Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 2 of 410
Found at i:405616 original size:44 final size:45
Alignment explanation
Indices: 405526--405654 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
405516 GACAGAACGA
*
405526 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
405572 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
405616 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
405655 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:407647 original size:16 final size:17
Alignment explanation
Indices: 407617--407649 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
407607 TTCATAAGTA
407617 TATATCAATTATTTCAT
1 TATATCAATTATTTCAT
407634 TATATCAA-TATTTCAT
1 TATATCAATTATTTCAT
407650 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATCAATTATTTCAT
Found at i:407995 original size:46 final size:46
Alignment explanation
Indices: 407935--408203 Score: 380
Period size: 46 Copynumber: 5.8 Consensus size: 46
407925 TTTGACATGA
* * * * *
407935 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TTTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGT
* *
407981 TGCCATGATATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* * *
408027 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGT
*
408073 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
408119 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
408165 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
408204 TTCAACCATG
Statistics
Matches: 205, Mismatches: 15, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
45 8 0.04
46 193 0.94
47 4 0.02
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
Found at i:408092 original size:92 final size:92
Alignment explanation
Indices: 407935--408203 Score: 423
Period size: 92 Copynumber: 2.9 Consensus size: 92
407925 TTTGACATGA
* * * * *
407935 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTTTCATGTTGCCATGATATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTATCATGTTGCCATGGTATCTTTCAAC
408000 CATGGTCTTATTCATTTCATATCACGT
66 CATGGTCTTATTCATTTCATATCACGT
* *
408027 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTATCATGTTGCCATGGTATCTTTCAAC
408092 CATGGTCTTATTCATTTCATATCACGT
66 CATGGTCTTATTCATTTCATATCACGT
* *
408119 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTC-TATCATGTTGCCATGGTATCTTTCAA
**
408183 CCATGGTCTTACACATTTCAT
65 CCATGGTCTTATTCATTTCAT
408204 TTCAACCATG
Statistics
Matches: 164, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
91 4 0.02
92 160 0.98
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.42
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTATCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTATTCATTTCATATCACGT
Found at i:408212 original size:72 final size:72
Alignment explanation
Indices: 408131--408275 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
408121 CCATGGTATC
408131 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
408196 CATTTCA
66 CATTTCA
408203 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
408268 CATTTCA
66 CATTTCA
408275 T
1 T
408276 ATCAGAGAGC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (72 bp):
TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
CATTTCA
Found at i:408213 original size:26 final size:26
Alignment explanation
Indices: 408177--408229 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
408167 CCATGGTATC
408177 TTTCAACCATGGTCTTACACATTTCA
1 TTTCAACCATGGTCTTACACATTTCA
408203 TTTCAACCATGGTCTTACACATTTCA
1 TTTCAACCATGGTCTTACACATTTCA
408229 T
1 T
408230 ATCAGGTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.40
Consensus pattern (26 bp):
TTTCAACCATGGTCTTACACATTTCA
Found at i:410113 original size:2 final size:2
Alignment explanation
Indices: 410106--410137 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
410096 CTTTCCTTAC
410106 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
410138 TAAATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:410469 original size:29 final size:30
Alignment explanation
Indices: 410412--410479 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
410402 CACCCTTAAA
* *
410412 ATATTTACACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
410442 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
410471 AGTATTTAC
1 A-TATTTAC
410480 TCTTGAGCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 16 0.47
30 18 0.53
ACGTcount: A:0.29, C:0.19, G:0.04, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:424308 original size:23 final size:22
Alignment explanation
Indices: 424252--424312 Score: 90
Period size: 21 Copynumber: 2.8 Consensus size: 22
424242 GACACATAAA
424252 GTGCCT-AAAACGACACACGAG
1 GTGCCTGAAAACGACACACGAG
*
424273 GTGCCTG-ATACGACACACGAG
1 GTGCCTGAAAACGACACACGAG
424294 GTGCCTGAAAAACGACACA
1 GTGCCTG-AAAACGACACA
424313 TAAAGTGCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 26 0.74
23 9 0.26
ACGTcount: A:0.36, C:0.28, G:0.25, T:0.11
Consensus pattern (22 bp):
GTGCCTGAAAACGACACACGAG
Found at i:424320 original size:23 final size:22
Alignment explanation
Indices: 424240--424324 Score: 84
Period size: 21 Copynumber: 3.9 Consensus size: 22
424230 TGATCAGTAG
*
424240 ACGACACATAAAGTGCCT-AAA
1 ACGACACACAAAGTGCCTGAAA
* * *
424261 ACGACACACGAGGTGCCTG-AT
1 ACGACACACAAAGTGCCTGAAA
* *
424282 ACGACACACGAGGTGCCTGAAAA
1 ACGACACACAAAGTGCCTG-AAA
*
424305 ACGACACATAAAGTGCCTGA
1 ACGACACACAAAGTGCCTGA
424325 TCAGTAAAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 35 0.66
22 1 0.02
23 17 0.32
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.13
Consensus pattern (22 bp):
ACGACACACAAAGTGCCTGAAA
Found at i:438563 original size:73 final size:71
Alignment explanation
Indices: 438374--438563 Score: 254
Period size: 72 Copynumber: 2.6 Consensus size: 71
438364 AAGCCTTTTT
* * * *
438374 ATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTCGAGCCTCAGGTCACGCTGAGGT
1 ATTTTTG-TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGT
*
438439 ATTTTCA
65 AATTTCA
* **
438446 ATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGT
1 ATTTTTGT-TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGT
438511 AATTTCA
65 AATTTCA
* *
438518 ATTTCTGTTTGTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGA
1 ATTTTTGTTT-TCAA-AATCAACTCATATTGCGAGAGGTGAGTTGA
438564 ACCTTTTAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
71 3 0.03
72 72 0.71
73 27 0.26
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (71 bp):
ATTTTTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTA
ATTTCA
Found at i:438747 original size:116 final size:117
Alignment explanation
Indices: 438539--438758 Score: 336
Period size: 116 Copynumber: 1.9 Consensus size: 117
438529 TCAAGAATCA
*
438539 ACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTTTACTTTTTCAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTTTACTTTTTCAAAATCAACTCATATTGC
* *
438604 GAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTTAAATTG
66 GAGAAGTGAGTCGAGCCTCAGGGCACGCTGAGGTATTTTTAGTTTTAAATTG
* * *
438656 ACTCATATTGCGAGAGGTGAGTT-AAGTCTTTTTATTTTT-GTTTTTCAAAATCAACTCATATTG
1 ACTCATATTGCGAGAGGTGAGTTGAA-CCTTTTAATTTTTACTTTTTCAAAATCAACTCATATTG
* * *
438719 CTAGAGGTGAGTCGAGCCTCAGGTCACGCTGAGGTATTTT
65 CGAGAAGTGAGTCGAGCCTCAGGGCACGCTGAGGTATTTT
438759 CAATTTTTGT
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
116 60 0.65
117 33 0.35
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (117 bp):
ACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTTTACTTTTTCAAAATCAACTCATATTGC
GAGAAGTGAGTCGAGCCTCAGGGCACGCTGAGGTATTTTTAGTTTTAAATTG
Found at i:438838 original size:315 final size:315
Alignment explanation
Indices: 438266--438864 Score: 1119
Period size: 315 Copynumber: 1.9 Consensus size: 315
438256 TTAATTGTTG
*
438266 TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGATGTATTTTTAG
1 TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAG
438331 TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTTGTTTTTCAAAATCAAC
66 TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTTGTTTTTCAAAATCAAC
438396 TCATATTGCTAGAGGTGAGTCGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTTTGTGTTTTAA
131 TCATATTGCTAGAGGTGAGTCGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTTTGTGTTTTAA
438461 TTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTGT
196 TTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTG-
*
438526 TTGTC-AAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTTTACT
260 TTGTCAAAAAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTTTACT
438581 TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAG
1 TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAG
*
438646 TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGTCTTTTTATTTTTGTTTTTCAAAATCAAC
66 TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTTGTTTTTCAAAATCAAC
438711 TCATATTGCTAGAGGTGAGTCGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTTTGTGTTTTAA
131 TCATATTGCTAGAGGTGAGTCGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTTTGTGTTTTAA
* *
438776 TTTCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGT
196 TTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTGT
*
