCGATTCAAAACTTTAAAAAATAATTTTTT
Found at i:5365129 original size:64 final size:63
Alignment explanation
Indices: 5364961--5365140 Score: 195
Period size: 64 Copynumber: 2.9 Consensus size: 63
5364951 AAAAAAATGA
* * * *
5364961 ATTTTTTTTG-TGCCGATGTTGAAGTGGCCGACAGCGATTGAAAACTTTAAAAAATAATTTTTT
1 ATTTTTTTTGATGCCGGTGTTGAAGTGGTCGACACCGATTCAAAAC-TTAAAAAATAATTTTTT
* *
5365024 ATTTTTTTTGGTGCCGGTGTTGAAGTGGTCGACATCGATTCAAAACTTAAAAAATGAA-TTTTT
1 ATTTTTTTTGATGCCGGTGTTGAAGTGGTCGACACCGATTCAAAACTTAAAAAAT-AATTTTTT
* ** * * * *
5365087 ATTTTTGTTTTATGTTGGTGTTGAAGTGGTGGGCACCTATTCAAAA-TAAAAAAA
1 ATTTTT-TTTGATGCCGGTGTTGAAGTGGTCGACACCGATTCAAAACTTAAAAAA
5365141 AAAAAATGGA
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
63 37 0.37
64 64 0.63
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (63 bp):
ATTTTTTTTGATGCCGGTGTTGAAGTGGTCGACACCGATTCAAAACTTAAAAAATAATTTTTT
Found at i:5365245 original size:14 final size:15
Alignment explanation
Indices: 5365226--5365260 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
5365216 GGCAAATGGA
5365226 GAAAAAAGAAAG-AT
1 GAAAAAAGAAAGAAT
*
5365240 GAAAAAGGAAAGAAT
1 GAAAAAAGAAAGAAT
5365255 GAAAAA
1 GAAAAA
5365261 TAAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (15 bp):
GAAAAAAGAAAGAAT
Found at i:5365387 original size:28 final size:28
Alignment explanation
Indices: 5365347--5365406 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
5365337 AAATAACAAG
*
5365347 TTTTAACCTTAAT-TATCCACC-AATCAAA
1 TTTTAACATTAATGT-TCCACCAAAT-AAA
5365375 TTTTAACATTAATGTTCCACCAAATAAA
1 TTTTAACATTAATGTTCCACCAAATAAA
5365403 TTTT
1 TTTT
5365407 GAAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (28 bp):
TTTTAACATTAATGTTCCACCAAATAAA
Found at i:5368019 original size:16 final size:17
Alignment explanation
Indices: 5367998--5368030 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5367988 AATTCGGGCC
5367998 CTTTCT-TTTTTCCTTT
1 CTTTCTCTTTTTCCTTT
*
5368014 CTTTCTCTTTTTTCTTT
1 CTTTCTCTTTTTCCTTT
5368031 TTATTTTGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
CTTTCTCTTTTTCCTTT
Found at i:5371355 original size:12 final size:11
Alignment explanation
Indices: 5371339--5371388 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
5371329 TTTTATTTTA
5371339 TTTTTCTTTCAT
1 TTTTTCTTTC-T
5371351 TTTTTC-TTCAT
1 TTTTTCTTTC-T
5371362 TTTTTCTTTCT
1 TTTTTCTTTCT
*
5371373 TTTTTCCTTCT
1 TTTTTCTTTCT
5371384 TTTTT
1 TTTTT
5371389 TTCTCAACTC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
11 27 0.75
12 9 0.25
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:5371365 original size:23 final size:23
Alignment explanation
Indices: 5371339--5371389 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
5371329 TTTTATTTTA
5371339 TTTTTCTTTCATTTTTT-CTTCAT
1 TTTTTCTTTC-TTTTTTCCTTCAT
*
5371362 TTTTTCTTTCTTTTTTCCTTCTT
1 TTTTTCTTTCTTTTTTCCTTCAT
5371385 TTTTT
1 TTTTT
5371390 TCTCAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTCTTTCTTTTTTCCTTCAT
Found at i:5371611 original size:34 final size:35
Alignment explanation
Indices: 5371530--5371612 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
5371520 GAGAGATGGT
*
5371530 CGAGAGTCGGATGGTGGGGGCATGAAGGAAAGGGC
1 CGAGAGTCGGATGGTGGGGGCATGAAGGAAAGAGC
* * * *
5371565 CGAGAGTTGGATGGTGGGGG-GTGCGAGG-GAGAGC
1 CGAGAGTCGGATGGTGGGGGCATG-AAGGAAAGAGC
5371599 CGAGAGTCGGATGG
1 CGAGAGTCGGATGG
5371613 AGGGTGGGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
34 19 0.46
35 22 0.54
ACGTcount: A:0.22, C:0.11, G:0.54, T:0.13
Consensus pattern (35 bp):
CGAGAGTCGGATGGTGGGGGCATGAAGGAAAGAGC
Found at i:5372934 original size:76 final size:76
Alignment explanation
Indices: 5372452--5373044 Score: 848
Period size: 76 Copynumber: 7.8 Consensus size: 76
5372442 GAAATTTAAA
* * * * *
5372452 AATACCTCGGTGTGCGACTCGAGGCTCAACCCACCTCTCGAATTATGAGTTGA-TCTTTGAAAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTTGAAAAA
* *
5372516 TAGAAATTGAA
66 TAGACATTGAG
* * * * * *
5372527 AATACCTCAACGTGTGACCCTAGGCTCAACTCACCTATTGGATTATGAGTTGA-TTTTTGAAAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTTGAAAAA
* *
5372591 TAGAAATTGAA
66 TAGACATTGAG
* *
5372602 AATACCTCAGCGTGCGACCCGCGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTTTTGAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGA--TTTTTTGAAA
*
5372667 AATAGACATTGAA
64 AATAGACATTGAG
* * * * *
5372680 AATACCTCAGCGTGTGACCTGAGGCTCAACTCATCTCTCGGATTATGAGTTAATTTTTTTGAAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGA-TTTTTTGAAAA
5372745 ATAGACATTGAG
65 ATAGACATTGAG
* * *
5372757 AATACCTCTGCGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTAATTTTTTTGAAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGA-TTTTTTGAAAA
5372822 ATAGACATTGAG
65 ATAGACATTGAG
**
5372834 AATACCTCAGCGTATGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTTGAAAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTTGAAAAA
* *
5372899 CAGGCATTGAG
66 TAGACATTGAG
5372910 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTTGAAAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTTGAAAAA
* *
5372975 CAGGCATTGAG
66 TAGACATTGAG
5372986 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTT
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTT
5373045 TTTGAAAGAT
Statistics
Matches: 478, Mismatches: 37, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
75 111 0.23
76 154 0.32
77 144 0.30
78 69 0.14
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (76 bp):
AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTTGAAAAA
TAGACATTGAG
Found at i:5373045 original size:153 final size:153
Alignment explanation
Indices: 5372452--5373044 Score: 870
Period size: 153 Copynumber: 3.9 Consensus size: 153
5372442 GAAATTTAAA
* * * * *
5372452 AATACCTCGGTGTGCGACTCGAGGCTCAACCCACCTCTCGAATTATGAGTTGA--TCTTTGAAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTTTGAAAA
* * * * * *
5372515 ATAGAAATTGAAAATACCTCAACGTGTGACCCTAGGCTCAACTCACCTATTGGATTATGAGTTGA
66 ATAGACATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGA
* *
5372580 -TTTTTGAAAAATAGAAATTGAA
131 TTTTTTGAAAAATAGACATTGAG
* *
5372602 AATACCTCAGCGTGCGACCCGCGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTTTTGAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGA-TTTTTTTGAAA
* * * *
5372667 AATAGACATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCATCTCTCGGATTATGAGTTA
65 AATAGACATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTG
5372732 ATTTTTTTGAAAAATAGACATTGAG
130 A-TTTTTTGAAAAATAGACATTGAG
* * *
5372757 AATACCTCTGCGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTAATTTTTTTGAAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTTTGAAAA
* *
5372822 ATAGACATTGAGAATACCTCAGCGTATGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGA
66 ATAGACATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGA
* *
5372887 TTTTTTGAAAAACAGGCATTGAG
131 TTTTTTGAAAAATAGACATTGAG
5372910 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGA-TTTTTTGAAAA
1 AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTTTGAAAA
* * * *
5372974 ACAGGCATTGAGAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGA
66 ATAGACATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGA
5373039 TTTTTT
131 TTTTTT
5373045 TTTGAAAGAT
Statistics
Matches: 403, Mismatches: 35, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
150 47 0.12
152 78 0.19
153 137 0.34
154 71 0.18
155 70 0.17
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (153 bp):
AATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGATTTTTTTGAAAA
ATAGACATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGAATTATGAGTTGA
TTTTTTGAAAAATAGACATTGAG
Found at i:5375122 original size:17 final size:17
Alignment explanation
Indices: 5375100--5375133 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5375090 TATTCCTAGA
5375100 TATCATGGAACCATGGT
1 TATCATGGAACCATGGT
5375117 TATCATGGAACCATGGT
1 TATCATGGAACCATGGT
5375134 CGTCCATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (17 bp):
TATCATGGAACCATGGT
Found at i:5375852 original size:17 final size:17
Alignment explanation
Indices: 5375830--5375863 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5375820 TATTCCAAGA
5375830 TATCATGGAACCATGGT
1 TATCATGGAACCATGGT
5375847 TATCATGGAACCATGGT
1 TATCATGGAACCATGGT
5375864 CGTCCATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (17 bp):
TATCATGGAACCATGGT
Found at i:5376072 original size:730 final size:731
Alignment explanation
Indices: 5374671--5376134 Score: 2849
Period size: 730 Copynumber: 2.0 Consensus size: 731
5374661 TCAGTGTCAA
5374671 TTAGAAGCTTTCGGGGAAATTGGCCTTATAACGTTCATGCCCCACATAGAAAAAAGGCCATGGAA
1 TTAGAAGCTTTCGGGGAAATTGGCCTTATAACGTTCATGCCCCACATAGAAAAAAGGCCATGGAA
5374736 AAGTCATGACATGAAGAGGGCGAAGGAGCTACATGAATTTTATCACCGTAAATTTGACACTTGTG
66 AAGTCATGACATGAAGAGGGCGAAGGAGCTACATGAATTTTATCACCGTAAATTTGACACTTGTG
5374801 ACATTTTCATGCGTAACTAATGCAGTCCATTTCCATCGTCAGCCAAGAATAACCAAGTCTCATAA
131 ACATTTTCATGCGTAACTAATGCAGTCCATTTCCATCGTCAGCCAAGAATAACCAAGTCTCATAA
*
5374866 TCTGCCTAGCCATAGTGAAACCATTGGCATGCGTTCCACAAATTCTTTCATGGACATCTTTAAGT
196 TCTACCTAGCCATAGTGAAACCATTGGCATGCGTTCCACAAATTCTTTCATGGACATCTTTAAGT
5374931 ATTCTTTTAGCTTCAACAGTGTCCACGCATATCAGGAGCATTTGATCTTTTCCTCTTTTGTATAT
261 ATTCTTTTAGCTTCAACAGTGTCCACGCATATCAGGAGCATTTGATCTTTTCCTCTTTTGTATAT
5374996 GATATCCCCATCAAGAACAAATCCAATCACCATTCTCCTGATCGTTCTTTTGTCATTCTTGTTTG
326 GATATCCCCATCAAGAACAAATCCAATCACCATTCTCCTGATCGTTCTTTTGTCATTCTTGTTTG
*
5375061 CTTGCTTGGGATACCTTTGATTATTGATATATTCCTAGATATCATGGAACCATGGTTATCATGGA
391 CTTGCTTGGGATACCTTTGATTATTGATATATTCCAAGATATCATGGAACCATGGTTATCATGGA
5375126 ACCATGGTCGTCCATCTGACTCATTCTCAATGCTAAAAAAATATGCGAGGACCTCATATATACTC
456 ACCATGGTCGTCCATCTGACTCATTCTCAATGCTAAAAAAATATGCGAGGACCTCATATATACTC
5375191 ATTTGGAGAGGCATTATTTTAGTTTCTCTGTTTGCTTTGAACATTGAAGCCAAGGTGGCCAGGGT
521 ATTTGGAGAGGCATTATTTTAGTTTCTCTGTTTGCTTTGAACATTGAAGCCAAGGTGGCCAGGGT
5375256 GTCAGTCAATTAGTTTTCTTCTCGTGGGAAGTAATTAAAAGTCACTCATTTGAATTCTTTGACCA
586 GTCAGTCAATTAGTTTTCTTCTCGTGGGAAGTAATTAAAAGTCACTCATTTGAATTCTTTGACCA
*
5375321 GTTTCGTAACAAGATCGTGATATTTGACTAATTTCGAATCCCTCACTTCTCAATCTTCACGGATT
651 GTTTCATAACAAGATCGTGATATTTGACTAATTTCGAATCCCTCACTTCTCAATCTTCACGGATT
5375386 TGATAAATCACTAATG
716 TGATAAATCACTAATG
5375402 TTAGAAGCTTTCGGGGAAATTGGCCTTATAACGTTCATGCCCCACATAGAAAAAAGGCCATGGAA
1 TTAGAAGCTTTCGGGGAAATTGGCCTTATAACGTTCATGCCCCACATAGAAAAAAGGCCATGGAA
*
5375467 AAGTCATGACATGAAGAGGGCGAAGGAGCTGCATGAATTTTATCACCGTAAATTTGACACTTGTG
66 AAGTCATGACATGAAGAGGGCGAAGGAGCTACATGAATTTTATCACCGTAAATTTGACACTTGTG
5375532 ACATTTTCATGCGTAACTAATGCAGTCCATTTCCATCGTCAGCCAAGAATAACCAAGTCTCATAA
131 ACATTTTCATGCGTAACTAATGCAGTCCATTTCCATCGTCAGCCAAGAATAACCAAGTCTCATAA
5375597 TCTACCTAGCCATAGTGAAACCATTGGCATGCGTTCCACAAATTCTTTCATGGACATCTTTAAGT
196 TCTACCTAGCCATAGTGAAACCATTGGCATGCGTTCCACAAATTCTTTCATGGACATCTTTAAGT
5375662 ATTC-TTTAGCTTCAACAGTGTCCACGCATATCAGGAGCATTTGATCTTTTCCTCTTTTGTATAT
261 ATTCTTTTAGCTTCAACAGTGTCCACGCATATCAGGAGCATTTGATCTTTTCCTCTTTTGTATAT
* *
5375726 GATATCCCCATCAAGAACAAATCCAATCGCCATTTTCCTGATCGTTCTTTTGTCATTCTTGTTTG
326 GATATCCCCATCAAGAACAAATCCAATCACCATTCTCCTGATCGTTCTTTTGTCATTCTTGTTTG
5375791 CTTGCTTGGGATACCTTTGATTATTGATATATTCCAAGATATCATGGAACCATGGTTATCATGGA
391 CTTGCTTGGGATACCTTTGATTATTGATATATTCCAAGATATCATGGAACCATGGTTATCATGGA
5375856 ACCATGGTCGTCCATCTGACTCATTCTCAATGCTAAAAAAATATGCGAGGACCTCATATATACTC