438841 TGTCAAAAAAATCAACTCGTATTG
261 TGTC-AAAAAATCAACTCATATTG
438865 TGAGCGGCGA
Statistics
Matches: 276, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
314 5 0.02
315 255 0.92
316 16 0.06
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (315 bp):
TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAG
TTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTTGTTTTTCAAAATCAAC
TCATATTGCTAGAGGTGAGTCGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTTTGTGTTTTAA
TTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTGT
TGTCAAAAAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTTTACT
Found at i:438885 original size:74 final size:74
Alignment explanation
Indices: 438702--439610 Score: 411
Period size: 72 Copynumber: 11.8 Consensus size: 74
438692 TTTGTTTTTC
* * *
438702 AAAATCAACTCATATTGCTAGAGGTGAGTCGAGCCTCAGG-TCACGCTGAGGTATTTTCAATTTT
1 AAAATCAACTCATATTG-TAGAGGTGAGTTGAGCCTCAGGCACACGCTGAGGTATTTTCAATTTC
***
438766 TG-TGT-TTT
65 TGTTGTCAAA
** *
438774 AATTTCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTAATTTCAATTTC
1 AAAATCAACTCATATTG-TAGAGGTGAGTTGAGCCTCAGGCACACGCTGAGGTATTTTCAATTTC
438838 TGTTGTCAAA
65 TGTTGTCAAA
* * * *
438848 AAAATCAACTCGTATTGTGAGCGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGT-AGAGGTGAGTTGAGCCTCAGG-CACACGCTGAGGTATTTTCAATTT
*
438913 CTGTTTTTCAATTTCTGCCTTTCA
64 CTG-TTGTCAA------------A
* * * ** ** * * * *
438937 AAAA-AAAATCGA-CTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGCTATTT
1 AAAATCAACTC-ATATTGTAGAG-GTGAGTTGAG-----CCTCAGG--CACACGCTGAGGTATTT
*
438999 TCAATTTCTGTCTTTCAAA
57 TCAATTTCTGT-TGTCAAA
* *
439018 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTAATTTCAATTTC
1 AAAATCAACTCATATTG-TAGAGGTGAGTTGAGCCTCAGGCACACGCTGAGGTATTTTCAATTTC
439082 TGTTGTCAAA
65 TGTTGTCAAA
* * * *
439092 AAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTT
1 AAAATCAACTCATATTG-TAGAGGTGAGTTGAGCCTCAGG-CACACGCTGAGGTATTTTCAATTT
*
439157 CTGTTTTTCAATTTCTGCCTTCA
64 CTG-TTGTCAA-----------A
* * ** *** * * * *
439180 AAAA-AATAATCA-ACTCATATTTCGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGGTAATTT
1 AAAATCA-ACTCATA-TTGTA-GAGGTGAGTTGAG-----CCTCAGGCACACGCTGAGGTATTTT
* **
439242 CGATTTCTGTT-T-TTA
58 CAATTTCTGTTGTCAAA
* * ** * *
439257 AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACACGCTGAGGTAATTTCAATTTC
1 AAAATCAACTCATATTG-TAGAGGTGAGTTGAGCCTCAGGCACACGCTGAGGTATTTTCAATTTC
*
439321 TGTTTTC--A
65 TGTTGTCAAA
* * ** * * ** *
439329 AAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAG-ACACATTGAGGTAATTTCAATTTC
1 AAAATCAACTCATATTG-TAGAGGTGAGTTGAGCCTCAGGCACACGCTGAGGTATTTTCAATTTC
*
439393 TGTTTTC--A
65 TGTTGTCAAA
* * ** * * *
439401 AAATTCAACTCATATTGCAAGAAATGAGTTGAGCCTTAAG-ACACGTTGAGGTATTTTCAATTTC
1 AAAATCAACTCATATTG-TAGAGGTGAGTTGAGCCTCAGGCACACGCTGAGGTATTTTCAATTTC
*
439465 TGTTTTCAAA
65 TGTTGTCAAA
* * *
439475 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTG-TAGAGGTGAGTTGAGCCTCAGG--CACACGCTGAGGTATTTTCAATT
*
439539 TCTGTCTTTCAAA
63 TCTGT-TGTCAAA
* * * * *
439552 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGTGGTATTTT
1 AAAATCAACTCATATTG-TAGAGGTGAGTTGAGCCTCAG-GCACACGCTGAGGTATTTT
439611 TTCAATTTAT
Statistics
Matches: 667, Mismatches: 103, Indels: 129
0.74 0.11 0.14
Matches are distributed among these distances:
72 227 0.34
73 7 0.01
74 109 0.16
75 25 0.04
76 73 0.11
77 88 0.13
78 6 0.01
81 6 0.01
82 13 0.02
83 2 0.00
87 5 0.01
88 31 0.05
89 6 0.01
90 2 0.00
91 23 0.03
92 5 0.01
93 39 0.06
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (74 bp):
AAAATCAACTCATATTGTAGAGGTGAGTTGAGCCTCAGGCACACGCTGAGGTATTTTCAATTTCT
GTTGTCAAA
Found at i:438922 original size:14 final size:14
Alignment explanation
Indices: 438903--438929 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
438893 CGCCGAGGTA
438903 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
438917 TTTTCAATTTCTG
1 TTTTCAATTTCTG
438930 CCTTTCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:438935 original size:14 final size:14
Alignment explanation
Indices: 438904--438937 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
438894 GCCGAGGTAT
**
438904 TTTCAATTTCTGTT
1 TTTCAATTTCTGCC
438918 TTTCAATTTCTGCC
1 TTTCAATTTCTGCC
438932 TTTCAA
1 TTTCAA
438938 AAAAAAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.56
Consensus pattern (14 bp):
TTTCAATTTCTGCC
Found at i:438985 original size:93 final size:93
Alignment explanation
Indices: 438845--439016 Score: 247
Period size: 93 Copynumber: 1.8 Consensus size: 93
438835 TTCTGTTGTC
* * * *
438845 AAAAAAATCAACTCGTATTGTGAGCGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGCTATTTTCAA
*
438910 TTTCTGTTTTTCAATTTCTGCCTTTCAA
66 TTTCTGTCTTTCAATTTCTGCCTTTCAA
* * * *
438938 AAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGCTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-TCACACGCCGAGCTATTTTCA
439002 ATTTCTGTCTTTCAA
65 ATTTCTGTCTTTCAA
439017 AAAAATCAAC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
92 2 0.03
93 67 0.97
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (93 bp):
AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGCTATTTTCAA
TTTCTGTCTTTCAATTTCTGCCTTTCAA
Found at i:439166 original size:14 final size:14
Alignment explanation
Indices: 439147--439173 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
439137 CGCCGAGGTA
439147 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
439161 TTTTCAATTTCTG
1 TTTTCAATTTCTG
439174 CCTTCAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:439198 original size:244 final size:238
Alignment explanation
Indices: 438704--439597 Score: 1030
Period size: 244 Copynumber: 3.8 Consensus size: 238
438694 TGTTTTTCAA
* * * * *
438704 AATCAACTCATATTGCTAGAGGTGAGTCGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTTTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGACACGCTGAGGTATTTTCAATTTCTGT
* ** *
438769 GTTT-TAATTTCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
65 -TTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
* * *
438833 ATTTCTGTTGTCAAAAAAATCAACTCGTATTGTGAGCGGCGAGTTGAGCCTCAGGTCACACGCCG
129 ATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCG
438898 AGGTATTTTCAATTTCTGTTTTTCAATTTCTGCCTTTCAAAAAAA-
194 AGGTATTTTCAATTTCTGTTTTTCAATTTCTGCC-TTCAAAAAAAT
* *
438943 AATCGACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGCTATTTTCAATTTCT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG---ACACGCTGAGGTATTTTCAATTTCT
439008 GTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
63 GT-TTT--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
*
439073 TTCAATTTCTGTTGTCAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
125 TTCAATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
439138 GCCGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCCTTCAAAAAAAT
190 GCCGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCCTTCAAAAAAAT
* * * *
439187 AATCAACTCATATTTCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCGATTTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGACACGCTGAGGTATTTTCAATTTCTGT
* * ** *
439252 TTTTAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAA
65 TTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
* * *** * * ***
439317 TTTCTGTTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAG--ACACATTGA
130 TTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGA
*
439378 GGTAATTTCAATTTCTG----------T-T---TTC---AAAAT
195 GGTATTTTCAATTTCTGTTTTTCAATTTCTGCCTTCAAAAAAAT
* ** * *
439405 --TCAACTCATATTGCAAGAAATGAGTTGAGCCTTAAGACACGTTGAGGTATTTTCAATTTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGACACGCTGAGGTATTTTCAATTTCTGT
* * *
439468 TTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATT
65 TTT--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAAT
* * * *
439532 TTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACA
125 TTCAATTTCTGT-TGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACA
439597 C
189 C
439598 ACTGTGGTAT
Statistics
Matches: 575, Mismatches: 61, Indels: 52
0.84 0.09 0.08
Matches are distributed among these distances:
216 56 0.10
217 1 0.00
218 39 0.07
220 25 0.04
221 7 0.01
223 34 0.06
224 1 0.00
225 5 0.01
235 22 0.04
237 34 0.06
238 2 0.00
239 98 0.17
241 30 0.05
242 24 0.04
243 10 0.02
244 185 0.32
245 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (238 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACACGCTGAGGTATTTTCAATTTCTGTT
TTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
TTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAG
GTATTTTCAATTTCTGTTTTTCAATTTCTGCCTTCAAAAAAAT
Found at i:439208 original size:167 final size:161
Alignment explanation
Indices: 438996--439573 Score: 504
Period size: 144 Copynumber: 3.7 Consensus size: 161
438986 CGCTGAGCTA
*
438996 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTCCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* **
439061 CGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGC
66 CGCTGAGGTAATTTCAATTTCTGTT-T-AAAAAAATCAACTCATATTGCGAGAAACGAGTTGAGC
* *
439126 CTCAGGTCACACGCCGAGGTATTTTCAATTTCTGT
129 CTCAAG--ACACGCCGAGGTAATTTCAATTTCTGT
* *
439161 TTTTCAATTTCTG-CCTTCAAAAAAATAATCAACTCATATTTCGAGAGGTGAGTTGAGCCTCGGG