456 ACCATGGTCGTCCATCTGACTCATTCTCAATGCTAAAAAAATATGCGAGGACCTCATATATACTC
5375921 ATTTGGAGAGGCATTATTTTAGTTTCTCTGTTTGCTTTGAACATTGAAGCCAAGGTGGCCAGGGT
521 ATTTGGAGAGGCATTATTTTAGTTTCTCTGTTTGCTTTGAACATTGAAGCCAAGGTGGCCAGGGT
* *
5375986 GTCAGTCAATTAGTTTTCTTCTTGTGGGAAGTAATTAAAAGTCACTCCTTTGAATTCTTTGACCA
586 GTCAGTCAATTAGTTTTCTTCTCGTGGGAAGTAATTAAAAGTCACTCATTTGAATTCTTTGACCA
5376051 GTTTCATAACAAGATCGTGATATTTGACTAATTTCGAATCCCTCACTTCTCAATCTTCACGGATT
651 GTTTCATAACAAGATCGTGATATTTGACTAATTTCGAATCCCTCACTTCTCAATCTTCACGGATT
5376116 TGATAAATCACTAATG
716 TGATAAATCACTAATG
5376132 TTA
1 TTA
5376135 AGTCCCAATA
Statistics
Matches: 725, Mismatches: 8, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
730 463 0.64
731 262 0.36
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (731 bp):
TTAGAAGCTTTCGGGGAAATTGGCCTTATAACGTTCATGCCCCACATAGAAAAAAGGCCATGGAA
AAGTCATGACATGAAGAGGGCGAAGGAGCTACATGAATTTTATCACCGTAAATTTGACACTTGTG
ACATTTTCATGCGTAACTAATGCAGTCCATTTCCATCGTCAGCCAAGAATAACCAAGTCTCATAA
TCTACCTAGCCATAGTGAAACCATTGGCATGCGTTCCACAAATTCTTTCATGGACATCTTTAAGT
ATTCTTTTAGCTTCAACAGTGTCCACGCATATCAGGAGCATTTGATCTTTTCCTCTTTTGTATAT
GATATCCCCATCAAGAACAAATCCAATCACCATTCTCCTGATCGTTCTTTTGTCATTCTTGTTTG
CTTGCTTGGGATACCTTTGATTATTGATATATTCCAAGATATCATGGAACCATGGTTATCATGGA
ACCATGGTCGTCCATCTGACTCATTCTCAATGCTAAAAAAATATGCGAGGACCTCATATATACTC
ATTTGGAGAGGCATTATTTTAGTTTCTCTGTTTGCTTTGAACATTGAAGCCAAGGTGGCCAGGGT
GTCAGTCAATTAGTTTTCTTCTCGTGGGAAGTAATTAAAAGTCACTCATTTGAATTCTTTGACCA
GTTTCATAACAAGATCGTGATATTTGACTAATTTCGAATCCCTCACTTCTCAATCTTCACGGATT
TGATAAATCACTAATG
Found at i:5385952 original size:15 final size:15
Alignment explanation
Indices: 5385907--5385952 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
5385897 AAATAAAAAT
*
5385907 AAAAAAAAGTATTTTA
1 AAAAAAAAATA-TTTA
5385923 AAATAAAAAA-ATTTA
1 AAA-AAAAAATATTTA
5385938 AAAAAAAAATATTTA
1 AAAAAAAAATATTTA
5385953 TTATACTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.22
15 12 0.44
16 4 0.15
17 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (15 bp):
AAAAAAAAATATTTA
Found at i:5386599 original size:12 final size:11
Alignment explanation
Indices: 5386579--5386637 Score: 57
Period size: 12 Copynumber: 5.3 Consensus size: 11
5386569 TTATTTTATA
*
5386579 TTTTTT-TTCT
1 TTTTTTCTTTT
*
5386589 TTTTTTCTTTCG
1 TTTTTTCTTT-T
5386601 TTTTTTCTTTT
1 TTTTTTCTTTT
*
5386612 GTTTTTCTTTT
1 TTTTTTCTTTT
*
5386623 TTTCCTTCTTTT
1 TTT-TTTCTTTT
5386635 TTT
1 TTT
5386638 CTCAACTCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 6 0.15
11 14 0.35
12 20 0.50
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:5386802 original size:35 final size:34
Alignment explanation
Indices: 5386763--5386982 Score: 218
Period size: 33 Copynumber: 6.5 Consensus size: 34
5386753 GATGGCGAGA
* * *
5386763 GGTGCGAGAAAGATGACCGAGAGTTGGATGGTAGG
1 GGTGCGAGAGAGAGGGCCGAGAGTTGGATGGT-GG
*
5386798 GGTGCGAGGGAGAGGGCCGAGAGTTGGATGGT-G
1 GGTGCGAGAGAGAGGGCCGAGAGTTGGATGGTGG
* *
5386831 GGTGCGAGAGATAGGGCCGAGAGTCGGATGGTGGGG
1 GGTGCGAGAGAGAGGGCCGAGAGTTGGATGGT--GG
* * *
5386867 AGGTGCGA-AG-GAGCGCCGAGTGTCGGATGGT-G
1 -GGTGCGAGAGAGAGGGCCGAGAGTTGGATGGTGG
* * *
5386899 GGTGTGAGAGAGAGGGCCAAGAGTCGGATGGT-G
1 GGTGCGAGAGAGAGGGCCGAGAGTTGGATGGTGG
*
5386932 GGTGCGAGAGAGAGGGCCGAGA-TTAGATGGTGGG
1 GGTGCGAGAGAGAGGGCCGAGAGTTGGATGGT-GG
* *
5386966 GGTGCCAGGGAGAGGGC
1 GGTGCGAGAGAGAGGGC
5386983 TGTGGCGATT
Statistics
Matches: 157, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
31 6 0.04
32 10 0.06
33 69 0.44
34 16 0.10
35 46 0.29
36 3 0.02
37 7 0.04
ACGTcount: A:0.22, C:0.11, G:0.53, T:0.15
Consensus pattern (34 bp):
GGTGCGAGAGAGAGGGCCGAGAGTTGGATGGTGG
Found at i:5386885 original size:68 final size:69
Alignment explanation
Indices: 5386763--5386953 Score: 214
Period size: 68 Copynumber: 2.8 Consensus size: 69
5386753 GATGGCGAGA
* * * * * * * *
5386763 GGTGCGAGAAAGATGACCGAGAGTTGGATGGT-AGGGGTGCGAGGGAGAGGGCCGAGAGTTGGAT
1 GGTGCGAGAGAGAGGGCCGAGAGTCGGATGGTGGGGGGTGCGAGAGAGAGCGCCGAGAGTCGGAT
5386827 GGTG
66 GGTG
* *
5386831 GGTGCGAGAGATAGGGCCGAGAGTCGGATGGTGGGGAGGTGCGA-AG-GAGCGCCGAGTGTCGGA
1 GGTGCGAGAGAGAGGGCCGAGAGTCGGATGGTGGGG-GGTGCGAGAGAGAGCGCCGAGAGTCGGA
5386894 TGGTG
65 TGGTG
* * *
5386899 GGTGTGAGAGAGAGGGCCAAGAGTCGGATGGT---GGGTGCGAGAGAGAGGGCCGAGA
1 GGTGCGAGAGAGAGGGCCGAGAGTCGGATGGTGGGGGGTGCGAGAGAGAGCGCCGAGA
5386954 TTAGATGGTG
Statistics
Matches: 104, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
64 7 0.07
65 3 0.03
66 9 0.09
68 75 0.72
69 3 0.03
70 7 0.07
ACGTcount: A:0.23, C:0.11, G:0.52, T:0.14
Consensus pattern (69 bp):
GGTGCGAGAGAGAGGGCCGAGAGTCGGATGGTGGGGGGTGCGAGAGAGAGCGCCGAGAGTCGGAT
GGTG
Found at i:5386948 original size:101 final size:101
Alignment explanation
Indices: 5386779--5386966 Score: 270
Period size: 101 Copynumber: 1.9 Consensus size: 101
5386769 AGAAAGATGA
* * * * *
5386779 CCGAGAGTTGGATGGTAGGGGTGCGAGGGAGAGGGCCGAGAGTTGGATGGTGGGTGCGAGAGATA
1 CCGAGAGTCGGATGGTA-GGGTGCGAGAGAGAGGGCCAAGAGTCGGATGGTGGGTGCGAGAGAGA
*
5386844 GGGCCGAGAGTCGGATGGTGGGGAGGTGCGAAGGAGCG
65 GGGCCGAGA-TCAGATGGTGGGGAGGTGCGAAGGAGCG
* *
5386882 CCGAGTGTCGGATGGT-GGGTGTGAGAGAGAGGGCCAAGAGTCGGATGGTGGGTGCGAGAGAGAG
1 CCGAGAGTCGGATGGTAGGGTGCGAGAGAGAGGGCCAAGAGTCGGATGGTGGGTGCGAGAGAGAG
*
5386946 GGCCGAGATTAGATGGTGGGG
66 GGCCGAGATCAGATGGTGGGG
5386967 GTGCCAGGGA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
100 11 0.14
101 51 0.67
103 14 0.18
ACGTcount: A:0.21, C:0.11, G:0.53, T:0.15
Consensus pattern (101 bp):
CCGAGAGTCGGATGGTAGGGTGCGAGAGAGAGGGCCAAGAGTCGGATGGTGGGTGCGAGAGAGAG
GGCCGAGATCAGATGGTGGGGAGGTGCGAAGGAGCG
Found at i:5387303 original size:30 final size:29
Alignment explanation
Indices: 5387262--5387371 Score: 118
Period size: 30 Copynumber: 3.8 Consensus size: 29
5387252 CCTCTAAGGC
*
5387262 CAAAATGTAAATAGTAAAAAGTTAAGGGGT
1 CAAAATATAAATAGTAAAAAGTTAA-GGGT
* *
5387292 TAAAATATAAATAGT-AAAAGTTTGAAAGGT
1 CAAAATATAAATAGTAAAAAG-TT-AAGGGT
* *
5387322 CAAAATATAAGTAATAAAAAGTT--GGGT
1 CAAAATATAAATAGTAAAAAGTTAAGGGT
*
5387349 CAAAATGTAAATAGTAAAAAGTT
1 CAAAATATAAATAGTAAAAAGTT
5387372 GCATTTTTTC
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
27 23 0.34
29 5 0.07
30 32 0.48
31 7 0.10
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (29 bp):
CAAAATATAAATAGTAAAAAGTTAAGGGT
Found at i:5387988 original size:29 final size:29
Alignment explanation
Indices: 5387955--5388038 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
5387945 ATAATTAGAC
5387955 CTAAATTTTAAATTTAAAAAATAAAAAGA
1 CTAAATTTTAAATTTAAAAAATAAAAAGA
** ** *
5387984 CTAAATTCTTAAAAAT-AAAAATTTAATGA
1 CTAAATT-TTAAATTTAAAAAATAAAAAGA
5388013 CTAAAATTTTAAATTTGTAAAAAATA
1 CT-AAATTTTAAA-TT-TAAAAAATA
5388039 CATCCACCTA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
29 24 0.57
30 11 0.26
31 1 0.02
32 6 0.14
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.35
Consensus pattern (29 bp):
CTAAATTTTAAATTTAAAAAATAAAAAGA
Found at i:5389008 original size:20 final size:19
Alignment explanation
Indices: 5388980--5389035 Score: 80
Period size: 18 Copynumber: 2.9 Consensus size: 19
5388970 TTTCCTTTAA
5388980 TTTATTAAAAATTGATAGAAT
1 TTTA-TAAAAATTGATA-AAT
5389001 TTTATAAAAA-TGATAAAT
1 TTTATAAAAATTGATAAAT
5389019 TTTATAAAAATT-ATAAA
1 TTTATAAAAATTGATAAA
5389036 ACATAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 18 0.53
19 6 0.18
20 6 0.18
21 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTATAAAAATTGATAAAT
Found at i:5389847 original size:22 final size:22
Alignment explanation
Indices: 5389812--5389856 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5389802 CACCACATGT
5389812 ATTTCTTTTATAAAAATATATA
1 ATTTCTTTTATAAAAATATATA
*
5389834 ATTT-TTTTATTAAATATATATA
1 ATTTCTTTTA-TAAAAATATATA
5389856 A
1 A
5389857 ACTTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTCTTTTATAAAAATATATA
Found at i:5389881 original size:15 final size:16
Alignment explanation
Indices: 5389851--5389883 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5389841 TATTAAATAT
*
5389851 ATATAAACTTTAAAAA
1 ATATAAACTATAAAAA
5389867 ATATAAA-TATAAAAA
1 ATATAAACTATAAAAA
5389882 AT
1 AT
5389884 TACAAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
ATATAAACTATAAAAA
Found at i:5390715 original size:19 final size:19
Alignment explanation
Indices: 5390693--5390730 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5390683 TGTTTTTGGA
5390693 AAATGATTTACTTTTCTAG
1 AAATGATTTACTTTTCTAG
5390712 AAATGATTTACTTTTCTAG
1 AAATGATTTACTTTTCTAG
5390731 TGTTTGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (19 bp):
AAATGATTTACTTTTCTAG
Found at i:5390832 original size:18 final size:18
Alignment explanation
Indices: 5390806--5390848 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
5390796 AAAAATTGTT
*
5390806 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
5390824 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
5390842 TTTATAT
1 TTTATAT
5390849 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:5395176 original size:77 final size:78
Alignment explanation
Indices: 5395065--5395220 Score: 305
Period size: 77 Copynumber: 2.0 Consensus size: 78
5395055 CACGTAAATT
5395065 TAACGAAAAATAAATACACTTATTAGTAAATTATTTTTTTTGAAAAAAATATTAGAATAAATACA
1 TAACGAAAAATAAATACACTTATTAGTAAATTATTTTTTTTGAAAAAAATATTAGAATAAATACA
5395130 ATATAAATATATG
66 ATATAAATATATG
5395143 TAACGAAAAAT-AATACACTTATTAGTAAATTATTTTTTTTGAAAAAAATATTAGAATAAATACA
1 TAACGAAAAATAAATACACTTATTAGTAAATTATTTTTTTTGAAAAAAATATTAGAATAAATACA
5395207 ATATAAATATATG
66 ATATAAATATATG
5395220 T
1 T
5395221 CTAACTAATT
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 67 0.86
78 11 0.14
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (78 bp):
TAACGAAAAATAAATACACTTATTAGTAAATTATTTTTTTTGAAAAAAATATTAGAATAAATACA
ATATAAATATATG
Found at i:5397121 original size:23 final size:24
Alignment explanation
Indices: 5397095--5397140 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
5397085 AAAAAGTTTT
5397095 AATAGAATTATTA-ATTTATAAAA
1 AATAGAATTATTATATTTATAAAA
* *
5397118 AATATAATTTTTATATTTATAAA
1 AATAGAATTATTATATTTATAAA
5397141 TTTTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AATAGAATTATTATATTTATAAAA
Found at i:5398720 original size:106 final size:108
Alignment explanation
Indices: 5398485--5398740 Score: 367
Period size: 109 Copynumber: 2.4 Consensus size: 108
5398475 NNNNNNNNNN
5398485 CCATTGACAGGCCAGCACCCAAAA-TTTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGAC
1 CCATTGACAGGCCAGCACCCAAAATTTTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGAC
*
5398549 ACGAAAAAAAAGAAAAAAAAATTCTAAATTGTACTGGGTGCCGG
66 ACGAAAAAAAAGAAAAAAAAATTCTAAACTGTA-TGGGTGCCGG
5398593 CCATTGACAGGCCAGCACCCAAAATTTTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGAC
1 CCATTGACAGGCCAGCACCCAAAATTTTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGAC
** *** * **
5398658 ACGAAAAAAAA-AGCAAATTTTTTTTTACTGT-TGGGTGCCGG
66 ACGAAAAAAAAGAAAAAAAAATTCTAAACTGTATGGGTGCCGG
* *
5398699 CCATTGACAGCCCAGCACCC-AAATTTTTTTTTCCTTTTTTTC
1 CCATTGACAGGCCAGCACCCAAAATTTTTTTTT-ATTTTTTTC
5398741 TTTTTTGTAT
Statistics
Matches: 135, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
105 12 0.09
106 37 0.27
108 35 0.26
109 51 0.38
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (108 bp):
CCATTGACAGGCCAGCACCCAAAATTTTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGAC
ACGAAAAAAAAGAAAAAAAAATTCTAAACTGTATGGGTGCCGG
Found at i:5405509 original size:15 final size:15
Alignment explanation