1 TTTTCAATTTCTGTCCTTC--AAAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
* ** * *
439225 ACACGCTGAGGTAATTTCGATTTCTGTTTTTAAAATTCAACTCATATTGCGAGAAATGAGTTGAG
63 ACACGCTGAGGTAATTTCAATTTCTGTTTAAAAAAATCAACTCATATTGCGAGAAACGAGTTGAG
*
439290 CCTCAAGACACGCTGAGGTAATTTCAATTTCTG-
128 CCTCAAGACACGCCGAGGTAATTTCAATTTCTGT
* ** * *
439323 -----------T-T--TTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGTCCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
** ** * * *
439372 CATTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCAAGAAATGAGTTGAGCCT
66 CGCTGAGGTAATTTCAATTTCTGTTTAAAAAAATCAACTCATATTGCGAGAAACGAGTTGAGCCT
* **
439437 TAAGACACGTTGAGG-----T--A-------
131 CAAGACACGCCGAGGTAATTTCAATTTCTGT
* *
439454 TTTTCAATTTCTGT-TTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTC
1 TTTTCAATTTCTGTCCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---
* *
439517 ACATGCTGAGGTATTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGA
63 ACACGCTGAGGTAATTTCAATTTCTG--TTT-AAAAAAATCAACTCATATTGCGAGA
439574 GGTGAGTTGA
Statistics
Matches: 346, Mismatches: 42, Indels: 64
0.77 0.09 0.14
Matches are distributed among these distances:
137 1 0.00
139 1 0.00
142 1 0.00
143 1 0.00
144 110 0.32
145 4 0.01
146 33 0.10
148 22 0.06
149 3 0.01
150 3 0.01
151 22 0.06
163 24 0.07
164 4 0.01
165 48 0.14
166 6 0.02
167 63 0.18
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (161 bp):
TTTTCAATTTCTGTCCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
CGCTGAGGTAATTTCAATTTCTGTTTAAAAAAATCAACTCATATTGCGAGAAACGAGTTGAGCCT
CAAGACACGCCGAGGTAATTTCAATTTCTGT
Found at i:439253 original size:91 final size:92
Alignment explanation
Indices: 439089--439255 Score: 248
Period size: 93 Copynumber: 1.8 Consensus size: 92
439079 TTCTGTTGTC
* *
439089 AAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTAATTTCAA
439154 TTTCTGTTTTTCAATTTCTGCCTTCAA
66 TTTCTGTTTTTCAATTTCTGCCTTCAA
* * * * *
439181 AAAAATAATCAACTCATATTTCGAGAGGTGAGTTGAGCCTC-GG-GACACGCTGAGGTAATTTCG
1 AAAAA-AATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTAATTTCA
439244 ATTTCTGTTTTT
65 ATTTCTGTTTTT
439256 AAAATTCAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
91 28 0.42
92 7 0.10
93 32 0.48
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (92 bp):
AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTAATTTCAA
TTTCTGTTTTTCAATTTCTGCCTTCAA
Found at i:439610 original size:77 final size:73
Alignment explanation
Indices: 439182--439585 Score: 483
Period size: 72 Copynumber: 5.5 Consensus size: 73
439172 TGCCTTCAAA
* ** ** * *
439182 AAAATAATCAACTCATATTTCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCGATT
1 AAAA-AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATT
439247 TCTGTTTT-
65 TCTGTTTTC
* * *
439255 TAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTT
439320 CTGTTTTC
66 CTGTTTTC
* * ** *
439328 -AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACATTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTT
439392 CTGTTTTC
66 CTGTTTTC
* * * *
439400 -AAAATTCAACTCATATTGCAAGAAATGAGTTGAGCCTTAAGACACGTTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTT
439464 CTGTTTTC
66 CTGTTTTC
* ** * *
439472 AAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCA
1 -AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG---ACACGCTGAGGTATTTTCA
439536 ATTTCTGTCTTTC
62 ATTTCTGT-TTTC
**
439549 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 -AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGC
439586 TTCAGATCAC
Statistics
Matches: 298, Mismatches: 26, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
72 197 0.66
73 4 0.01
74 32 0.11
76 25 0.08
77 40 0.13
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (73 bp):
AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTT
CTGTTTTC
Found at i:440493 original size:32 final size:32
Alignment explanation
Indices: 440454--440547 Score: 138
Period size: 31 Copynumber: 3.0 Consensus size: 32
440444 ACCCCCCCAA
440454 AAAAACCTAACCCCCAAAAAAAAAG-AAAAAAG
1 AAAAACCTAA-CCCCAAAAAAAAAGAAAAAAAG
*
440486 AAAAACCTAACCCAAAAAAAAAAGAAAAAAAG
1 AAAAACCTAACCCCAAAAAAAAAGAAAAAAAG
**
440518 AAAAACCTAA-CCCAAAAAAAACTAAAAAAA
1 AAAAACCTAACCCCAAAAAAAAAGAAAAAAA
440548 CCCTAGCCAC
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
31 30 0.53
32 27 0.47
ACGTcount: A:0.72, C:0.19, G:0.04, T:0.04
Consensus pattern (32 bp):
AAAAACCTAACCCCAAAAAAAAAGAAAAAAAG
Found at i:440507 original size:31 final size:32
Alignment explanation
Indices: 440454--440538 Score: 145
Period size: 32 Copynumber: 2.7 Consensus size: 32
440444 ACCCCCCCAA
*
440454 AAAAACCTAACCCCCAAAAAAAAAG-AAAAAAG
1 AAAAACCTAA-CCCAAAAAAAAAAGAAAAAAAG
440486 AAAAACCTAACCCAAAAAAAAAAGAAAAAAAG
1 AAAAACCTAACCCAAAAAAAAAAGAAAAAAAG
440518 AAAAACCTAACCCAAAAAAAA
1 AAAAACCTAACCCAAAAAAAA
440539 CTAAAAAAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 13 0.25
32 38 0.75
ACGTcount: A:0.72, C:0.20, G:0.05, T:0.04
Consensus pattern (32 bp):
AAAAACCTAACCCAAAAAAAAAAGAAAAAAAG
Found at i:440534 original size:19 final size:19
Alignment explanation
Indices: 440480--440535 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
440470 AAAAAAAAGA
440480 AAAAAGAAAAACCTAACCC
1 AAAAAGAAAAACCTAACCC
*
440499 AAAAA-AAAAA--GAA---
1 AAAAAGAAAAACCTAACCC
440512 AAAAAGAAAAACCTAACCC
1 AAAAAGAAAAACCTAACCC
440531 AAAAA
1 AAAAA
440536 AAACTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
13 5 0.17
14 5 0.17
16 4 0.14
18 5 0.17
19 10 0.34
ACGTcount: A:0.73, C:0.18, G:0.05, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAAACCTAACCC
Found at i:441110 original size:2 final size:2
Alignment explanation
Indices: 441105--441129 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
441095 TAAATACTAT
441105 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
441130 TTTAAATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:441113 original size:39 final size:37
Alignment explanation
Indices: 441032--441141 Score: 116
Period size: 39 Copynumber: 2.9 Consensus size: 37
441022 TTTAGGTATT
* *
441032 TTATATATAT-TATGTATATATTTTTTAATGCCATTAG
1 TTATATATATATATGTATATA-TTTTAAATACCATTAG
* * *
441069 TTATATATTTCTCATGTATATATTCTTAAATACTATTA-
1 TTATATATATAT-ATGTATATATT-TTAAATACCATTAG
*
441107 TATATATATATATATATATATATTTTAAATACCAT
1 T-TATATATATATATGTATATATTTTAAATACCAT
441142 ATTGTGTATA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
37 19 0.31
38 14 0.23
39 28 0.46
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (37 bp):
TTATATATATATATGTATATATTTTAAATACCATTAG
Found at i:441152 original size:39 final size:37
Alignment explanation
Indices: 441028--441160 Score: 112
Period size: 39 Copynumber: 3.5 Consensus size: 37
441018 TTTTTTTAGG
* *
441028 TATT-TTATATATATTATGTATATATTTTTTAATGCCA
1 TATTGTTATATATATTATGTATATA-TTTTAAATACCA
* *
441065 T-TAGTTATATATTTCTCATGTATATATTCTTAAATA-C-
1 TATTGTTATATATAT-T-ATGTATATATT-TTAAATACCA
* *
441102 TATTATATATATATATATATATATATATTTTAAATACCA
1 TATTGT-TATATATAT-TATGTATATATTTTAAATACCA
441141 TATTGTGTATATATTATTAT
1 TATTGT-TATATA-TATTAT
441161 TACAAATTAT
Statistics
Matches: 76, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
36 1 0.01
37 18 0.24
38 17 0.22
39 37 0.49
40 3 0.04
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (37 bp):
TATTGTTATATATATTATGTATATATTTTAAATACCA
Found at i:441196 original size:21 final size:20
Alignment explanation
Indices: 441166--441207 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
441156 ATTATTACAA
*
441166 ATTATTACTATTGCTAGTATT
1 ATTATAACTATTGCTA-TATT
*
441187 ATTATAACTATTGTTATATT
1 ATTATAACTATTGCTATATT
441207 A
1 A
441208 GTGTATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTATAACTATTGCTATATT
Found at i:445691 original size:18 final size:18
Alignment explanation
Indices: 445665--445734 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
445655 ATTTGGTCAT
445665 TTTAATAAAACATTTTGA
1 TTTAATAAAACATTTTGA
* * *
445683 TTTACTAAAATAATTTGGTCA
1 TTTAATAAAA-CATTT--TGA
445704 TTTTAATAAAACATTTTGA
1 -TTTAATAAAACATTTTGA
*
445723 TTTACTAAAACA
1 TTTAATAAAACA
445735 ACGATTTTGG
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
18 20 0.49
19 6 0.15
21 6 0.15
22 9 0.22
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (18 bp):
TTTAATAAAACATTTTGA
Found at i:445697 original size:40 final size:40
Alignment explanation
Indices: 445653--445732 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
445643 GATCACCTAG
445653 TAATTTGGTCATTTTAATAAAACATTTTGATTTACTAAAA
1 TAATTTGGTCATTTTAATAAAACATTTTGATTTACTAAAA
445693 TAATTTGGTCATTTTAATAAAACATTTTGATTTACTAAAA
1 TAATTTGGTCATTTTAATAAAACATTTTGATTTACTAAAA
445733 CAACGATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (40 bp):
TAATTTGGTCATTTTAATAAAACATTTTGATTTACTAAAA
Found at i:445719 original size:21 final size:21
Alignment explanation
Indices: 445655--445719 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
445645 TCACCTAGTA
445655 ATTTGGTCATTTTAATAAAAC
1 ATTTGGTCATTTTAATAAAAC
* * *
445676 ATTT--TGA-TTTACTAAAATA
1 ATTTGGTCATTTTAATAAAA-C
445695 ATTTGGTCATTTTAATAAAAC
1 ATTTGGTCATTTTAATAAAAC
445716 ATTT
1 ATTT
445720 TGATTTACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
18 9 0.26