Indices: 5405489--5405518 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5405479 AGACAAAGAA
5405489 AAGATGTTAAGATTT
1 AAGATGTTAAGATTT
5405504 AAGATGTTAAGATTT
1 AAGATGTTAAGATTT
5405519 TCTCCCTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (15 bp):
AAGATGTTAAGATTT
Found at i:5406339 original size:259 final size:257
Alignment explanation
Indices: 5405867--5406359 Score: 652
Period size: 259 Copynumber: 1.9 Consensus size: 257
5405857 TTTTTTTCTT
** * *
5405867 TTTTTTTGTTTTTTATTTTTTTGTTTTTGCACTTTTCCAATCACTTTTTTTTGTGGAAAATATTT
1 TTTTTTTGTTTTGAATTTTTCTGTTTTTGCACTTTTCCAATCACTTTTTTTTGTAGAAAATATTT
** * * * * *
5405932 TTCTACTTTCCAAGAGAGTGTCAAGAATCAATATGTAAAATTTCAGATTATTTGAAAAATACCCA
66 TTCTACAGTCCAAGAGAGTGCCAAGAAGCAATATATAAAATTTCAAATCATTTGAAAAATACCCA
* ** *
5405997 CTAAAAAATATTTTTTTTTAAAAACTTTTTGGTAAAAAAAAGTTGTTTTGAGGTTGTTTGCTGGA
131 CTAAAAAATATTTTCTTCAAAAAACTTTTTGGTAAAAAAAAGTTGTTTTCAGGTTGTTTGCTGGA
* *
5406062 AATCAATAGATTAGAACACAAAGAACCCCTAAAACGCTCAAATCTTACATTAAATCTAATTC
196 AATCAATAGATAAGAACACAAAGAACACCTAAAACGCTCAAATCTTACATTAAATCTAATTC
* *
5406124 TTTTTTT-TTTTGAATTTTTCTGTTTTTGCACTTTTTCGATCAC-TTTTTTT-TAG-AAATATTT
1 TTTTTTTGTTTTGAATTTTTCTGTTTTTGCACTTTTCCAATCACTTTTTTTTGTAGAAAATATTT
* * *
5406185 TTCTAGAGTCTAAGAGAGTGCCAAGAAGCAATATATAAAATTTTAAATCATTTGAAAAACGTTTA
66 TTCTACAGTCCAAGAGAGTGCCAAGAAGCAATATATAAAATTTCAAATCATTTGAAAAA----TA
* *
5406250 CCGACTAAAAAATATTTTCTTCAAAAAACTTTTTGGGTAAAAAAAAAGTTGTTTTCAGTTTGTTT
127 CCCACTAAAAAATATTTTCTTCAAAAAACTTTTT-GGT-AAAAAAAAGTTGTTTTCAGGTTGTTT
* ** *
5406315 GTTGGAAATCAATTTATAAGAACACAAAGAGCACCTAAAACGCTC
190 GCTGGAAATCAATAGATAAGAACACAAAGAACACCTAAAACGCTC
5406360 CAATTTGATA
Statistics
Matches: 202, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
253 57 0.28
254 2 0.01
255 7 0.03
256 31 0.15
257 39 0.19
258 3 0.01
259 63 0.31
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (257 bp):
TTTTTTTGTTTTGAATTTTTCTGTTTTTGCACTTTTCCAATCACTTTTTTTTGTAGAAAATATTT
TTCTACAGTCCAAGAGAGTGCCAAGAAGCAATATATAAAATTTCAAATCATTTGAAAAATACCCA
CTAAAAAATATTTTCTTCAAAAAACTTTTTGGTAAAAAAAAGTTGTTTTCAGGTTGTTTGCTGGA
AATCAATAGATAAGAACACAAAGAACACCTAAAACGCTCAAATCTTACATTAAATCTAATTC
Found at i:5407001 original size:10 final size:11
Alignment explanation
Indices: 5406986--5407031 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
5406976 AACTAAATCC
5406986 TTTCTCTC-AA
1 TTTCTCTCAAA
*
5406996 TTTCTCTCTAA
1 TTTCTCTCAAA
5407007 TATTCTCTCAAA
1 T-TTCTCTCAAA
*
5407019 TTCCTCTCAAA
1 TTTCTCTCAAA
5407030 TT
1 TT
5407032 CCCATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 8 0.25
11 14 0.44
12 10 0.31
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (11 bp):
TTTCTCTCAAA
Found at i:5407012 original size:12 final size:10
Alignment explanation
Indices: 5406986--5407028 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
5406976 AACTAAATCC
5406986 TTTCTCTCAA
1 TTTCTCTCAA
5406996 TTTCTCTCTAA
1 TTTCTCTC-AA
5407007 TATTCTCTCAAA
1 T-TTCTCTC-AA
*
5407019 TTCCTCTCAA
1 TTTCTCTCAA
5407029 ATTCCCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 10 0.34
11 9 0.31
12 10 0.34
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:5408888 original size:18 final size:18
Alignment explanation
Indices: 5408865--5408908 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5408855 ATGCCAGGTG
*
5408865 TGTATCCTAACCATTTTA
1 TGTATCCTAACCATTATA
*
5408883 TGTATCCTAACCCTTATA
1 TGTATCCTAACCATTATA
*
5408901 TGTTTCCT
1 TGTATCCT
5408909 TTTCCTAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (18 bp):
TGTATCCTAACCATTATA
Found at i:5409384 original size:49 final size:49
Alignment explanation
Indices: 5409329--5409449 Score: 215
Period size: 49 Copynumber: 2.5 Consensus size: 49
5409319 GTTTATATTA
* *
5409329 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTAAATATTTTGATATTATTTC
5409378 ATGTAATAAAATACAAAATAGTTTATTTTAAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTAAATATTTTGATATTATTTC
*
5409427 ATTTAATAAAATACAAAATAGTT
1 ATGTAATAAAATACAAAATAGTT
5409450 AATATTCTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 69 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTAAATATTTTGATATTATTTC
Found at i:5410078 original size:126 final size:125
Alignment explanation
Indices: 5409813--5410226 Score: 650
Period size: 125 Copynumber: 3.3 Consensus size: 125
5409803 CCCAAACATG
*
5409813 CTACTGTAGCAAAAGTGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* * * *
5409878 TTG-AAGTGTTTTTTATACTATTTGCTTAGAAATGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAACT-TTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
*
5409938 CTACTGTAGCAAAAGCGCATCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
5410003 TTGAAACATTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAAC-TTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* ** * * *
5410064 CTACTGTAGTAAAAGTACGTCCACGTGGAAGCGATTTCAGAAATTCTTCTGATAAAGTATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* *
5410129 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAACTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * *
5410189 CTACTGTATCAAAAACGTGTCCACGTGGGAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
5410227 CTTAATAAAT
Statistics
Matches: 265, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
125 149 0.56
126 115 0.43
127 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
TTGAAACTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:5410430 original size:6 final size:6
Alignment explanation
Indices: 5410412--5410444 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
5410402 AAAATCCTAA
5410412 AACCCT AAACCCT AACCCT AACCCT AACCCT AA
1 AACCCT -AACCCT AACCCT AACCCT AACCCT AA
5410445 AAACCCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.15
Consensus pattern (6 bp):
AACCCT
Found at i:5415247 original size:3 final size:3
Alignment explanation
Indices: 5415241--5415278 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5415231 ACTTTTGTTG
5415241 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5415279 TGTTTTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5415450 original size:3 final size:3
Alignment explanation
Indices: 5415444--5415481 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5415434 ACTTTTGTTG
*
5415444 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5415482 TGTTTTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5415923 original size:44 final size:44
Alignment explanation
Indices: 5415852--5415970 Score: 116
Period size: 44 Copynumber: 2.7 Consensus size: 44
5415842 TTAATCCGAC
* * * *
5415852 CCACTACAACTTCAGAGG-TATAGGATTTGTTGCTTCAATCTA-CT
1 CCACTGCAACTTCA-AGGAGATAAGATTTGTTGCTTCAAT-AAGCT
* * * *
5415896 CCATTGTAACTTCAAGGAGATGAGATTTGTAGCTTCAATAAGCT
1 CCACTGCAACTTCAAGGAGATAAGATTTGTTGCTTCAATAAGCT
* *
5415940 CCACTGCAACTTTAGGGAGATAAGATTTGTT
1 CCACTGCAACTTCAAGGAGATAAGATTTGTT
5415971 ATAGTAAATT
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
43 4 0.07
44 55 0.93
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTCAAGGAGATAAGATTTGTTGCTTCAATAAGCT
Found at i:5416273 original size:11 final size:11
Alignment explanation
Indices: 5416257--5416285 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
5416247 TTGGGCAAGT
5416257 TTTGATAGACG
1 TTTGATAGACG
5416268 TTTGATAGACG
1 TTTGATAGACG
5416279 TTTGATA
1 TTTGATA
5416286 AACATAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (11 bp):
TTTGATAGACG
Found at i:5426599 original size:21 final size:21
Alignment explanation
Indices: 5426573--5426617 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
5426563 AGAATAATAT
*
5426573 TAATAATAATGAT-AGTATAAA
1 TAATAATAATAATAAG-ATAAA
5426594 TAATAATAATAATAAGATAAA
1 TAATAATAATAATAAGATAAA
5426615 TAA
1 TAA
5426618 ATAAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (21 bp):
TAATAATAATAATAAGATAAA
Found at i:5429043 original size:43 final size:43
Alignment explanation
Indices: 5428982--5429278 Score: 459
Period size: 43 Copynumber: 6.8 Consensus size: 43
5428972 TTTTGGAAAT
*
5428982 AAACGCCGCTATAGATCATGACTTTTAGTGGCGCTTCTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTCTCCCAC
*
5429025 AAACGCCGCTATAGATCATAACTTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTCTCCCAC
*
5429068 AAATGCCGCTATAATAGATCATGACTTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGC--T-ATAGATCATGACTTTTAGCGGCGCTTCTCCCAC
* * *
5429114 AAACGCCGCTATAGATTATGACTTTTAGTGGCGCTTATCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTCTCCCAC
* *
5429157 AAACGCCACTATAGATCATGACTTTTAACGGCGCTTCTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTCTCCCAC
* * *
5429200 AGACGTCGGTATAGATCATGACTTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTCTCCCAC
*
5429243 AAATGCCGCTATAGATCATGACTTTTAGCGGCGCTT
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTT
5429279 TTTTTTAAAC
Statistics
Matches: 229, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
43 187 0.82
44 1 0.00
45 1 0.00
46 40 0.17
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTCTCCCAC
Found at i:5429683 original size:21 final size:21
Alignment explanation
Indices: 5429625--5429695 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
5429615 TTCTGCTTTG
***
5429625 CTCTGCTTCCCTCGCTAAAGC
1 CTCTGCTTCCCTCGCTGCTGC
*
5429646 CTCTGCTTCTCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
*
5429667 CTCTACTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
*
5429688 ATCTGCTT
1 CTCTGCTT
5429696 TAAGTTGTAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.07, C:0.42, G:0.15, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCTGC
Found at i:5429725 original size:9 final size:9
Alignment explanation
Indices: 5429711--5429901 Score: 138
Period size: 9 Copynumber: 22.2 Consensus size: 9
5429701 TGTAGTTGTA
5429711 TTATGTAAG
1 TTATGTAAG
5429720 TTATGTAAG
1 TTATGTAAG
*
5429729 TTGTGT-A-
1 TTATGTAAG
5429736 TTATGTAAG
1 TTATGTAAG
5429745 TTATGTAAG
1 TTATGTAAG
*
5429754 TTATGT--C
1 TTATGTAAG
*
5429761 TTATGTAGG
1 TTATGTAAG
5429770 TTATGTAAG
1 TTATGTAAG
*
5429779 TTAAGT-A-
1 TTATGTAAG
5429786 TTATGTAAG
1 TTATGTAAG
5429795 TTATGTAAG
1 TTATGTAAG
*
5429804 TT-T-T-TG
1 TTATGTAAG
*
5429810 TT-TGTGTA-
1 TTATGT-AAG
*
5429818 TTATGTAAC
1 TTATGTAAG
* *
5429827 TTATATAAT
1 TTATGTAAG
*
5429836 TTATGTAGG
1 TTATGTAAG
*
5429845 TTATG-CA-
1 TTATGTAAG
5429852 TTATGTAAG
1 TTATGTAAG
5429861 TTATGTAAG
1 TTATGTAAG
5429870 TTATTATGTAAG
1 ---TTATGTAAG
**
5429882 TTATGTTGG
1 TTATGTAAG
5429891 TTATGTAAG
1 TTATGTAAG
5429900 TT
1 TT
5429902 GTGATATGAT
Statistics
Matches: 144, Mismatches: 22, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
6 4 0.03
7 23 0.16
8 9 0.06
9 99 0.69
12 9 0.06
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:5429737 original size:25 final size:25
Alignment explanation
Indices: 5429707--5429901 Score: 166
Period size: 25 Copynumber: 7.6 Consensus size: 25
5429697 AAGTTGTAGT
*
5429707 TGTATTATGTAAGTTATGTAAGTTG
1 TGTATTATGTAAGTTATGTAAGTTA
5429732 TGTATTATGTAAGTTATGTAAGTTA
1 TGTATTATGTAAGTTATGTAAGTTA
* *
5429757 TGTCTTATGTAGGTTATGTAAGTTA
1 TGTATTATGTAAGTTATGTAAGTTA
* *
5429782 AGTATTATGTAAGTTATGTAAGTTTT
1 TGTATTATGTAAGTTATGTAAG-TTA
* *
5429808 TGT-TTGTGT-A-TTATGTAACTTA
1 TGTATTATGTAAGTTATGTAAGTTA
* * *
5429830 TATAATTTATGTAGGTTATG-CA-TTA
1 TGT-A-TTATGTAAGTTATGTAAGTTA
5429855 TGTAAGTTATGTAAGTTATTATGTAAGTTA
1 TGT-A-TTATGTAAG---TTATGTAAGTTA
*