19 6 0.18
21 10 0.29
22 9 0.26
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (21 bp):
ATTTGGTCATTTTAATAAAAC
Found at i:445721 original size:22 final size:22
Alignment explanation
Indices: 445656--445721 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
445646 CACCTAGTAA
445656 TTTGGTCATTTTAATAAAACAT
1 TTTGGTCATTTTAATAAAACAT
* * *
445678 TTT-G--A-TTTACTAAAATAA
1 TTTGGTCATTTTAATAAAACAT
445696 TTTGGTCATTTTAATAAAACAT
1 TTTGGTCATTTTAATAAAACAT
445718 TTTG
1 TTTG
445722 ATTTACTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
18 13 0.38
19 2 0.06
21 2 0.06
22 17 0.50
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (22 bp):
TTTGGTCATTTTAATAAAACAT
Found at i:451870 original size:26 final size:27
Alignment explanation
Indices: 451810--451883 Score: 105
Period size: 26 Copynumber: 2.7 Consensus size: 27
451800 AAAAACAGCT
*
451810 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTAATACCCCTATG-ATGGA
*
451838 AAATTACTGTTATACCCCTATG-TGGA
1 AAATTACTGTAATACCCCTATGATGGA
*
451864 AAATTACTGAAATACCCCTA
1 AAATTACTGTAATACCCCTA
451884 GGGTTAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 22 0.52
28 20 0.48
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (27 bp):
AAATTACTGTAATACCCCTATGATGGA
Found at i:453635 original size:27 final size:29
Alignment explanation
Indices: 453591--453647 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
453581 TAAAACAGTT
* *
453591 TAAAAGATGACAAAAATAGTAGT-AATAA
1 TAAAAGATAACAAAAATAATAGTAAATAA
*
453619 TAAAA-ATAACAATAATAATAGTAAATAA
1 TAAAAGATAACAAAAATAATAGTAAATAA
453647 T
1 T
453648 GCTAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.63, C:0.04, G:0.09, T:0.25
Consensus pattern (29 bp):
TAAAAGATAACAAAAATAATAGTAAATAA
Found at i:455219 original size:2 final size:2
Alignment explanation
Indices: 455212--455240 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
455202 TGCTAACAAT
455212 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
455241 TTTGGGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:456956 original size:3 final size:3
Alignment explanation
Indices: 456948--457014 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
456938 AAAATGCATA
456948 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
456996 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
457015 GTAGTAGTAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:459837 original size:25 final size:25
Alignment explanation
Indices: 459790--459837 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
459780 AATCAAAATT
** **
459790 TTAAAATCAATTATCTTCTTTAATA
1 TTAAAATCAATTAAATTAATTAATA
459815 TTAAAATCAATTAAATTAATTAA
1 TTAAAATCAATTAAATTAATTAA
459838 AAATAAATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (25 bp):
TTAAAATCAATTAAATTAATTAATA
Found at i:460214 original size:2 final size:2
Alignment explanation
Indices: 460207--460233 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
460197 TCAAACATTC
460207 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
460234 AACAAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:460261 original size:16 final size:17
Alignment explanation
Indices: 460237--460269 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
460227 AGAGAGAAAC
*
460237 AAAACAAAACCA-AAAA
1 AAAAAAAAACCACAAAA
460253 AAAAAAAAACCACAAAA
1 AAAAAAAAACCACAAAA
460270 GAAGACCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAACCACAAAA
Found at i:461666 original size:25 final size:26
Alignment explanation
Indices: 461629--461680 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
461619 ATTCAATAAT
*
461629 AAATATATAATTATT-TTTAAAAATA
1 AAATATATAATTATTGTGTAAAAATA
* *
461654 AAATATTTTATTATTGTGTAAAAATA
1 AAATATATAATTATTGTGTAAAAATA
461680 A
1 A
461681 CTTTTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
AAATATATAATTATTGTGTAAAAATA
Found at i:463426 original size:22 final size:21
Alignment explanation
Indices: 463401--463441 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
463391 AGGTGATGTT
*
463401 ATTTTTATTCTATTGATTCATA
1 ATTTTAATT-TATTGATTCATA
463423 ATTTTAATTTATTGATTCA
1 ATTTTAATTTATTGATTCA
463442 ATTTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTTTAATTTATTGATTCATA
Found at i:463427 original size:21 final size:18
Alignment explanation
Indices: 463403--463449 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 18
463393 GTGATGTTAT
463403 TTTTATTCTATTGATTCATAA
1 TTTTATT-TATTGATTC--AA
463424 TTTTAATTTATTGATTCAA
1 TTTT-ATTTATTGATTCAA
463443 TTTTATT
1 TTTTATT
463450 AAGTAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.12
19 6 0.24
21 13 0.52
22 3 0.12
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTATTTATTGATTCAA
Found at i:463862 original size:18 final size:21
Alignment explanation
Indices: 463834--463887 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
463824 TGATTTGTAA
*
463834 AATTAAAATTAAA-A-ATTAT
1 AATTAATATTAAATATATTAT
*
463853 -ATTAATATTAAATATTTTAT
1 AATTAATATTAAATATATTAT
463873 AATTAATATTAAATA
1 AATTAATATTAAATA
463888 AAAAATGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 11 0.37
19 1 0.03
20 4 0.13
21 14 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTAATATTAAATATATTAT
Found at i:475252 original size:26 final size:26
Alignment explanation
Indices: 475223--475273 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
475213 AAATCAAATA
* *
475223 GTTTAAAAGAAATAATATTTAAAAGG
1 GTTTAAAAGAAATAACATGTAAAAGG
* *
475249 GTTTAAGATAAATAACATGTAAAAG
1 GTTTAAAAGAAATAACATGTAAAAG
475274 AGAAATTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.53, C:0.02, G:0.16, T:0.29
Consensus pattern (26 bp):
GTTTAAAAGAAATAACATGTAAAAGG
Found at i:475396 original size:2 final size:2
Alignment explanation
Indices: 475389--475417 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
475379 AGAGTTTAAA
475389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
475418 ACAATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:477508 original size:46 final size:44
Alignment explanation
Indices: 477404--477511 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
477394 TGTCTTTGAC
** * * *
477404 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
477448 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
477494 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
477512 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:483649 original size:46 final size:44
Alignment explanation
Indices: 483545--483652 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
483535 TGTCTTTGAC
** * * *
483545 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
483589 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
483635 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
483653 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:487192 original size:31 final size:31
Alignment explanation
Indices: 487154--487216 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
487144 AAGTACAAAA
487154 ATGCCCTGAAAATAGTTAGAAGGCTTTTGAT
1 ATGCCCTGAAAATAGTTAGAAGGCTTTTGAT
*
487185 ATGCCCTGAAAATAGTTAGAAGGTTTTTGAT
1 ATGCCCTGAAAATAGTTAGAAGGCTTTTGAT
487216 A
1 A
487217 AGTGTGTAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (31 bp):
ATGCCCTGAAAATAGTTAGAAGGCTTTTGAT
Found at i:488210 original size:137 final size:136
Alignment explanation
Indices: 487939--488224 Score: 527
Period size: 137 Copynumber: 2.1 Consensus size: 136
487929 TATTGGGCCT
** *
487939 AAGCCCATTCAGGTAATAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
488004 AGCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAAC
66 AGCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAAAATCAGTAAAC
488069 ATATGC
131 ATATGC
488075 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
488140 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAAAATCAGTAAA
66 AG-CCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAAAATCAGTAAA
488205 CATATGC
130 CATATGC
488212 AAGCCCATTTGGG
1 AAGCCCATTTGGG
488225 GAGACTACTC
Statistics
Matches: 145, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
136 64 0.44
137 81 0.56
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAAAATCAGTAAAC
ATATGC
Found at i:490160 original size:26 final size:26
Alignment explanation
Indices: 490000--490159 Score: 261
Period size: 26 Copynumber: 6.2 Consensus size: 26
489990 CATGAAATTC
490000 TTATCATG-AA-ATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
490024 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
490050 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
490076 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
490102 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* * *
490128 TTATCAAGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
490154 TTATCA
1 TTATCA
490160 ATTTGTATCA
Statistics
Matches: 129, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
24 8 0.06
25 2 0.02
26 119 0.92
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:495928 original size:26 final size:26
Alignment explanation
Indices: 495892--496027 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
495882 CATGATATTC
495892 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
495918 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
495944 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
495970 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
495996 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
496022 TTATCA
1 TTATCA
496028 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:499880 original size:7 final size:7
Alignment explanation
Indices: 499868--499895 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
499858 TTAAACCAAT
499868 AATAAAC
1 AATAAAC
499875 AATAAAC
1 AATAAAC
499882 AATAAAC
1 AATAAAC
499889 AATAAAC
1 AATAAAC
499896 GGTATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (7 bp):
AATAAAC
Found at i:502599 original size:5 final size:5
Alignment explanation
Indices: 502589--502617 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
502579 GGGGTGAAAG
502589 GAAGA GAAGA GAAGA GAAGA GAAG- GAAGA
1 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA
502618 AAAAGGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:503604 original size:6 final size:6
Alignment explanation
Indices: 503595--503621 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
503585 TTATAATTAT
503595 ATTGTA ATTGTA ATTGTA ATTGTA ATT
1 ATTGTA ATTGTA ATTGTA ATTGTA ATT
503622 CTCTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (6 bp):
ATTGTA
Found at i:503604 original size:23 final size:23
Alignment explanation
Indices: 503568--503615 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
503558 GGACATATTT
*
503568 TTATATTTATATTGTATTTATAA
1 TTATATTTATATTGTAATTATAA
*
503591 TTATATTGTA-ATTGTAATTGTAA
1 TTATATT-TATATTGTAATTATAA
503614 TT
1 TT
503616 GTAATTCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (23 bp):
TTATATTTATATTGTAATTATAA
Found at i:503608 original size:17 final size:17
Alignment explanation
Indices: 503568--503621 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
503558 GGACATATTT
* *
503568 TTATATTTATATTGTAT
1 TTATAATTATATTGTAA
503585 TTATAATTATATTGTAA
1 TTATAATTATATTGTAA
* *
503602 TTGTAATTGTAATTGTAA
1 TTATAATTAT-ATTGTAA
503620 TT
1 TT
503622 CTCTTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 23 0.72
18 9 0.28
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.57
Consensus pattern (17 bp):
TTATAATTATATTGTAA
Found at i:507599 original size:17 final size:17
Alignment explanation
Indices: 507579--507617 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
507569 ATATTTACCA
507579 ATTTATTAAAAATTTAT
1 ATTTATTAAAAATTTAT
507596 ATTTATTAAAAATTTAT
1 ATTTATTAAAAATTTAT
*
507613 CTTTA
1 ATTTA
507618 ACATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATTAAAAATTTAT
Found at i:510907 original size:17 final size:18
Alignment explanation
Indices: 510885--510923 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
510875 TTTGAAAACA
*
510885 AAAAATAT-CTTATAATT
1 AAAAATATACTTACAATT
510902 AAAAATATAACTTACAATT
1 AAAAATAT-ACTTACAATT
510921 AAA
1 AAA
510924 TTAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
19 11 0.58
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATATACTTACAATT
Found at i:512243 original size:26 final size:24
Alignment explanation
Indices: 512213--512262 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
512203 AAATAAAAAA
*
512213 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
512239 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
512263 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:512282 original size:21 final size:20
Alignment explanation
Indices: 512241--512288 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
512231 TCAAATATAT
* *
512241 TTAAAAACATAAAAACAAATA
1 TTAAAAAAATAAAAA-TAATA
512262 TTAAAACAAATAAAAATAATA
1 TTAAAA-AAATAAAAATAATA
*
512283 CTAAAA
1 TTAAAA
512289 TAATTCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TTAAAAAAATAAAAATAATA
Found at i:512326 original size:35 final size:33
Alignment explanation
Indices: 512262--512326 Score: 78
Period size: 35 Copynumber: 1.9 Consensus size: 33
512252 AAAACAAATA
*
512262 TTAAAACAAATAAAAATAATACTAAAATAATTC
1 TTAAAACAAATAAAAATAATAATAAAATAATTC
*
512295 TTAAAAC-AATACACAAATTAATAATATAATAA
1 TTAAAACAAATA-A-AAA-TAATAATAAAATAA
512327 AAATGGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 4 0.15
33 8 0.30
34 3 0.11
35 12 0.44
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (33 bp):
TTAAAACAAATAAAAATAATAATAAAATAATTC
Found at i:520943 original size:29 final size:28
Alignment explanation
Indices: 520910--520969 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
520900 ATAGAGATCT
* *
520910 AATCAAATTAGTCTTTATACTATTAAATA
1 AATCAAATTAATCTTTATACTACTAAA-A
* *
520939 AATCAATTTAATTTTTATACTACTAAAA
1 AATCAAATTAATCTTTATACTACTAAAA
520967 AAT
1 AAT
520970 TCAGATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.42
Consensus pattern (28 bp):
AATCAAATTAATCTTTATACTACTAAAA
Found at i:525579 original size:89 final size:88
Alignment explanation
Indices: 525442--525630 Score: 222
Period size: 89 Copynumber: 2.2 Consensus size: 88
525432 AAACTTAAAA
* * * * * *
525442 AAAAAAACAATTAAGCCC--CCTTTTTTTTGCACTCATTTGAGCATTTGAACTTTTAAAATGCAT
1 AAAAAAACAATTAAACCCATACTTTTTTTTGCACTAAATTGAGCACTTGAACTTTCAAAATGCAT
* *
525505 CAAAAAG-GCCTTCAAACTTCTTC
66 AAAAAAGAGCCTT-AAAATTCTTC
* *
525528 AAAAAAAGCAATTAAACCCATACTTTTTTTTGCACTAAATTGGGTACTTGAACTTTCAAAATGCA
1 AAAAAAA-CAATTAAACCCATACTTTTTTTTGCACTAAATTGAGCACTTGAACTTTCAAAATGCA
** *
525593 TAAAAAAGATTCTTAAAATTTTTC
65 TAAAAAAGAGCCTTAAAATTCTTC
525617 AAAAAAACAATTAA
1 AAAAAAACAATTAA
525631 GGCGCTGGTC
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
86 7 0.08
87 10 0.12
88 7 0.08
89 59 0.69
90 3 0.03
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.33
Consensus pattern (88 bp):
AAAAAAACAATTAAACCCATACTTTTTTTTGCACTAAATTGAGCACTTGAACTTTCAAAATGCAT
AAAAAAGAGCCTTAAAATTCTTC
Found at i:526085 original size:38 final size:38
Alignment explanation
Indices: 526001--526085 Score: 86
Period size: 39 Copynumber: 2.2 Consensus size: 38
525991 TTTTGGTATG
* *
526001 ATAATTTTTATAAGTTTTTTTACGAAATTTATATTTCT
1 ATAATTTTAATAAGTTTTCTTACGAAATTTATATTTCT
*
526039 TTACATTTTGAATAA-TTTTCTTACG-AATTTATAAATTT-T
1 ATA-ATTTT-AATAAGTTTTCTTACGAAATTTAT--ATTTCT
526078 ATAATTTT
1 ATAATTTT
526086 TTAATATTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
38 14 0.36
39 17 0.44
40 8 0.21
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (38 bp):
ATAATTTTAATAAGTTTTCTTACGAAATTTATATTTCT
Found at i:526088 original size:19 final size:17
Alignment explanation
Indices: 526066--526150 Score: 57
Period size: 17 Copynumber: 4.7 Consensus size: 17
526056 TTCTTACGAA
526066 TTTATAAATTTTATAATTT
1 TTTA-AAATTTTATAA-TT
* *
526085 TTTAATATTTCTAT-ATA
1 TTTAAAATTT-TATAATT
*
526102 TTTAAAATTTTTATGATTT
1 TTTAAAA-TTTTAT-AATT
*
526121 TTATAAAATTTTACAA-T
1 TT-TAAAATTTTATAATT
526138 TTTAATAATTTTA
1 TTTAA-AATTTTA
526151 CGATTTTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.06
17 20 0.38
18 10 0.19
19 15 0.28
20 5 0.09
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (17 bp):
TTTAAAATTTTATAATT
Found at i:526099 original size:28 final size:27
Alignment explanation
Indices: 526068--526140 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 27
526058 CTTACGAATT
526068 TATAAATTTTATAATTTTTTAAT-ATTTC
1 TATAAATTTTA-AATTTTTT-ATGATTTC
* * *
526096 TATATA-TTTAAAATTTTTATGATTTT
1 TATAAATTTTAAATTTTTTATGATTTC
526122 TATAAAATTTTACAATTTT
1 TAT-AAATTTTA-AATTTT
526141 AATAATTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
25 2 0.06
26 14 0.39
27 6 0.17
28 9 0.25
29 5 0.14
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (27 bp):
TATAAATTTTAAATTTTTTATGATTTC
Found at i:526159 original size:19 final size:18
Alignment explanation
Indices: 526102--526159 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
526092 TTTCTATATA
*
526102 TTTAAAATTTTTATGATTT
1 TTTAAAA-TTTTACGATTT
*
526121 TTATAAAATTTTAC-A-AT
1 TT-TAAAATTTTACGATTT
526138 TTTAATAATTTTACGATTT
1 TTTAA-AATTTTACGATTT
526157 TTT
1 TTT
526160 TCTAATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 3 0.09
17 11 0.34
18 2 0.06
19 11 0.34
20 5 0.16
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTAAAATTTTACGATTT
Found at i:534810 original size:17 final size:17
Alignment explanation
Indices: 534788--534822 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
534778 AATAAATTAT
534788 TAAAAAT-TTATAAAAAA
1 TAAAAATATTA-AAAAAA
534805 TAAAAATATTAAAAAAA
1 TAAAAATATTAAAAAAA
534822 T
1 T
534823 TGGTTCAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAATATTAAAAAAA
Found at i:540036 original size:19 final size:22
Alignment explanation
Indices: 540012--540052 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
540002 TAAGTTTTTT
540012 AAAAAT-TTAAA-TAT-ATTAA
1 AAAAATGTTAAAGTATAATTAA
540031 AAAAATGTTAAAGTATAATTAA
1 AAAAATGTTAAAGTATAATTAA
540053 TTTTATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 5 0.26
21 3 0.16
22 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (22 bp):
AAAAATGTTAAAGTATAATTAA
Found at i:540185 original size:19 final size:19
Alignment explanation
Indices: 540163--540266 Score: 51
Period size: 17 Copynumber: 5.8 Consensus size: 19
540153 TAAATCTATT
540163 AAAATTTTAAATATATTAA
1 AAAATTTTAAATATATTAA