5429885 TGTTGGTTATGTAAGTT
1 TG-T-ATTATGTAAGTT
5429902 GTGATATGAT
Statistics
Matches: 137, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
22 4 0.03
23 8 0.06
24 1 0.01
25 91 0.66
26 5 0.04
27 7 0.05
28 5 0.04
29 1 0.01
30 14 0.10
31 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (25 bp):
TGTATTATGTAAGTTATGTAAGTTA
Found at i:5429739 original size:16 final size:17
Alignment explanation
Indices: 5429711--5429901 Score: 121
Period size: 16 Copynumber: 11.1 Consensus size: 17
5429701 TGTAGTTGTA
5429711 TTATGTAAGTTATGTAAG
1 TTATGT-AGTTATGTAAG
*
5429729 TTGTGTA-TTATGTAAG
1 TTATGTAGTTATGTAAG
*
5429745 TTATGTAAGTTATGT--C
1 TTATGT-AGTTATGTAAG
5429761 TTATGTAGGTTATGTAAG
1 TTATGTA-GTTATGTAAG
*
5429779 TTAAGTA-TTATGTAAG
1 TTATGTAGTTATGTAAG
*
5429795 TTATGTAAGTT-T-T-TG
1 TTATGT-AGTTATGTAAG
* *
5429810 TTTGTGTA-TTATGTAAC
1 -TTATGTAGTTATGTAAG
* * *
5429827 TTATATAATTTATGTAGG
1 TTATGT-AGTTATGTAAG
*
5429845 TTATGCA-TTATGTAAG
1 TTATGTAGTTATGTAAG
5429861 TTATGTAAGTTATTATGTAAG
1 TTATGT-AG---TTATGTAAG
*
5429882 TTATGTTGGTTATGTAAG
1 TTATG-TAGTTATGTAAG
5429900 TT
1 TT
5429902 GTGATATGAT
Statistics
Matches: 135, Mismatches: 19, Indels: 38
0.70 0.10 0.20
Matches are distributed among these distances:
14 2 0.01
15 4 0.03
16 65 0.48
17 7 0.05
18 41 0.30
21 15 0.11
22 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (17 bp):
TTATGTAGTTATGTAAG
Found at i:5429878 original size:12 final size:12
Alignment explanation
Indices: 5429861--5429885 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5429851 ATTATGTAAG
5429861 TTATGTAAGTTA
1 TTATGTAAGTTA
5429873 TTATGTAAGTTA
1 TTATGTAAGTTA
5429885 T
1 T
5429886 GTTGGTTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:5429957 original size:30 final size:30
Alignment explanation
Indices: 5429914--5429980 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
5429904 GATATGATAT
* *
5429914 AAATTACGTAAGTTAAGAAATCTAATCTTA
1 AAATTATGCAAGTTAAGAAATCTAATCTTA
** * *
5429944 AAATTATGCAAGTTTTGAAATTTGATCTTA
1 AAATTATGCAAGTTAAGAAATCTAATCTTA
*
5429974 ATATTAT
1 AAATTAT
5429981 ACAATTTTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (30 bp):
AAATTATGCAAGTTAAGAAATCTAATCTTA
Found at i:5430043 original size:30 final size:31
Alignment explanation
Indices: 5430007--5430070 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
5429997 GTAAGTTATG
*
5430007 TAATTTATGCAAGTTATG-AAATTTGAACTT
1 TAATTTATACAAGTTATGTAAATTTGAACTT
* *
5430037 TAATTTATATAAGTTATGTAAATTTTAACTT
1 TAATTTATACAAGTTATGTAAATTTGAACTT
5430068 TAA
1 TAA
5430071 AATAAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (31 bp):
TAATTTATACAAGTTATGTAAATTTGAACTT
Found at i:5430089 original size:22 final size:21
Alignment explanation
Indices: 5430062--5430103 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5430052 ATGTAAATTT
5430062 TAACTTTAAAATAAATTAAAAA
1 TAACTTTAAAATAAA-TAAAAA
* *
5430084 TAACTTTGAATTAAATAAAA
1 TAACTTTAAAATAAATAAAA
5430104 TATTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
TAACTTTAAAATAAATAAAAA
Found at i:5430191 original size:28 final size:28
Alignment explanation
Indices: 5430159--5430247 Score: 98
Period size: 28 Copynumber: 3.2 Consensus size: 28
5430149 TTAAATAAAA
5430159 TATTTAAAATATAACTTTGAATACAATT
1 TATTTAAAATATAACTTTGAATACAATT
* *
5430187 TATTTAATTAAGTA-AA--TTAAATA-AA-A
1 TATTTAA--AA-TATAACTTTGAATACAATT
5430213 TATTTAAAATATAACTTTGAATACAATT
1 TATTTAAAATATAACTTTGAATACAATT
5430241 TATTTAA
1 TATTTAA
5430248 TTAGGTAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
23 2 0.04
24 4 0.08
26 13 0.27
27 4 0.08
28 20 0.41
30 4 0.08
31 2 0.04
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (28 bp):
TATTTAAAATATAACTTTGAATACAATT
Found at i:5430218 original size:54 final size:54
Alignment explanation
Indices: 5430146--5430261 Score: 223
Period size: 54 Copynumber: 2.1 Consensus size: 54
5430136 TTTGTCATTC
5430146 AAATTAAATAAAATATTTAAAATATAACTTTGAATACAATTTATTTAATTAAGT
1 AAATTAAATAAAATATTTAAAATATAACTTTGAATACAATTTATTTAATTAAGT
*
5430200 AAATTAAATAAAATATTTAAAATATAACTTTGAATACAATTTATTTAATTAGGT
1 AAATTAAATAAAATATTTAAAATATAACTTTGAATACAATTTATTTAATTAAGT
5430254 AAATTAAA
1 AAATTAAA
5430262 AACAAAACAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (54 bp):
AAATTAAATAAAATATTTAAAATATAACTTTGAATACAATTTATTTAATTAAGT
Found at i:5432963 original size:115 final size:115
Alignment explanation
Indices: 5432754--5433112 Score: 601
Period size: 115 Copynumber: 3.1 Consensus size: 115
5432744 AAAAGTATAC
* * *
5432754 TATTAGTGGCGCTTTCTTAGAAGCGCCGCAATATATATTAACGGAAACGCTGCGTTTAAATCTTG
1 TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTGCGTTTAAATCTTG
*
5432819 ATGTATACTGGATTTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
66 ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
* * * * * *
5432869 TATTAGCGGCACTTGCTAAGAAGCGCCGCAAGATATATTAACCTAAACGTTGCGTTTAGATCTTG
1 TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTGCGTTTAAATCTTG
* * *
5432934 ACGTATACTGGAATTAGTGGCATTTACGAGAAATCGCCGCTAAATCATAT
66 ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
5432984 TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTGCGTTTAAATCTTG
1 TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTGCGTTTAAATCTTG
5433049 ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
66 ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
5433099 TATTAGCGGCGCTT
1 TATTAGCGGCGCTT
5433113 ATTTGTTAGC
Statistics
Matches: 222, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
115 222 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (115 bp):
TATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTAACCGAAACGCTGCGTTTAAATCTTG
ATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGCCGCTAAATCATAT
Found at i:5434563 original size:45 final size:45
Alignment explanation
Indices: 5434503--5434593 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
5434493 TGTTGCGTCC
* *
5434503 TTCTTGCCCAATTTCTTGAATTCCCAAATCCGTAAATCGCCTCCT
1 TTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCCTCCT
* *
5434548 TTCTTGCCTAATTTCTTGAAATCCGAAATCCCTAAATCGCCTCCT
1 TTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCCTCCT
5434593 T
1 T
5434594 CCTCCTTCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (45 bp):
TTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCCTCCT
Found at i:5435122 original size:37 final size:37
Alignment explanation
Indices: 5435072--5435156 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
5435062 CTGTCGATGG
*
5435072 GTTACTGTTTTCCTGCATTTTTTTGGCATACTGGTCT
1 GTTACTGTTTTCCTGCATTTTTTAGGCATACTGGTCT
*
5435109 GTTACTATTTTCCTGCATTTTTTAGGCATACTGGTCT
1 GTTACTGTTTTCCTGCATTTTTTAGGCATACTGGTCT
5435146 GTTACTGTTTT
1 GTTACTGTTTT
5435157 GTAGAAATCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.13, C:0.18, G:0.18, T:0.52
Consensus pattern (37 bp):
GTTACTGTTTTCCTGCATTTTTTAGGCATACTGGTCT
Found at i:5448019 original size:42 final size:42
Alignment explanation
Indices: 5447960--5448156 Score: 288
Period size: 42 Copynumber: 4.6 Consensus size: 42
5447950 GTCATATCAA
*
5447960 GGCGTTTATTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGT
1 GGCGTTTATTTCTAAGCGCCGCTAAAGAACATGATCTTTAGT
*
5448002 GGCGTTTATTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGT
1 GGCGTTTATTTCTAAGCGCCGCTAAAGAACATGATCTTTAGT
* * *
5448044 GGCGTTTATTTTTTTAGCGCCGCTAAAGAACATGATCTTTAGC
1 GGCGTTTA-TTTCTAAGCGCCGCTAAAGAACATGATCTTTAGT
*
5448087 GGCGTTT-TTTCTAAGCGCCGCTAAAGAACATGATCTTTAGG
1 GGCGTTTATTTCTAAGCGCCGCTAAAGAACATGATCTTTAGT
* *
5448128 GGCGTTTTTTTCTGTAAGCGCCGCAAAAG
1 GGCGTTTATTTC--TAAGCGCCGCTAAAG
5448157 TTTGCGACGT
Statistics
Matches: 143, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
41 38 0.27
42 54 0.38
43 37 0.26
44 14 0.10
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (42 bp):
GGCGTTTATTTCTAAGCGCCGCTAAAGAACATGATCTTTAGT
Found at i:5448113 original size:84 final size:85
Alignment explanation
Indices: 5447960--5448156 Score: 292
Period size: 85 Copynumber: 2.3 Consensus size: 85
5447950 GTCATATCAA
* * *
5447960 GGCGTTTA-TTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCGTTTATTTCTAAGCGCCGC
1 GGCGTTTATTTTTTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTTCTAAGCGCCGC
* *
5448024 TAAAGAACATGGTCTTTAGT
66 TAAAGAACATGATCTTTAGG
*
5448044 GGCGTTTATTTTTTTAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTCTAAGCGCCGC
1 GGCGTTTATTTTTTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTTCTAAGCGCCGC
5448108 TAAAGAACATGATCTTTAGG
66 TAAAGAACATGATCTTTAGG
*
5448128 GGCGTTT-TTTTCTGTAAGCGCCGCAAAAG
1 GGCGTTTATTTT-T-TAAGCGCCGCTAAAG
5448157 TTTGCGACGT
Statistics
Matches: 102, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
83 4 0.04
84 48 0.47
85 50 0.49
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (85 bp):
GGCGTTTATTTTTTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTATTTCTAAGCGCCGC
TAAAGAACATGATCTTTAGG
Found at i:5448532 original size:20 final size:20
Alignment explanation
Indices: 5448489--5448530 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
5448479 GGCCATGTTT
5448489 GGGG-AATTGTTAGGGATTA
1 GGGGAAATTGTTAGGGATTA
*
5448508 GGGGAAATT-TTAGGGATTT
1 GGGGAAATTGTTAGGGATTA
5448527 GGGG
1 GGGG
5448531 GAGAATGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.24, C:0.00, G:0.45, T:0.31
Consensus pattern (20 bp):
GGGGAAATTGTTAGGGATTA
Found at i:5450003 original size:36 final size:35
Alignment explanation
Indices: 5449942--5450017 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
5449932 ACCCAAAATA
*
5449942 ATAAACATTAAACCATAATCCCTAAAACTCTAAACC
1 ATAAACATTAAACCATAATCCCTAAAA-ACTAAACC
* *
5449978 ATAAACATTAAATCATAAAT-TCTAAAAACTAAACC
1 ATAAACATTAAACCAT-AATCCCTAAAAACTAAACC
*
5450013 CTAAA
1 ATAAA
5450018 ATAAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 11 0.31
36 21 0.60
37 3 0.09
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (35 bp):
ATAAACATTAAACCATAATCCCTAAAAACTAAACC
Found at i:5450639 original size:46 final size:47
Alignment explanation
Indices: 5450572--5450663 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 47
5450562 GGCGCTTCTT
5450572 CAAAAACGCCGCTAAAACCCTGAGCATTAGCTGCGC-TTTCCAAAAC
1 CAAAAACGCCGCTAAAACCCTGAGCATTAGCTGCGCTTTTCCAAAAC
5450618 CAAAAACGCCGCTAAAACCCTGAGCATTAGCTGCGCTTTTCCAAAA
1 CAAAAACGCCGCTAAAACCCTGAGCATTAGCTGCGCTTTTCCAAAA
5450664 ACGACGCTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 36 0.80
47 9 0.20
ACGTcount: A:0.35, C:0.32, G:0.15, T:0.18
Consensus pattern (47 bp):
CAAAAACGCCGCTAAAACCCTGAGCATTAGCTGCGCTTTTCCAAAAC
Found at i:5450687 original size:87 final size:81
Alignment explanation
Indices: 5450434--5450715 Score: 302
Period size: 80 Copynumber: 3.4 Consensus size: 81
5450424 AAAAATAGAG
*
5450434 CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAACCCTGAGCATTAGCTGCGCTTTTCCAAAAAC
1 CATTAGCGGCGCTT-TCCAAAAACGCCGCTAAAACCCTGAGCATTAGCTGCGCTTTTCCAAAAAC
5450499 GACGCTAAAGCCCCATT
65 GACGCTAAAGCCCCATT
* * ** * *
5450516 CATTAGCGGGGGTTTTTAAAAACGCCGCTAAAA--ATAGAGCATTAGCGGCGCTTCTT-CAAAAA
1 CATTAGCGGCGCTTTCCAAAAACGCCGCTAAAACCCT-GAGCATTAGCTGCGCTT-TTCCAAAAA
* * * *
5450578 CGCCGCTAAAACCCTGA-G
64 CGACGCTAAAGCCC-CATT
*
5450596 CATTAGCTGCGCTTTCCAAAACCAAAAACGCCGCTAAAACCCTGAGCATTAGCTGCGCTTTTCCA
1 CATTAGCGGCGCTTT------CCAAAAACGCCGCTAAAACCCTGAGCATTAGCTGCGCTTTTCCA
5450661 AAAACGACGCTAAAGCCCCATT
60 AAAACGACGCTAAAGCCCCATT
** *
5450683 CATTAGCGGCGCTTTTTAAAAAACGCCACTAAA
1 CATTAGCGGCGC-TTTCCAAAAACGCCGCTAAA
5450716 GCCTCGAAAA
Statistics
Matches: 162, Mismatches: 24, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
79 1 0.01
80 46 0.28
81 21 0.13
82 26 0.16
86 19 0.12
87 45 0.28
88 4 0.02
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (81 bp):
CATTAGCGGCGCTTTCCAAAAACGCCGCTAAAACCCTGAGCATTAGCTGCGCTTTTCCAAAAACG
ACGCTAAAGCCCCATT
Found at i:5450718 original size:41 final size:41
Alignment explanation
Indices: 5450399--5450715 Score: 281
Period size: 41 Copynumber: 7.7 Consensus size: 41
5450389 ATATTTTTTT
*
5450399 GCGGCGCATTTTT-AAAAACGCCGCTAAAA--ATAGAGCATTA
1 GCGGCGC-TTTTTCAAAAACGCCGCTAAAACCCT-GAGCATTA
*
5450439 GCGGCGCTTCTTCAAAAACGCCGCTAAAACCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCTGAGCATTA
* * * * * *
5450480 GCTGCGCTTTTCCAAAAACGACGCTAAAGCCC-CATTCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCTGA-GCATTA
* * *
5450521 GCGGGGGTTTTT-AAAAACGCCGCTAAAA--ATAGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCT-GAGCATTA
*
5450560 GCGGCGCTTCTTCAAAAACGCCGCTAAAACCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCTGAGCATTA
* **
5450601 GCTGCGCTTTCCAAAACCAAAAACGCCGCTAAAACCCTGAGCATTA
1 GCGGCGCTTT-----TTCAAAAACGCCGCTAAAACCCTGAGCATTA
* * * * * *
5450647 GCTGCGCTTTTCCAAAAACGACGCTAAAGCCC-CATTCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCTGA-GCATTA
* *
5450688 GCGGCGCTTTTTAAAAAACGCCACTAAA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAA
5450716 GCCTCGAAAA
Statistics
Matches: 226, Mismatches: 36, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
39 18 0.08
40 56 0.25
41 111 0.49
42 2 0.01
46 39 0.17
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAACCCTGAGCATTA
Found at i:5464315 original size:44 final size:44
Alignment explanation
Indices: 5464260--5464486 Score: 305
Period size: 44 Copynumber: 5.2 Consensus size: 44
5464250 AAAAGCAACC
* * * *
5464260 GATCCTGTCTTCATGTATTTGCATGAAGTAGATTAAAGAT-AGTA
1 GATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATGA-CA
* * *
5464304 GATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATGGCA
1 GATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATGACA
* * *
5464348 TATCTTGTCTTCATGTATTGGCATGAAGAAGATCGAAGATGACA
1 GATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATGACA
* *
5464392 GATCTTGTCTTCATGTATTGACATGGAGTAGATCAAAGATGACA
1 GATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATGACA
* *
5464436 GATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGA-AACA
1 GATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATGACA
5464479 GATCTTGT
1 GATCTTGT
5464487 NNNNNNNNNN
Statistics
Matches: 162, Mismatches: 20, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
43 11 0.07
44 151 0.93
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (44 bp):
GATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATGACA
Found at i:5464703 original size:44 final size:44
Alignment explanation
Indices: 5464640--5464990 Score: 395
Period size: 44 Copynumber: 7.9 Consensus size: 44
5464630 NNNNNNNNNN
*
5464640 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATGGC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATGGC
* * * *
5464684 AGATCTTGTCTTCATGTATTGGCATAAAGAAGATCAAAGATGAC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATGGC
* * *
5464728 ATATCTTGTCTTCATGTATTGACAT-AGAGTAGATCAAAGATGGC
1 AGATCTTGTCTTCATGTATTGGCATGA-AGTAGATCGAAGATGGC
*
5464772 AGATCTTGTCTTCATGTATTAGCATGAAGTAGATCGAAGATGGC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATGGC
* * *
5464816 AGATCTTATCTTCATGTATTGGCATGAAGTAGATCAAAGATAGC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATGGC
* * *
5464860 AGATATTGTCTTCATGTATTGGTATGAAGTAGATC-AGAGATAGC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGA-AGATGGC
* * ** **
5464904 AGATCTTATCTTTCCA--TACTGGTGGTGAAGTAGATCGAAGATAAC
1 AGATCTTGTC-TT-CATGTATTGG-CATGAAGTAGATCGAAGATGGC
* * * *
5464949 AGATCTTATCTTCCTGTATCGGTAGTGAAGTAGATCGAAGAT
1 AGATCTTGTCTTCATGTATTGGCA-TGAAGTAGATCGAAGAT
5464991 ACAAGTCTTA
Statistics
Matches: 266, Mismatches: 31, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
43 3 0.01
44 209 0.79
45 51 0.19
46 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (44 bp):
AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATGGC
Found at i:5464877 original size:132 final size:133
Alignment explanation
Indices: 5464640--5464991 Score: 444
Period size: 132 Copynumber: 2.6 Consensus size: 133
5464630 NNNNNNNNNN
*
5464640 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATGGCAGATCTTGTCTTCATGTATTG
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATGGCAGATCTTATCTTCATGTATTG
* * * *
5464705 GCATAAAGAAGATCAAAGAT-GACATATCTTGTCTTCATGTATTGACAT-AGAGTAGATCAAAGA
66 GCATGAAGTAGATCAAAGATAGACAGATATTGTCTTCATGTATTGACATGA-AGTAGATCAAAGA
*
5464768 TGGC
130 TAGC
* *
5464772 AGATCTTGTCTTCATGTATTAGCATGAAGTAGATCGAAGATGGCAGATCTTATCTTCATGTATTG
1 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATGGCAGATCTTATCTTCATGTATTG
** *
5464837 GCATGAAGTAGATCAAAGATAG-CAGATATTGTCTTCATGTATTGGTATGAAGTAGATCAGAGAT
66 GCATGAAGTAGATCAAAGATAGACAGATATTGTCTTCATGTATTGACATGAAGTAGATCAAAGAT
5464901 AGC
131 AGC
* * * ** *
5464904 AGATCTTATCTTTCCA--TACTGGTGGTGAAGTAGATCGAAGATAACAGATCTTATCTTCCTGTA
1 AGATCTTGTC-TT-CATGTATTGG-CGTGAAGTAGATCGAAGATGGCAGATCTTATCTTCATGTA
* * *
5464967 TCGGTAGTGAAGTAGATCGAAGATA
63 TTGGCA-TGAAGTAGATCAAAGATA
5464992 CAAGTCTTAT
Statistics
Matches: 192, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
132 130 0.68
133 43 0.22
134 19 0.10
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (133 bp):
AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATGGCAGATCTTATCTTCATGTATTG
GCATGAAGTAGATCAAAGATAGACAGATATTGTCTTCATGTATTGACATGAAGTAGATCAAAGAT
AGC
Found at i:5466505 original size:3 final size:3
Alignment explanation
Indices: 5466493--5466533 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
5466483 ATGTTATACC
*
5466493 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5466534 TCTATATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:5467890 original size:29 final size:28
Alignment explanation
Indices: 5467857--5467918 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
5467847 AAAAAGCCAT
*
5467857 ATTTTTTCAA-AATTTACCGAAATGGGTC
1 ATTTTTT-AATAATTTAACGAAATGGGTC
* *
5467885 ACTTTTTTAATTATTTAACGGAATGGGTC
1 A-TTTTTTAATAATTTAACGAAATGGGTC
5467914 ATTTT
1 ATTTT
5467919 CCGCGAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (28 bp):
ATTTTTTAATAATTTAACGAAATGGGTC
Found at i:5468153 original size:22 final size:22
Alignment explanation
Indices: 5468120--5468175 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
5468110 TTTTCACAAA
*
5468120 CAAATATTCTCTCAATTTCTTTC
1 CAAA-ATTCTCTCAATTTCCTTC
5468143 CAAAATTCTCTCAATTTCCTTC
1 CAAAATTCTCTCAATTTCCTTC
*
5468165 CGAAATTCTCT
1 CAAAATTCTCT
5468176 TAAACTCTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.27, C:0.29, G:0.02, T:0.43
Consensus pattern (22 bp):
CAAAATTCTCTCAATTTCCTTC
Found at i:5468186 original size:30 final size:30
Alignment explanation
Indices: 5468150--5468208 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
5468140 TTCCAAAATT
* * *
5468150 CTCTCAATTTCCTTCCGAAATTCTCTTAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTTAAA
5468180 CTCTCAAATTCCTTCCAAAATCCTCTTAA
1 CTCTCAAATTCCTTCCAAAATCCTCTTAA
5468209 TTTCCTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.32, G:0.02, T:0.37
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTTAAA
Found at i:5468227 original size:52 final size:52
Alignment explanation
Indices: 5468128--5468227 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 52
5468118 AACAAATATT
* * * ** *
5468128 CTCTCAATTTCTTTCCAAAATTCTCTCAATTTCCTTCCGAAATTCTCTTAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCTTAAA
*
5468180 CTCTCAAATTCCTTCCAAAATCCTCTTAATTTCCTTCAAAAAATCTCT
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCT
5468228 CAAATCCATA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.29, C:0.30, G:0.01, T:0.40
Consensus pattern (52 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCTTAAA
Found at i:5469238 original size:7 final size:7
Alignment explanation
Indices: 5469226--5469264 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
5469216 AGTGGATTGA
5469226 TATTTAG
1 TATTTAG
5469233 TATTTAG
1 TATTTAG
5469240 TATTTAG
1 TATTTAG
5469247 TATTTAG
1 TATTTAG
5469254 TATTTAG
1 TATTTAG
5469261 TATT
1 TATT
5469265 ATGTATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (7 bp):
TATTTAG
Found at i:5470508 original size:29 final size:29
Alignment explanation
Indices: 5470428--5470943 Score: 618
Period size: 29 Copynumber: 17.9 Consensus size: 29
5470418 TTCTGATATT
*
5470428 ATTTGATTAAAAACCCTAA-CCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
5470456 ATTTAATTAAAAACCC-AAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
5470484 ATTTAATTAAAAACACTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
5470513 ATTTAATTAAAAACCCTAACCCTAGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
**
5470542 ATTTAATT-AAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AACCCTAATTTA
* * *
5470571 ATTTGATTAAAAACCATAACCCTAGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* *
5470600 ATTTAATTAAAAATCCTAACCCTTATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
**
5470629 ATTTAATT-AAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AACCCTAATTTA
* * *
5470658 ATTTGATTAAAAACCATAACCCTAGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* *
5470687 ATTTAATTAAAAATCCTAACCCTTATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
**
5470716 ATTTAATT-AAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AACCCTAATTTA
*
5470745 ATTTAATTAAAAACCCTAACTCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
5470774 ATTTAATTAAAAACCCTAACCCTAGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* * **
5470803 ATTTAATT-AAAACTCTAAACACTAACCTA
1 ATTTAATTAAAAACCCT-AACCCTAATTTA
**
5470832 ATTTAATT-AAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AACCCTAATTTA
*
5470861 ATTTAATTAAAAACCCTAACCCTAGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* *
5470890 ATTTAATT-AAAACCCTAAATCCTAATCTA
1 ATTTAATTAAAAACCCT-AACCCTAATTTA
*
5470919 ATTTGATT-AAAACCCTAAACCCTAA
1 ATTTAATTAAAAACCCT-AACCCTAA
5470944 CCTAATTTNN
Statistics
Matches: 421, Mismatches: 56, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
27 2 0.00
28 76 0.18
29 313 0.74
30 30 0.07
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (29 bp):
ATTTAATTAAAAACCCTAACCCTAATTTA
Found at i:5470591 original size:87 final size:87
Alignment explanation
Indices: 5470428--5470943 Score: 733
Period size: 87 Copynumber: 6.0 Consensus size: 87
5470418 TTCTGATATT
* * **
5470428 ATTTGATTAAAAACCCTAA-CCTAATTTAATTTAATTAAAAACCC-AAA-CCTAATTTAATTTAA
1 ATTTAATTAAAAACCCTAACCCTAGTTTAATTTAATT-AAAACCCTAAACCCTAACCTAATTTAA
5470490 TTAAAAA-CACTAACCCTAATTTA
65 TTAAAAACCA-TAACCCTAATTTA
*
5470513 ATTTAATTAAAAACCCTAACCCTAGTTTAATTTAATTAAAACCCTAAACCCTAACCTAATTTGAT
1 ATTTAATTAAAAACCCTAACCCTAGTTTAATTTAATTAAAACCCTAAACCCTAACCTAATTTAAT
*
5470578 TAAAAACCATAACCCTAGTTTA
66 TAAAAACCATAACCCTAATTTA
* *
5470600 ATTTAATTAAAAATCCTAACCCTTA-TTTAATTTAATTAAAACCCTAAACCCTAACCTAATTTGA
1 ATTTAATTAAAAACCCTAACCC-TAGTTTAATTTAATTAAAACCCTAAACCCTAACCTAATTTAA
*
5470664 TTAAAAACCATAACCCTAGTTTA
65 TTAAAAACCATAACCCTAATTTA
*