* *
540182 AAAATGTT-AA-GTA-TAA
1 AAAATTTTAAATATATTAA
* *
540198 CAAATTTTAAA-ATTTTAA
1 AAAATTTTAAATATATTAA
* * * *
540216 TATA-TTTAATATATTTTTA
1 AAAATTTTAA-ATATATTAA
*
540235 AAAA--TTAAATATTTTAA
1 AAAATTTTAAATATATTAA
* *
540252 AAAATGTTAAGTATA
1 AAAATTTTAAATATA
540267 ACTAATTTTA
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
16 9 0.14
17 22 0.34
18 12 0.18
19 22 0.34
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (19 bp):
AAAATTTTAAATATATTAA
Found at i:540255 original size:18 final size:18
Alignment explanation
Indices: 540221--540256 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
540211 TTTAATATAT
*
540221 TTAATATATTTTTAAAAA
1 TTAATATATTTTAAAAAA
540239 TTAA-ATATTTTAAAAAA
1 TTAATATATTTTAAAAAA
540256 T
1 T
540257 GTTAAGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATATATTTTAAAAAA
Found at i:540261 original size:70 final size:71
Alignment explanation
Indices: 540169--540311 Score: 252
Period size: 70 Copynumber: 2.0 Consensus size: 71
540159 TATTAAAATT
*
540169 TTAAATATATTAAAAAATGTTAAGTATAACAAATTTTAAAATTTTAATATATTTAATATA-TTTT
1 TTAAATATATTAAAAAATGTTAAGTATAACAAATTTTAAAATTTTAATATATTCAATATATTTTT
540233 TAAAAA
66 TAAAAA
* *
540239 TTAAATATTTTAAAAAATGTTAAGTATAACTAATTTTAAAATTTTAATATATTCAATATATTTTT
1 TTAAATATATTAAAAAATGTTAAGTATAACAAATTTTAAAATTTTAATATATTCAATATATTTTT
540304 TAAAAA
66 TAAAAA
540310 TT
1 TT
540312 TATTTAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
70 57 0.83
71 12 0.17
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (71 bp):
TTAAATATATTAAAAAATGTTAAGTATAACAAATTTTAAAATTTTAATATATTCAATATATTTTT
TAAAAA
Found at i:540305 original size:21 final size:20
Alignment explanation
Indices: 540280--540349 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 20
540270 AATTTTAAAA
540280 TTTTAATATATTCAATATATT
1 TTTTAATATATT-AATATATT
* * * **
540301 TTTTAA-AAATTTATTTAAAA
1 TTTTAATATATTAATAT-ATT
*
540321 TTTTAATTTATTTAATATATT
1 TTTTAATATA-TTAATATATT
540342 TTTTAATA
1 TTTTAATA
540350 GGTAAAGAGA
Statistics
Matches: 34, Mismatches: 12, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
19 3 0.09
20 11 0.32
21 15 0.44
22 5 0.15
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAATATATTAATATATT
Found at i:540391 original size:17 final size:17
Alignment explanation
Indices: 540369--540401 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
540359 AAAAAAGATT
540369 TTTTAATATAT-TTAAAA
1 TTTTAA-ATATGTTAAAA
540386 TTTTAAATATGTTAAA
1 TTTTAAATATGTTAAA
540402 GAAAATGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTTAAATATGTTAAAA
Found at i:548748 original size:20 final size:19
Alignment explanation
Indices: 548720--548757 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
548710 AATATTAAAA
548720 TTTTTTAGTTCAAACAATT
1 TTTTTTAGTTCAAACAATT
*
548739 TTTTTCTAGTTCAATCAAT
1 TTTTT-TAGTTCAAACAAT
548758 CTAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.13, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTTTTAGTTCAAACAATT
Found at i:553151 original size:18 final size:18
Alignment explanation
Indices: 553128--553187 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
553118 AGATGTTCGA
553128 CTTGGATTTCTCTGAAAC
1 CTTGGATTTCTCTGAAAC
* * *
553146 CTTGGATTTCCCAGAGAC
1 CTTGGATTTCTCTGAAAC
553164 CTTGGATTTCT-TCGAAAC
1 CTTGGATTTCTCT-GAAAC
553182 CTTGGA
1 CTTGGA
553188 GATCCTCAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (18 bp):
CTTGGATTTCTCTGAAAC
Found at i:556327 original size:14 final size:16
Alignment explanation
Indices: 556308--556341 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
556298 TGATGAGCTT
556308 CAGCTT-GTTCAA-AG
1 CAGCTTGGTTCAATAG
556322 CAGCTTGGTTCAATAG
1 CAGCTTGGTTCAATAG
556338 CAGC
1 CAGC
556342 CACATGAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 6 0.33
16 6 0.33
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (16 bp):
CAGCTTGGTTCAATAG
Found at i:562952 original size:26 final size:26
Alignment explanation
Indices: 562906--562958 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
562896 TCAAACATGC
*
562906 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAAGGGT
* *
562932 ATTTCGGT-AATTTATCTCCTAAGGGT
1 ATTTAGGTCAATTTAAC-CCTAAGGGT
562958 A
1 A
562959 AAACTATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAAGGGT
Found at i:564476 original size:32 final size:32
Alignment explanation
Indices: 564439--564503 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
564429 AATGCTTACC
564439 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
564471 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
564503 A
1 A
564504 AATGCATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:569300 original size:119 final size:119
Alignment explanation
Indices: 569134--569854 Score: 1244
Period size: 119 Copynumber: 6.1 Consensus size: 119
569124 GCCGCAGTAC
* *
569134 AGCAGATCTATCCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTATTT
1 AGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
569199 ACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTCTCAGATAT
66 ACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTCTCAGATAT
* *
569253 AGAAGATCTAACCTTCAGATGTTTATACTAAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
1 AGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
569318 ACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTCTCAGATAT
66 ACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTCTCAGATAT
* *
569372 AGAAGATCTAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
1 AGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
* * *
569437 ATAAGAAAAAAATCGAGGACATAGTAGATTTGGCTCTCAGATGTTCTCAGATAT
66 ACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTCTCAGATAT
* * * *
569491 AGCAGATCTAACCTTCAGACGTTTAGACTTAAGCAGATCCAAGATGATTTGGTATTCTTGTGTCT
1 AGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
569556 ACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTCTCAGATAT
66 ACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTCTCAGATAT
*
569610 AGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTAGTATTCTTGTGTTT
1 AGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
* * *
569675 ATAAGAAACAAATCGAGGACATAGTAGATTTGGCTCTCAGACGTTCTCAGATAT
66 ACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTCTCAGATAT
*
569729 AGCAGATCTAACCTTCAGATGTTTAGACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
1 AGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
* * * *
569794 ACAAGAAACAAATCGAGGACATAGCAGATTTGATTCTCAGGTGTTCTTAGATAT
66 ACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTCTCAGATAT
569848 AGCAGAT
1 AGCAGAT
569855 TTGATTCTCA
Statistics
Matches: 567, Mismatches: 35, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 567 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (119 bp):
AGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
ACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTCTCAGATAT
Found at i:569855 original size:32 final size:32
Alignment explanation
Indices: 569814--569887 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
569804 AATCGAGGAC
*
569814 ATAGCAGATTTGATTCTCAGGTGTTCTTAGAT
1 ATAGCAGATTTGATTCTCAAGTGTTCTTAGAT
569846 ATAGCAGATTTGATTCTCAAGTGTTCTTAGAT
1 ATAGCAGATTTGATTCTCAAGTGTTCTTAGAT
569878 ATAGCAGATT
1 ATAGCAGATT
569888 AGACTCTTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.39
Consensus pattern (32 bp):
ATAGCAGATTTGATTCTCAAGTGTTCTTAGAT
Found at i:569903 original size:32 final size:32
Alignment explanation
Indices: 569814--569904 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 32
569804 AATCGAGGAC
*
569814 ATAGCAGATTTGATTCTCAGGTGTTCTTAGAT
1 ATAGCAGATTTGATTCTCAGATGTTCTTAGAT
569846 ATAGCAGATTTGATTCTCA-AGTGTTCTTAGAT
1 ATAGCAGATTTGATTCTCAGA-TGTTCTTAGAT
* * *
569878 ATAGCAGATTAGACTCTTAGATGTTCT
1 ATAGCAGATTTGATTCTCAGATGTTCT
569905 CAAACAGACT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
32 52 0.98
33 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (32 bp):
ATAGCAGATTTGATTCTCAGATGTTCTTAGAT
Found at i:570019 original size:83 final size:83
Alignment explanation
Indices: 569878--570031 Score: 236
Period size: 83 Copynumber: 1.9 Consensus size: 83
569868 GTTCTTAGAT
* * * * **
569878 ATAGCAGATTAGACTCTTAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGTTTAC
1 ATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGATTTAGCATCCTTGTACTTAC
569943 AAGGAACAAATTGAGGAC
66 AAGGAACAAATTGAGGAC
* *
569961 ATAGCAGATTTGACTCTCAGATGTTCTCAAACAGACTCAAGATGATTTAGTATCCTTGTACTTAC
1 ATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGATTTAGCATCCTTGTACTTAC
570026 AAGGAA
66 AAGGAA
570032 AACAAATCAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 63 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (83 bp):
ATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGATTTAGCATCCTTGTACTTAC
AAGGAACAAATTGAGGAC
Found at i:571881 original size:11 final size:11
Alignment explanation
Indices: 571867--571968 Score: 59
Period size: 11 Copynumber: 8.8 Consensus size: 11
571857 ATTTCACATA
571867 TATTATATATT
1 TATTATATATT
571878 TATTGAT-TATT
1 TATT-ATATATT
571889 TATATATATATT
1 TAT-TATATATT
*
571901 GT-TT-TACATGT
1 -TATTATATAT-T
*
571912 TATTTTATATT