5470687 ATTTAATTAAAAATCCTAACCCTTA-TTTAATTTAATTAAAACCCTAAACCCTAACCTAATTTAA
1 ATTTAATTAAAAACCCTAACCC-TAGTTTAATTTAATTAAAACCCTAAACCCTAACCTAATTTAA
* *
5470751 TTAAAAACCCTAACTCTAATTTA
65 TTAAAAACCATAACCCTAATTTA
* *
5470774 ATTTAATTAAAAACCCTAACCCTAGTTTAATTTAATTAAAACTCTAAACACTAACCTAATTTAAT
1 ATTTAATTAAAAACCCTAACCCTAGTTTAATTTAATTAAAACCCTAAACCCTAACCTAATTTAAT
* **
5470839 T-AAAACCCTAAACCCTAACCTA
66 TAAAAACCAT-AACCCTAATTTA
* * *
5470861 ATTTAATTAAAAACCCTAACCCTAGTTTAATTTAATTAAAACCCTAAATCCTAATCTAATTTGAT
1 ATTTAATTAAAAACCCTAACCCTAGTTTAATTTAATTAAAACCCTAAACCCTAACCTAATTTAAT
*
5470926 T-AAAACCCTAAACCCTAA
66 TAAAAACCAT-AACCCTAA
5470944 CCTAATTTNN
Statistics
Matches: 402, Mismatches: 22, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
85 25 0.06
86 29 0.07
87 344 0.86
88 4 0.01
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (87 bp):
ATTTAATTAAAAACCCTAACCCTAGTTTAATTTAATTAAAACCCTAAACCCTAACCTAATTTAAT
TAAAAACCATAACCCTAATTTA
Found at i:5470769 original size:24 final size:23
Alignment explanation
Indices: 5470732--5470776 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
5470722 TTAAAACCCT
5470732 AAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAA
5470755 AAACCCTAACTCTAATTTAATT
1 AAACCCTAAC-CTAATTTAATT
5470777 TAATTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (23 bp):
AAACCCTAACCTAATTTAATTAA
Found at i:5471161 original size:29 final size:28
Alignment explanation
Indices: 5471138--5471305 Score: 203
Period size: 29 Copynumber: 5.9 Consensus size: 28
5471128 TAAAACCCTA
**
5471138 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAATTTAATTTAATT-AAAACCCT
*
5471167 AACCCTAATTTAATTTAATTAAAAATCCT
1 AACCCTAATTTAATTTAATT-AAAACCCT
* *
5471196 AACCCTAGTTTAA-TTAATTAAAACTCT
1 AACCCTAATTTAATTTAATTAAAACCCT
**
5471223 AAACCCTAACCTAATTTAATTAAAACCCT
1 -AACCCTAATTTAATTTAATTAAAACCCT
* *
5471252 AAACCCTAATATAATTTGATTAAAAACCCT
1 -AACCCTAATTTAATTTAATT-AAAACCCT
5471282 AACCCTAATTTAATTTAATTAAAA
1 AACCCTAATTTAATTTAATTAAAA
5471306 NNNNNNNNNN
Statistics
Matches: 121, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
27 6 0.05
28 20 0.17
29 87 0.72
30 8 0.07
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.33
Consensus pattern (28 bp):
AACCCTAATTTAATTTAATTAAAACCCT
Found at i:5471240 original size:57 final size:59
Alignment explanation
Indices: 5471119--5471305 Score: 249
Period size: 58 Copynumber: 3.2 Consensus size: 59
5471109 NNNNNNNNNN
**
5471119 TAATTTAATT-AAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATT
1 TAATTTAATTAAAAACCCTAAACCCTAATATAATTTAATTAAAAACCCTAACCCTAATT
* * * * **
5471177 TAATTTAATTAAAAATCCT-AACCCTAGTTTAA-TTAATT-AAAACTCTAAACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAATATAATTTAATTAAAAACCCT-AACCCTAATT
*
5471234 TAATTTAATT-AAAACCCTAAACCCTAATATAATTTGATTAAAAACCCTAACCCTAATT
1 TAATTTAATTAAAAACCCTAAACCCTAATATAATTTAATTAAAAACCCTAACCCTAATT
5471292 TAATTTAATTAAAA
1 TAATTTAATTAAAA
5471306 NNNNNNNNNN
Statistics
Matches: 109, Mismatches: 14, Indels: 11
0.81 0.10 0.08
Matches are distributed among these distances:
56 14 0.13
57 35 0.32
58 43 0.39
59 17 0.16
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.33
Consensus pattern (59 bp):
TAATTTAATTAAAAACCCTAAACCCTAATATAATTTAATTAAAAACCCTAACCCTAATT
Found at i:5471268 original size:86 final size:87
Alignment explanation
Indices: 5471119--5471305 Score: 306
Period size: 86 Copynumber: 2.2 Consensus size: 87
5471109 NNNNNNNNNN
*
5471119 TAATTTAATTAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTA
1 TAATTTAATTAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATATAATTTA
* *
5471184 ATTAAAAATCCTAACCCTAGTT
66 ATTAAAAACCCTAACCCTAATT
*
5471206 TAA-TTAATTAAAACTCTAAACCCTAACCTAATTTAATT-AAAACCCTAAACCCTAATATAATTT
1 TAATTTAATTAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAATATAATTT
*
5471269 GATTAAAAACCCTAACCCTAATT
65 AATTAAAAACCCTAACCCTAATT
5471292 TAATTTAATTAAAA
1 TAATTTAATTAAAA
5471306 NNNNNNNNNN
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
85 8 0.09
86 72 0.77
87 13 0.14
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.33
Consensus pattern (87 bp):
TAATTTAATTAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATATAATTTA
ATTAAAAACCCTAACCCTAATT
Found at i:5474732 original size:125 final size:126
Alignment explanation
Indices: 5474505--5474776 Score: 439
Period size: 125 Copynumber: 2.2 Consensus size: 126
5474495 GCAATTTGAC
*
5474505 ACTATTTGCTCAG-AAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCGAAATCGCA
1 ACTATTTGCTCAGAAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTACCGAAATCGCA
*
5474569 TCCACGAAGGCACGATTTCACAATTTCTTCTCATATAGCATCCTGGTATG-AGCGATTTTAT
66 TCCACGAAGGCACGATTGCACAATTTCTTCTCATATAGCATCCTGGTA-GAAGCGATTTTAT
*
5474630 ACTATTTGCTCAGAAAACGTCAAAAAA-AATTATTTCTTACATGACCAACTGTACCGAAATCGCA
1 ACTATTTGCTCAGAAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTACCGAAATCGCA
*
5474694 TCCACGAGGGCACGATTGCACAATTTCTTCTC-TGATAGCATCCTGGTAGAAGCGATTTTAT
66 TCCACGAAGGCACGATTGCACAATTTCTTCTCAT-ATAGCATCCTGGTAGAAGCGATTTTAT
5474755 ACTATTTGAC-CA-AAAACGTCAA
1 ACTATTTG-CTCAGAAAACGTCAA
5474777 CTCCAAATAA
Statistics
Matches: 139, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
124 12 0.09
125 113 0.81
126 14 0.10
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (126 bp):
ACTATTTGCTCAGAAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTACCGAAATCGCA
TCCACGAAGGCACGATTGCACAATTTCTTCTCATATAGCATCCTGGTAGAAGCGATTTTAT
Found at i:5484404 original size:51 final size:50
Alignment explanation
Indices: 5484340--5484522 Score: 258
Period size: 51 Copynumber: 3.6 Consensus size: 50
5484330 TATCGATGAA
*
5484340 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGT
* * * * * *
5484391 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATATGGT
*
5484442 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGT
*
5484493 CACGTATGTAGTACTATGTGAAGGCTACTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTA
5484523 TGTGAAGGCT
Statistics
Matches: 114, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
50 1 0.01
51 112 0.98
52 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATGGT
Found at i:5484516 original size:102 final size:102
Alignment explanation
Indices: 5484340--5484747 Score: 421
Period size: 102 Copynumber: 3.9 Consensus size: 102
5484330 TATCGATGAA
* *
5484340 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTAC
*
5484405 TAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGAT
* * *
5484442 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACGTATGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTAC
* ** *
5484507 TATGTGAAGGCTACTATGTGAAGGCTACTACGTGAATCGTAAAATTTAAT
66 TAAGTGAAGGCTACTATGT----G-TAC--C--G-A--G-AAGCTTTGAT
* * *
5484557 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCG--GAATGATGAGTCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGATG-GTCACATGTGTAGTA
* * * *
5484620 CTAGGTGCAGGCTACTATGCGTACC-AAATAGCTTTGAT
65 CTAAGTGAAGGCTACTATGTGTACCGAGA-AGCTTTGAT
* * *
5484658 CACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGGATGAAA--ATGGTCACATGTGTAGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-CCGAT-AAATGATGGTCACATGTGTAGT
* * *
5484721 ACTACGTGCAGGCTACTATGTGAACCG
64 ACTAAGTGAAGGCTACTATGTGTACCG
5484748 GTTACCATTG
Statistics
Matches: 258, Mismatches: 28, Indels: 39
0.79 0.09 0.12
Matches are distributed among these distances:
100 1 0.00
101 41 0.16
102 118 0.46
103 4 0.02
105 2 0.01
106 1 0.00
107 4 0.02
109 4 0.02
110 1 0.00
111 1 0.00
112 1 0.00
113 7 0.03
114 31 0.12
115 42 0.16
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGAT
Found at i:5484523 original size:14 final size:14
Alignment explanation
Indices: 5484504--5484542 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
5484494 ACGTATGTAG
5484504 TACTATGTGAAGGC
1 TACTATGTGAAGGC
5484518 TACTATGTGAAGGC
1 TACTATGTGAAGGC
*
5484532 TACTACGTGAA
1 TACTATGTGAA
5484543 TCGTAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (14 bp):
TACTATGTGAAGGC
Found at i:5484615 original size:50 final size:51
Alignment explanation
Indices: 5484518--5484738 Score: 204
Period size: 50 Copynumber: 4.4 Consensus size: 51
5484508 ATGTGAAGGC
* * * * * *
5484518 TACTATGTGAAGGCTACTACGTGAATCGTAA--AATTTAATCACGTGTGTAG
1 TACTATGTGCAGGCTACTACGTGTATCGGAATGAA-TGAGTCACATGTGTAG
5484568 TACTATGTGCAGGCTACTACGTGTATCGGAATG-ATGAGTCACATGTGTAG
1 TACTATGTGCAGGCTACTACGTGTATCGGAATGAATGAGTCACATGTGTAG
* * * ** ** * *
5484618 TACTAGGTGCAGGCTACTATGCGTA-CCAAATAGCTTTGA-TCACGTGTGTAA
1 TACTATGTGCAGGCTACTACGTGTATCGGAAT-G-AATGAGTCACATGTGTAG
5484669 TACTATGTGCAGGCTACTACGTGTATCGG-ATGAAAATG-GTCACATGTGTAG
1 TACTATGTGCAGGCTACTACGTGTATCGGAATG--AATGAGTCACATGTGTAG
*
5484720 TACTACGTGCAGGCTACTA
1 TACTATGTGCAGGCTACTA
5484739 TGTGAACCGG
Statistics
Matches: 138, Mismatches: 25, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
49 4 0.03
50 65 0.47
51 65 0.47
52 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (51 bp):
TACTATGTGCAGGCTACTACGTGTATCGGAATGAATGAGTCACATGTGTAG
Found at i:5484664 original size:101 final size:100
Alignment explanation
Indices: 5484555--5484740 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 100
5484545 GTAAAATTTA
*
5484555 ATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATG-ATGAGTCACATGTGTAGT
1 ATCACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGG-ATGAATG-GTCACATGTGTAGT
*
5484619 ACTAGGTGCAGGCTACTATGCGTACCAAATAGCTTTG
64 ACTACGTGCAGGCTACTATGCGTACCAAATAGCTTTG
5484656 ATCACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTCACATGTGTAGT
1 ATCACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGGATG--AATGGTCACATGTGTAGT
5484721 ACTACGTGCAGGCTACTATG
64 ACTACGTGCAGGCTACTATG
5484741 TGAACCGGTT
Statistics
Matches: 80, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
100 3 0.04
101 41 0.51
102 33 0.41
103 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (100 bp):
ATCACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGGATGAATGGTCACATGTGTAGTAC
TACGTGCAGGCTACTATGCGTACCAAATAGCTTTG
Found at i:5484679 original size:51 final size:49
Alignment explanation
Indices: 5484555--5484738 Score: 165
Period size: 51 Copynumber: 3.7 Consensus size: 49
5484545 GTAAAATTTA
* **
5484555 ATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGATG
1 ATCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCCAAATGATG
* * * *
5484604 AGTCACATGTGTAGTACTAGGTGCAGGCTACTATGCGTA-CCAAATAGCTTTG
1 A-TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCCAAAT-G--ATG
* * * *
5484656 ATCACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGGATGAA-AATG
1 ATCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATC-CA--AATGATG
* * *
5484707 GTCACATGTGTAGTACTACGTGCAGGCTACTA
1 ATCACGTGTGTAGTACTATGTGCAGGCTACTA
5484739 TGTGAACCGG
Statistics
Matches: 108, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
49 5 0.05
50 34 0.31
51 62 0.57
52 4 0.04
53 1 0.01
55 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
ATCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCCAAATGATG
Found at i:5484721 original size:216 final size:215
Alignment explanation
Indices: 5484340--5484744 Score: 573
Period size: 216 Copynumber: 1.9 Consensus size: 215
5484330 TATCGATGAA
*
5484340 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGA-AAATAATGGTCACATGTGTAGTAC
* * * * *
5484405 TAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTAC
65 TAAGTGAAGGCTACTATGCGTACCGAAAAGCTTTGATCACGTGTGTAATACTATGTGAAGGCTAC
* *
5484470 TACGTGTACCGATAAATGATGGTCACGTATGTAGTACTATGTGAAGGCTACTATGTGAAGGCTAC
130 TACGTGTACCGATAAA-GATGGTCACATATGTAGTACTACGTGAAGGCTACTATGTGAAGGCTAC
5484535 TACGTGAATCGTAAAATTTAAT
194 TACGTGAATCGTAAAATTTAAT
* * * *
5484557 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCG-GAATGATGAGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAAAATAATG-GTCACATGTGTAGTAC
* * *
5484621 TAGGTGCAGGCTACTATGCGTACC-AAATAGCTTTGATCACGTGTGTAATACTATGTGCAGGCTA
65 TAAGTGAAGGCTACTATGCGTACCGAAA-AGCTTTGATCACGTGTGTAATACTATGTGAAGGCTA
* * *
5484685 CTACGTGTATCGGATGAAA-ATGGTCACATGTGTAGTACTACGTGCAGGCTACTATGTGAA
129 CTACGTGTA-CCGAT-AAAGATGGTCACATATGTAGTACTACGTGAAGGCTACTATGTGAA
5484745 CCGGTTACCA
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
215 8 0.05
216 115 0.69
217 40 0.24
218 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (215 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAAAATAATGGTCACATGTGTAGTACT
AAGTGAAGGCTACTATGCGTACCGAAAAGCTTTGATCACGTGTGTAATACTATGTGAAGGCTACT
ACGTGTACCGATAAAGATGGTCACATATGTAGTACTACGTGAAGGCTACTATGTGAAGGCTACTA
CGTGAATCGTAAAATTTAAT
Found at i:5484849 original size:33 final size:33
Alignment explanation
Indices: 5484811--5484934 Score: 124
Period size: 33 Copynumber: 3.5 Consensus size: 33
5484801 ATGTGAAAGG
5484811 GGTTGCTAAGTGCTGATTCCTCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCTCGAATCATTGGT
* * *
5484844 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAAG-
1 GGTTGCTAAGTGCTGATTCC-TCGAATC----AT-TG----GT
5484886 GGTTGCTAAGTGCTGATTCCTCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCTCGAATCATTGGT
5484919 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
5484935 ATCCACCGAT
Statistics
Matches: 74, Mismatches: 6, Indels: 22
0.73 0.06 0.22
Matches are distributed among these distances:
32 1 0.01
33 35 0.47
34 5 0.07
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
41 5 0.07
42 19 0.26
43 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCTCGAATCATTGGT
Found at i:5484889 original size:75 final size:74
Alignment explanation
Indices: 5484766--5484942 Score: 284
Period size: 75 Copynumber: 2.4 Consensus size: 74
5484756 TGACTATAAA
* * *
5484766 GGTGGTTGCTACGTGCTAATTCCACCGTAATTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCC
1 GGTGGTTGCTAAGTGCTGA-TCCACCGTAATTTAAATGTGAAAAGGGTTGCTAAGTGCTGATTCC
5484831 TCGAATCATT
65 TCGAATCATT
5484841 GGTGGTTGCTAAGTGCTGATCCCACCGT-ATCTTAAATGTGAAAAGGGTTGCTAAGTGCTGATTC
1 GGTGGTTGCTAAGTGCTGAT-CCACCGTAAT-TTAAATGTGAAAAGGGTTGCTAAGTGCTGATTC
5484905 CTCGAATCATT
64 CTCGAATCATT
5484916 GGTGGTTGCTAAGTGCTGAATCCACCG
1 GGTGGTTGCTAAGTGCTG-ATCCACCG
5484943 ATAACGGATA
Statistics
Matches: 96, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
74 3 0.03
75 91 0.95
76 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.32
Consensus pattern (74 bp):
GGTGGTTGCTAAGTGCTGATCCACCGTAATTTAAATGTGAAAAGGGTTGCTAAGTGCTGATTCCT
CGAATCATT
Found at i:5485886 original size:49 final size:49
Alignment explanation
Indices: 5485777--5485926 Score: 192
Period size: 49 Copynumber: 3.0 Consensus size: 49
5485767 ACATGTGAAC
* *
5485777 ATGTGATTATGTGATTCCGTATAAGACCATAGCTGGGTGGGCTATGGCATCGGT
1 ATGTGA-TATGTGATTACGTGTAAGACCATAGC----TGGGCTATGGCATCGGT
* *
5485831 AAGTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGT
1 ATGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGT
* * *
5485880 ATGTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 ATGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCG
5485927 AGAAAACGAA
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
49 59 0.67
53 24 0.27
54 5 0.06
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (49 bp):
ATGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGT
Found at i:5489522 original size:24 final size:24
Alignment explanation
Indices: 5489494--5489545 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5489484 TTAGTAAGTC
* *
5489494 AAATAAACTATACTAATAAGTGCT
1 AAATAAACTATACTAATAAATACT
* *
5489518 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
5489542 AAAT
1 AAAT
5489546 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:5491459 original size:31 final size:31
Alignment explanation
Indices: 5491421--5491486 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
5491411 CTTTATCAAT
5491421 ATAGGGTTCCTCATATCAGTTTGAGGATTGA
1 ATAGGGTTCCTCATATCAGTTTGAGGATTGA
5491452 ATAGGGTTCCTCATATCAGTTTGAGGATTGA
1 ATAGGGTTCCTCATATCAGTTTGAGGATTGA
5491483 ATAG
1 ATAG
5491487 AGGGTACTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (31 bp):
ATAGGGTTCCTCATATCAGTTTGAGGATTGA
Found at i:5492510 original size:132 final size:132
Alignment explanation
Indices: 5492354--5492621 Score: 527
Period size: 132 Copynumber: 2.0 Consensus size: 132
5492344 TATAAATGAT
5492354 ACAAACTTCAACAACAAAGATTTCAGGTTAAACTTAGGAGCAAATTCATCCCTCTGTTATAAAAG
1 ACAAACTTCAACAACAAAGATTTCAGGTTAAACTTAGGAGCAAATTCATCCCTCTGTTATAAAAG
5492419 CGAGCAATTTAGTCTTACATTTAATTTCAAAGCAGAAAAGGGATACCCACAAGGGGATTATGAAC
66 CGAGCAATTTAGTCTTACATTTAATTTCAAAGCAGAAAAGGGATACCCACAAGGGGATTATGAAC
5492484 AA
131 AA
5492486 ACAAACTTCAACAACAAAGATTTCAGGTTAAACTTAGGAGCAAATTCATCCCTCTGTTATAAAAG
1 ACAAACTTCAACAACAAAGATTTCAGGTTAAACTTAGGAGCAAATTCATCCCTCTGTTATAAAAG
*
5492551 CGAGCAATTTAGTCTTACATTTAATTTCAAAGCAGAAAAGGGATACCCACAAGGGGATTATGAAT
66 CGAGCAATTTAGTCTTACATTTAATTTCAAAGCAGAAAAGGGATACCCACAAGGGGATTATGAAC
5492616 AA
131 AA
5492618 ACAA
1 ACAA
5492622 GCTGATTCAG
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 135 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (132 bp):
ACAAACTTCAACAACAAAGATTTCAGGTTAAACTTAGGAGCAAATTCATCCCTCTGTTATAAAAG
CGAGCAATTTAGTCTTACATTTAATTTCAAAGCAGAAAAGGGATACCCACAAGGGGATTATGAAC
AA
Found at i:5492952 original size:47 final size:48
Alignment explanation
Indices: 5492870--5492967 Score: 137
Period size: 47 Copynumber: 2.0 Consensus size: 48
5492860 AACTAAAAAA
* *
5492870 GAAAACTAAAAAAAGGGGGGAGATGAACGATTTTTTAACTAAGATTTAGG
1 GAAAACTAAAAAAA--GAGGAGATGAACGAGTTTTTAACTAAGATTTAGG
5492920 GAAAACTAAAAAAA-AGGAGATGAAC-AGGTTTTTAACTAAGATTTAGG
1 GAAAACTAAAAAAAGAGGAGATGAACGA-GTTTTTAACTAAGATTTAGG
5492967 G
1 G
5492968 TTTAAAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
46 1 0.02
47 30 0.67
50 14 0.31
ACGTcount: A:0.46, C:0.06, G:0.24, T:0.23
Consensus pattern (48 bp):
GAAAACTAAAAAAAGAGGAGATGAACGAGTTTTTAACTAAGATTTAGG
Found at i:5500371 original size:18 final size:18
Alignment explanation
Indices: 5500348--5500383 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5500338 AAAAGTTAAT
5500348 TTCCAAAAAAGGTTTGGA
1 TTCCAAAAAAGGTTTGGA
5500366 TTCCAAAAAAGGTTTGGA
1 TTCCAAAAAAGGTTTGGA
5500384 CAGCTTGCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (18 bp):
TTCCAAAAAAGGTTTGGA
Found at i:5508025 original size:19 final size:20
Alignment explanation
Indices: 5507983--5508025 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
5507973 TTTGAATACT
* * *
5507983 TTTAAAATATTTTTTTTATT
1 TTTAAAATATATTTTTAATG
5508003 TTTAAAATA-ATTTTTAATG
1 TTTAAAATATATTTTTAATG
5508022 TTTA
1 TTTA
5508026 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTAAAATATATTTTTAATG
Found at i:5508365 original size:23 final size:22
Alignment explanation
Indices: 5508339--5508396 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 22
5508329 GGGCCGCTGA
*
5508339 TATTAGGCCTGTTGGGCTACTGG
1 TATTAGGCCTGCTGGGC-ACTGG
* *
5508362 TATTGGGTCTGCTGGGCACTGG
1 TATTAGGCCTGCTGGGCACTGG
* *
5508384 CATT-GGGCTGCTG
1 TATTAGGCCTGCTG
5508397 TGTTGGGCCG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 8 0.27
22 8 0.27
23 14 0.47
ACGTcount: A:0.10, C:0.19, G:0.38, T:0.33
Consensus pattern (22 bp):
TATTAGGCCTGCTGGGCACTGG
Found at i:5508388 original size:22 final size:22
Alignment explanation
Indices: 5508351--5508396 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5508341 TTAGGCCTGT
*
5508351 TGGGCTACTGGTATTGGGTCTGC
1 TGGGCTACTGGCATTGGG-CTGC
5508374 TGGGC-ACTGGCATTGGGCTGC
1 TGGGCTACTGGCATTGGGCTGC
5508395 TG
1 TG
5508397 TGTTGGGCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 11 0.50
23 5 0.23
ACGTcount: A:0.09, C:0.20, G:0.41, T:0.30
Consensus pattern (22 bp):
TGGGCTACTGGCATTGGGCTGC
Found at i:5508791 original size:35 final size:35
Alignment explanation
Indices: 5508734--5508878 Score: 125
Period size: 35 Copynumber: 4.2 Consensus size: 35
5508724 GTGATGACGA
* * * *
5508734 GGGGTGCGAGAGAGATGACCAAGAGTCAGATGGTG
1 GGGGTGCGAGAGAAAGGGCCAAGAGTCGGATGGTG
* *
5508769 GGGGTGCGAGGGAAAGGGCCAAGAGTTGGATGGT-
1 GGGGTGCGAGAGAAAGGGCCAAGAGTCGGATGGTG
* * * *
5508803 -GGGTGCGAGAGAGAGGGTCGAGAGTCTGATGGTG
1 GGGGTGCGAGAGAAAGGGCCAAGAGTCGGATGGTG
* * * *
5508837 GGGATGCCA-AGGAAAGGGCCGAGAGTCGGATGATG
1 GGGGTGCGAGA-GAAAGGGCCAAGAGTCGGATGGTG
*
5508872 AGGGTGC
1 GGGGTGC
5508879 CAAGGAGAGG
Statistics
Matches: 87, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
33 27 0.31
34 1 0.01
35 59 0.68
ACGTcount: A:0.25, C:0.11, G:0.50, T:0.14
Consensus pattern (35 bp):
GGGGTGCGAGAGAAAGGGCCAAGAGTCGGATGGTG
Found at i:5508814 original size:68 final size:68
Alignment explanation
Indices: 5508735--5508868 Score: 178
Period size: 68 Copynumber: 2.0 Consensus size: 68
5508725 TGATGACGAG
* * * * *
5508735 GGGTGCGAGAGAGATGACCAAGAGTCAGATGGTGGGGGTGCGAGGGAAAGGGCCAAGAGTTGGAT
1 GGGTGCGAGAGAGAGGACCAAGAGTCAGATGGTGGGGATGCCAAGGAAAGGGCCAAGAGTCGGAT
5508800 GGT
66 GGT
** * * *
5508803 GGGTGCGAGAGAGAGGGTCGAGAGTCTGATGGTGGGGATGCCAAGGAAAGGGCCGAGAGTCGGAT
1 GGGTGCGAGAGAGAGGACCAAGAGTCAGATGGTGGGGATGCCAAGGAAAGGGCCAAGAGTCGGAT
5508868 G
66 G
5508869 ATGAGGGTGC
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.25, C:0.11, G:0.49, T:0.14
Consensus pattern (68 bp):
GGGTGCGAGAGAGAGGACCAAGAGTCAGATGGTGGGGATGCCAAGGAAAGGGCCAAGAGTCGGAT
GGT
Found at i:5508827 original size:33 final size:33
Alignment explanation
Indices: 5508735--5508838 Score: 102
Period size: 33 Copynumber: 3.1 Consensus size: 33
5508725 TGATGACGAG
* * * *
5508735 GGGTGCGAGAGAGATGACCAAGAGTCAGATGGT
1 GGGTGCGAGAGAAAGGGCCAAGAGTCTGATGGT
*
5508768 GGGGGTGCGAGGGAAAGGGCCAAGAGT-TGGATGGT
1 --GGGTGCGAGAGAAAGGGCCAAGAGTCT-GATGGT
* * *
5508803 GGGTGCGAGAGAGAGGGTCGAGAGTCTGATGGT
1 GGGTGCGAGAGAAAGGGCCAAGAGTCTGATGGT
5508836 GGG
1 GGG
5508839 GATGCCAAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
33 30 0.52
34 1 0.02
35 27 0.47
ACGTcount: A:0.24, C:0.10, G:0.51, T:0.15
Consensus pattern (33 bp):
GGGTGCGAGAGAAAGGGCCAAGAGTCTGATGGT
Found at i:5509204 original size:30 final size:29
Alignment explanation
Indices: 5509163--5509274 Score: 156
Period size: 29 Copynumber: 3.8 Consensus size: 29
5509153 CTTCTGAGGC
*
5509163 CAAAATGTAAATAGTGAAAAGTTAAGGGGT
1 CAAAATGTAAATAGTAAAAAGTT-AGGGGT
*
5509193 CAAAATATAAATAGTAAAAAAGTTGAGGGGT
1 CAAAATGTAAATAGT-AAAAAGTT-AGGGGT
5509224 CAAAA-GTAAATAGTAAAAAGTT-GGCGGT
1 CAAAATGTAAATAGTAAAAAGTTAGG-GGT
5509252 CAAAATGTAAATAGTAAAAAGTT
1 CAAAATGTAAATAGTAAAAAGTT
5509275 GTATTTTTTC
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.03
28 8 0.11
29 25 0.33
30 22 0.29
31 18 0.24
ACGTcount: A:0.50, C:0.04, G:0.22, T:0.23
Consensus pattern (29 bp):
CAAAATGTAAATAGTAAAAAGTTAGGGGT
Found at i:5509263 original size:59 final size:59
Alignment explanation
Indices: 5509163--5509275 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
5509153 CTTCTGAGGC
*
5509163 CAAAATGTAAATAGTGAAAAGTTAAGGGGTCAAAATATAAATAGTAAAAAAGTTGAGGGGT