1 TATTATATATT
571923 ATATCTATTATATT
1 -TAT-TA-TATATT
*
571937 TCTTATATATT
1 TATTATATATT
*
571948 TA-TATTACATTT
1 TATTA-TATA-TT
571960 TATTATATA
1 TATTATATA
571969 ATATTTATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 25
0.69 0.07 0.24
Matches are distributed among these distances:
10 7 0.10
11 28 0.39
12 24 0.34
13 6 0.08
14 6 0.08
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (11 bp):
TATTATATATT
Found at i:571978 original size:46 final size:47
Alignment explanation
Indices: 571873--571988 Score: 121
Period size: 46 Copynumber: 2.4 Consensus size: 47
571863 CATATATTAT
* *
571873 ATATTTATTGATTATTTATATATATATTGTTTTACATGTTATTTTATATT
1 ATATTTATT-A-TATTTAT-TATATATTGTTTTACATGTTATATTATATA
* *
571923 ATATCTATTATATTTCTTATATATT-TATATTACAT-TT-TATTATATA
1 ATATTTATTATATTTATTATATATTGT-T-TTACATGTTATATTATATA
*
571969 ATATTTATTATATTTTTTAT
1 ATATTTATTATATTTATTAT
571989 TCATTTTATG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
46 26 0.45
47 11 0.19
48 12 0.21
49 1 0.02
50 8 0.14
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (47 bp):
ATATTTATTATATTTATTATATATTGTTTTACATGTTATATTATATA
Found at i:571994 original size:35 final size:38
Alignment explanation
Indices: 571932--572003 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 38
571922 TATATCTATT
*
571932 ATATTTCTTATATATTTATATTACATTTTAT-TATATA
1 ATATTTATTATATATTTATATTACATTTTATGTATATA
*
571969 ATATTTATTATAT-TTTTTATT-CATTTTATGTATAT
1 ATATTTATTATATATTTATATTACATTTTATGTATAT
572004 CATGTATCGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 8 0.25
36 12 0.38
37 12 0.38
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (38 bp):
ATATTTATTATATATTTATATTACATTTTATGTATATA
Found at i:572049 original size:20 final size:19
Alignment explanation
Indices: 572016--572053 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
572006 TGTATCGCCA
572016 ATTATATTATTTATGTTTAT
1 ATTATATTATTTAT-TTTAT
572036 ATTATA-TATATTATTTTA
1 ATTATATTAT-TTATTTTA
572054 AAAAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
ATTATATTATTTATTTTAT
Found at i:578738 original size:21 final size:21
Alignment explanation
Indices: 578712--578755 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
578702 AAAATATATG
578712 TATAAATAATATAAAATAAAA
1 TATAAATAATATAAAATAAAA
* *
578733 TATAAATAGTTTAAAATAAAA
1 TATAAATAATATAAAATAAAA
578754 TA
1 TA
578756 ATGTATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TATAAATAATATAAAATAAAA
Found at i:580547 original size:23 final size:22
Alignment explanation
Indices: 580521--580568 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
580511 ACAATGAGGC
580521 TTTGGTAAAAATTATA-AATTTAT
1 TTTGGTAAAAATT-TAGAA-TTAT
* *
580544 TTTGTTAAATATTTAGAATTAT
1 TTTGGTAAAAATTTAGAATTAT
580566 TTT
1 TTT
580569 AAATTTATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (22 bp):
TTTGGTAAAAATTTAGAATTAT
Found at i:585480 original size:93 final size:93
Alignment explanation
Indices: 585368--585539 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
585358 CGCCCATAAG
* *
585368 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
585433 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
585461 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
585526 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
585540 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:585536 original size:46 final size:46
Alignment explanation
Indices: 585361--585536 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
585351 TGTAACCCGC
* * *
585361 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
585407 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
585457 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
585500 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
585537 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:593045 original size:93 final size:93
Alignment explanation
Indices: 592933--593104 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
592923 CGCCCATAAG
* *
592933 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
592998 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
593026 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
593091 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
593105 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:593101 original size:46 final size:46
Alignment explanation
Indices: 592926--593101 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
592916 TGTAACCCGC
* * *
592926 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
592972 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
593022 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
593065 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
593102 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:596831 original size:25 final size:28
Alignment explanation
Indices: 596794--596860 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 28
596784 AAAAAAATAT
*
596794 TAATACAATATAA-ATAAT-ATATATGCCA
1 TAATA-AA-ATAATATAATAATATATGACA
*
596822 T-ATAAAATAATATAATAATATATGATA
1 TAATAAAATAATATAATAATATATGACA
596849 TAATAAAATAAT
1 TAATAAAATAAT
596861 GTATTTTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 4 0.12
26 7 0.21
27 12 0.35
28 11 0.32
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.34
Consensus pattern (28 bp):
TAATAAAATAATATAATAATATATGACA
Found at i:596844 original size:20 final size:20
Alignment explanation
Indices: 596821--596860 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
596811 TATATATGCC
*
596821 ATATAAAATAATATAATAAT
1 ATATAAAATAATAAAATAAT
* *
596841 ATATGATATAATAAAATAAT
1 ATATAAAATAATAAAATAAT
596861 GTATTTTCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
ATATAAAATAATAAAATAAT
Found at i:599087 original size:24 final size:24
Alignment explanation
Indices: 599049--599198 Score: 103
Period size: 24 Copynumber: 6.2 Consensus size: 24
599039 ATGATTTTCT
599049 TTTTATATACGTTATTTATTTTAAAC
1 TTTTATATA--TTATTTATTTTAAAC
*
599075 TTTTACATATTATTTATTTTAAA-
1 TTTTATATATTATTTATTTTAAAC
* * *
599098 TTTATATACATTATGTA-GTTAAAC
1 TTT-TATATATTATTTATTTTAAAC
599122 TATTTTATATATTATTTATTTTAAACC
1 --TTTTATATATTATTTATTTTAAA-C
* * *
599149 CTCT-T-TATTAGTTATTTTAAA-
1 TTTTATATATTATTTATTTTAAAC
* * * *
599170 TTGTTCTACATTGTTTATTTTAAAT
1 TT-TTATATATTATTTATTTTAAAC
599195 TTTT
1 TTTT
599199 TTTATATAAT
Statistics
Matches: 98, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 24 0.24
24 40 0.41
25 15 0.15
26 16 0.16
27 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (24 bp):
TTTTATATATTATTTATTTTAAAC
Found at i:599138 original size:49 final size:48
Alignment explanation
Indices: 599050--599146 Score: 133
Period size: 49 Copynumber: 2.0 Consensus size: 48
599040 TGATTTTCTT
* * *
599050 TTTATATACGTTATTTATTTTAAACTTTTACATATTATTTATTTTAAA
1 TTTATATACATTATGTATGTTAAACTTTTACATATTATTTATTTTAAA
*
599098 TTTATATACATTATGTA-GTTAAACTATTTTATATATTATTTATTTTAAA
1 TTTATATACATTATGTATGTTAAAC--TTTTACATATTATTTATTTTAAA
599147 CCCTCTTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 6 0.14
48 15 0.35
49 22 0.51
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (48 bp):
TTTATATACATTATGTATGTTAAACTTTTACATATTATTTATTTTAAA
Found at i:601380 original size:19 final size:20
Alignment explanation
Indices: 601356--601395 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
601346 GATAAATTTA
*
601356 TACATAG-ATACTTGTCATT
1 TACATAGAATACTTGCCATT
601375 TACATAGAATACTTGCCATT
1 TACATAGAATACTTGCCATT
601395 T
1 T
601396 GTATATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (20 bp):
TACATAGAATACTTGCCATT
Found at i:603182 original size:30 final size:30
Alignment explanation
Indices: 603121--603182 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
603111 TTAATAGGGT
**
603121 ATTCAAATCACTTTTCAAATTTCACTTTCA
1 ATTCAAATCACTTTTCAAATTTCACAATCA
* *
603151 ATTCAAAATCACTTTTCCATTTTCA-AATCA
1 ATTC-AAATCACTTTTCAAATTTCACAATCA
603181 AT
1 AT
603183 ATACAATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (30 bp):
ATTCAAATCACTTTTCAAATTTCACAATCA
Found at i:603999 original size:22 final size:21
Alignment explanation
Indices: 603952--604063 Score: 72
Period size: 22 Copynumber: 5.4 Consensus size: 21
603942 TTCTATGCTT
* * *
603952 TGTTTCTTTTGTTT-CCTTTT
1 TGTTTCTTTTATTTAGCTTTC
*
603972 TCTTTCTTTTATTTGAGCTTTC
1 TGTTTCTTTTATTT-AGCTTTC
* *
603994 TGTTTCTTTTCTAT-GC-TT-
1 TGTTTCTTTTATTTAGCTTTC
** *
604012 TGTTTCTTTT-TGTTTCCTTTT
1 TGTTTCTTTTAT-TTAGCTTTC
*
604033 TCTTTCTTTTATTTGAGCTTTC
1 TGTTTCTTTTATTT-AGCTTTC
604055 TGTTTCTTT
1 TGTTTCTTT
604064 CCTTTTGTTT
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
17 1 0.01
18 11 0.16
19 3 0.04
20 16 0.23
21 11 0.16
22 28 0.40
ACGTcount: A:0.04, C:0.16, G:0.10, T:0.70
Consensus pattern (21 bp):
TGTTTCTTTTATTTAGCTTTC
Found at i:604033 original size:61 final size:61
Alignment explanation
Indices: 603941--604082 Score: 241
Period size: 61 Copynumber: 2.3 Consensus size: 61
603931 CTGTTCTTCA
603941 TTTCTATGCTTTGTTTC-TTTTGTTTCCTTTTTCTTTCTTTTATTTGAGCTTTCTGTTTCT
1 TTTCTATGCTTTGTTTCTTTTTGTTTCCTTTTTCTTTCTTTTATTTGAGCTTTCTGTTTCT
604001 TTTCTATGCTTTGTTTCTTTTTGTTTCCTTTTTCTTTCTTTTATTTGAGCTTTCTGTTTCT