1 CAAAATGTAAATAGTAAAAAGTT-AGGGGTCAAAATATAAATAGT-AAAAAGTTGAGGGGT
*
5509224 CAAAA-GTAAATAGTAAAAAGTT-GGCGGTCAAAATGTAAATAGTAAAAAGTTG
1 CAAAATGTAAATAGTAAAAAGTTAGG-GGTCAAAATATAAATAGTAAAAAGTTG
5509276 TATTTTTTCC
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
58 11 0.22
59 17 0.35
60 16 0.33
61 5 0.10
ACGTcount: A:0.50, C:0.04, G:0.23, T:0.23
Consensus pattern (59 bp):
CAAAATGTAAATAGTAAAAAGTTAGGGGTCAAAATATAAATAGTAAAAAGTTGAGGGGT
Found at i:5509332 original size:13 final size:13
Alignment explanation
Indices: 5509314--5509339 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5509304 TATAACATAG
5509314 AAAAACAAAAACA
1 AAAAACAAAAACA
5509327 AAAAACAAAAACA
1 AAAAACAAAAACA
5509340 CTAATGGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAACA
Found at i:5510920 original size:20 final size:19
Alignment explanation
Indices: 5510892--5510947 Score: 80
Period size: 18 Copynumber: 2.9 Consensus size: 19
5510882 TTTCCTTTAA
5510892 TTTATTAAAAATTGATAGAAT
1 TTTA-TAAAAATTGATA-AAT
5510913 TTTATAAAAA-TGATAAAT
1 TTTATAAAAATTGATAAAT
5510931 TTTATAAAAATT-ATAAA
1 TTTATAAAAATTGATAAA
5510948 ACACCTCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 18 0.53
19 6 0.18
20 6 0.18
21 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTATAAAAATTGATAAAT
Found at i:5511279 original size:124 final size:125
Alignment explanation
Indices: 5511135--5511405 Score: 370
Period size: 124 Copynumber: 2.2 Consensus size: 125
5511125 TTTTTTCGAG
* * * ** * *
5511135 TTGACGTTTCTG-GTTAAATAGTGGGAAATCGCTTCTACTAGGATGCTATTTAAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTAGAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGT
* *
5511199 GAAATAGTGGCCTCGTGGACGCGATTTCGCTACAG-TGGTCATGT-GAGAAATAA-TTTTTT
65 GAAATAGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAG-GAAATAATTTTTTT
* * *
5511258 TTGACGTTTTCTGAGGAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTAGAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGT
*
5511323 GAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTT
65 GAAATAGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTT
5511384 TTGACGTTTCTGAGCAAATAGT
1 TTGACGTTTCTGAGCAAATAGT
5511406 NNNNNNNNNN
Statistics
Matches: 130, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
123 6 0.05
124 79 0.61
125 32 0.25
126 13 0.10
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTAGAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTG
AAATAGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTT
Found at i:5515934 original size:28 final size:28
Alignment explanation
Indices: 5515851--5516269 Score: 429
Period size: 28 Copynumber: 15.8 Consensus size: 28
5515841 NNNNTAGGTT
5515851 AGGTTAGGGTTTTTAATTTAATTAAAATA
1 AGGTTAGGGTTTTTAATTTAATT-AAATA
*
5515880 AGGTTAGGGTTTTTAA--T--TTAAGT-
1 AGGTTAGGGTTTTTAATTTAATTAAATA
5515903 AGGTTAGGGTTTTTAATTTAATTAAATA
1 AGGTTAGGGTTTTTAATTTAATTAAATA
* ** *
5515931 AGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGTTAGGGTTTTTAATTTAATTAAATA
*
5515959 AGGTTAAGGTTTTTAATTTAATTAAATA
1 AGGTTAGGGTTTTTAATTTAATTAAATA
5515987 AGGTTAGGGTTTTTAATTTAATTAAAATA
1 AGGTTAGGGTTTTTAATTTAATT-AAATA
*
5516016 AGGTTAGGGTTTTTAA--T--TTAAGT-
1 AGGTTAGGGTTTTTAATTTAATTAAATA
* ** *
5516039 AGGTTAGGGTTTTTAATTTAAGTAGGTC
1 AGGTTAGGGTTTTTAATTTAATTAAATA
*
5516067 AGGTTAGGGTTTTTAATTTAATTAAATT
1 AGGTTAGGGTTTTTAATTTAATTAAATA
* *
5516095 AGGTTAGGGTTTTTAATTAAATTAAATT
1 AGGTTAGGGTTTTTAATTTAATTAAATA
* * ** *
5516123 AGGTTAGTGTTTTTAATTAAATTAGGTC
1 AGGTTAGGGTTTTTAATTTAATTAAATA
5516151 AGGTTAGGGTTTTTAATTTAATT--A-A
1 AGGTTAGGGTTTTTAATTTAATTAAATA
* *
5516176 A--TTAGGGTTTCTAA-TT-A---AGTA
1 AGGTTAGGGTTTTTAATTTAATTAAATA
*
5516197 GGGTTAGGGTTTTTAATTTAATTAAAATA
1 AGGTTAGGGTTTTTAATTTAATT-AAATA
*
5516226 AGGTTAGGGTTTTTAA--T--TTAAGT-
1 AGGTTAGGGTTTTTAATTTAATTAAATA
5516249 AGGTTAGGGTTTTTAATTTAA
1 AGGTTAGGGTTTTTAATTTAA
5516270 GTAGGTNNNN
Statistics
Matches: 330, Mismatches: 35, Indels: 52
0.79 0.08 0.12
Matches are distributed among these distances:
21 2 0.01
22 2 0.01
23 72 0.22
24 11 0.03
25 11 0.03
27 12 0.04
28 165 0.50
29 55 0.17
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (28 bp):
AGGTTAGGGTTTTTAATTTAATTAAATA
Found at i:5516097 original size:136 final size:133
Alignment explanation
Indices: 5515850--5516269 Score: 559
Period size: 136 Copynumber: 3.2 Consensus size: 133
5515840 NNNNNTAGGT
5515850 TAGGTTAGGGTTTTTAATTTAATTAAAATAAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTTT
1 TAGGTTAGGGTTTTTAATTTAATTAAAATAAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTTT
* * * ** *
5515915 TTAATTTAATTAAATAAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAAGGTTTTTAATTTAA
66 TTAATTTAAGT-AGT-AGGTTAGGGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTTAA
5515980 TTAAA
129 TTAAA
5515985 TAAGGTTAGGGTTTTTAATTTAATTAAAATAAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTT
1 T-AGGTTAGGGTTTTTAATTTAATTAAAATAAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTT
*
5516050 TTTAATTTAAGTAGGTCAGGTTAGGGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTAA
65 TTTAATTTAAGTA-GT-AGGTTAGGGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTTA
5516115 ATTAAA
128 ATTAAA
* * ** * * **
5516121 TTAGGTTAGTGTTTTTAATTAAATT-AGGTCAGGTTAGGGTTTTTAATTTAATTAAATTAGGGTT
1 -TAGGTTAGGGTTTTTAATTTAATTAAAATAAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTT
* *
5516185 TCTAA-TTAAGTAG--GGTTAGGGTTTTTAATTTAATTAAAATAAGGTTAGGGTTTTTAA--T--
65 TTTAATTTAAGTAGTAGGTTAGGGTTTTTAATTTAATT-AAATTAGGTTAGGGTTTTTAATTTAA
*
5516243 TTAAG
129 TTAAA
5516248 TAGGTTAGGGTTTTTAATTTAA
1 TAGGTTAGGGTTTTTAATTTAA
5516270 GTAGGTNNNN
Statistics
Matches: 259, Mismatches: 22, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
126 20 0.08
127 4 0.02
130 22 0.08
131 20 0.08
133 1 0.00
134 7 0.03
135 39 0.15
136 145 0.56
137 1 0.00
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (133 bp):
TAGGTTAGGGTTTTTAATTTAATTAAAATAAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTTT
TTAATTTAAGTAGTAGGTTAGGGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTTAATT
AAA
Found at i:5519117 original size:14 final size:15
Alignment explanation
Indices: 5519100--5519133 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5519090 AATAAATATC
5519100 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
5519114 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
5519129 TAAAA
1 TAAAA
5519134 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:5519360 original size:22 final size:22
Alignment explanation
Indices: 5519330--5519371 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5519320 ATTTGGAGAT
*
5519330 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
5519352 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
5519372 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:5519379 original size:30 final size:30
Alignment explanation
Indices: 5519343--5519401 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
5519333 TTGAAGGAAA
* * *
5519343 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGAAAATTGAGAGT
5519373 TTGAGAGAATTTTGGAAGAAAATTGAGAG
1 TTGAGAGAATTTTGGAAGAAAATTGAGAG
5519402 AATTTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGAAAATTGAGAGT
Found at i:5519396 original size:52 final size:51
Alignment explanation
Indices: 5519321--5519423 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
5519311 TTAATATGGA
* * * *
5519321 TTTGGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGAAAATTGAGAGAATTTTGGAAGGGAA-TTGAGAG
*
5519372 TTTGAGAGAATTTTGGAAGAAAATTGAGAGAATTTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGAAAATTGAGAGAATTTTGGAAGGGAATTGAGAG
5519424 AATTTTTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 37 0.82
53 4 0.09
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGAAAATTGAGAGAATTTTGGAAGGGAATTGAGAG
Found at i:5519398 original size:22 final size:22
Alignment explanation
Indices: 5519373--5519441 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
5519363 ATTTGAGAGT
* *
5519373 TTGAGAGAATTTTGGAAGAAAA
1 TTGAGAGAATTTTTGAAGGAAA
*
5519395 TTGAGAGAATTTTTGAAGGGAA
1 TTGAGAGAATTTTTGAAGGAAA
5519417 TTGAGAGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTTGAAGGAAA
5519439 TTG
1 TTG
5519442 TTTTTGAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (22 bp):
TTGAGAGAATTTTTGAAGGAAA
Found at i:5520364 original size:21 final size:20
Alignment explanation
Indices: 5520330--5520368 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5520320 CGAGTATTTC
5520330 TTTTATAAAAATATATAATT
1 TTTTATAAAAATATATAATT
*
5520350 TTTTATTAAATATATATAA
1 TTTTA-TAAAAATATATAA
5520369 ACTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTATAAAAATATATAATT
Found at i:5520393 original size:15 final size:16
Alignment explanation
Indices: 5520363--5520395 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5520353 TATTAAATAT
*
5520363 ATATAAACTTTAAAAA
1 ATATAAACTATAAAAA
5520379 ATATAAA-TATAAAAA
1 ATATAAACTATAAAAA
5520394 AT
1 AT
5520396 CACGAAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
ATATAAACTATAAAAA
Found at i:5523106 original size:6 final size:6
Alignment explanation
Indices: 5523095--5523124 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5523085 GAATAAATAC
5523095 AATATA AATATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA
5523125 TGTCCAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:5525499 original size:23 final size:24
Alignment explanation
Indices: 5525473--5525518 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
5525463 AAAAAGTTTT
5525473 AATAGAATTATTA-ATTTATAAAA
1 AATAGAATTATTATATTTATAAAA
* *
5525496 AATATAATTTTTATATTTATAAA
1 AATAGAATTATTATATTTATAAA
5525519 TTTTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AATAGAATTATTATATTTATAAAA
Found at i:5531828 original size:9 final size:9
Alignment explanation
Indices: 5531814--5531844 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5531804 GTTAAACGAA
5531814 TCGAGTTAT
1 TCGAGTTAT
*
5531823 TCGAGTTAA
1 TCGAGTTAT
5531832 TCGAGTTAT
1 TCGAGTTAT
5531841 TCGA
1 TCGA
5531845 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:5532167 original size:30 final size:30
Alignment explanation
Indices: 5532131--5532194 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
5532121 AAACCTTTTA
* **
5532131 TTTTCCCCCAAAATTTTTACTCCCTCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTAACAC
* *
5532161 TTTTCCCCTAAAACTTTTATTCCCTAACAC
1 TTTTCCCCCAAAACTTTTACTCCCTAACAC
5532191 TTTT
1 TTTT
5532195 ATTCTCTTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.36, G:0.00, T:0.42
Consensus pattern (30 bp):
TTTTCCCCCAAAACTTTTACTCCCTAACAC
Found at i:5532187 original size:16 final size:16
Alignment explanation
Indices: 5532166--5532198 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5532156 CCCACTTTTC
5532166 CCCTAAAACTTTTATT
1 CCCTAAAACTTTTATT
*
5532182 CCCTAACACTTTTATT
1 CCCTAAAACTTTTATT
5532198 C
1 C
5532199 TCTTCCCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.42
Consensus pattern (16 bp):
CCCTAAAACTTTTATT
Found at i:5532262 original size:16 final size:16
Alignment explanation
Indices: 5532243--5532273 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5532233 TTCCCCCTCC
*
5532243 AATTTTTTTTTTAAAT
1 AATTATTTTTTTAAAT
5532259 AATTATTTTTTTAAA
1 AATTATTTTTTTAAA
5532274 ATTTTTAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTATTTTTTTAAAT
Done.