1 TTTCTATGCTTTGTTTCTTTTTGTTTCCTTTTTCTTTCTTTTATTTGAGCTTTCTGTTTCT
* * *
604062 TTCCTTTTGTTTTGTTTCTTT
1 TTTC-TATGCTTTGTTTCTTT
604083 ATTTTACTTT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
60 17 0.22
61 46 0.60
62 14 0.18
ACGTcount: A:0.04, C:0.16, G:0.10, T:0.70
Consensus pattern (61 bp):
TTTCTATGCTTTGTTTCTTTTTGTTTCCTTTTTCTTTCTTTTATTTGAGCTTTCTGTTTCT
Found at i:604111 original size:3 final size:3
Alignment explanation
Indices: 604103--604138 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
604093 ATGTTTTGTT
604103 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
604139 TTATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:604143 original size:3 final size:3
Alignment explanation
Indices: 604137--604171 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
604127 ATAATAATAA
*
604137 TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
604172 CTTAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:604206 original size:15 final size:15
Alignment explanation
Indices: 604188--604216 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
604178 TAAAAAGTAA
604188 ACAAATATATGTATT
1 ACAAATATATGTATT
604203 ACAAATATATGTAT
1 ACAAATATATGTAT
604217 ATATATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
ACAAATATATGTATT
Found at i:604274 original size:3 final size:3
Alignment explanation
Indices: 604266--604299 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
604256 TGTCTTTATT
604266 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
604300 TATCATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:605568 original size:21 final size:21
Alignment explanation
Indices: 605544--605586 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
605534 AAGAATATGA
605544 TCATCGCATTTGTGTTTAGTG
1 TCATCGCATTTGTGTTTAGTG
605565 TCATCGCATTTGTGTTTAGTG
1 TCATCGCATTTGTGTTTAGTG
605586 T
1 T
605587 AGTTGGTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (21 bp):
TCATCGCATTTGTGTTTAGTG
Found at i:613901 original size:18 final size:19
Alignment explanation
Indices: 613878--613923 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
613868 AAAACCTTAG
613878 TTTTTCCTTTTTCTTTT-C
1 TTTTTCCTTTTTCTTTTCC
*
613896 TTTTT-CTCCTTTCTTTTCC
1 TTTTTCCT-TTTTCTTTTCC
*
613915 CTTTTCCTT
1 TTTTTCCTT
613924 ATTTTCGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
17 2 0.09
18 13 0.59
19 5 0.23
20 2 0.09
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTCCTTTTTCTTTTCC
Found at i:614187 original size:3 final size:3
Alignment explanation
Indices: 614181--614236 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
614171 AATACTAATA
*
614181 ATT ATT ATT ATT ATT A-T ATAT ATT ATT ATT ATT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
614226 ATT ATT ATT AT
1 ATT ATT ATT AT
614237 CAATAATAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:618832 original size:34 final size:34
Alignment explanation
Indices: 618789--618857 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
618779 ATGTAACAAA
618789 TGAATAAGTCTATAAAAAGTTCTAGTATTTATTC
1 TGAATAAGTCTATAAAAAGTTCTAGTATTTATTC
618823 TGAATAAGTCTATAAAAAGTTCTAGTATTTATTC
1 TGAATAAGTCTATAAAAAGTTCTAGTATTTATTC
618857 T
1 T
618858 ACTTGGGTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (34 bp):
TGAATAAGTCTATAAAAAGTTCTAGTATTTATTC
Found at i:621340 original size:18 final size:18
Alignment explanation
Indices: 621315--621374 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
621305 AGATGTTCGA
621315 CTTGGATTTCTCCGAAAC
1 CTTGGATTTCTCCGAAAC
* * *
621333 CATGGATTTC-CCAGAGAT
1 CTTGGATTTCTCC-GAAAC
621351 CTTGGATTTCTCCGAAAC
1 CTTGGATTTCTCCGAAAC
621369 CTTGGA
1 CTTGGA
621375 GATCCTCGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 2 0.06
18 30 0.88
19 2 0.06
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (18 bp):
CTTGGATTTCTCCGAAAC
Found at i:621468 original size:18 final size:18
Alignment explanation
Indices: 621445--621481 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
621435 ACGGCTTGAC
621445 TGTTCCGGTTATTTGGTT
1 TGTTCCGGTTATTTGGTT
621463 TGTTCCGGTTATTTGGTT
1 TGTTCCGGTTATTTGGTT
621481 T
1 T
621482 ATGAAATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.11, G:0.27, T:0.57
Consensus pattern (18 bp):
TGTTCCGGTTATTTGGTT
Found at i:623700 original size:105 final size:105
Alignment explanation
Indices: 623518--623726 Score: 355
Period size: 105 Copynumber: 2.0 Consensus size: 105
623508 TCTTTATTCC
* * *
623518 TTGTTTTGTGGATTATATAACGAATATTAATGTACGATAATATTTTGGTATTGTTTATACTTTAA
1 TTGTTTTGTGGATTATATAACGAATATTAATGTACGATAATATTTTGATATTGTTTATACCTCAA
623583 AACAAATATAAGATAACCAACAAGTTATTCGAATGAGTGT
66 AACAAATATAAGATAACCAACAAGTTATTCGAATGAGTGT
* *
623623 TTGTTTTGTGGATTATATAACGAATATTGATGTACGATAATATTTTTATATTGTTTATACCTCAA
1 TTGTTTTGTGGATTATATAACGAATATTAATGTACGATAATATTTTGATATTGTTTATACCTCAA
* *
623688 AACAAATATAAGATAACGAGCAAGTTATTCGAATGAGTG
66 AACAAATATAAGATAACCAACAAGTTATTCGAATGAGTG
623727 GTATTAGACT
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
105 97 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (105 bp):
TTGTTTTGTGGATTATATAACGAATATTAATGTACGATAATATTTTGATATTGTTTATACCTCAA
AACAAATATAAGATAACCAACAAGTTATTCGAATGAGTGT
Found at i:631399 original size:19 final size:18
Alignment explanation
Indices: 631375--631418 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
631365 AATATGAATA
631375 AAATTTATCTACCCAAAT
1 AAATTTATCTACCCAAAT
* *
631393 AAGATTTATCTATCTAAAT
1 AA-ATTTATCTACCCAAAT
631412 AAATTTA
1 AAATTTA
631419 AAATATATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATTTATCTACCCAAAT
Found at i:636082 original size:14 final size:15
Alignment explanation
Indices: 636060--636088 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
636050 TTGGTCAATG
636060 TTTAGGATTTAGGGT
1 TTTAGGATTTAGGGT
636075 TTTA-GATTTAGGGT
1 TTTAGGATTTAGGGT
636089 AAAAATACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (15 bp):
TTTAGGATTTAGGGT
Found at i:636963 original size:18 final size:18
Alignment explanation
Indices: 636937--637009 Score: 65
Period size: 18 Copynumber: 4.1 Consensus size: 18
636927 ATGATGATCC
* *
636937 TAACGAAAATAATATTAG
1 TAACAAAAATAATAATAG
* *
636955 TAACAAAAATCATAATAT
1 TAACAAAAATAATAATAG
* * * *
636973 TAATATAAATAATCATAT
1 TAACAAAAATAATAATAG
*
636991 TAATAAAAATAATAATAG
1 TAACAAAAATAATAATAG
637009 T
1 T
637010 GGAAACGAGA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (18 bp):
TAACAAAAATAATAATAG
Found at i:646713 original size:13 final size:13
Alignment explanation
Indices: 646695--646723 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
646685 AAAGGAAGAA
646695 AATAAAATTGCAT
1 AATAAAATTGCAT
646708 AATAAAATTGCAT
1 AATAAAATTGCAT
646721 AAT
1 AAT
646724 CTTACTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (13 bp):
AATAAAATTGCAT
Found at i:650415 original size:132 final size:132
Alignment explanation
Indices: 650156--650530 Score: 454
Period size: 132 Copynumber: 2.8 Consensus size: 132
650146 TGAAAACCTA
* * * * * ** *
650156 AAGGAATATTCGATTGTTTTGAGCAGACGAGGAATTATAACCCAACACGATAGGGCA-TGATTCC
1 AAGGGATATTCGATTATTTTAAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACT-ATTCC
* *** * * ** * *
650220 -CGAATTGTCAAACGCCAAATAT--TACATTCGTTTTAAATG-ATTTTTAGAAGATATGCGTGAA
65 GCGAATTGCCAAATATCGAATATCGT-C-TTCGTTTTAAA-GAATTTTTAAAAGGCATGAGTAAA
650281 ATTTTG
127 ATTTTG
* *
650287 AAGGGATATTTGATTATTTTAAGCAAACGAGAAATTGCAACCCAGCACGTTAGGGCACTATTCCG
1 AAGGGATATTCGATTATTTTAAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACTATTCCG
*
650352 CGAATTGCCAAATATCGAATATCGTCTTTGTTTTAAAGAATTTTTAAAAGGCATGAGTAAAATTT
66 CGAATTGCCAAATATCGAATATCGTCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTAAAATTT
650417 TG
131 TG
* *
650419 AAGGGATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCACTATTCCG
1 AAGGGATATTCGATTATTTTAAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACTATTCCG
* *
650484 CGAATTGCCAAATATCGAGTCTCGTCTTCGTTTTAAAGAATTTTTAA
66 CGAATTGCCAAATATCGAATATCGTCTTCGTTTTAAAGAATTTTTAA
650531 TAATAATTAT
Statistics
Matches: 211, Mismatches: 28, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
131 53 0.25
132 156 0.74
133 1 0.00
134 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (132 bp):
AAGGGATATTCGATTATTTTAAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACTATTCCG
CGAATTGCCAAATATCGAATATCGTCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTAAAATTT
TG
Found at i:650820 original size:3 final size:3
Alignment explanation
Indices: 650812--650853 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
650802 AATGATAAAA
* * *
650812 AAT AAT AAT GAC AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
650854 GCAATGATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:650829 original size:12 final size:12
Alignment explanation
Indices: 650799--650846 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
650789 AAACAACACG
*
650799 AACAATGATAA-
1 AACAATAATAAT
650810 AA-AATAATAAT
1 AACAATAATAAT
*
650821 GACAATAATAAT
1 AACAATAATAAT
*
650833 AATAATAATAAT
1 AACAATAATAAT
650845 AA
1 AA
650847 TGATAATGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 7 0.23
11 3 0.10
12 21 0.68
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (12 bp):
AACAATAATAAT
Done.